https://www-user.pas.rochester.edu/~gosia/mediawiki/index.php?feed=atom&target=Hayes&title=Special%3AContributionsGOSIA - User contributions [en]2026-07-08T07:20:07ZFrom GOSIAMediaWiki 1.16.0https://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2015-10-13T15:54:42Z<p>Hayes: /* Downloads */ Changed to proper download links for Rachel</p>
<hr />
<div><span><font color="FF0000">Please contribute to this wiki! If you would like an account, please [[Special:UserLogin | request an account]] and then [mailto:abraunhayes@gmail.com send an email to an administrator]. (The number of requests by spam-bots necessitates an email for a quick response.)</font></span><br />
<br />
Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.<br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
[[Rachel_GUI | Rachel ]] is the graphical user interface for Gosia. New Gosia users should start by installing the GUI.<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[common_mistakes | Common mistakes in Gosia calculations]]<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120510) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120510.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* The current version of Rachel, the Gosia interface, can be downloaded as a zip file or a Git repository here: [https://github.com/adamhayes/Rachel master branch] . Feel free to fork and contribute.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2013-02-11T23:36:29Z<p>Hayes: Better links to the videos. Streaming on Youtube now.</p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a demo of Rachel's capabilities, watch [http://youtu.be/moVVC-GODzQ The Rachel Video on Youtube], or [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html Download the mp4 (9MB)].<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. Versions 1.* have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Get the latest release version from the [[Gosia#Downloads | Downloads section on the Main Page]].<br />
<br />
==Version notes==<br />
<br />
The [[Gui_release_notes | version notes page]] gives a history of Rachel updates. Known issues are given for each version, as well as the current version.<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
A script was added by Mitch Allmond that compiles and sets up Rachel, Gosia and Elast in one step. First, un-tar the distribution:<br />
<br />
<pre><br />
% tar -xvf rachel_distribution_1.3.0.tar<br />
</pre><br />
<br />
or similar for the correct version number. Move into the new Rachel directory and run compile-all.sh:<br />
<br />
<pre><br />
% cd rachel_distribution_1.3.0<br />
% ./compile-all.sh<br />
</pre><br />
<br />
You will be prompted if any previous setup information needs to be overwritten.<br />
<br />
Rachel has been installed successfully on a number of Linux and OS X systems. Most problems are related to the level scheme graphics. Refer to [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends] for remedies. You can view or submit detailed installation notes for any particular operating system. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When changing to version 1.0 or later, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data. Subsequent versions will have the automatic upgrading reinstated.<br />
<br />
==Graphics Issues==<br />
<br />
If you do not see a level scheme diagram after loading a level scheme or a saved session, click "Examine fig. window" once. The level scheme should then appear.<br />
<br />
If it does not, or if the level scheme window buttons (zoom, pan, etc.) do not work, you may need to change the graphics back-end. The matplotlib graphics library used for the level scheme and particle detector layout comes with several choices of back-ends. <br />
<br />
*On OS X machines, "macosx" may work best.<br />
*On Ubuntu, GTKAgg works best, but the user must click "Examine fig. window" 'once' after loading a level scheme or saved session.<br />
<br />
The back-end is in the matplotlibrc file in the .matplotlib directory, or will be, after you start Rachel for the first time.<br />
<br />
<pre><br />
hayes@Sobchak:~$ cd .matplotlib/<br />
hayes@Sobchak:~/.matplotlib$ ll<br />
total 116K<br />
drwxr-xr-x 3 hayes hayes 4.0K Nov 5 12:30 ./<br />
drwxr-xr-x 125 hayes hayes 12K Nov 5 12:53 ../<br />
-rw-r--r-- 1 hayes hayes 92K Oct 27 13:13 fontList.cache<br />
-rw-r--r-- 1 hayes hayes 17 Aug 19 02:09 matplotlibrc<br />
drwxrwxr-x 2 hayes hayes 4.0K Oct 27 13:13 tex.cache/<br />
hayes@Sobchak:~/.matplotlib$ cat matplotlibrc <br />
backend : GTKAgg<br />
hayes@Sobchak:~/.matplotlib$ <br />
</pre><br />
<br />
Change the backend line as desired. The choices are found <br />
<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, many of which have already been added to versions 1.0 and later. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2013-02-11T23:23:55Z<p>Hayes: /* How to get the Rachel package */ Made the download link go right to the download section on the main page.</p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. Versions 1.* have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Get the latest release version from the [[Gosia#Downloads | Downloads section on the Main Page]].<br />
<br />
==Version notes==<br />
<br />
The [[Gui_release_notes | version notes page]] gives a history of Rachel updates. Known issues are given for each version, as well as the current version.<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
A script was added by Mitch Allmond that compiles and sets up Rachel, Gosia and Elast in one step. First, un-tar the distribution:<br />
<br />
<pre><br />
% tar -xvf rachel_distribution_1.3.0.tar<br />
</pre><br />
<br />
or similar for the correct version number. Move into the new Rachel directory and run compile-all.sh:<br />
<br />
<pre><br />
% cd rachel_distribution_1.3.0<br />
% ./compile-all.sh<br />
</pre><br />
<br />
You will be prompted if any previous setup information needs to be overwritten.<br />
<br />
Rachel has been installed successfully on a number of Linux and OS X systems. Most problems are related to the level scheme graphics. Refer to [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends] for remedies. You can view or submit detailed installation notes for any particular operating system. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When changing to version 1.0 or later, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data. Subsequent versions will have the automatic upgrading reinstated.<br />
<br />
==Graphics Issues==<br />
<br />
If you do not see a level scheme diagram after loading a level scheme or a saved session, click "Examine fig. window" once. The level scheme should then appear.<br />
<br />
If it does not, or if the level scheme window buttons (zoom, pan, etc.) do not work, you may need to change the graphics back-end. The matplotlib graphics library used for the level scheme and particle detector layout comes with several choices of back-ends. <br />
<br />
*On OS X machines, "macosx" may work best.<br />
*On Ubuntu, GTKAgg works best, but the user must click "Examine fig. window" 'once' after loading a level scheme or saved session.<br />
<br />
The back-end is in the matplotlibrc file in the .matplotlib directory, or will be, after you start Rachel for the first time.<br />
<br />
<pre><br />
hayes@Sobchak:~$ cd .matplotlib/<br />
hayes@Sobchak:~/.matplotlib$ ll<br />
total 116K<br />
drwxr-xr-x 3 hayes hayes 4.0K Nov 5 12:30 ./<br />
drwxr-xr-x 125 hayes hayes 12K Nov 5 12:53 ../<br />
-rw-r--r-- 1 hayes hayes 92K Oct 27 13:13 fontList.cache<br />
-rw-r--r-- 1 hayes hayes 17 Aug 19 02:09 matplotlibrc<br />
drwxrwxr-x 2 hayes hayes 4.0K Oct 27 13:13 tex.cache/<br />
hayes@Sobchak:~/.matplotlib$ cat matplotlibrc <br />
backend : GTKAgg<br />
hayes@Sobchak:~/.matplotlib$ <br />
</pre><br />
<br />
Change the backend line as desired. The choices are found <br />
<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, many of which have already been added to versions 1.0 and later. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2013-02-11T23:21:35Z<p>Hayes: Added Rachel info at the top.</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
[[Rachel_GUI | Rachel ]] is the graphical user interface for Gosia. New Gosia users should start by installing the GUI.<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[common_mistakes | Common mistakes in Gosia calculations]]<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120510) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120510.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_distribution_1.3.1.tar Rachel release version 1.3.1], the graphical interface for Gosia. See also the [[Gui_release_notes | Version notes]] page for new features.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel,_a_GUI_for_GosiaRachel, a GUI for Gosia2013-02-11T23:14:46Z<p>Hayes: moved Rachel, a GUI for Gosia to Rachel GUI: Can't link to the old name (because of a comma?).</p>
<hr />
<div>#REDIRECT [[Rachel GUI]]</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2013-02-11T23:14:46Z<p>Hayes: moved Rachel, a GUI for Gosia to Rachel GUI: Can't link to the old name (because of a comma?).</p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. Versions 1.* have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Get the latest release version from the [http://www-user.pas.rochester.edu/~gosia/mediawiki/ Main Page].<br />
<br />
==Version notes==<br />
<br />
The [[Gui_release_notes | version notes page]] gives a history of Rachel updates. Known issues are given for each version, as well as the current version.<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
A script was added by Mitch Allmond that compiles and sets up Rachel, Gosia and Elast in one step. First, un-tar the distribution:<br />
<br />
<pre><br />
% tar -xvf rachel_distribution_1.3.0.tar<br />
</pre><br />
<br />
or similar for the correct version number. Move into the new Rachel directory and run compile-all.sh:<br />
<br />
<pre><br />
% cd rachel_distribution_1.3.0<br />
% ./compile-all.sh<br />
</pre><br />
<br />
You will be prompted if any previous setup information needs to be overwritten.<br />
<br />
Rachel has been installed successfully on a number of Linux and OS X systems. Most problems are related to the level scheme graphics. Refer to [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends] for remedies. You can view or submit detailed installation notes for any particular operating system. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When changing to version 1.0 or later, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data. Subsequent versions will have the automatic upgrading reinstated.<br />
<br />
==Graphics Issues==<br />
<br />
If you do not see a level scheme diagram after loading a level scheme or a saved session, click "Examine fig. window" once. The level scheme should then appear.<br />
<br />
If it does not, or if the level scheme window buttons (zoom, pan, etc.) do not work, you may need to change the graphics back-end. The matplotlib graphics library used for the level scheme and particle detector layout comes with several choices of back-ends. <br />
<br />
*On OS X machines, "macosx" may work best.<br />
*On Ubuntu, GTKAgg works best, but the user must click "Examine fig. window" 'once' after loading a level scheme or saved session.<br />
<br />
The back-end is in the matplotlibrc file in the .matplotlib directory, or will be, after you start Rachel for the first time.<br />
<br />
<pre><br />
hayes@Sobchak:~$ cd .matplotlib/<br />
hayes@Sobchak:~/.matplotlib$ ll<br />
total 116K<br />
drwxr-xr-x 3 hayes hayes 4.0K Nov 5 12:30 ./<br />
drwxr-xr-x 125 hayes hayes 12K Nov 5 12:53 ../<br />
-rw-r--r-- 1 hayes hayes 92K Oct 27 13:13 fontList.cache<br />
-rw-r--r-- 1 hayes hayes 17 Aug 19 02:09 matplotlibrc<br />
drwxrwxr-x 2 hayes hayes 4.0K Oct 27 13:13 tex.cache/<br />
hayes@Sobchak:~/.matplotlib$ cat matplotlibrc <br />
backend : GTKAgg<br />
hayes@Sobchak:~/.matplotlib$ <br />
</pre><br />
<br />
Change the backend line as desired. The choices are found <br />
<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, many of which have already been added to versions 1.0 and later. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Normalization_of_yield_dataNormalization of yield data2012-09-21T13:28:50Z<p>Hayes: /* Introduction */ Added important note that this article assumes efficiency-corrected yields</p>
<hr />
<div>==Introduction==<br />
<br />
''In this "Normalization of yield data" article it is assumed that the user is passing efficiency-corrected gamma-ray yields to Gosia, but there are other ways that data can be used.''<br />
<br />
Any arbitrary overall normalization of the gamma-ray yield data is acceptable, unless the user is trying to normalize to the collision partner's gamma-ray yields or to the elastic cross section. This is because Gosia fits one overall normalization constant to all yield data, representing the factors of beam current, beam time, etc.<br />
<br />
==Ge detector solid-angle corrections==<br />
<br />
If all of the Ge detectors span the same solid angle, then all of the data will be consistent if each count is efficiency-corrected by dividing by the relative efficiency <math>\epsilon (E_\gamma)</math> with an arbitrary overall normalization. However, if two data sets from different detector ''[[physical_germanium_type | types]]'' are included, then the following additional correction is necessary, since Gosia calculates (OP,INTI) yield per unit Ge solid angle and expects the same yield per unit solid angle in fitting (OP,MINI).<br />
<br />
Gosia expects to read "corrected" yields of <br />
<br />
<math>Y = N_{raw} / [\epsilon(E_\gamma) \Delta\Omega_{Ge}]</math>,<br />
<br />
where <math>Y</math> is the "corrected yield," <math>N_{raw}</math> is the measured count, <math>\epsilon(E_\gamma)</math> is the relative (or absolute) Ge detector efficiency and <math>\Delta\Omega_{Ge}</math> is the solid angle subtended by the germanium detector. Here, the solid angle is in units of sr (steradians). Obviously, if all Ge detectors span the same solid angle, then the <math>\Delta\Omega_{Ge}</math> term can be absorbed into the arbitrary overall normalization.<br />
<br />
However, if two or more of the Ge detectors subtend different solid angles, the <math>\Delta\Omega_{Ge}</math> term should be included.<br />
<br />
In cases where the overall normalization doesn't matter, the efficiency can absorb the solid angle and be taken on a scale of 0 < efficiency < 4pi, ''but the solid angle factor must not be included twice.''<br />
<br />
===Exceptions and warnings===<br />
<br />
If the data sets are from detector clusters (see OP,RAW in the user manual), all of the Ge crystals in the cluster should be of the same physical type. This is because Gosia gives output and expects data from the user representing the count per unit solid angle ''of the crystal type,'' not of the total cluster solid angle.<br />
<br />
It is not clear how to handle summed Ge clusters of ''different physical types'' in Gosia.<br />
<br />
The OP,RAW command can be used to pass data to Gosia without an efficiency correction and/or for summed clusters. The solid angle divisors are still required, and for each cluster should be taken as <math>\Delta\Omega_{crystal}</math>&mdash;the solid angle of a single Ge detector in the cluster!</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-08-14T20:05:58Z<p>Hayes: /* Downloads */ updated to rachel 1.2.0</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[common_mistakes | Common mistakes in Gosia calculations]]<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120510) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120510.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.2.0.tar Rachel release version 1.2.0], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-05-25T20:38:30Z<p>Hayes: </p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.2.0==<br />
