The 'txt' keyword of the calculator is working for spec.
This option is still not working for phagen due to stdout
descriptor hardcoded in the Fortran code of phagen. Will
fix it later.
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 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.
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
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.
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 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
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 call to the run function in libspec cannot be done
with unzip the OrderedDict values. It creates memory address
confusion and the program is killed by the os with a message:
"Operating system error: Cannot allocate memory
Allocation would exceed memory limit"
To fix, we shall call the run function with each argument well specified
between the parentheses.
* Started port of the previous CI.bash
* Also fix bug in spec.f (stdout was closed so nothing appeared on screen
at the second call to libspec)
* Work on test suite
- utils to create clusters are tested
- PED calculator for polar and azimutal scans are tested
Sylvain Tricot
Sylvain Tricot