src issueshttps://gitlab.psi.ch/OPAL/src/-/issues2021-11-03T13:20:02+01:00https://gitlab.psi.ch/OPAL/src/-/issues/687No values assigned to dispersion2021-11-03T13:20:02+01:00krausNo values assigned to dispersionAll values for the dispersion in statistics file are zero everywhere. The reason is that no values are assigned.All values for the dispersion in statistics file are zero everywhere. The reason is that no values are assigned.2022.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/685Output file names for LossDataSink can't have prefixed dots if no extension i...2022-03-17T08:55:14+01:00krausOutput file names for LossDataSink can't have prefixed dots if no extension is providedInstead of correct paths an empty string is returned in `ElementBase::getOutputFN()`if the paths start with a prefixed dot such as e.g. `../` and the file name doesn't include an extension. The user shouldn't have to use a file name with...Instead of correct paths an empty string is returned in `ElementBase::getOutputFN()`if the paths start with a prefixed dot such as e.g. `../` and the file name doesn't include an extension. The user shouldn't have to use a file name with extension, the extension is provided by Opal anyway to support both ascii and HDF5 output.2022.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/684Beam stripping physics in OPAL-t2022-07-08T10:15:01+02:00ext-calvo_ppedro.calvo@ciemat.esBeam stripping physics in OPAL-tBeam stripping interactions are currently restricted to OPAL-cycl.
`VACUUM` element must be adapted to extend the beam stripping physics algorithm to beam lines in OPAL-t.Beam stripping interactions are currently restricted to OPAL-cycl.
`VACUUM` element must be adapted to extend the beam stripping physics algorithm to beam lines in OPAL-t.2022.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/683Variables of incident particles in OPAL-t elements2021-10-04T07:56:36+02:00ext-calvo_ppedro.calvo@ciemat.esVariables of incident particles in OPAL-t elementsPosition and time variables of incident particles in OPAL-t elements must be adjusted to correspond to the physical boundary of the element.
There are different ways of saving the particles according to each element: `MONITOR` implement...Position and time variables of incident particles in OPAL-t elements must be adjusted to correspond to the physical boundary of the element.
There are different ways of saving the particles according to each element: `MONITOR` implementation is correct, `FLEXIBLECOLLIMATOR` records one step after the element input, `DEGRADER` currently do not save incident particles.
All elements should have the same structure to store the incident particles in the output file.2022.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/682Somethings wrong with the algorithm for spatial monitors2021-09-20T09:25:15+02:00krausSomethings wrong with the algorithm for spatial monitorslongitudinal phase space
![chopped](/uploads/b6883e5e1ef686cc053393a5cd3dc1d7/chopped.png)longitudinal phase space
![chopped](/uploads/b6883e5e1ef686cc053393a5cd3dc1d7/chopped.png)2022.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/681Use ENABLEHDF5 in OPAL-T2022-02-13T11:50:30+01:00krausUse ENABLEHDF5 in OPAL-TThere is an option ENABLEHDF5 which should allow to disable all HDF5 output. This option doesn’t seem to be supported in OPAL-T.There is an option ENABLEHDF5 which should allow to disable all HDF5 output. This option doesn’t seem to be supported in OPAL-T.2022.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/680Remove interactive mode, replace it with additional help option.2022-02-04T16:05:23+01:00krausRemove interactive mode, replace it with additional help option.The interactive mode is presumably not used by anyone. I propose therefore to remove it and add instead an option to print the help for commands on the command line.
Additionally I noticed that Opal crashes while printing the help messa...The interactive mode is presumably not used by anyone. I propose therefore to remove it and add instead an option to print the help for commands on the command line.
Additionally I noticed that Opal crashes while printing the help messages. The reason is that the type names `predefined string`, `upper case string` and `upper case string array` are longer than 16 characters. However the user doesn't have to know what these types represent, they are simply strings and string arrays respectively.2022.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/679OPAL header is not printed in interactive mode2021-08-27T14:01:20+02:00gsellOPAL header is not printed in interactive mode### Summary