(not yet released)<br />
<br />
===Expected Changes===<br />
<br />
The normalization of calculated yields to experimental yields in the GUI now matches the normalization used by Gosia. The previous Rachel versions weighted yields by their fractional errors when calculating the normalizations. This can make plotting and understanding the chi-squared values confusing. For example, when low-intensity gamma-ray yields are poorly reproduced, the high-intensity yields can appear to be poorly reproduced.<br />
<br />
The new method in version 1.2.0 weights the individual yields' contributions to the normalization factor by their intensity only.<br />
<br />
<br />
<br />
<br />
<br />
<br />
==Version 1.1.5==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
None<br />
<br />
====Bug-fixes====<br />
<br />
A bug that affected only the fitting and corrected yield calculations has been fixed. Occasionally, but not always, this bug resulted in incorrect yield data being passed to Gosia using the "Write Gosia yld file" button, which would affect fitting. It did not affect integrated yield calculations, simulations or plotting, and the integrated yield function still gave the correct chi-squared value. <br />
<br />
See the recommendations section below.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions to date, the sensitivity map (OP,MAP) is calculated in the same Gosia call that does a fit (OP,MINI). This works in most cases, but it may cause errors occasionally in inverse-kinematics calculations. (This is not confirmed, but the error will be reported if it occurs.) The sensitivity map will be calculated in a separate call in the next bug-fix version.<br />
<br />
Level schemes that do not have spins in order of increasing energy within a band, e.g. 1-, 0-, 3-, 2-..., will cause errors in generating the Gosia input, and the full yield data set may not be passed to Gosia for fitting matrix elements. The expected date for the bug fix is not known. In the meantime, separate each state to a separate band. (It may be sufficient to separate the ground state and put it in band #1, then put all remaining states in another band.) Be sure to check the K values that the GUI has assumed and normalization constants for the Alaga rule compared to the in-band rotor model.<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with this version.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
Refer to the bug-fix above. To correct possible errors in prior fits, do the following 'if a fit has been performed'.<br />
No corrections are needed if a fit has not been performed with an earlier version.<br />
<br />
# Rewrite the Gosia yield file using the button "Write Gosia yld file."<br />
# Re-run the "Make corrected yields" calculation.<br />
# Re-run the "Fit" calculation.<br />
# Re-run any error calculations that have been done.<br />
# Before comparing experimental yields to calculated yields (plotting, etc.), re-run "Integrated yields" to update the calculated yields for the new matrix elements.<br />
# Save the session.<br />
<br />
The new fitted matrix elements can be compared to previous calculations to see if the bug had affected fits.<br />
<br />
To migrate from a beta version to this version, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.4==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
The user must now answer "y" or "n" when asked whether to save the session upon exiting. This helps to prevent accidentally overwriting the session file.<br />
<br />
====Bug-fixes====<br />
<br />
All yield data are properly displayed when plotting yields for merged bands.<br />
<br />
Some previous versions did not parse comments properly in detector array files has been fixed. This bug had made it impossible to import a few of the array files that come with the Rachel package.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.4.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.4, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.3==<br />
<br />
===Known bugs and issues===<br />
<br />
''The following bug affects the plotting function, but does not affect the accuracy of calculations.''<br />
<br />
In some cases, plots of gamma-ray yields will not show all of the data for merged bands. For example, if odd-spin states in band "b" are merged into the even spin states of band "a," a plot of the yield data for the merged band "a" may not show the yields from the states of the original band "b." <br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.3.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
It is now possible to add in-band matrix elements of any multipolarity that conserves parity, i.e., E2, E4, E6 and M1. There was no accuracy error associated with this bug.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.3, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-05-16T18:09:32Z<p>Hayes: /* Downloads */ Updated to manual version 2012 05 10</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[common_mistakes | Common mistakes in Gosia calculations]]<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120510) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120510.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.5.tar Rachel release version 1.1.5], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_format_matrix_fileRachel format matrix file2012-05-03T14:39:45Z<p>Hayes: Added general format description and format for coupled (dependent) matrix elements</p>
<hr />
<div>Rachel can import a matrix from a text file. Currently the Rachel format below is the only one supported, but in the future it will be possible to read the level scheme and matrix from a Gosia input file.<br />
<br />
The format of the matrix file is shown below by example.<br />
<br />
<pre><br />
g 0.0 g 2.0 E2 0.7 master 0.01 5.<br />
g 2.0 g 2.0 E2 0.1 master -5. 5. <br />
g 2.0 g 4.0 E2 0.5 master 0.01 5.0<br />
g 4.0 g 4.0 E2 0.2 fixed <br />
a 4.0 a 5.0 E2 0.3 master 0.01 10.0<br />
a 4.0 a 5.0 M1 0.4 coupled E2 a 4.0 a 5.0<br />
</pre><br />
<br />
The general format is<br />
<br />
<pre><br />
initial_band_name initial_spin final_band_name final_spin multipole_code value "fixed"<br />
</pre><br />
<br />
(omitting quotation marks) for a fixed-value matrix element (not to be fitted),<br />
<br />
<pre><br />
initial_band_name initial_spin final_band_name final_spin multipole_code value "master" lower_limit upper_limit<br />
</pre><br />
<br />
(omitting quotation marks) for a master matrix element and<br />
<br />
<pre><br />
(same first 6 fields as above) "coupled" master_multipole master_initial_band master_initial_spin master_final_band master_final_spin<br />
</pre><br />
<br />
(omitting quotation marks) for a matrix element coupled to a master matrix element.<br />
<br />
The fixed/master/coupled status can be changed later in the GUI.<br />
<br />
The matrix element value is in units of powers of e, b and nuclear magnetons.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_format_matrix_fileRachel format matrix file2012-05-03T14:26:24Z<p>Hayes: Created page with "Rachel can import a matrix from a text file. Currently the Rachel format below is the only one supported, but in the future it will be possible to read the level scheme and matr..."</p>
<hr />
<div>Rachel can import a matrix from a text file. Currently the Rachel format below is the only one supported, but in the future it will be possible to read the level scheme and matrix from a Gosia input file.<br />
<br />
The format of the matrix file is shown below by example.<br />
<br />
<pre><br />
g 0.0 g 2.0 E2 0.7 master 0.01 5.<br />
g 2.0 g 2.0 E2 0.1 master -5. 5. <br />
g 2.0 g 4.0 E2 0.5 master 0.01 5.0<br />
g 4.0 g 4.0 E2 0.0 fixed <br />
</pre><br />
<br />
The general format is<br />
<br />
<pre><br />
initial_band_name initial_spin final_band_name final_spin multipole_code value coupling_code [lower_limit upper_limit]<br />
</pre><br />
<br />
The matrix element value is in units of powers of e, b and nuclear magnetons.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_format_level_scheme_fileRachel format level scheme file2012-05-03T14:22:50Z<p>Hayes: </p>
<hr />
<div>See also [[rachel_format_matrix_file | Rachel format matrix file]].<br />
<br />
Rachel can read both Radware AGS ascii level scheme files and a simple human-readable level scheme file. The Rachel-format level scheme file is most easily understood from the following example:<br />
<br />
<pre><br />
# Not a real level scheme!<br />
75 184 # The Z and A number must appear first<br />
band1 0.5 + 0.0 # The ground 1/2+ state at 0 keV<br />
band1 1.5 + 100.0 # The first excited 3/2+ state at 100 keV<br />
band1 2.5 + 200.0<br />
a 2.5 - 250.0 # All states in one band must have the same parity<br />
a 3.5 - 350.0 # The second band will be named "a".<br />
a 4.5 - 450.0<br />
band1 3.5 + 300.0 # States can appear in any order<br />
</pre><br />
<br />
When the file is read into Rachel, a new band is created any time a new band name is encountered. It is useful to arrange levels in bands to simplify defining initial matrix elements using a rotor model. (Gosia is not aware of bands.) <br />
<br />
Levels can appear in any order.<br />
<br />
Choose short band names (about 8 characters or fewer) to make the level scheme display clearly. These band names will be referenced in [[rachel_yield_data_files | gamma-ray yield data files]].<br />
<br />
Note the following requirements:<br />
<br />
All levels with the same band name must have the same parity, or an error will be produced.<br />
<br />
There may be only one state of a given spin in a single band.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-05-02T14:41:38Z<p>Hayes: /* Downloads */ updated manual to May 1 2012</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[common_mistakes | Common mistakes in Gosia calculations]]<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120501) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120501.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.5.tar Rachel release version 1.1.5], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-04-30T15:14:16Z<p>Hayes: /* Known bugs and issues */</p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.5==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
None<br />
<br />
====Bug-fixes====<br />
<br />
A bug that affected only the fitting and corrected yield calculations has been fixed. Occasionally, but not always, this bug resulted in incorrect yield data being passed to Gosia using the "Write Gosia yld file" button, which would affect fitting. It did not affect integrated yield calculations, simulations or plotting, and the integrated yield function still gave the correct chi-squared value. <br />
<br />
See the recommendations section below.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions to date, the sensitivity map (OP,MAP) is calculated in the same Gosia call that does a fit (OP,MINI). This works in most cases, but it may cause errors occasionally in inverse-kinematics calculations. (This is not confirmed, but the error will be reported if it occurs.) The sensitivity map will be calculated in a separate call in the next bug-fix version.<br />
<br />
Level schemes that do not have spins in order of increasing energy within a band, e.g. 1-, 0-, 3-, 2-..., will cause errors in generating the Gosia input, and the full yield data set may not be passed to Gosia for fitting matrix elements. The expected date for the bug fix is not known. In the meantime, separate each state to a separate band. (It may be sufficient to separate the ground state and put it in band #1, then put all remaining states in another band.) Be sure to check the K values that the GUI has assumed and normalization constants for the Alaga rule compared to the in-band rotor model.<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with this version.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
Refer to the bug-fix above. To correct possible errors in prior fits, do the following 'if a fit has been performed'.<br />
No corrections are needed if a fit has not been performed with an earlier version.<br />
<br />
# Rewrite the Gosia yield file using the button "Write Gosia yld file."<br />
# Re-run the "Make corrected yields" calculation.<br />
# Re-run the "Fit" calculation.<br />
# Re-run any error calculations that have been done.<br />
# Before comparing experimental yields to calculated yields (plotting, etc.), re-run "Integrated yields" to update the calculated yields for the new matrix elements.<br />
# Save the session.<br />
<br />
The new fitted matrix elements can be compared to previous calculations to see if the bug had affected fits.<br />
<br />
To migrate from a beta version to this version, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.4==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
The user must now answer "y" or "n" when asked whether to save the session upon exiting. This helps to prevent accidentally overwriting the session file.<br />
<br />
====Bug-fixes====<br />
<br />
All yield data are properly displayed when plotting yields for merged bands.<br />
<br />
Some previous versions did not parse comments properly in detector array files has been fixed. This bug had made it impossible to import a few of the array files that come with the Rachel package.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.4.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.4, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.3==<br />
<br />
===Known bugs and issues===<br />
<br />
''The following bug affects the plotting function, but does not affect the accuracy of calculations.''<br />
<br />
In some cases, plots of gamma-ray yields will not show all of the data for merged bands. For example, if odd-spin states in band "b" are merged into the even spin states of band "a," a plot of the yield data for the merged band "a" may not show the yields from the states of the original band "b." <br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.3.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
It is now possible to add in-band matrix elements of any multipolarity that conserves parity, i.e., E2, E4, E6 and M1. There was no accuracy error associated with this bug.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.3, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-04-30T15:06:50Z<p>Hayes: /* Known bugs and issues */</p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.5==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
None<br />
<br />
====Bug-fixes====<br />
<br />
A bug that affected only the fitting and corrected yield calculations has been fixed. Occasionally, but not always, this bug resulted in incorrect yield data being passed to Gosia using the "Write Gosia yld file" button, which would affect fitting. It did not affect integrated yield calculations, simulations or plotting, and the integrated yield function still gave the correct chi-squared value. <br />
<br />
See the recommendations section below.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions to date, the sensitivity map (OP,MAP) is calculated in the same Gosia call that does a fit (OP,MINI). This works in most cases, but it may cause errors occasionally in inverse-kinematics calculations. (This is not confirmed, but the error will be reported if it occurs.) The sensitivity map will be calculated in a separate call in the next bug-fix version.<br />
<br />
Level schemes that do not have spins in order of increasing energy within a band, e.g. 1-, 0-, 3-, 2-..., will cause errors in generating the Gosia input, and the full yield data set may not be passed to Gosia for fitting matrix elements. The expected date for the bug fix is not known. In the meantime, separate each state to a separate band.<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with this version.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
