Commit Graph

149 Commits

Author SHA1 Message Date
Sylvain Tricot 7b104d5b20 Add LEED calculator
The Low Energy Electron Diffraction spectroscopy is now included
with Matrix Inversion algoriyhm only for now.
2024-01-25 09:48:44 +01:00
Sylvain Tricot 6c7038cdde Simplify the version mechanism.
No "setuptools-scm" anymore. The version is read by a subprocess
command or using package metadata or the VERSION file.
I still don't know if this is my last attempt to make the
version number reliable...
2023-12-01 10:24:21 +01:00
Sylvain Tricot 44b424e3c6 Increase the lmax in Phagen.
The lmax value is increased from 50 to 80 (for very high energies)
2023-12-01 10:22:06 +01:00
Sylvain Tricot af72a764e5 Fix the stereographic projection issue.
The matplotlib function changed. A new keyword is needed
to make the plotting "pcolormesh" function works. This keyword is
"shading='gouraud'"
2023-12-01 10:19:22 +01:00
Sylvain Tricot 5f19198dec Remove the creation of output file "fort.354"
This file was created for debugging purposes by the renormalization
procedure. But since it had one line per diffusion path, its size
could rapidly become an issue.
The line is simply commented in the code.
2023-06-19 14:50:08 +02:00
Sylvain Tricot 893d012c99 Remove stderr output for 'git describe' call 2023-06-02 11:33:22 +02:00
Sylvain Tricot d61408e594 Remove 'print' calls in version.py 2023-06-02 11:14:21 +02:00
Sylvain Tricot 3811c4baf0 Restore pip.freeze and setup.py in src/
Since those files are still required for an
editable install (make devel)
2023-06-02 11:03:08 +02:00
Sylvain Tricot 7d9662ae37 Merge branch 'devel' of https://git.ipr.univ-rennes1.fr/epsi/msspec_python3 into devel
Required since changes were made uptream while trying to push local changes
2023-06-02 10:53:38 +02:00
Sylvain Tricot 5b76612c72 Change the version mechanism.
setuptools_scm is no longer used to get the version
of msspec. This commit is an attempt to sanitize this.
2023-06-02 10:49:09 +02:00
kmdunseath cb0b432041 Added file src/msspec/spec/fortran/eig/common/save_eigenvalues.f
which writes the eigenvalues to a fortran stream file called
eigenvalues.dat, facilitating reading by a python script.

Added call to save_eigenvalues in src/msspec/spec/fortran/eig/common/eig_mat_ms.f
2023-06-01 15:52:11 +02:00
Sylvain Tricot 39ba8c3983 Merge tag '1.7.post13' into devel
1.7.post13
2023-03-29 11:45:17 +02:00
Sylvain Tricot cf74431c31 Fix new dtype values for Numpy.
Numpy does not allow anylonger types np.int or np.float.
These are replaced simply by int and float python native types.
2023-03-29 11:41:52 +02:00
Sylvain Tricot d1e52eae86 Switch to pyprojetc.toml
The packaging uses now the modern pyproject.toml and setup.cfg files.
The setup.py is deprecated.
2022-10-27 14:45:38 +02:00
Sylvain Tricot 6f254e688e Change the version mechanism 2022-10-26 17:15:24 +02:00
Sylvain Tricot c455b3bdfa Fix bug with matplotlib > 3.4.3
In newer versions of matplotlib, the autoscale was not working.
Changing "autoscale" to False simply fixes the bug...
2022-10-25 16:21:38 +02:00
Sylvain Tricot bbc8a92382 Merge tag '1.7.post12' into devel
1.7.post12
2022-10-06 18:27:24 +02:00
Sylvain Tricot 2bdc9943b9 Fix numpy bug with alen()
* The numpy.alen() function is deprecated. We use len() instead
* The use of pkg_resources is discouraged. We use importlib.metadata
  instead. I also removed setuptools_scm get_version. I switch to
  a simple call to "git describe", easier now that we use git flow
* The build fails with python3.10 if compiling wx from sources.
  A fix in the Makefile will be proposed in a future commit.
2022-10-06 18:19:16 +02:00
Sylvain Tricot c0d5e97b35 Merge tag '1.7.post11' into devel
1.7.post11
2022-10-05 13:55:33 +02:00
Sylvain Tricot a4351f5606 Add a "light" installation of msspec
This is similar to a "devel" installation, but only the
virtualenv is created and the msspec package is installed
inside (not in edit mode). Bindings to the Fortran code
are not built.

