Scripts 'run_plovasp.sh' have been replaced by a template in which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.
Matrices parsed by the config-parser are interpreted as transformation
matrices for each ion in the shell. If only one matrix is defined
(by TRANSFORM) it is copied for every ion.
Whether a matrix is real or complex is derived from its dimensions
consistently with other parameters of the shell (such as 'nm = 2*l + 1').
Transformation matrices are stored as complex in any case.
TRANSFILE option provides a filename containing transformation
matrices for all ions of a projected shell.
The parser simply reads the numbers into a 2d-array which is left
for interpretation at a later stage.
A description of the option 'TRANSFILE' is added to 'config.rst'.
Also, the description of options 'RTRANSFORM' and 'CTRANSFORM' is
modified. They are now combined into a single option 'TRANSFORM'.
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.
If option DOSMESH is specified a projected DOS for each shell
will be output. Energy mesh parameters are given in DOSMESH as
DOSMESH = [EMIN EMAX] N_POINTS
The parameters in the brackets [] are optional. If only the number
of points is specified the energy range is taken to be the same
as the projection energy window.
When PROJCAR is read it assigns the orbitals by their corresponding
labels. These labels are now added to the dictionary 'proj_params'.
Although they are not used currently they can be handy when it comes
to identifying the character of the orbitals.
Also, the order of orbital labels for p- and d-orbitals was changed
to conform to the convention of the old PROCAR file.