Refer to the bug-fix above. To correct possible errors in prior fits, do the following 'if a fit has been performed'.<br />
No corrections are needed if a fit has not been performed with an earlier version.<br />
<br />
# Rewrite the Gosia yield file using the button "Write Gosia yld file."<br />
# Re-run the "Make corrected yields" calculation.<br />
# Re-run the "Fit" calculation.<br />
# Re-run any error calculations that have been done.<br />
# Before comparing experimental yields to calculated yields (plotting, etc.), re-run "Integrated yields" to update the calculated yields for the new matrix elements.<br />
# Save the session.<br />
<br />
The new fitted matrix elements can be compared to previous calculations to see if the bug had affected fits.<br />
<br />
To migrate from a beta version to this version, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.4==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
The user must now answer "y" or "n" when asked whether to save the session upon exiting. This helps to prevent accidentally overwriting the session file.<br />
<br />
====Bug-fixes====<br />
<br />
All yield data are properly displayed when plotting yields for merged bands.<br />
<br />
Some previous versions did not parse comments properly in detector array files has been fixed. This bug had made it impossible to import a few of the array files that come with the Rachel package.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.4.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.4, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.3==<br />
<br />
===Known bugs and issues===<br />
<br />
''The following bug affects the plotting function, but does not affect the accuracy of calculations.''<br />
<br />
In some cases, plots of gamma-ray yields will not show all of the data for merged bands. For example, if odd-spin states in band "b" are merged into the even spin states of band "a," a plot of the yield data for the merged band "a" may not show the yields from the states of the original band "b." <br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.3.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
It is now possible to add in-band matrix elements of any multipolarity that conserves parity, i.e., E2, E4, E6 and M1. There was no accuracy error associated with this bug.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.3, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-04-30T15:00:57Z<p>Hayes: </p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.5==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
None<br />
<br />
====Bug-fixes====<br />
<br />
A bug that affected only the fitting and corrected yield calculations has been fixed. Occasionally, but not always, this bug resulted in incorrect yield data being passed to Gosia using the "Write Gosia yld file" button, which would affect fitting. It did not affect integrated yield calculations, simulations or plotting, and the integrated yield function still gave the correct chi-squared value. <br />
<br />
See the recommendations section below.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions to date, the sensitivity map (OP,MAP) is calculated in the same Gosia call that does a fit (OP,MINI). This works in most cases, but it may cause errors occasionally in inverse-kinematics calculations. (This is not confirmed, but the error will be reported if it occurs.) The sensitivity map will be calculated in a separate call in the next bug-fix version.<br />
<br />
Level schemes that have the spins not in order of increasing energy within a band, e.g. 1-, 0-, 3-, 2-..., will cause errors in generating the Gosia input, and the full yield data set may not be passed to Gosia for fitting matrix elements. The bug will be fixed in the next bug-fix version. In the meantime, separate each state to a separate band.<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with this version.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
Refer to the bug-fix above. To correct possible errors in prior fits, do the following 'if a fit has been performed'.<br />
No corrections are needed if a fit has not been performed with an earlier version.<br />
<br />
# Rewrite the Gosia yield file using the button "Write Gosia yld file."<br />
# Re-run the "Make corrected yields" calculation.<br />
# Re-run the "Fit" calculation.<br />
# Re-run any error calculations that have been done.<br />
# Before comparing experimental yields to calculated yields (plotting, etc.), re-run "Integrated yields" to update the calculated yields for the new matrix elements.<br />
# Save the session.<br />
<br />
The new fitted matrix elements can be compared to previous calculations to see if the bug had affected fits.<br />
<br />
To migrate from a beta version to this version, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.4==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
The user must now answer "y" or "n" when asked whether to save the session upon exiting. This helps to prevent accidentally overwriting the session file.<br />
<br />
====Bug-fixes====<br />
<br />
All yield data are properly displayed when plotting yields for merged bands.<br />
<br />
Some previous versions did not parse comments properly in detector array files has been fixed. This bug had made it impossible to import a few of the array files that come with the Rachel package.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.4.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.4, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.3==<br />
<br />
===Known bugs and issues===<br />
<br />
''The following bug affects the plotting function, but does not affect the accuracy of calculations.''<br />
<br />
In some cases, plots of gamma-ray yields will not show all of the data for merged bands. For example, if odd-spin states in band "b" are merged into the even spin states of band "a," a plot of the yield data for the merged band "a" may not show the yields from the states of the original band "b." <br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.3.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
It is now possible to add in-band matrix elements of any multipolarity that conserves parity, i.e., E2, E4, E6 and M1. There was no accuracy error associated with this bug.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.3, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-04-30T13:48:29Z<p>Hayes: /* Known bugs and issues */</p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.5==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
None<br />
<br />
====Bug-fixes====<br />
<br />
A bug that affected only the fitting and corrected yield calculations has been fixed. Occasionally, but not always, this bug resulted in incorrect yield data being passed to Gosia using the "Write Gosia yld file" button, which would affect fitting. It did not affect integrated yield calculations, simulations or plotting, and the integrated yield function still gave the correct chi-squared value. <br />
<br />
See the recommendations section below.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions to date, the sensitivity map (OP,MAP) is calculated in the same Gosia call that does a fit (OP,MINI). This works in most cases, but it may cause errors occasionally in inverse-kinematics calculations. (This is not confirmed, but the error will be reported if it occurs.) The sensitivity map will be calculated in a separate call in the next bug-fix version.<br />
<br />
Level schemes that have the spins not in order of increasing energy, e.g. 1-, 0-, 3-, 2-..., in the ground band may likely cause errors in Gosia calculations, and the full yield data set may not be passed to Gosia for fitting matrix elements. The bug will be fixed in the next bug-fix version. In the meantime, put the ground state in one band (band #1 as usual) and the remaining states in the band in another band.<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with this version.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
Refer to the bug-fix above. To correct possible errors in prior fits, do the following 'if a fit has been performed'.<br />
No corrections are needed if a fit has not been performed with an earlier version.<br />
<br />
# Rewrite the Gosia yield file using the button "Write Gosia yld file."<br />
# Re-run the "Make corrected yields" calculation.<br />
# Re-run the "Fit" calculation.<br />
# Re-run any error calculations that have been done.<br />
# Before comparing experimental yields to calculated yields (plotting, etc.), re-run "Integrated yields" to update the calculated yields for the new matrix elements.<br />
# Save the session.<br />
<br />
The new fitted matrix elements can be compared to previous calculations to see if the bug had affected fits.<br />
<br />
To migrate from a beta version to this version, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.4==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
The user must now answer "y" or "n" when asked whether to save the session upon exiting. This helps to prevent accidentally overwriting the session file.<br />
<br />
====Bug-fixes====<br />
<br />
All yield data are properly displayed when plotting yields for merged bands.<br />
<br />
Some previous versions did not parse comments properly in detector array files has been fixed. This bug had made it impossible to import a few of the array files that come with the Rachel package.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.4.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.4, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.3==<br />
<br />
===Known bugs and issues===<br />
<br />
''The following bug affects the plotting function, but does not affect the accuracy of calculations.''<br />
<br />
In some cases, plots of gamma-ray yields will not show all of the data for merged bands. For example, if odd-spin states in band "b" are merged into the even spin states of band "a," a plot of the yield data for the merged band "a" may not show the yields from the states of the original band "b." <br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.3.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
It is now possible to add in-band matrix elements of any multipolarity that conserves parity, i.e., E2, E4, E6 and M1. There was no accuracy error associated with this bug.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.3, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-03-05T16:09:48Z<p>Hayes: updated to 1.1.5 rachel</p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.5==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
None<br />
<br />
====Bug-fixes====<br />
<br />
A bug that affected only the fitting and corrected yield calculations has been fixed. Occasionally, but not always, this bug resulted in incorrect yield data being passed to Gosia using the "Write Gosia yld file" button, which would affect fitting. It did not affect integrated yield calculations, simulations or plotting, and the integrated yield function still gave the correct chi-squared value. <br />
<br />
See the recommendations section below.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with this version.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
Refer to the bug-fix above. To correct possible errors in prior fits, do the following 'if a fit has been performed'.<br />
No corrections are needed if a fit has not been performed with an earlier version.<br />
<br />
# Rewrite the Gosia yield file using the button "Write Gosia yld file."<br />
# Re-run the "Make corrected yields" calculation.<br />
# Re-run the "Fit" calculation.<br />
# Re-run any error calculations that have been done.<br />
# Before comparing experimental yields to calculated yields (plotting, etc.), re-run "Integrated yields" to update the calculated yields for the new matrix elements.<br />
# Save the session.<br />
<br />
The new fitted matrix elements can be compared to previous calculations to see if the bug had affected fits.<br />
<br />
To migrate from a beta version to this version, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.4==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
The user must now answer "y" or "n" when asked whether to save the session upon exiting. This helps to prevent accidentally overwriting the session file.<br />
<br />
====Bug-fixes====<br />
<br />
All yield data are properly displayed when plotting yields for merged bands.<br />
<br />
Some previous versions did not parse comments properly in detector array files has been fixed. This bug had made it impossible to import a few of the array files that come with the Rachel package.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.4.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.4, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.3==<br />
<br />
===Known bugs and issues===<br />
<br />
''The following bug affects the plotting function, but does not affect the accuracy of calculations.''<br />
<br />
In some cases, plots of gamma-ray yields will not show all of the data for merged bands. For example, if odd-spin states in band "b" are merged into the even spin states of band "a," a plot of the yield data for the merged band "a" may not show the yields from the states of the original band "b." <br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.3.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
It is now possible to add in-band matrix elements of any multipolarity that conserves parity, i.e., E2, E4, E6 and M1. There was no accuracy error associated with this bug.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.3, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2012-03-05T15:56:09Z<p>Hayes: updated to 1.1.5 rachel</p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. Versions 1.* have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Release version 1.1.5 is now available. This version does not read beta-version files, but level schemes and matrices can be ported following the instructions in the 2012 version of the Gosia manual. Refer to the [[gui_release_notes | release notes]] for the change in this version and known issues.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.5.tar Rachel 1.1.5 download]<br />
<br />
==Version notes==<br />
<br />
The [[Gui_release_notes | version notes page]] gives a history of Rachel updates. Known issues are given for each version, as well as the current version.<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
Rachel has been installed successfully on the following systems. You can view or submit detailed installation notes for these or other systems. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When changing to version 1.0 or later, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data. Subsequent versions will have the automatic upgrading reinstated.<br />
<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, many of which have already been added to versions 1.0 and later. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-03-05T15:55:20Z<p>Hayes: updated to 1.1.5 rachel</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[common_mistakes | Common mistakes in Gosia calculations]]<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120125) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120125.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.5.tar Rachel release version 1.1.5], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gosia_errorsGosia errors2012-03-04T17:52:59Z<p>Hayes: Created page with "The errors described below are reported in the output file, and/or in the terminal as a Gosia calculation terminates. ==Exceeding the range of conversion coefficients== When us..."</p>
<hr />
<div>The errors described below are reported in the output file, and/or in the terminal as a Gosia calculation terminates.<br />
