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.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commitDetails
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.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commitDetails
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.
epsi-builds/msspec_python3/pipeline/head This commit looks goodDetails
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.
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.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commitDetails
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.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commitDetails
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.
Instead of returning a panda dataframe, return both a list
of [x0, y0, x1, y1,...] values for all the calculations and the
corresponding dict of parameters
epsi-builds/msspec_python3/pipeline/head This commit looks goodDetails
It is impossible to compute the crosssection if LMAX > 30.
This is due to a lack of precision in the djmn.f subroutine which
is written in simple precision. This commit is a first step to promote
this subroutine and all its dependensices to doucle precision.
epsi-builds/msspec_python3/pipeline/head This commit looks goodDetails
Just began to rewrite the topmost Makefile which will provide
targets for:
* runing the tests
* creating the Python venv
* building and installing the code
* building the manual and the website
Makefiles in subfolder were also upgraded to fix some issues in
target filenames.
epsi-builds/msspec_python3/pipeline/head This commit looks goodDetails
Makefiles are easier to maintain, I eventually prefer using GNU Make
instead of scons. SConstruct files will be removed when makefiles will
be ready in a future commit.
epsi-builds/msspec_python3/pipeline/head There was a failure building this commitDetails
The automatic resizing is not working very well in WXPython along with
matplotlib with the WxAgg backend. It is an attempt to improve this but
does not change anything unfortunately. This is a problem of WX + mpl.
When setting calc.spec_parameters.iprint=3, Spec prints out a huge
amount of information about path taken into account using the series
expansion algorithm.
Some files were not closed in spec at the end of the program. This
caused some troubles in runing the phagen-spec cycle several times.
A function (CLOSE_ALL_FILES) was added in misc.f to force opened
units in the range [7,200] to be closed before exiting the main
subroutine.
The Curve comparison is possible through R-Factor analysis.
Further comparison like shape analysis, similarity index... will
be included later.
Data export is now possible through the gui menu or as a method of
the Data object.
X, Y, Z axes were not in the right-hand orientation and the
Z-stack for drawing axes was not updated resulting in strange
graphical output (axis could "jump" over another instead of being
drawn behind)
A module (cli.py) is used to provide an entry point for the msspec
package. It is here to be PEX-compatible (https://github.com/pantsbuild/pex)
that may be used to provide a zero-install msspec distribution.
F2PY can generate inconsistent suffix for *.so files due to a
different version of numpy if not the same as the one used
in the virtualenv. The workaround is to remove the
"cpython-36m-x86_64-linux-gnu"-like part of the name. The import
mechanism works well without. This is a tiny hack though.
The f2py *.so suffix is not consistent with python virtualenv version.
By using the source dir it is easier to fix manually since the *.so are not
installed
The sys module should be imported first to decalre msspec
path as soon as possible. It enables to load the version module
necessary to avoid hardcoded version number in the setup.py file.
Please note that this import order is not pep8 compliant.
A new keyword in TMatrixParameters allows to use an external
file for the potential energy of atoms. It should be used like
this:
calc.tmatrix_parameters.potential = 'spkkr'
calc.tmatrix_parameters.potential_file = 'Cu.pot' # the name does not matter
The version 2.1 of Phagen is now used. Some updates in the
original code (bakup in phagen_scf_2.1_dp.f.orig file) have been
made to allow the making of the python extension.
Every changes are commented by a line begining by "CST"
To deal with the case of previously installed version of msspec,
the order in which the version is checked has changed.
1- test if we can infer the version from the SCM
2- check if a VERSION file exists
3- take the version from the distribution
The version is now not hardcoded anymore in the python module. We use
setuptools_scm or pkg_resources instead.
There was also a bug in the linkage for PED with matrix inversion using
external lapack.
Finally, the install script install now requirements and all requirements
are stored in the requirements.txt file. setup.py looks inside to set its
"install_requires" keyword.
It is now possible to use an external lapack version. If using
directly the Makefile, use
make pybinding USE_MKL=1 LINKER_FLAGS=-L$(MKLROOT) -lmkl_core -lmkl_intel_lp64 -lmkl_sequential
If using the install script, you can choose to edit each option of the compilation
The PED spectroscopy by the matrix inversion algorithm is now
included.
This commit also includes:
* some changes in default values in parameters.py for eigval_ipwm, eigval_method
in SpecParameters and phi in SourceParameters
* a modification in the cluster viewer: the mouse wheel allows to change the
transparency and see the emitter
* in utils.py, the hemispherical_cluster function has a new keyword that allows
to create cylindrical clusters
It was impossible to perform an energy scan in EIG spectroscopy.
The calculator and calcio modules were corrected.
We can now compute the spectral radius vs energy with and without
renormalization for EIG spectroscopy mode
The G_n, Sigma_n, Z_n and Lowdin K^2 methods are supported for
the inversion algorithm.
This commit fixes also several issues in the GUI and in the
hemispherical_cluster function
In src/msspec/spec/fortran/eig/common/, modified eig_mat_ms.f to call subroutines in new
files diagonalize_matrix.f and renormalization.f to implement renormalization in the
eigenvalue "spectroscopy"
The msspec/spec/fortran folder is totally different now. Most of the
fortran subroutines are in their own file and are located in different folders
The Makefile has been rewritten and can generate 3 libraries:
- one for Photoelectron Diffration in series expansion
- two for Eigen value calculation with matrix inversion and power method
The installation script does not try anymore to create a virtual environment.
A message at the begining recommends to the user to be in a virtual env. That way
it is possible to use virtualenv, conda, python - m venv or none of this to
create (or not) a virtual environment. It's up to the user.
The script is simpler and *should* be POSIX compliant
Files that have been modified in this commit:
- Makefile
- src/Makefile
- src/msspec/spec/fortran/Makefile
- src/msspec/phagen/fortran/Makefile
- src/install.sh
Sylvain Tricot
sylvain tricot
sylvain tricot
Kevin Dunseath