OPAL header is not printed in interactive mode
### Steps to reproduce
Run opal without argumante
### What is the current *bug* behavior?
No header printed
### What is the expected *correct* behavior?
Print header### Summary
OPAL header is not printed in interactive mode
### Steps to reproduce
Run opal without argumante
### What is the current *bug* behavior?
No header printed
### What is the expected *correct* behavior?
Print headerOPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/678Clang does not support option -fno-aggressive-loop-optimizations2021-08-26T15:08:52+02:00gsellClang does not support option -fno-aggressive-loop-optimizationsClang does not support the option `-fno-aggressive-loop-optimizations`.Clang does not support the option `-fno-aggressive-loop-optimizations`.OPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/677Linking issues on macOS2021-08-26T15:09:45+02:00gsellLinking issues on macOSCMake is not reliable in finding needed libraries for HDF5 and Boost. As a workaround `librt` has been added to `HDF5_LIBRARIES` and `Boost_LIBRARIES`, but `librt` is not needed (and not available on macOS).CMake is not reliable in finding needed libraries for HDF5 and Boost. As a workaround `librt` has been added to `HDF5_LIBRARIES` and `Boost_LIBRARIES`, but `librt` is not needed (and not available on macOS).OPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/676Clang 12 compiler warnings on macOS2021-08-27T14:00:12+02:00gsellClang 12 compiler warnings on macOSOPAL doesn't compile on macOS with current Clang/Xcode 12:
- if compiled for production PAssert() is defined empty and Clang complains about unused variables
- declarations of virtual methods are missing in same base classesOPAL doesn't compile on macOS with current Clang/Xcode 12:
- if compiled for production PAssert() is defined empty and Clang complains about unused variables
- declarations of virtual methods are missing in same base classesOPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/675TrackBack not working correctly2022-02-21T17:42:05+01:00krausTrackBack not working correctlyI am trying to run a simulation forward then take the output distribution and run it backwards to confirm that I am setting up the simulation correctly — it should just return to the same initial distribution.
When running the simulatio...I am trying to run a simulation forward then take the output distribution and run it backwards to confirm that I am setting up the simulation correctly — it should just return to the same initial distribution.
When running the simulation with trackback on, the dipoles bend the reference particle the correct direction, and bend the actual particle distribution in the opposite direction.
Here are Sirepo simulations for the forward and backward. I've confirmed that my conversion script to go from the final distribution in the .h5 file to the initial distribution in a .txt file format for the FROMFILE distribution source is correct.
[AWA_TBA_Drive_Beamline_Backtrack.zip](/uploads/37feb8cf2e1da03a0ccbc7a8dd2038f7/AWA_TBA_Drive_Beamline_Backtrack.zip)2022.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/674CMake configuration file fixes2021-08-18T11:51:33+02:00gsellCMake configuration file fixes### Summary
Linking with static libraries fails
### Steps to reproduce
* Build all required software with the build recipes
* run cmake (static libs enabled by default)
* compile
### What is the current *bug* behavior?
Linking faile...### Summary
Linking with static libraries fails
### Steps to reproduce
* Build all required software with the build recipes
* run cmake (static libs enabled by default)
* compile
### What is the current *bug* behavior?
Linking failed.
The boost libraries must not be specified lexicographical (`chrono timer` doesn't work).
CMake does not always detect all libraries required to link with a static `libhdf5.a`.
Old CMake version have issues to detect current boost libraries.OPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/673Add option to disable deletion of particles when exiting transversally2021-09-07T13:08:13+02:00krausAdd option to disable deletion of particles when exiting transversallyIn Opal-T all particles that exit an element transversally are deleted. With this feature request an option should be added with which the user can disable this behavior per element. This can be used e.g. for alpha magnets.In Opal-T all particles that exit an element transversally are deleted. With this feature request an option should be added with which the user can disable this behavior per element. This can be used e.g. for alpha magnets.2022.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/672OPAL 2021.1 release2022-01-20T11:35:20+01:00gsellOPAL 2021.1 release**source code and binary**
* [x] create branch 2021.1
* [x] create issue "Release version 2021.1.0" and merge request
* [x] update version string in Doxyfile
* [x] update the version string in CMakeLists.txt and commit
* [x] wa...**source code and binary**
* [x] create branch 2021.1
* [x] create issue "Release version 2021.1.0" and merge request
* [x] update version string in Doxyfile
* [x] update the version string in CMakeLists.txt and commit
* [x] wait for approval of MR and merge