<br />
==Exceeding the range of conversion coefficients==<br />
<br />
When using the built-in internal conversion coefficient calculation function, there may be frequent reports similar to the following.<br />
<br />
<pre><br />
Warning Egamma= 0.8596 exceeds range of conversion coefficients table for shell N7 <br />
0.8596 2.174E-03 5.586E-03 1.299E-02 1.212E-02 3.128E-02<br />
</pre><br />
<br />
This does not necessarily indicate an accuracy error in Gosia calculations. The internal conversion coefficients reported after the warnings can be checked for accuracy. Accuracy errors in [[internal_conversion | internal conversion coefficients]] should only be large near K, L,... edges and for very low gamma-ray energies. (reference needed)</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Common_mistakesCommon mistakes2012-03-04T15:44:15Z<p>Hayes: </p>
<hr />
<div>==Too many fit parameters (e.g. forgetting the overall normalization parameter)==<br />
<br />
This problem will not cause an error to be reported by Gosia.<br />
<br />
If the system is not overdetermined, then fits will not represent a true minimum. With more than a few fit parameters, the system must be very overdetermined using many experiments or scattering angle ranges, etc.<br />
<br />
A common mistake is to forget that Gosia must fit the overall normalization of cross section to measured gamma-ray counts. (This effectively includes the total beam dose, detector efficiencies, etc.) If, for example, Gosia is used to try to fit the B(E2) in a two-state calculation, this overall normalization parameter will adjust to allow any B(E2) value at the chi-squared minimum. The fit will converge, and Gosia will not report an error, but the fitted B(E2) will be meaningless.<br />
<br />
Using Gosia 2 in two-state systems with measured yields for both the projectile and the target is designed to overcome this problem.<br />
<br />
==Insufficient integration accuracy==<br />
<br />
This problem will not cause an error to be reported by Gosia.<br />
<br />
Gosia does not test that the [[integrated_yields | integrated yields]] (the accurate yields or cross sections integrated over the energy loss in the target and the solid angle of the scattered particle) are converged. Usually, the most sensitive set is the angular meshpoints, but this is not always the case.<br />
<br />
===Integration meshpoints===<br />
<br />
Gosia does not test convergence for the user's chosen integration meshpoints. <br />
<br />
If the integrated yields are not converged, then the predicted cross sections will be inaccurate, and this will also cause an inaccurate fit via the [[corrected_yields | corrected yields]].<br />
<br />
There are two ways to test for convergence:<br />
<br />
# The Rachel interface chooses sufficient meshpoints in energy and scattering angle for convergence, but possibly more than necessary. Generating an input with Rachel, or running all calculations in Rachel 'should' always give converged calculations. Rachel also has a built-in test, option "ti" in the Tools button menu, that will test the convergence for a choice of meshpoints. However, sometimes Gosia does not have sufficient memory for this test for very large level schemes, and it must be performed with a subset of the bands.<br />
<br />
# The only certain test that there are sufficient meshpoints for convergence is to look at the integrated yields (OP,INTI) with an increasing number of meshpoints 'for each experiment'. Once the required meshpoint spacing is found, calculation time can be minimized by choosing the fewest required.<br />
<br />
Once the meshpoint requirement has been found, it does not need to be tested again for OP,CORR [[corrected_yields | corrected yields]] or any other function.<br />
<br />
===Integration meshpoint subdivisions===<br />
<br />
The meshpoint [[integration_subdivisions | subdivisions]] can be tested to see if increasing the number of subdivisions will allow for fewer required meshpoints. Increasing the number of meshpoints significantly increases the calculation time, but increasing the number of subdivisions does not. (It is probably wisest to pick 50 or 100 subdivisions and then test for the required number of meshpoints for convergence.)<br />
<br />
===Convergence of the coupled-channels calculations===<br />
<br />
In order to ensure convergence in the point cross sections, it is best to prevent Gosia from trying to reduce the step-size used in the collision trajectory. This is done by adding the "INT," control to the CONT section of the input. (Refer to "CONT" in the Gosia manual.) To turn off the step-size reduction, add<br />
<br />
<pre><br />
INT,X.<br />
1, 1000<br />
2, 1000<br />
...<br />
</pre><br />
<br />
where X is the number of experiments in the input, and 1, 2, ... are the experiment numbers 1 through X. The decimal point is required after X.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Common_mistakesCommon mistakes2012-03-04T14:26:24Z<p>Hayes: </p>
<hr />
<div>==Too many fit parameters (forgetting the overall normalization parameter)==<br />
<br />
This problem will not cause an error to be reported by Gosia.<br />
<br />
If the system is not overdetermined, then fits will not represent a true minimum. With more than a few fit parameters, the system must be very overdetermined using many experiments or scattering angle ranges, etc.<br />
<br />
A common mistake is to forget that Gosia must fit the overall normalization of cross section to measured gamma-ray counts. (This effectively includes the total beam dose, detector efficiencies, etc.) If, for example, Gosia is used to try to fit the B(E2) in a two-state calculation, this overall normalization parameter will adjust to allow any B(E2) value at the chi-squared minimum. The fit will converge, and Gosia will not report an error, but the fitted B(E2) will be meaningless.<br />
<br />
Using Gosia 2 in two-state systems with measured yields for both the projectile and the target is designed to overcome this problem.<br />
<br />
==Insufficient integration accuracy==<br />
<br />
This problem will not cause an error to be reported by Gosia.<br />
<br />
Gosia does not test that the [[integrated_yields | integrated yields]] (the accurate yields or cross sections integrated over the energy loss in the target and the solid angle of the scattered particle) are converged. Usually, the most sensitive set is the angular meshpoints, but this is not always the case.<br />
<br />
===Integration meshpoints===<br />
<br />
Gosia does not test convergence for the user's chosen integration meshpoints. <br />
<br />
If the integrated yields are not converged, then the predicted cross sections will be inaccurate, and this will also cause an inaccurate fit via the [[corrected_yields | corrected yields]].<br />
<br />
There are two ways to test for convergence:<br />
<br />
# The Rachel interface chooses sufficient meshpoints in energy and scattering angle for convergence, but possibly more than necessary. Generating an input with Rachel, or running all calculations in Rachel 'should' always give converged calculations. Rachel also has a built-in test, option "ti" in the Tools button menu, that will test the convergence for a choice of meshpoints. However, sometimes Gosia does not have sufficient memory for this test for very large level schemes, and it must be performed with a subset of the bands.<br />
<br />
# The only certain test that there are sufficient meshpoints for convergence is to look at the integrated yields (OP,INTI) with an increasing number of meshpoints 'for each experiment'. Once the required meshpoint spacing is found, calculation time can be minimized by choosing the fewest required.<br />
<br />
Once the meshpoint requirement has been found, it does not need to be tested again for OP,CORR [[corrected_yields | corrected yields]] or any other function.<br />
<br />
===Integration meshpoint subdivisions===<br />
<br />
The meshpoint [[integration_subdivisions | subdivisions]] can be tested to see if increasing the number of subdivisions will allow for fewer required meshpoints. Increasing the number of meshpoints significantly increases the calculation time, but increasing the number of subdivisions does not. (It is probably wisest to pick 50 or 100 subdivisions and then test for the required number of meshpoints for convergence.)<br />
<br />
===Convergence of the coupled-channels calculations===<br />
<br />
In order to ensure convergence in the point cross sections, it is best to prevent Gosia from trying to reduce the step-size used in the collision trajectory. This is done by adding the "INT," control to the CONT section of the input. (Refer to "CONT" in the Gosia manual.) To turn off the step-size reduction, add<br />
<br />
<pre><br />
INT,X.<br />
1, 1000<br />
2, 1000<br />
...<br />
</pre><br />
<br />
where X is the number of experiments in the input, and 1, 2, ... are the experiment numbers 1 through X. The decimal point is required after X.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Common_mistakesCommon mistakes2012-03-04T14:21:06Z<p>Hayes: </p>
<hr />
<div>==Too many fit parameters (forgetting the overall normalization parameter)==<br />
<br />
This problem will not cause an error to be reported by Gosia.<br />
<br />
If the system is not overdetermined, then fits will not represent a true minimum. With more than a few fit parameters, the system must be very overdetermined using many experiments or scattering angle ranges, etc.<br />
<br />
A common mistake is to forget that Gosia must fit the overall normalization of cross section to measured gamma-ray counts. (This effectively includes the total beam dose, detector efficiencies, etc.) If, for example, Gosia is used to try to fit the B(E2) in a two-state calculation, this overall normalization parameter will adjust to allow any B(E2) value at the chi-squared minimum. The fit will converge, and Gosia will not report an error, but the fitted B(E2) will be meaningless.<br />
<br />
Using Gosia 2 in two-state systems with measured yields for both the projectile and the target is designed to overcome this problem.<br />
<br />
==Insufficient integration accuracy==<br />
<br />
This problem will not cause an error to be reported by Gosia.<br />
<br />
Gosia does not test that the [[integrated_yields | integrated yields]] (the accurate yields or cross sections integrated over the energy loss in the target and the solid angle of the scattered particle) are converged. Usually, the most sensitive set is the angular meshpoints, but this is not always the case.<br />
<br />
===Integration meshpoints===<br />
<br />
Gosia does not test convergence for the user's chosen integration meshpoints. <br />
<br />
If the integrated yields are not converged, then the predicted cross sections will be inaccurate, and this will also cause an inaccurate fit via the [[corrected_yields | corrected yields]].<br />
<br />
There are two ways to test for convergence:<br />
<br />
# The Rachel interface chooses sufficient meshpoints in energy and scattering angle for convergence, but possibly more than necessary. Generating an input with Rachel, or running all calculations in Rachel 'should' always give converged calculations. Rachel also has a built-in test, option "ti" in the Tools button menu, that will test the convergence for a choice of meshpoints. However, sometimes Gosia does not have sufficient memory for this test for very large level schemes, and it must be performed with a subset of the bands.<br />
<br />
# The only certain test that there are sufficient meshpoints for convergence is to look at the integrated yields (OP,INTI) with an increasing number of meshpoints 'for each experiment'. Once the required meshpoint spacing is found, calculation time can be minimized by choosing the fewest required.<br />
<br />
Once the meshpoint requirement has been found, it does not need to be tested again for OP,CORR [[corrected_yields | corrected yields]] or any other function.<br />
<br />
===Integration meshpoint subdivisions===<br />
<br />
The meshpoint [[integration_subdivisions | subdivisions]] can be tested to see if increasing the number of subdivisions will allow for fewer required meshpoints. Increasing the number of meshpoints significantly increases the calculation time, but increasing the number of subdivisions does not. (It is probably wisest to pick 50 or 100 subdivisions and then test for the required number of meshpoints for convergence.)</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Common_mistakesCommon mistakes2012-03-03T15:12:53Z<p>Hayes: </p>
<hr />
<div><br />
==Too many fit parameters (forgetting the overall normalization parameter)==<br />
<br />
If the system is not overdetermined, then fits will not represent a true minimum. With more than a few fit parameters, the system must be very overdetermined using many experiments or scattering angle ranges, etc.<br />
<br />
A common mistake is to forget that Gosia must fit the overall normalization of cross section to measured gamma-ray counts. (This effectively includes the total beam dose, detector efficiencies, etc.) If, for example, Gosia is used to try to fit the B(E2) in a two-state calculation, this overall normalization parameter will adjust to allow any B(E2) value at the chi-squared minimum. The fit will converge, and Gosia will not report an error, but the fitted B(E2) will be meaningless.<br />
<br />
Using Gosia 2 in two-state systems with measured yields for both the projectile and the target is designed to overcome this problem.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Common_mistakesCommon mistakes2012-03-03T15:12:38Z<p>Hayes: Created page with " This page will be updated soon. ==Too many fit parameters (forgetting the overall normalization parameter)== If the system is not overdetermined, then fits will not represent ..."</p>
<hr />
<div><br />
This page will be updated soon.<br />
<br />
==Too many fit parameters (forgetting the overall normalization parameter)==<br />
<br />
If the system is not overdetermined, then fits will not represent a true minimum. With more than a few fit parameters, the system must be very overdetermined using many experiments or scattering angle ranges, etc.<br />
<br />
A common mistake is to forget that Gosia must fit the overall normalization of cross section to measured gamma-ray counts. (This effectively includes the total beam dose, detector efficiencies, etc.) If, for example, Gosia is used to try to fit the B(E2) in a two-state calculation, this overall normalization parameter will adjust to allow any B(E2) value at the chi-squared minimum. The fit will converge, and Gosia will not report an error, but the fitted B(E2) will be meaningless.<br />
<br />
Using Gosia 2 in two-state systems with measured yields for both the projectile and the target is designed to overcome this problem.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-03-03T15:06:24Z<p>Hayes: /* Selected special topics */</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[common_mistakes | Common mistakes in Gosia calculations]]<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120125) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120125.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.4.tar Rachel release version 1.1.4], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-03-03T12:47:17Z<p>Hayes: changed the order of subsections</p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.4==<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
===Changes===<br />
<br />
The user must now answer "y" or "n" when asked whether to save the session upon exiting. This helps to prevent accidentally overwriting the session file.<br />
<br />
====Bug-fixes====<br />
<br />
All yield data are properly displayed when plotting yields for merged bands.<br />
<br />
