-In triqs version 2.2 array_views no longer own the memory they point to
This means that array variables that are local to a function should always
be returned as arrray and never as an array_view
* Added a new input format for the list of ions. It is now possible
to group ions (like this [1 2] [5 6]) that are considered
equivalent in the solver. This has required changing the internal
variable 'ion_list' to a dictionary 'ions' which can later be
enhanced by other features (such as specifying ions by element name).
-consistent indends in all cmake files
-add static analyzer checks with both cppcheck and clang-tidy
-add dynamic analyzer checks with Address Sanitizer and option ASAN
-add dynamic analyzer checks with Undefined Behavior Sanitizer and option UBSAN
-Further Cleaning and Comments
Was failing test srvo3_transp on centos:
File "/home/build/dft_tools/python/sumk_dft_tools.py", line 947, in <dictcomp>
for direction in self.directions}
AttributeError: 'module' object has no attribute 'full'
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.
dos_wannier_basis and dos_parproj_basis now
return a complex spectral function as the
orbital-resolved DOS; the files have now 3
columns: omega, real, imag
In the calculation of the Hamiltonian correction to the total energy
the arrays were not always aligned if the number of bands varied inside
the energy window.
* 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
extract_G_loc(), total_density(), and calc_mu() support
now real frequency data, which is necessary for DMFT
when a real frequency impurity solver is used.
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.
Function 'calc_density_correction()' has now two options.
VASP-type calculations include not only a density-matrix correction
(which is defined differently compared to Wien2K) but also a correction
to the band energy.
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'.
At one step of the orthogonaliztion procedure two matrix multiplications
have been replaced with one matrix multiplication and a element-wise
multiplication of a vector and a matrix.
Fermi weights are output next to eigenvalues. They will be needed
for the calculation of the KS density matrix in the charge
self-consistency implementation.
The part responsible for generating a mapping between the shell/ions
and block projector matrices has now been relocated to a separate
method 'get_block_matrix_map()'. This simplifies the source code
and makes testing easier.
The mapping for NORMION = True has been implemented.
Also, the orthogonalization loop has been fixed. First of all,
orthogonalization should be done separately for each block map 'bl_map'.
Second, one has to take into account that the orbital dimensions of the
block matrix can vary from block to block. To make that the overlap
matrix is non-singular one, thus, has to pass to
'orthogonalize_projector_matrix()' only a view of a submatrix of 'pmat'
corresponding to the current block.
Two tests to check the simplest cases have been added.
The implementation of the mapping of a set of projectors (belonging
to different shells and ions) onto a block matrix in the
orthogonalization routine has been generalized. Now, an implementation
of the choice between the full orthogoanlization and per-site one
is straightforward: it is just a matter of defining a proper mapping.
The mapping scheme itself is described in the doc-string of method
'ProjectorGroup.orthogonalize()'
There was a very nasty bug in the preparation of the block matrix
'p_mat'. The point is that this matrix is created once for all k-points
with the band dimension being the maximum possible. However, only
a part of the matrix is used at every k-point but the orthogonalization
is done for the whole matrix. The problem was that if the number of
bands for a given k-point was smaller than that for the next k-point
them for the next k-point some part of 'p_mat' still contained data from
the previous step, which messed up the orthonormalization. Now, 'p_mat'
is set to zero at each step of the loop.
Also, property 'nion' was added to ProjectorShell since it is used
very often.
First of all, suite '_plotools' is now split into three separate suites
'_plotools', '_proj_shell', '_proj_group', following the changes made
into the structure of the code.
Second, the two tests in 'test_projshells.py' have been fixed to conform
to the recent modifications in the code and input files.
Added missing import of ProjectorGroup and ProjectorShell to
'plotools.py'.
Moved separate routines 'orthogonalize_projector_matrix()'
and 'select_bands()' into class ProjectorGroup because these
routines are anyway not used elsewhere outside this class.
The classes ProjectorShell and ProjectorGroup are now defined in
different source files. This makes 'plotools.py' only contain
routines that control the data flows, including consistency checks
and output.