* [x] tag version 2021.1.0
* [x] upload source tar-ball to `/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/src`
* [x] compile new binary for Linux
* [x] upload Linux binary package to `/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/package/`
* [x] compile new binary for macOS
* [x] upload macOS binary package to `/afs/psi.ch/project/amas/webhosting/Downloads/OPAL/package/`
**manual/documentation**
* [x] setup a new branch for the new version of the manual
* [x] fix version, branches and links in `Manual.attributes`
* [x] clone repository into `/afs/psi.ch/project/amas/webhosting/opal/Documentation/x.y` and checkout new branch (`git clone https://gitlab.psi.ch/OPAL/documentation/manual.git`)
* [x] add links to the binaries in the wiki
* [x] update https://gitlab.psi.ch/OPAL/src/wikis/For-Developers/Compile-OPAL
* [x] compile the change log/release notes and publish it in the wiki: https://gitlab.psi.ch/OPAL/src/wikis/ReleaseNotes
* [x] review the file `src/addToDoxygenMainPage.h`
* [x] build Doxygen documentation
* [x] update https://gitlab.psi.ch/OPAL/src/wikis/home
* [x] update https://gitlab.psi.ch/OPAL/src/wikis/regression-tests
**tracker**
* [x] new milestone for `OPAL x.(y+1)`
* [x] update labels and milestones in issues
**regression-tests**
* [x] create new branch x.y
* [x] setup the regression-tests to run the new version on opalrunner.psi.ch
**varia**
* [x] PSI module
* [x] write e-mail to mailing listOPAL 2021.1gsellgsellhttps://gitlab.psi.ch/OPAL/src/-/issues/671Energy range for gas stripping2021-07-16T12:59:43+02:00ext-calvo_ppedro.calvo@ciemat.esEnergy range for gas strippingThe energy range check for gas stripping in `computeCrossSectionBohr` must be performed in energy units of keV/umaThe energy range check for gas stripping in `computeCrossSectionBohr` must be performed in energy units of keV/umaOPAL 2021.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.eshttps://gitlab.psi.ch/OPAL/src/-/issues/670Simulations broken2021-07-08T13:43:09+02:00ext-calvo_ppedro.calvo@ciemat.esSimulations brokenAfter implementing !497 the energy assignment in the `BEAM` command is never true, so all simulations and [regression tests](http://amas.web.psi.ch/opal/regressionTests/master/results_2021-07-07_22-30.xml) fail.
cc: @krausAfter implementing !497 the energy assignment in the `BEAM` command is never true, so all simulations and [regression tests](http://amas.web.psi.ch/opal/regressionTests/master/results_2021-07-07_22-30.xml) fail.
cc: @krausOPAL 2021.1snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/src/-/issues/668Different initial distribution with same input file2022-02-14T09:42:39+01:00albajacas_aarnau.albajacas@psi.chDifferent initial distribution with same input file### Summary
When running regression tests multiple times, some parameters of the initial distribution are different at each run, even though `SEED` is the default. Initial differences are small, but they diverge with time and can yield ...### Summary
When running regression tests multiple times, some parameters of the initial distribution are different at each run, even though `SEED` is the default. Initial differences are small, but they diverge with time and can yield larger-than-machine-precision errors in the final time-step, which makes it harder to reproduce results and run regression tests (e.g. see OPAL/src#658).
### Steps to reproduce
By running the regression test [`Distribution-Gauss-1.in`](https://gitlab.psi.ch/OPAL/regression-tests/-/blob/master/RegressionTests/Distribution-Gauss-1/Distribution-Gauss-1.in) several times one can see that the initial bunch is not the same at each run (see image below).
However, this only happens when I run the tests on 4 cores. When running the test on 1 or 2 cores the initial distribution is the same at every run. So I suspect that this might be due to differences in timing of communication between processors.
Comparison of the initial bunch between three runs on 4 cores:
![comparison](/uploads/dd69f637b7e16b6b39cdd4ff2e2aeb5e/comparison.png)2022.1krauskraushttps://gitlab.psi.ch/OPAL/src/-/issues/667Dependencies on Cyclotron.h2021-06-30T14:07:55+02:00snuverink_jjochem.snuverink@psi.chDependencies on Cyclotron.hI noticed that when Cyclotron.h is changed, lots of unrelated classes like Solenoid need to be recompiled. The dependency chain need to be cleaned.I noticed that when Cyclotron.h is changed, lots of unrelated classes like Solenoid need to be recompiled. The dependency chain need to be cleaned.OPAL 2021.1snuverink_jjochem.snuverink@psi.chsnuverink_jjochem.snuverink@psi.chhttps://gitlab.psi.ch/OPAL/src/-/issues/666Refactoring method for cyclotron output field files2021-06-30T10:34:53+02:00ext-calvo_ppedro.calvo@ciemat.esRefactoring method for cyclotron output field filesOutput file gnu.out is written by different field map types. A new method could be added to avoid duplication of the code, separating the reading of the field map and the writing of the output.Output file gnu.out is written by different field map types. A new method could be added to avoid duplication of the code, separating the reading of the field map and the writing of the output.OPAL 2021.1ext-calvo_ppedro.calvo@ciemat.esext-calvo_ppedro.calvo@ciemat.es