Some previous versions did not parse comments properly in detector array files has been fixed. This bug had made it impossible to import a few of the array files that come with the Rachel package.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.4.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.4, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.3==<br />
<br />
===Known bugs and issues===<br />
<br />
''The following bug affects the plotting function, but does not affect the accuracy of calculations.''<br />
<br />
In some cases, plots of gamma-ray yields will not show all of the data for merged bands. For example, if odd-spin states in band "b" are merged into the even spin states of band "a," a plot of the yield data for the merged band "a" may not show the yields from the states of the original band "b." <br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.3.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
It is now possible to add in-band matrix elements of any multipolarity that conserves parity, i.e., E2, E4, E6 and M1. There was no accuracy error associated with this bug.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.3, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-03-03T12:46:04Z<p>Hayes: added 1.1.4</p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.4==<br />
<br />
===Changes===<br />
<br />
The user must now answer "y" or "n" when asked whether to save the session upon exiting. This helps to prevent accidentally overwriting the session file.<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.4.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
This version is backward-compatible with all versions 1.0 and later.<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
All yield data are properly displayed when plotting yields for merged bands.<br />
<br />
Some previous versions did not parse comments properly in detector array files has been fixed. This bug had made it impossible to import a few of the array files that come with the Rachel package.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.4, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.3==<br />
<br />
===Known bugs and issues===<br />
<br />
''The following bug affects the plotting function, but does not affect the accuracy of calculations.''<br />
<br />
In some cases, plots of gamma-ray yields will not show all of the data for merged bands. For example, if odd-spin states in band "b" are merged into the even spin states of band "a," a plot of the yield data for the merged band "a" may not show the yields from the states of the original band "b." <br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.3.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
It is now possible to add in-band matrix elements of any multipolarity that conserves parity, i.e., E2, E4, E6 and M1. There was no accuracy error associated with this bug.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.3, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-03-03T12:38:34Z<p>Hayes: changed to version 1.1.4</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120125) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120125.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.4.tar Rachel release version 1.1.4], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2012-03-03T12:37:43Z<p>Hayes: changed to version 1.1.4</p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. Versions 1.* have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Release version 1.1.4 is now available. This version does not read beta-version files, but level schemes and matrices can be ported following the instructions in the 2012 version of the Gosia manual. Refer to the [[gui_release_notes | release notes]] for the change in this version and known issues.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.4.tar Rachel 1.1.4 download]<br />
<br />
==Version notes==<br />
<br />
The [[Gui_release_notes | version notes page]] gives a history of Rachel updates. Known issues are given for each version, as well as the current version.<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
Rachel has been installed successfully on the following systems. You can view or submit detailed installation notes for these or other systems. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When changing to version 1.0 or later, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data. Subsequent versions will have the automatic upgrading reinstated.<br />
<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, many of which have already been added to versions 1.0 and later. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-02-24T13:56:45Z<p>Hayes: </p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.3==<br />
<br />
===Known bugs and issues===<br />
<br />
''The following bug affects the plotting function, but does not affect the accuracy of calculations.''<br />
<br />
In some cases, plots of gamma-ray yields will not show all of the data for merged bands. For example, if odd-spin states in band "b" are merged into the even spin states of band "a," a plot of the yield data for the merged band "a" may not show the yields from the states of the original band "b." <br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.3.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
It is now possible to add in-band matrix elements of any multipolarity that conserves parity, i.e., E2, E4, E6 and M1. There was no accuracy error associated with this bug.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.3, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2012-02-24T13:45:20Z<p>Hayes: changed to v 1.1.3</p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. Versions 1.* have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Release version 1.1.3 is now available. This version does not read beta-version files, but level schemes and matrices can be ported following the instructions in the 2012 version of the Gosia manual. Refer to the [[gui_release_notes | release notes]] for the change in this version and known issues.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.3.tar Rachel 1.1.3 download]<br />
<br />
==Version notes==<br />
<br />
The [[Gui_release_notes | version notes page]] gives a history of Rachel updates. Known issues are given for each version, as well as the current version.<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
Rachel has been installed successfully on the following systems. You can view or submit detailed installation notes for these or other systems. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When changing to version 1.0 or later, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data. Subsequent versions will have the automatic upgrading reinstated.<br />
<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, many of which have already been added to versions 1.0 and later. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-02-24T13:44:00Z<p>Hayes: /* Downloads */ changed to rachel 1.1.3</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120125) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120125.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.3.tar Rachel release version 1.1.3], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2012-02-24T13:13:55Z<p>Hayes: </p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. Versions 1.* have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Release version 1.1.2 is now available. This version does not read beta-version files, but level schemes and matrices can be ported following the instructions in the 2012 version of the Gosia manual. Refer to the [[gui_release_notes | release notes]] for the change in this version and known issues.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.2.tar Rachel 1.1.2 download]<br />
<br />
==Version notes==<br />
<br />
The [[Gui_release_notes | version notes page]] gives a history of Rachel updates. Known issues are given for each version, as well as the current version.<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
Rachel has been installed successfully on the following systems. You can view or submit detailed installation notes for these or other systems. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When changing to version 1.0 or later, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data. Subsequent versions will have the automatic upgrading reinstated.<br />
<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, many of which have already been added to versions 1.0 and later. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-02-02T16:29:41Z<p>Hayes: added 1.1.2</p>
<hr />
<div>These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.2==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.2.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes caused the deorientation coefficient calculation to fail has been fixed. Calculations were accurate in previous versions, but sometimes could not be read from the Gosia output.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.2, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2012-02-02T16:27:08Z<p>Hayes: changes to reflect v. 1.1.2</p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. Versions 1.* have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Release version 1.1.2 is now available. This version does not read beta-version files, but level schemes and matrices can be ported following the instructions in the 2012 version of the Gosia manual. Refer to the [[gui_release_notes | release notes]] for the change in this version and known issues.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.2.tar Rachel 1.1.2 download]<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
Rachel has been installed successfully on the following systems. You can view or submit detailed installation notes for these or other systems. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When changing to version 1.0 or later, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data. Subsequent versions will have the automatic upgrading reinstated.<br />
<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, many of which have already been added to versions 1.0 and later. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-02-02T16:23:23Z<p>Hayes: /* Downloads */ update to rachel 1.1.2</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120125) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120125.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.2.tar Rachel release version 1.1.2], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2012-02-02T16:21:46Z<p>Hayes: update for 1.1.2</p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. The release-candidate version, expected in the September of 2011, will have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Release version 1.1.2 is now available. This version does not read beta-version files, but level schemes and matrices can be ported following the instructions in the 2012 version of the Gosia manual. Refer to the [[gui_release_notes | release notes]] for the change in this version and known issues.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.2.tar Rachel 1.1.2 download]<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
Rachel has been installed successfully on the following systems. You can view or submit detailed installation notes for these or other systems. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When the release candidate becomes available, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data.<br />
<br />
In the release versions, automatic upgrading of saved sessions will be reinstated.<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, ''some'' of which will be incorporated in the first [[rachel_release_candidate | release candidate] version. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2012-02-01T20:03:03Z<p>Hayes: </p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines. A Windows version is not planned.<br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. The release-candidate version, expected in the September of 2011, will have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Release version 1.1.1 is now available. This version does not read beta-version files, but level schemes and matrices can be ported following the instructions in the 2012 version of the Gosia manual. Refer to the [[gui_release_notes | release notes]] for the change in this version and known issues.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.1.tar Rachel 1.1.1 download]<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
Rachel has been installed successfully on the following systems. You can view or submit detailed installation notes for these or other systems. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When the release candidate becomes available, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data.<br />
<br />
In the release versions, automatic upgrading of saved sessions will be reinstated.<br />
<br />
==Capabilities of version 1==<br />
<br />
Note that there are major simplifications in the Ge detector array setup and data loading.<br />
<br />
* Human-readable data files that are robust for changes in the experimental setup and level scheme<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* A user-expandable library of detector arrays (Tigress, Miniball, Gammasphere...)<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and [[Rachel_yield_data_files | Rachel text format]] including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls, optional pop-up guidance and guided prompts<br />
* A searchable help function<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, ''some'' of which will be incorporated in the first [[rachel_release_candidate | release candidate] version. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-02-01T19:48:44Z<p>Hayes: changed from beta" to release version of GUI in text</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120125) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120125.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.1.tar Rachel release version 1.1.1], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed. The current version can be found in the download section above. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-01-30T13:59:15Z<p>Hayes: </p>
<hr />
<div><br />
These versions are listed from newest to oldest.<br />
<br />
=Versions 1.x=<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
===Description===<br />
<br />
See version 1.0.<br />
<br />
====Bug-fixes====<br />
<br />
A bug that sometimes prevented correlated errors from being read from the Gosia output has been fixed.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Gui_release_notesGui release notes2012-01-30T13:35:22Z<p>Hayes: </p>
<hr />
<div>=Versions 1.x=<br />
<br />
==Version 1.1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
==Version 1.1==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.1.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
<br />
===Description===<br />
<br />
See version 1.0<br />
<br />
====Bug-fixes====<br />
<br />
A bug in adding interband matrix elements is fixed. Version 1.0 did not include all allowed couplings.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.1, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
==Version 1.0==<br />
<br />
===Known bugs and issues===<br />
<br />
In all versions, it is possible to save an empty session over an existing session. Frequent backups of the working directory should be made.<br />
<br />
This version is not backward-compatible with the beta versions; users must re-define the experimental<br />
definitions. Level and matrix data CAN be exported from beta versions and imported to this version. All<br />
later versions are expected to preserve backward compatibility with version 1.0.<br />
Plots of collision functions cannot be generated for all states.<br />
<br />
