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docs(plovasp): add various fxies to PLOVasp documentation

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19
doc/guide/conv_vasp.rst
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@ -22,7 +22,7 @@ Interface with VASP
spin-polarized projectors have not been tested.
A detailed description of the VASP converter tool PLOVasp can be found
in :ref:`plovasp`. Here, a quick-start guide is presented.
in the :ref:`PLOVasp User's Guide <plovasp>`. Here, a quick-start guide is presented.
The VASP interface relies on new options introduced since version
5.4.x. In particular, a new INCAR-option `LOCPROJ`
@ -55,11 +55,12 @@ harmonics are:
* `f`-states: `fy(3x2-y2)`, `fxyz`, `fyz2`, `fz3`,
`fxz2`, `fz(x2-y2)`, `fx(x2-3y2)`.
For projector type `Pr 2`, one should also set `LORBIT = 14` in INCAR
and provide parameters `EMIN`, `EMAX` which, in this case, define an
energy range (window) corresponding to the valence states. Note that as in the case
of DOS calculation the position of the valence states depends on the
Fermi level.
For projector type `Pr 2`, one should also set `LORBIT = 14` in the INCAR file
and provide parameters `EMIN`, `EMAX`, defining, in this case, an
energy range (energy window) corresponding to the valence states.
Note that, as in the case
of a DOS calculation, the position of the valence states depends on the
Fermi level, which can usually be found at the end of the OUTCAR file.
For example, in case of SrVO3 one may first want to perform a self-consistent
calculation, then set `ICHARGE = 1` and add the following additional
@ -88,7 +89,7 @@ Post-processing of `LOCPROJ` data is generally done as follows:
#. Prepare an input file `<name>.cfg` (e.g., `plo.cfg`) that describes the definition
of your impurity problem (more details below).
#. Extract the value of the Fermi level from OUTCAR and paste at the end of
#. Extract the value of the Fermi level from OUTCAR and paste it at the end of
the first line of LOCPROJ.
#. Run :program:`plovasp` with the input file as an argument, e.g.:
@ -103,7 +104,7 @@ These files are needed for the converter that will be invoked in your
DMFT script.
The format of input file `<name>.cfg` is described in details in
:ref:`plovasp`. Here we just give a simple example for the case
the :ref:`User's Guide <plovasp>`. Here we just consider a simple example for the case
of SrVO3:
.. literalinclude:: images_scripts/srvo3.cfg
@ -119,7 +120,7 @@ parameters are required
- **EWINDOW**: energy window in which the projectors are normalized;
note that the energies are defined with respect to the Fermi level.
Option **TRANSFORM** is optional but here it is specified to extract
Option **TRANSFORM** is optional but here, it is specified to extract
only three :math:`t_{2g}` orbitals out of five `d` orbitals given by
:math:`l = 2`.

105
doc/guide/plovasp.rst
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@ -3,35 +3,33 @@
PLOVasp
=======
The general purpose of the PLOVasp tool is to transform
raw, non-normalized projectors generated by VASP into normalized
projectors corresponding to user-defined projected localized orbitals (PLO).
The PLOs can then be used for DFT+DMFT calculations with or without
charge self-consistency. PLOVasp also provides some utilities
for basic analysis of the generated projectors, such as outputting
density matrices, local Hamiltonians, and projected
density of states.
The general purpose of the PLOVasp tool is to transform raw, non-normalized
projectors generated by VASP into normalized projectors corresponding to
user-defined projected localized orbitals (PLO). The PLOs can then be used for
DFT+DMFT calculations with or without charge self-consistency. PLOVasp also
provides some utilities for basic analysis of the generated projectors, such as
outputting density matrices, local Hamiltonians, and projected density of
states.
PLOs are determined by the energy window in which the raw projectors
are normalized. This allows to define either atomic-like strongly
localized Wannier functions (large energy window) or extended
Wannier functions focusing on selected low-energy states (small
energy window).
PLOs are determined by the energy window in which the raw projectors are
normalized. This allows to define either atomic-like strongly localized Wannier
functions (large energy window) or extended Wannier functions focusing on
selected low-energy states (small energy window).
In PLOVasp all projectors sharing the same energy window are combined
into a `projector group`. Technically, this allows one to define
several groups with different energy windows for the same set of
raw projectors. Note, however, that DFTtools does not support projector
groups at the moment but this feature might appear in future releases.
In PLOVasp, all projectors sharing the same energy window are combined into a
`projector group`. Technically, this allows one to define several groups with
different energy windows for the same set of raw projectors. Note, however,
that DFTtools does not support projector groups at the moment but this feature
might appear in future releases.
A set of projectors defined on sites realted to each other either by symmetry
or by sort along with a set of :math:`l`, :math:`m` quantum numbers forms a
`projector shell`. There could be several projectors shells in a
projector group, implying that they will be normalized within
the same energy window.
A set of projectors defined on sites related to each other either by symmetry
or by an atomic sort, along with a set of :math:`l`, :math:`m` quantum numbers,
forms a `projector shell`. There could be several projectors shells in a
projector group, implying that they will be normalized within the same energy
window.
Projector shells and groups are specified by a user-defined input file
whose format is described below.
Projector shells and groups are specified by a user-defined input file whose
format is described below.
Input file format
-----------------
@ -51,8 +49,8 @@ A PLOVasp input file can contain three types of sections:
there should be no more than one projector group.
#. **[Shell <Ns>]**: contains parameters of a projector shell labelled
with `<Ns>`. If there is only one group section and one shell section,
the group section can be omitted and its required parameters can be
given inside the single shell section.
the group section can be omitted but in this case, the group required
parameters must be provided inside the shell section.