It is intended to use msspec functions to create clusters but
without having to install wx.
2022-10-05 13:40:22 +02:00
Sylvain Tricot adb73f7fd8 Merge branch 'feature/polarization' into devel
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
2022-02-15 17:30:12 +01:00
Sylvain Tricot 9787e99d2e Added the binding for polarization keyword.
The polarization keyword may be None, 'linear_qOz', 'linear_xOy' or
'circular'. The IPOL parameter in spec.dat is set accordingly to
0, 1, -1 or 2 respectively.
2022-02-15 15:37:28 +01:00
Sylvain Tricot 4b75be2045 Changed 'python' command in sdist target.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
The 'python' command might not be the true interpreter. It is
better to use the provided PYTHON_EXE command.
2022-02-15 15:34:30 +01:00
Sylvain Tricot 39074f75b6 Fixed some minor bugs.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
Fixed some bugs. The correlation expansion version now compiles!
The shared object is imported in the calculator.py module.
2022-02-09 19:08:22 +01:00
Sylvain Tricot 6986dde636 Added main anf Makefile rules for CE. 2022-02-09 19:07:03 +01:00
Sylvain Tricot d09ba1b590 Added main_phd_ns_ce.f
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
This file was updated to be compatible with Python bindings.
The begining of the file is identical to the series expansion
version, so it was copied from there.
2022-02-09 14:35:26 +01:00
Sylvain Tricot f4f204305e Added lapack_axb.f
This file is the same as for the matrix inversion.
2022-02-09 14:34:52 +01:00
Sylvain Tricot 2b6a8b6e05 Added phddif_ce.f file.
The file was updated to be compatible with Python bindings.
2022-02-09 14:19:30 +01:00
Sylvain Tricot 9ebf6c6bc3 Added coumat.f and treat_phd.f
Those 2 files were copied from the phd_se version since
they are identical.
2022-02-09 14:18:22 +01:00
Sylvain Tricot 998fdbee88 Added ms_cor.f file.
The file ms_cor.f was updated to be compatible with Python
bindings.
2022-02-09 13:46:03 +01:00
Sylvain Tricot b1f34aef6a Added mpis.f file.
The file mpis.f was updated to be compatible with Python
bindings. The module CORREXP_MOD was created and is now
allocated in memalloc/allocation.f. The parameter NLMM was
added to dim_mod.f.
2022-02-09 13:39:28 +01:00
Sylvain Tricot 58e9731ffd Added gaunt_st.f file.
The file gaunt_st.f was updated to be compatible with Python
bindings. The module GAUNT_C was created.
2022-02-09 13:24:07 +01:00
Sylvain Tricot 0b889681d1 Added corexp1.f file
The file corexp1.f was updated to be compatible with Python
bindings.
2022-02-09 13:11:17 +01:00
Sylvain Tricot f262f96004 Added and updated corexp.f
The file corexp.f was updated to be compatible with Python
bindings.
2022-02-09 13:08:06 +01:00
Sylvain Tricot e3c0accbcb Added and updated coefpq.f
The file coefpq.f was updated to be compatible with Python
bindings. The common /Q_ARRAY/ was refactored as a module in
memalloc/modules.f and allocated in memalloc/allocation.f.
2022-02-09 12:22:05 +01:00
Sylvain Tricot 39eb3dc9d8 Added and updated cmngr.f
The file cmngr.f was updated to be compatible with Python bindings.
2022-02-09 12:02:24 +01:00
Sylvain Tricot 1dba5cbe47 Added files common to SE and CE.
5 files are common to Series Expansion and Correlation Expansion
algortithms. They are now in the dedicated phd_ce_noso_nosp_nosym
folder.
2022-02-09 11:43:35 +01:00
Sylvain Tricot ca1fd04163 Modified cut_cylinder and cut_plane functions.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
cut_cylinder and cut_plane functions were too slow due to
lists modifications in for loops. Implementation was modified
a bit while keeping the same API.
For now, cutting a cylinder for an axis 'x' or 'y' is not supported
anymore.
2022-02-08 15:20:32 +01:00
Sylvain Tricot a657b1874e Changed memory requirements. 2022-02-08 15:19:26 +01:00
Sylvain Tricot 74ca8f467f Removed malloc NPH_M parameter.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
In get_theta_phi_scan, the malloc keyword was given
with NPH_M=8000. It was enough for most of calculations
but it was also impossible to change in cases where more
memory was needed. The keyword is now removed so that
it can be direclty specified by the user if needed.
The default value was increased to 8000 instead of 2000.
2021-12-13 18:51:12 +01:00
Sylvain Tricot 38023dcd52 Bug in matplotlib 3.5.0
epsi-builds/msspec_python3/pipeline/head This commit looks good Details
There is presumably a bug when using pcolormesh
with msspec in matplotlib 3.5.0. The stereo projection
does not work properly and the CPU is rising at 100% as
well as the memory usage. Meanwhile, the event loop of Wx
is affected freezing the GUI. Reverting to last stable 3.4.3
version fixes the problem for now. A true fix should be found
asap.
2021-12-02 12:20:40 +01:00
Sylvain Tricot 75c599de95 Added 'other_parameters' keyword in _get_scan.
epsi-builds/msspec_python3/pipeline/head This commit looks good Details
This allows to set or modify any option right before runing
Phagen and Spec. Mostly for debug purposes.
2021-11-30 17:53:47 +01:00
Sylvain Tricot e36373a576 Fixed bug in 'mean_free_path' option.
It was impossible to enter a numerical value.
The 'allowed_values' keyword was set in the definition
of the 'mean_free_path' parameter, I commented it to
allow any value for this option.
2021-11-30 16:56:20 +01:00
Sylvain Tricot 925d694099 Added 'other_parameters' keyword to any scan.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
This keyword is a dictionary allowing any option
to be passed to Phagen or Spec just before runing
the calculation. It is usefull to pass special options
that are for example set automatically otherwise.
2021-11-30 16:26:10 +01:00
Sylvain Tricot 7567b920a1 Add Lapack/Blas compilation flag. 2021-11-30 16:21:05 +01:00
Sylvain Tricot 369e743197 Removed all f-strings.
By replacing f-strings by the standard ".format" call,
the package can be now compatible with python3.5
2021-09-27 17:49:48 +02:00
Sylvain Tricot a57b8d138b Fix bug in "msspec -p" command.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
When using python options (like "-c" for example), all
arguments from the command line were not passed to the
launch_script function because of missing double quotes
around the $@ array.
2021-09-20 11:17:26 +02:00
Sylvain Tricot 4b23806482 Specify gfortran executables for f2py3
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
2021-07-21 23:06:41 +02:00
Sylvain Tricot df5c0de8b7 Fix bug, the rank was not set properly 2021-07-21 23:06:12 +02:00
Sylvain Tricot 0e04dd4a75 Remove config of logging in looper
epsi-builds/msspec_python3/pipeline/head There was a failure building this commit Details
Because it overriveded the global logging level...
2021-07-21 10:45:34 +02:00