The "fully-automatic" loading of yield data reports Ge detector numbers that are 1 larger than the correct number. This is misleading but does not cause any accuracy errors.<br />
<br />
===Description===<br />
<br />
Faster setup of calculations.<br />
<br />
Defining complicated detector arrays can be done in one operation.<br />
<br />
A library of detector types and arrays is included.<br />
<br />
Loading of all experimental yield data can be done in one operation.<br />
<br />
Simulations now use the standard definition of Ge efficiency.<br />
<br />
Simulated yield tables are clearer.<br />
<br />
Stopping power and exit energy are calculated by Elast automatically.<br />
<br />
The Rochester SRIM server can be called for more accurate stopping power data.<br />
<br />
Thick-target experiments are handled accurately, including backscatter detection from the surface.<br />
<br />
The correction to the gamma angular distribution now includes the motion of the emitting nucleus.<br />
<br />
Deorientation coefficients and lifetimes can be calulated in a few seconds.<br />
<br />
====Bug-fixes====<br />
<br />
Merging, deleting and reordering of bands are allowed at any time.<br />
<br />
Any number of bands can be merged. (See restrictions regarding duplicate spin states and different-parity<br />
states in one band.)<br />
<br />
Malfunctions during plotting of yield data are fixed. The overall normalization for all data sets is now<br />
used in plots comparing measured and predicted yields.<br />
<br />
The reported chi-squared values are properly-weighted on plots and in reports. (Chi-squared and<br />
normalization was done correctly in fits in all versions.)<br />
<br />
It is no longer necessary to reload yield data after changing the level scheme, unless new states are<br />
added.<br />
<br />
===Recommendations===<br />
<br />
To migrate from a beta version to version 1.0, export the level scheme and matrix, then import them into a<br />
new session in this version.<br />
<br />
=Beta Versions=<br />
<br />
==Version 2.0.8.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The GUI allows only simple changes to the level scheme after the matrix and experiment have been defined (adding and deleting of bands). The release candidate (expected September 2011) has the ability to merge and reorder bands at any time.<br />
<br />
If the level scheme is changed after calculated or experimental yield data are in memory, the user must reload the experimental data and generate new calculated yields. This has been fixed in the release candidate version (expected September 2011).<br />
<br />
===Description===<br />
<br />
This version uses a more accurate estimate of a typical Ge detector's ''intrinsic'' efficiency (based on Gammasphere's efficiency) to give approximate "raw" count rates. The total counts (for 100% efficienct detectors) were found to agree with perturbation calculations for weakly-coupled two-state systems, where the perturbation method is accurate.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are working with simulated data, refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for a description of the new output format and the meaning of terms.<br />
<br />
<br />
==Version 2.0.7.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
None<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.6.beta. <br />
<br />
# The simulated yield data are now updated properly. <br />
# The simulated data now include the proper Ge detector solid angle factor. Simulated yield data are corrected by dividing the simulated raw counts by a factor of <math>\epsilon \Delta\Omega_\gamma</math>, where <math>\epsilon</math> is the approximate intrinsic efficiency (<math>0<\epsilon <1</math>) and <math>\Delta\Omega_\gamma</math> is the solid angle subtended by the Ge detector. In previous Rachel versions, the absence of the solid angle factor would cause a systematic disagreement between Ge detectors only if they subtended different solid angles.<br />
<br />
Refer to the recommendations section if you are working with simulated yield data.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.6.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
If you are not working with simulated data, no corrections are needed.<br />
<br />
ONLY if simulated data are in use, re-run the simulated data calculation. Answer "yes" to the prompt to re-integrate the yield data.<br />
<br />
<br />
==Version 2.0.6.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
When calculating simulated yields, the new simulated yield data in session (and saved session file) will not be updated unless the user answers "y" to the prompt "Re-integrate the predicted yields? [Y/n]:" This may or may not affect subsequent fits to the simulated data, depending on the changes to the matrix, experimental parameters, detector arrangements, etc. The new simulated data are written correctly to the terminal and to the gosia yield file, so fits would not be affected, but a large disagreement between simulated data and calculated yields could appear on plots. ''Remedy: always choose to re-integrated the yields when calculating simulated yield data.''<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.5.beta. <br />
<br />
Refer to the notes for "Version 2.0.5.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.5.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
===Recommendations===<br />
<br />
After replacing an older version of Rachel with this version, re-integrate the calculated yields in memory by selecting "Integrated yields" and "Run gosia input" and clicking "Go." This will update the calculated yields and overwrite any erroneous calculated yields that may be in memory from the bug.<br />
<br />
==Version 2.0.5.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
The bug in version 2.0.4.beta is still not completely fixed. See below. A new version will be released probably in mid-June 2011. Refer to this post in the Gosia forum to see how to correct for the bug:<br />
<br />
[http://www-user.pas.rochester.edu/~gosia/phpBB3/viewtopic.php?f=9&t=9 Forum post on correcting for the bug]<br />
<br />
===Description===<br />
<br />
This is a bug-fix version relative to 2.0.4.beta, and some user prompts and output information is clarified. <br />
<br />
The GUI now correctly informs you of the choices of kinematic solutions for inverse kinematics cases. The safe energy is reported before asking for the initial beam energy.<br />
<br />
Refer to the notes for "Version 2.0.4.beta" below for the details of the bug fix and the recommended solution to update your session files.<br />
<br />
This version preserves the same backward compatibility with older session files as did version 2.0.4.beta.<br />
<br />
This is expected to be the last beta release before a significantly upgraded release version expected in July.<br />
<br />
==Version 2.0.4.beta==<br />
<br />
===Known bugs and issues===<br />
<br />
This version has one known bug: if the user selects "View gosia input" or "Save gosia input" for some types of calculations, such as "Integrated yields," inaccurate point yields would be stored in memory after the operation. This could be more or less apparent, depending on how accurate the point-scattering approximation is for the experiments defined. The absolute cross sections then reported on plots could then be extremely inaccurate.<br />
<br />
After running "Integrated yields" with "Run gosia input" selected, the calculated yields and absolute cross sections on plots would (again) be accurate.<br />
<br />
This bug does not affect real yield data or simulated yield data. This bug would not affect fitting of matrix elements, since the ''corrected'' yields used by Gosia are stored in an external file only.<br />
<br />
====Remedies====<br />
<br />
# Upgrade to version 2.0.5.beta.<br />
# Re-run the "Integrated yields" calculation to store accurately-calculated yields in memory. (Save the session.) This will update all calculated data in memory and on plots.</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_GUIRachel GUI2012-01-30T13:30:28Z<p>Hayes: /* How to get the Rachel package */</p>
<hr />
<div>==General description==<br />
<br />
[[File:Guisnapshot.png|thumb|right|A snapshot of the alpha version GUI.]]<br />
<br />
For a very short video demo of capabilities, refer to the "advertising video": [http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
The Rachel interface facilitates [http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html fast setup of Gosia calculations] and data analysis using push-button controls with guided input and 'plain language' warnings during setup. It is currently undergoing beta-testing. The GUI ''optionally'' uses a modified Gosia version based on release 20081208.10, called 20081208.10.a. This modified Gosia source code is distributed with the Rachel package. Rachel is written in Python 2.6 and is expected to be Python 2.7 compliant. It runs under Linux and Unix (OS X) machines, but it has ''not'' been tested under Windows. <br />
<br />
A 64-bit processor is essential, because Gosia runs fastest and most accurately on 64-bit machines. The release-candidate version, expected in the September of 2011, will have many structural changes in the code, allowing more automation, more general particle detector options and fewer user prompts for standard operations. <br />
<br />
[[File:Typicalgosiainput.png|thumb|right|Excerpt of a typical Gosia input for a collective system.]]While gosia.20081208 incorporates the [[OP,BRIC]] command to read internal conversion data from BrIcc data files, removing the burden of entering ICC interpolation data by the user, the GUI allows the greatest possible automation by prompts for pre-defined or user-defined germanium detector crystals or arrays, calculation of Zeigler stopping power data, optimum meshpoint selection for yield calculations, transformation of rectilinear detector definition to laboratory-frame spherical-polar interpolation coordinates, etc. For standard problems, the burden on the user is reduced to entering nuclear level and matrix data for simulations (including optional data-set simulation) and real experimental data for fitting of matrix elements. For collective systems, where the matrix definition often includes several hundred lines of matrix elements, rotor parameters can be given to reduce the setup time for the initial guesses of matrix element values. This also eliminates the need for the user to re-index the reduced matrix elements by hand as changes are made to the matrix or level scheme.<br />
<br />
==How to get the Rachel package==<br />
<br />
Release version 1.1.1 is now available. This version does not read beta-version files, but level schemes and matrices can be ported following the instructions in the 2012 version of the Gosia manual. Refer to the [[gui_release_notes | release notes]] for the change in this version and known issues.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.1.tar Rachel 1.1.1 download]<br />
<br />
==Installation notes==<br />
<br />
===General===<br />
<br />
Rachel has been installed successfully on the following systems. You can view or submit detailed installation notes for these or other systems. (Please link them to a separate Wiki page.)<br />
<br />
If the default python environment set in the rachel.py executable is not appropriate, the following error will appear:<br />
<br />
<pre><br />
% [path].rachel.py<br />
/usr/bin/env: python2.6: No such file or directory<br />
%<br />
</pre><br />
<br />
The correct Python environment can be invoked by typing instead:<br />
<br />
<pre><br />
% [python] [path].rachel.py<br />
</pre><br />
<br />
where [python] is the Python executable with the correct path and [path] is the path to the rachel.py executable where the user installed it.<br />
<br />
===Installation notes for other Linux/Unix systems===<br />
<br />
* [[rachel_installation_ubuntu | Ubuntu]]<br />
* [[rachel_installation_open_suse | OpenSuse]]<br />
* [[rachel_installation_fedora | Fedora]]<br />
* [[rachel_installation_mac_os_x | Mac OS X]]<br />
<br />
The final tests that all necessary libraries and codes are installed are usually the following:<br />
<br />
* Load a level scheme and see that the level scheme window is drawn properly. Rarely, after loading a level scheme with no errors (e.g. using one of the example files included in the Rachel distribution), the user must click "Examine fig. window" once to create the level scheme window. On most systems, with the correct libraries installed, the level scheme display pops up when a valid level scheme is loaded with no errors. If the GUI starts and can load and draw the level diagram without errors, then it is unlikely that there are any missing libraries. Also note that on some systems the matplotlib back-end must be changed. This is done by editing the <tt>~/.matplotlib/matplotlibrc</tt> file so that the back-end line reads<br />
<br />
<pre><br />
backend : [backend]<br />
</pre><br />
<br />
where <tt>[backend]</tt> may be one of several back-ends described here: [http://matplotlib.sourceforge.net/faq/installing_faq.html#backends matplotlib backends]. Usually <tt>TkAgg</tt> works except on Mac OS X. Refer to [[rachel_installation_mac_os_x | Mac OS X]].<br />
<br />
* After running a calculation ("integration"), test the yield-plotting feature using the "Plot yields" button. If there is an error finding gnuplot, install gnuplot on the system so that it is in the user's path, i.e., that it can be invoked by typing "gnuplot" at the terminal prompt.<br />
<br />
<br />
==GUI version backward compatibility==<br />
<br />
In the beta versions, the GUI preserves backward-compatibility of the saved session files, so that users can upgrade the GUI without having to rebuild the session.<br />
<br />
When the release candidate becomes available, users will have to rebuild their sessions, because of major changes in the internal structure that cannot be automatically upgraded. This can be aided by the export/import tools for the level and matrix data.<br />
<br />
In the release versions, automatic upgrading of saved sessions will be reinstated.<br />
<br />
==Beta version capabilities==<br />
<br />
* Azimuthally symmetric particle detection<br />
* Partitioning particle-detector data by azimuthal angle<br />
* Graphical definition of rectilinear or irregular-shaped particle detectors [[File:rectilineardetectorexample.png|thumb|right|A user-defined rectilinear detector automatically transformed into the laboratory spherical polar coordinates for Gosia. Black edge is the "exact" shape; red lines are the azimuthal range samples passed to Gosia.]]<br />
* 4pi experiments (e.g. experiments with no particle detection)<br />
* Normal or inverse kinematics experiments<br />
* A user-expandable library of standard Ge crystals e.g. Gammasphere<br />
* Data from summed 4pi arrays<br />
* Efficiency-corrected gamma-ray data only<br />
* Experiment planning aids<br />
** Generation of simulated data based on a proposed beam run<br />
** Optional quasi-Gaussian random scatter in simulated data<br />
** Estimated precision of the proposed measurement<br />
* Accuracy testing to determine if Gosia will be appropriate for a planned experiment<br />
* Fitting and correlated error estimations<br />
* Reading level schemes and gamma-ray data from Radware AGS files and including<br />
** Branching ratio data<br />
** Previously measured EM matrix elements, including the measured phases<br />
** Lifetime data for ''excited states'' (not the ground state lifetime)<br />
** Mixing ratios<br />
* Several supported data file formats<br />
** [Radware] AGS format<br />
** [[Rachel format nuclear data files]]<br />
** Gosia format (experimental yield and fitted matrix element data)<br />
* Instantly generating plots of experimental vs. predicted yields via gnuplot [[File:plottingexample.png|thumb|right|A zoomed view of a plot of yield vs. spin in a rotational band generated from the Gosia output and experimental data.]]<br />