Section [General]
"""""""""""""""""
@ -61,11 +59,11 @@ The entire section is optional and it contains three parameters:
* **BASENAME** (string): provides a base name for output files.
Default filenames are :file:`vasp.*`.
* **DOSMESH** ([float float] integer): if this parameter is given
projected density of states for each projected orbital will be
* **DOSMESH** ([float float] integer): if this parameter is given,
the projected density of states for each projected orbital will be
evaluated and stored to files :file:`pdos_<n>.dat`, where `n` is the
orbital number. The energy
mesh is defined by three numbers: `EMIN` `EMAX` `NPOINTS`. The first two
orbital index. The energy
mesh is defined by three numbers: `EMIN` `EMAX` `NPOINTS`. The first two
can be omitted in which case they are taken to be equal to the projector
energy window. **Important note**: at the moment this option works
only if the tetrahedron integration method (`ISMEAR = -4` or `-5`)
@ -78,7 +76,7 @@ There are no required parameters in this section.
Section [Shell]
"""""""""""""""
This section specifies a projector shell. Each shell section must be
This section specifies a projector shell. Each `[Shell]` section must be
labeled by an index, e.g. `[Shell 1]`. These indices can then be referenced
in a `[Group]` section.
@ -87,17 +85,17 @@ In each `[Shell]` section two parameters are required:
* **IONS** (list of integer): indices of sites included in the shell.
The sites can be given either by a list of integers `IONS = 5 6 7 8`
or by a range `IONS = 5..8`. The site indices must be compatible with
POSCAR file.
the POSCAR file.
* **LSHELL** (integer): :math:`l` quantum number of the desired local states.
It is important that a given combination of site indices and local states
given by `LSHELL` must be present in LOCPROJ file.
given by `LSHELL` must be present in the LOCPROJ file.
There are additional optional parameters that allow one to transform
the local states:
* **TRANSFORM** (matrix): local transformation matrix applied to all states
in the projector shell. The matrix is defined by (multiline) block
in the projector shell. The matrix is defined by a (multiline) block
of floats, with each line corresponding to a row. The number of columns
must be equal to :math:`2 l + 1`, with :math:`l` given by `LSHELL`. Only real matrices
are allowed. This parameter can be useful to select certain subset of
@ -105,14 +103,14 @@ the local states:
* **TRANSFILE** (string): name of the file containing transformation
matrices for each site. This option allows for a full-fledged functionality
when it comes to local state transformations. The format of this file
is described in :ref:`transformation_file`.
is described :ref:`below <transformation_file>`.
Section [Group]
"""""""""""""""
Each defined projector shell must be part of a projector group. In the current
implementation of DFTtools only a single group is supported which can be
labeled by any integer, e.g. `[Group 1]`. This implies that all projector shells
implementation of DFTtools only a single group (labelled by any integer, e.g. `[Group 1]`)
is supported. This implies that all projector shells
must be included in this group.
Required parameters for any group are the following:
@ -121,16 +119,17 @@ Required parameters for any group are the following:
All defined shells must be grouped.
* **EWINDOW** (float float): the energy window specified by two floats: bottom
and top. All projectors in the current group are going to be normalized within
this window.
this window. *Note*: This option must be specified inside the `[Shell]` section
if only one shell is defined and the `[Group]` section is omitted.
Optional group parameters:
* **NORMALIZE** (True/False): specifies whether projectors in the group are
to be noramlized. The default value is **True**.
to be normalized. The default value is **True**.
* **NORMION** (True/False): specifies whether projectors are normalized on
a per-site (per-ion) basis. That is, if `NORMION = True` the orthogonality
a per-site (per-ion) basis. That is, if `NORMION = True`, the orthogonality
condition will be enforced on each site separately but the Wannier functions
on different sites will not be orthogonal. If `NORMION = False` Wannier functions
on different sites will not be orthogonal. If `NORMION = False`, the Wannier functions
on different sites included in the group will be orthogonal to each other.
@ -140,15 +139,29 @@ File of transformation matrices
"""""""""""""""""""""""""""""""
.. warning::
The description below applies only to collinear cases (i.e. without spin-orbit
coupling). In this case the matrices are spin-independent.
The description below applies only to collinear cases (i.e., without spin-orbit
coupling). In this case, the matrices are spin-independent.
The file specified by option `TRANSFILE` contains transformation matrices
for each ion. Each line must contain a series of floats whose number is either equal to
the number of orbitals :math:`N_{orb}` (in this case the transformation matrices
are assumed to be real) or to :math:`2 N_{orb}` (for the complex transformation matrices).
The number of lines :math:`N` must be a multiple of the number of ions :math:`N_{ion}`
The total number of lines :math:`N` must be a multiple of the number of ions :math:`N_{ion}`
and the ratio :math:`N / N_{ion}`, then, gives the dimension of the transformed
orbital space. The lines with floats can be separated by any number of empty or
comment lines which are ignored.
comment lines (starting from `#`), which are ignored.
A very simple example is a transformation matrix that selects the :math:`t_{2g}` manifold.
For two correlated sites, one can define the file as follows:
::
# Site 1
1.0 0.0 0.0 0.0 0.0
0.0 1.0 0.0 0.0 0.0
0.0 0.0 0.0 1.0 0.0
# Site 2
1.0 0.0 0.0 0.0 0.0
0.0 1.0 0.0 0.0 0.0
0.0 0.0 0.0 1.0 0.0