In some MPI implementations the self-consistent run of `sc_dmft.py`
resulted in random freezings. This issue was fixed by polling the
VASP lock file only on the master node.
Also, better exception handling is implemented, allowing all nodes
to exit properly in case of error.
The k-phases turned out to be already included at VASP level.
The previous changes are commented out. However, the dependence
of `ProjectorShell` on `kmesh` and `struct` remains and the tests
are fixed accordingly.
* Fixed obvious bugs:
-- forgotten 'import re'
-- import user script by name from string
-- 'import converter' instead of 'import plovasp...'
* Number of iterations provided by the bash-script now has
an affect.
* Added a possibility to specify an alternative cfg-file
This test suite is based on V d-projectors in SrVO3.
The data have been recalculated to obtain the correct format
of LOCPROJ.
Also, some small but important changes are introduced to
the LOCPROJ parser and class ElectronicStructure.
Specifically, eigenvalues, Fermi-weights, and Fermi level are
now read from LOCPROJ instead of EIGENVAL and DOSCAR.
Besides, LOCPROJ now provides the value of NCDIJ instead of
NSPIN.
Basically, with these changes EIGENVAL and DOSCAR are no longer
needed. Although corresponding parseres will remain in 'vaspio.py'
they will not be used for standard operations.
To make it work one has to create a symlink in 'dft/converters/plovasp'
pointing to the built library 'atm.so'.
Also, one has to use 'from <modulename> import <function>' inside
the test itself to avoid problems with module name substitutions.
The local Hamiltonian is now output after the density matrix.
This is mainly needed for debug purposes. At a later stage the
output should be better formatted and controlled.
At the main SC script 'sc_dmft.py' requires importing a user DMFT
script as a module. Ideally, this should be implemented in a different
way so that the user script imports a function from the self-consistent
script.
Noramlly, the Fermi energy is read from DOSCAR. However, this does
not work in case of a self-consistent calculation in which DOSCAR
is not written between iterations. One of the options is
to modify slightly the output to LOCPROJ and add EFERMI to the
first line.
Since 'n_orbitals' can be a 2D array in case of spin-polarized
calculations, one should use 'numpy.max' instead of 'max' to
extract the maximum number of bands.
In the new version of VASP LOCPROJ contains the eigenvalues and
Fermi weights. Also, during a charge self-consistency calculation
the file EIGENVAL is not written at intermediate iterations. It is,
thus, preferential to use LOCPROJ to get the named data.
At the moment, EIGENVAL will still be used if it is complete but
in the future this dependence should be removed completely.
The band indices should be converted to Fortran convention,
i.e. starting from 1, in the output files because the are
used in the density matrix file which is read by a Fortran code.
The format of LOCPROJ has been modified again (in VASP 5.4.2
build from Dec 02, 2015).
Now, there is an additional line before each projector block
providing the spin, k-, and band indices, as well as
eigenvalues and Fermi weights.
Scripts 'run_plovasp.sh' have been replaced by a template in which
the path must be set by the user.
Also, .gitignore has been added to example 'lunio3'.
It was incorrect to ascribe VASP atomic sort to corr_shell['sort'],
the latter having a different meaning. According to the terminology of
Wien2k a sort determines an equivalence class of atoms.
Since the implementation at the moment does not support symmetries
the atom index is now used as a 'sort' index to make sure that all shells
remain inequivalent.
The files from the original vasp-interface repository are reshuffled in
accord with the directory structure of dft_tools. Some of the directories,
such as 'test' (unit tests for the interface), 'examples' (simple examples for
the development purposes) are temporarily placed into 'python/vasp' directory
to avoid confusion with integral tests and examples of dft_tools.
Import of 'json' is fixed to conform python distributions without
'simplejson'.
Also, the full path is used for 'converter_tools' for the moment while
'vasp_converter' is not part of 'dft_tools'.
It seems that not all distributions of python come with a 'simplejson' module.
Now, if this module is not found the import falls back to module 'json'.
At the moment, symmetries are not supported by the interface.
Instead, some dummy parameters are generated and the symmetry is turned off.
'misc_input' is only partially implemented because it contains
some data which is not required for the correct functioning of DftTools.
This preliminary version is untested and might not even run.
Here, almost all relevant input (apart from symmetries and miscellaneous)
is implemented and conventions adpoted in DftTools are accomodated.
Method 'nelect_window()' now correctly takes into account a subset
of bands selected by the energy window.
Also, the number of electrons is now output to a '*.grX' file.
The data for a projected shell (output to a '*.pgX' file) contains
now the ion sort corresponding to this shell.
Also, 'check_data_consistency()' was fixed by correcting the
reference to list 'type_of_ion' (which is now copied to ElectronicStructure).
Added a check to 'check_data_consistency()' that verifies
that each shell contains only one sort of ions.
Also added a non-functioning test (implementation is commented)
for the function.
It requires a full set of VASP files for an example with multiple atom sorts.
'read_data()' is a generator interpreting a file as a sequence of
floats. Lines starting with '#' are ignored.
'read_header_and_data()' reads the header string until a line
"# END ...", initializes a generator 'read_data()', and returns
them.
'vasp_converter.py' is based on the existing 'wien2k_converter.py'.
Methods 'read_header_and_data()' and 'read_data()' for reading input files
are added. The first method returns a JSON-header and a generator 'read_data()'
returning floats from the plain-data part of the file.
'main()' now calls a function 'output_as_text()' responsible for storing
both a ctrl- and plo-files ('ctrl_output()' and 'plo_output()', respectively).
Added function 'ctrl_ouput()' which stores data common for all correlated
shells into a file '<basename>.ctrl'.
At the moment, only a very basic header is output.
The signature of 'plo_output()' is also modified to include an instance
of class 'ElectronicStructre' containing important information on
the lattice structure, Efermi, and k-points.
Parsing of two optional parameters (BASENAME and EFERMI) from section [General] from the config-file
is implemented. If this section is not found the parameters are set to their
default values, which is 'vasp' for BASENAME and nothing for EFERMI.
Appropriate test is added to the 'inpconf' test suite.
A description of the output file formats is added to the documentation.
In particular, the outline of JSON headers for projector-group (*.plog<Ng>)
and control (*.ctrl) files are given.
The names of the test suites have been prefixed with an underscore
to avoid name conflicts with corresponding modules.
Also an attempt to make a scan of all tests has been made by
creating a 'test_all.py' script that is supposed to discover all
test cases and run them. Unfortunately, this does not work as expected
because many tests use input files assumed to be found in the current
directory, which is not true if the tests are run from a different
(parent) directory.
This can be fixed by either forcing the change of directory (but it
seems that 'unittest' does not have this functionality) or
prepending input file names with the current module directory.
Subroutine 'kpoints_output()' is added to 'plotools.py' and is invoked
from 'main.py'.
K-points are output in a separate file <basename>.kpoints that is
common to all PLO groups. If present, tetrahedron data is also stored.
Generation and orthogonalization of PLOs should be separated
because some quantities (such as the LDA density matrix) are calculated
using the original raw projectors.
The orthogonalization routine is now called from 'main.py'.
In the previous commit the calculation of 'nelect' was implemented
incorrectly. The sum over k-points must also contain k-weights
and a spin factor (2.0 for ns = 1).
The calculation of 'nelect' is now implemented as a separate method
of ProjectorGroup.
Output of PLO groups into a text file is added to 'plo_output()'.
The file format is provisional and can change in future versions.
Also, an attribute 'nelect' providing the number of electrons in
the selected energy window is added to ProjectorGroup.