* Automated generation of stopping power and internal conversion input for Gosia<br />
* Push-button controls<br />
* A searchable help function<br />
* Saving the entire session to a file<br />
* Undo/Redo of most functions and crash recovery<br />
<br />
<br />
Using Rachel, the user will be able to build a level scheme from either a hand-written text file and/or a Radware AGS file, define the experimental setup and import relative-efficiency-corrected gamma-ray data from Rachel-format text and/or AGS files. The matrix and fit parameters can be defined by push-buttons and prompts or imported from a Rachel-format matrix file. Gosia will then be run by push-button GUI controls. Most prompts will be preceded by help information, suggestions, or warnings. <br />
<br />
For experiments that fit the capabilities above, the user can view the Gosia inputs to learn the format, but will not be required to type any input code. Experienced Gosia users can export a GUI-generated input skeleton file and abandon the GUI to use the more advanced capabilities of Gosia.<br />
<br />
==Upgrade strategy==<br />
<br />
Upgrades are being made to incorporate all of the capabilities of Gosia, with a focus on the most commonly used features. Prioritization of the upgrades eventually will be directed primarily by [[software upgrade voting|votes]] cast by the user community. Users are encouraged to submit requested upgrades to handle present features of Gosia that are not already included, ''as well as new functions that Gosia does not handle, but which could be incorporated via the GUI.''<br />
<br />
This voting plan has not been implemented yet. Users are encouraged to suggest desired upgrades through the Forum or the [[rachel_desired_upgrades | desired upgrades]] page to steer the software development.<br />
<br />
===Planned upgrades===<br />
<br />
There are a number of planned upgrades, ''some'' of which will be incorporated in the first [[rachel_release_candidate | release candidate] version. The upgrade plan and priorities will be changed based on user feedback and bug reports. <br />
<br />
# More accurate stopping power calculations for low-Z beams.<br />
# Improved graphics including<br />
## a transition from matplotlib graphics to pyGtk in the level scheme window<br />
## clickable objects in the level scheme diagram<br />
# Addition of Ge clusters with libraries of array geometries (Gammasphere, Agata, Miniball etc.)<br />
# Plot functions to visualize fit conflicts in the data<br />
# Improved object structure for Ge detectors. This will reduce the burden on the user by automatically updating the data set passed to Gosia as the level scheme and matrix change.<br />
# Optional setting of symbolic matrix definitions, whereas now the matrix is stored numerically. This will allow greater user control by allowing tuning of model parameters, e.g. <gam|E2|gsb> = M1 + a*M2, where 'a' can be adjusted by the user.<br />
# Optional simple distributed processing of some functions. This will allow the user to set a maximum number of independent processes to speed up separable calculations (integrated yields, corrected yields and experiment simulations) by issuing a separate call to Gosia for each process<ref>True distributed computing is not handled by the current version of Gosia</ref>.<br />
<br />
==Videos, manual and run-time help==<br />
<br />
===Quick advertising and demos===<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/calculation_in_2_minutes.html Fast setup of Gosia calculations]<br />
<br />
===Help with Rachel on this Wiki===<br />
<br />
Use the search function to the left, or start here.<br />
<br />
[[rachel_selected_topics | Selected help topics for Rachel]]<br />
<br />
===Tutorial videos===<br />
<br />
[[rachel_1.0_tutorial_videos | New Tutorial videos]] are being produced for version 1.0. These will be much shorter and more focused than the old videos.<br />
<br />
You can still watch [[rachel_beta_tutorial_videos | beta-version tutorial videos]], but there have been many changes. General procedures are similar. These old videos contain more topics per video, so some are quite long.<br />
<br />
===The manual===<br />
<br />
The Rachel manual has been incorporated into the [[Gosia_Manual | Gosia manual]]. <br />
<br />
===Other help resources===<br />
<br />
Run-time help is available using the Help button. Users are encouraged to submit suggestions for additional help data.<br />
<br />
===Experiment planning and accuracy testing tools===<br />
<br />
The simulation tools have been improved since the recording of these video tutorials. The user will find extra prompts for the details of the planned beam run, and estimated absolute measured counts will be calculated and displayed. The display format looks like the following:<br />
<br />
<pre><br />
Experiment 1<br />
Target excitation by Z,A = 54,136 at 517 MeV. Mean scattering angle = 45.0 deg.<br />
Detector 1<br />
Single crystal at theta, phi = 45.0, 45.0 deg. Solid angle = 0.06 sr.<br />
This simulation does not include random gaussian scatter. Counts represent the cross sections calculated by Gosia. <br />
Transition | Gammas incident | Fraction of | Observed Counts <br />
| on Ge detectors | Gamma Incident | <br />
Initial Final | | Energy **Detector Gammas | <br />
Band Spin Band Spin | Counts *Error | (keV) Efficiency Detected | Rate(Hz) Counts ***Error <br />
-------------------------------------------------------------------------------------------------------------------------<br />
gsb 1.5 gsb 0.5 4.662e+06 2.332e+05 100.0 0.00049 0.09962 1.075e+00 4.644e+05 6.815e+02<br />
gsb 2.5 gsb 0.5 1.570e+07 7.848e+05 200.0 0.00179 0.36853 1.339e+01 5.784e+06 2.405e+03<br />
a 2.5 gsb 0.5 1.079e+04 5.647e+02 250.0 0.00189 0.38907 9.719e-03 4.199e+03 6.480e+01<br />
a 2.5 gsb 1.5 9.816e+02 7.705e+01 150.0 0.00135 0.27823 6.322e-04 2.731e+02 1.653e+01<br />
a 2.5 b 3.5 4.689e+05 2.376e+04 75.0 0.00015 0.0312 3.387e-02 1.463e+04 1.210e+02<br />
</pre><br />
<br />
The "Observed Counts" are calculated using the efficiency curve from the detector library or a detector created by the user. The "Detector Efficiency" <math>\epsilon</math> is the usual definition. Possion counting errors are based on the observed counts, while additional error on the ''total'' efficiency-corrected counts may be added by the user.<br />
<br />
Refer to the page [[Rachel_simulated_yield_output | Rachel simulated yield output]] for more information about simulations with the GUI.<br />
<br />
===Troubleshooting===<br />
<br />
For troubleshooting help, refer to the [[rachel_troubleshooting | troubleshooting]] page, or use the search box at the left.<br />
<br />
==Bug reports==<br />
<br />
Check the [[gui_release_notes | release notes]] page for a history of bugs and bug-fix versions.<br />
<br />
Users are encouraged to submit bug reports via the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum]. The operation that revealed the bug should be reported, and the session file saved before this operation should be included if possible.<br />
<br />
==Links==<br />
<br />
[http://www.pas.rochester.edu/~hayes/beta_rachel/main_ad.html The Rachel advertising video]<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/GosiaGosia2012-01-30T13:29:54Z<p>Hayes: /* Downloads */ updated to rachel 1.1.1</p>
<hr />
<div><span style="color:#F00000">Follow @GosiaCoulex on [http://twitter.com/#!/GosiaCoulex Twitter] for new version announcements and bug-fixes.</span><br />
<br />
Gosia is the primary analysis code for planning experiments and analyzing data for nuclear structure physics using [[low-energy Coulomb excitation]] experiments. It is suited for both planning experiments and analysis of Coulomb excitation data. The original version was written at the University of Rochester in 1979--1980 by [[Tomasz Czosnyka]], [http://www.pas.rochester.edu/~cline/ D. Cline] and [http://www.turpion.org/links/ca4ad02e0d0fafd70a31c549cf4b3c4c_0.phtml C.Y. Wu]. T. Czosnyka maintained the code until his untimely death in 2006. [[What_is_Gosia | Learn more...]].<br />
<br />
==What Gosia can do for the experimenter==<br />
<br />
===Experiment planning and simulation===<br />
<br />
The GOSIA suite of codes are ideally suited to the design and planning of<br />
heavy-ion induced Coulomb excitation experiments as well as the subsequent<br />
analysis. Coulomb excitation experiments can seem deceptively simple,<br />
especially for few-state problems, leading some experimenters to fall into <br />
analysis traps or collecting data that have less than optimal sensitivity to<br />
the goals of the experiment. The [[experiment_planning | Experiment planning]] page identifies potential pitfalls<br />
in the design and analysis of Coulomb excitation experiments. <br />
<br />
===Analysis of Coulomb excitation data===<br />
<br />
The motivation for development of Gosia was to<br />
implement the capability to extract measured<br />
<math>E\lambda</math><br />
matrix elements model-independently from Coulomb excitation data. The first<br />
major task required to achieve this goal was to design experiments covering a<br />
wide dynamic range of Coulomb excitation strength that provide sufficient<br />
experimental data to overdetermine the many unknown matrix elements.<br />
Experimental techniques were developed to achieve this requirement in the<br />
1980's and primarily involved Coulomb excitation measurements over a wide<br />
range of both scattering angle and unexcited nucleus<br />
<math>Z</math> value. The second major task was the development of Gosia to<br />
model-independently extract the matrix elements via a least-squares search of<br />
the data. During the 1980's and early 1990's the ready availability of beam<br />
time at heavy-ion accelerator facilities, the availability of high-efficiency<br />
<math>p-\gamma</math> detector facilities, and access to fast computer systems needed for the Gosia<br />
least-squares searches, enabled the first model-independent extraction of<br />
<math>E\lambda</math><br />
matrix elements from multiple Coulomb excitation data. <br />
<br />
[[Model_independent_analysis | Model-independent analysis]]<br />
<br />
[[Model_dependent_analysis | Model-dependent analysis]]<br />
<br />
==Selected special topics==<br />
<br />
Other topics can be found using the search box at the left.<br />
<br />
[[Integrated_yields | Interpreting the "integrated yields" output]]<br />
<br />
[[normalization_of_yield_data | Normalization of gamma-ray yield data]]<br />
<br />
==Downloads==<br />
<br />
Note that Gosia version numbers are coded as YYYYMMDD.N, where N is a minor update or bug-fix on the original YYYYMMDD version. For example, version 20110524.2 was released on 2011-11-07. ''Some recent releases have an incorrect message "LATEST REVISION- JUNE 2006" in the output file header.''<br />
<br />
(Right-click to download source codes.)<br />
<br />
* The current version (20120125) of the [http://www.pas.rochester.edu/~cline/Gosia/Gosia_Manual_20120125.pdf Gosia manual]<br />
* The latest release (20110524.2) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia_20110524.2.f Gosia]<br />
* The latest release (2_20081208.14) of [http://www.pas.rochester.edu/%7Ehayes/gosia_versions/gosia2_20081208.14.f Gosia2], for analysing simultaneous Coulomb excitation of target and projectile, using a common normalization.<br />
* [http://www.pas.rochester.edu/~hayes/rachel_1/rachel_1.1.1.tar Rachel release version 1.1.1], the graphical interface for Gosia. See also the [[Gui | Rachel]] page.<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/pawel-06-mod.f Pawel], the Gosia version to treat excitation of a nucleus in an isomer state<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gosia_arm.for ANNL (Anneal)], a special version of Gosia developed by Rich Ibbotson that uses simulated annealing techniques to locate minima<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/sigma.f Sigma], the 2006 Fortran source code for deducing the quadrupole invariants from the E2 matrix elements determined by Gosia<br />
* [http://www.pas.rochester.edu/%7Ecline/Research/GOSIAcodes/gremlin.f GREMLIN], the gamma-ray detector efficiency code developed for use with GOSIA in 1987 by Alexander Kavka<br />
<br />
* The set of [http://www.pas.rochester.edu/~hayes/gosia_downloads/fit_demo_2011.tar demonstration files] to accompany the Gosia tutorial in chapter 14 of the Gosia Manual<br />
<br />
==Installing Gosia==<br />
<br />
Installation of Gosia requires only the following steps:<br />
<br />
# Compiling gosia with a Fortran compiler<br />
# Setting the default path or alias to find Gosia, if desired. (See also the path requirements for [[Gui|Rachel]] and the [[rachel setup file]].)<br />
<br />
Most standard Fortran 77 compilers will produce a working Gosia executable. GNU <br />
<tt>g77</tt> is recommended, but is becoming deprecated on newer machines. The newer,<br />
more commonly used <tt>gfortran</tt> will also work. Intel Fortran should work, but is not recommended, because future error trapping patches may not work well with the Intel compiler. For more information about<br />
compiling and standard builds, refer to the page [[compiling gosia | Compiling Gosia]].<br />
<br />
== User support ==<br />
<br />
===The graphical interface for Gosia===<br />
<br />
A [[Gui | GUI (Graphical User Interface) called Rachel]] has been developed and is currently undergoing beta-testing. Novice Gosia users can use this interface to develop properly formatted template Gosia input files. These can be modified by comparing the input lines to the Gosia manual instructions, or Gosia can be run entirely from within the GUI for many typical [[simulation (experiment planning)]] and analysis problems.<br />
<br />
===Example Gosia input files===<br />
<br />
Chapter 14 of the current [[Gosia Manual]] contains an annotated example input, a flowchart of the procedures that must be run during analysis of data and a tutorial based on a set of example files which can be obtained on the [[Gosia_tutorials]] page.<br />
<br />
===The Gosia Forum===<br />
<br />
The new gosia forum can be found [http://www-user.pas.rochester.edu/~gosia/phpBB3/index.php here.] As described on the [[Gosia_users'_forum]] page, the Forum is the appropriate place to post requests for help with specific Gosia calculations and for experienced users to give answers and advice.<br />
<br />
==Maintenance of the Gosia codes==<br />
<br />
The Gosia codes are maintained by the [[Gosia_Steering_Committee]].<br />
<br />
==Purpose of the Gosia Wiki==<br />
<br />
While the Wiki will eventually mirror much of the content of the [http://www.pas.rochester.edu/%7Ecline/Gosia/2011manual20110428.pdf Gosia Manual], the purpose is not to reproduce the manual in its entirety. The Gosia Manual should still be considered the primary reference for running Gosia. The advantage of the Wiki format is that an unlimited number of pages can be added here by interested users on special topics that are not appropriate for a users' manual. These may include<br />
<br />
* Examples of Gosia input and output for common calculations, such as <br />
** input file templates<br />
** common detector definitions<br />
** proper data set normalizations<br />
** fitting strategies for systems with many matrix elements<br />
* Solutions for difficult calculations, such as extreme inverse kinematics cases<br />
* More detailed theory notes<br />
<br />
* Examples of the use of [[Pawel]], [[ANNL]] and other codes in the Gosia suite<br />
<br />
Wiki users are encouraged to contribute anything that should be of general interest to the Gosia user community and to move solved problems from the Forum if they may be of general interest.<br />
<br />
==Help for the Wiki user==<br />
<br />
Consult the page [[Wiki_formatting]] for basic formatting instructions to contribute to this Wiki.<br />
<br />
==Links==<br />
<br />
Some of the following pages will be absorbed into the pages on the new Wiki server.<br />
<br />
* The [http://www.slcj.uw.edu.pl/en/0.html Warsaw Heavy Ion Laboratory] page and the<br />
* [http://www.slcj.uw.edu.pl/gosia_workshop 2008 Gosia Workshop] at Warsaw<br />
* The [http://www.ikp.uni-koeln.de/~warr/gosia/ Cologne Gosia page]<br />
* and the [http://www.pas.rochester.edu/~cline/Gosia/index.html Rochester Gosia page]<br />
<br />
<br />
==Notes==<br />
<br />
<references/></div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_1.0_tutorial_videosRachel 1.0 tutorial videos2012-01-30T10:20:09Z<p>Hayes: /* Procedures in the usual order */</p>
<hr />
<div>These tutorials are listed by procedure, in the typical ordering of procedures. They are all in MP4 format. If they do not play properly, you probably need a new browser plugin for MP4.<br />
<br />
Please suggest other topics for tutorial videos through the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum.]<br />
<br />
The approximate running time is shown after each link.<br />
<br />
===Procedures in the usual order===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/installation.html Installation] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/read_level_schemes.html Level schemes] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_matrix.html Adding the matrix] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/set_fit_parameters.html Setting fit parameters] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_experiments.html Adding experiments] 7 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/stopping_power.html Calculating accurate stopping power, exit energy and range] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/define_ge_crystals.html Defining Ge detector types] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/attach_ge_detectors.html Attaching Ge detectors and arrays (laboratory positions)] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/nuclear_data.html Adding nuclear data to a fit] 4 minutes.<br />
Adding previously-measured lifetime or matrix element data is usually vital to finding a unique fit in few-state systems.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/op_gdet.html Passing germanium types to Gosia] 1 minute. Be sure to do this before the following steps!<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/loading_yield_data.html Loading yield data and passing the data to Gosia] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/simulation.html Simulating gamma-ray yield data] 4 minutes. This can be used for predicting count rates, testing the ability to fit matrix elements in a planned experiment, etc.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/integrated_yields.html Calculating gamma-ray yields] 3 minutes. This calculation uses a full integration over the particle detector, Ge detector and energy loss in the target. These are the yields that should be compared to data.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/corrected_yields.html Calculating "corrected" yields from yield data and the normalization constants.] 3 minutes. This is the first step in fitting matrix elements to experimental data. These two steps should be repeated every time a fit is done.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/fitting.html Fitting matrix elements to experimental data.] 9 minutes. Be sure to calculate the normalization constants before fitting. This is shown in the corrected yields tutorial.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/error_calculations.html Diagonal and correlated error calculations.] 4 minutes.<br />
<br />
===Other functions===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/math_interpreter.html Using the math interpreter] 2 minutes</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_1.0_tutorial_videosRachel 1.0 tutorial videos2012-01-29T21:43:20Z<p>Hayes: /* Procedures in the usual order */</p>
<hr />
<div>These tutorials are listed by procedure, in the typical ordering of procedures. They are all in MP4 format. If they do not play properly, you probably need a new browser plugin for MP4.<br />
<br />
Please suggest other topics for tutorial videos through the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum.]<br />
<br />
The approximate running time is shown after each link.<br />
<br />
===Procedures in the usual order===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/installation.html Installation] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/read_level_schemes.html Level schemes] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_matrix.html Adding the matrix] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/set_fit_parameters.html Setting fit parameters] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_experiments.html Adding experiments] 7 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/stopping_power.html Calculating accurate stopping power, exit energy and range] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/define_ge_crystals.html Defining Ge detector types] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/attach_ge_detectors.html Attaching Ge detectors and arrays (laboratory positions)] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/nuclear_data.html Adding nuclear data to a fit] 4 minutes.<br />
Adding previously-measured lifetime or matrix element data is usually vital to finding a unique fit in few-state systems.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/op_gdet.html Passing germanium types to Gosia] 1 minute. Be sure to do this before the following steps!<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/loading_yield_data.html Loading yield data and passing the data to Gosia] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/simulation.html Simulating gamma-ray yield data] 4 minutes. This can be used for predicting count rates, testing the ability to fit matrix elements in a planned experiment, etc.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/integrated_yields.html Calculating gamma-ray yields] 3 minutes. This calculation uses a full integration over the particle detector, Ge detector and energy loss in the target. These are the yields that should be compared to data.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/corrected_yields.html Calculating "corrected" yields from yield data and the normalization constants.] 3 minutes. This is the first step in fitting matrix elements to experimental data. These two steps should be repeated every time a fit is done.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/error_calculations.html Diagonal and correlated error calculations.] 4 minutes.<br />
<br />
===Other functions===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/math_interpreter.html Using the math interpreter] 2 minutes</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_1.0_tutorial_videosRachel 1.0 tutorial videos2012-01-29T20:51:48Z<p>Hayes: /* Procedures in the usual order */</p>
<hr />
<div>These tutorials are listed by procedure, in the typical ordering of procedures. They are all in MP4 format. If they do not play properly, you probably need a new browser plugin for MP4.<br />
<br />
Please suggest other topics for tutorial videos through the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum.]<br />
<br />
The approximate running time is shown after each link.<br />
<br />
===Procedures in the usual order===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/installation.html Installation] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/read_level_schemes.html Level schemes] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_matrix.html Adding the matrix] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/set_fit_parameters.html Setting fit parameters] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_experiments.html Adding experiments] 7 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/stopping_power.html Calculating accurate stopping power, exit energy and range] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/define_ge_crystals.html Defining Ge detector types] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/attach_ge_detectors.html Attaching Ge detectors and arrays (laboratory positions)] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/nuclear_data.html Adding nuclear data to a fit] 4 minutes.<br />
Adding previously-measured lifetime or matrix element data is usually vital to finding a unique fit in few-state systems.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/op_gdet.html Passing germanium types to Gosia] 1 minute. Be sure to do this before the following steps!<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/loading_yield_data.html Loading yield data and passing the data to Gosia] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/simulation.html Simulating gamma-ray yield data] 4 minutes. This can be used for predicting count rates, testing the ability to fit matrix elements in a planned experiment, etc.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/integrated_yields.html Calculating gamma-ray yields] 3 minutes. This calculation uses a full integration over the particle detector, Ge detector and energy loss in the target. These are the yields that should be compared to data.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/corrected_yields.html Calculating "corrected" yields from yield data and the normalization constants.] 3 minutes. This is the first step in fitting matrix elements to experimental data. These two steps should be repeated every time a fit is done.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/fitting.html Fitting matrix elements to experimental data.] 7 minutes.<br />
<br />
===Other functions===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/math_interpreter.html Using the math interpreter] 2 minutes</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_1.0_tutorial_videosRachel 1.0 tutorial videos2012-01-29T20:06:38Z<p>Hayes: </p>
<hr />
<div>These tutorials are listed by procedure, in the typical ordering of procedures. They are all in MP4 format. If they do not play properly, you probably need a new browser plugin for MP4.<br />
<br />
Please suggest other topics for tutorial videos through the [http://www-user.pas.rochester.edu/~gosia/phpBB3/ Gosia forum.]<br />
<br />
The approximate running time is shown after each link.<br />
<br />
===Procedures in the usual order===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/installation.html Installation] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/read_level_schemes.html Level schemes] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_matrix.html Adding the matrix] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/set_fit_parameters.html Setting fit parameters] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_experiments.html Adding experiments] 7 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/stopping_power.html Calculating accurate stopping power, exit energy and range] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/define_ge_crystals.html Defining Ge detector types] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/attach_ge_detectors.html Attaching Ge detectors and arrays (laboratory positions)] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/nuclear_data.html Adding nuclear data to a fit] 4 minutes.<br />
Adding previously-measured lifetime or matrix element data is usually vital to finding a unique fit in few-state systems.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/op_gdet.html Passing germanium types to Gosia] 1 minute. Be sure to do this before the following steps!<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/loading_yield_data.html Loading yield data and passing the data to Gosia] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/simulation.html Simulating gamma-ray yield data] 4 minutes. This can be used for predicting count rates, testing the ability to fit matrix elements in a planned experiment, etc.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/integrated_yields.html Calculating gamma-ray yields] 3 minutes. This calculation uses a full integration over the particle detector, Ge detector and energy loss in the target. These are the yields that should be compared to data.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/corrected_yields.html Calculating "corrected" yields from yield data and the normalization constants.] 3 minutes. This is the first step in fitting matrix elements to experimental data. These two steps should be repeated every time a fit is done.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/fitting.html Fitting matrix elements to experimental data.] minutes.<br />
<br />
===Other functions===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/math_interpreter.html Using the math interpreter] 2 minutes</div>Hayeshttps://www-user.pas.rochester.edu/~gosia/mediawiki/index.php/Rachel_1.0_tutorial_videosRachel 1.0 tutorial videos2012-01-29T20:02:05Z<p>Hayes: /* Procedures in the usual order */</p>
<hr />
<div>These tutorials are listed by procedure, in the typical ordering of procedures. They are all in MP4 format. If they do not play properly, you probably need a new browser plugin for MP4.<br />
<br />
The approximate running time is shown after each link.<br />
<br />
===Procedures in the usual order===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/installation.html Installation] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/read_level_schemes.html Level schemes] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_matrix.html Adding the matrix] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/set_fit_parameters.html Setting fit parameters] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/add_experiments.html Adding experiments] 7 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/stopping_power.html Calculating accurate stopping power, exit energy and range] 5 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/define_ge_crystals.html Defining Ge detector types] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/attach_ge_detectors.html Attaching Ge detectors and arrays (laboratory positions)] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/nuclear_data.html Adding nuclear data to a fit] 4 minutes.<br />
Adding previously-measured lifetime or matrix element data is usually vital to finding a unique fit in few-state systems.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/op_gdet.html Passing germanium types to Gosia] 1 minute. Be sure to do this before the following steps!<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/loading_yield_data.html Loading yield data and passing the data to Gosia] 4 minutes<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/simulation.html Simulating gamma-ray yield data] 4 minutes. This can be used for predicting count rates, testing the ability to fit matrix elements in a planned experiment, etc.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/integrated_yields.html Calculating gamma-ray yields] 3 minutes. This calculation uses a full integration over the particle detector, Ge detector and energy loss in the target. These are the yields that should be compared to data.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/corrected_yields.html Calculating "corrected" yields from yield data and the normalization constants.] 3 minutes. This is the first step in fitting matrix elements to experimental data. These two steps should be repeated every time a fit is done.<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/fitting.html Fitting matrix elements to experimental data.] minutes.<br />
<br />
===Other functions===<br />
<br />
[http://www.pas.rochester.edu/~hayes/rachel_1_videos/math_interpreter.html Using the math interpreter] 2 minutes</div>Hayes