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docs(plovasp): add various fxies to PLOVasp documentation
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@ 22,7 +22,7 @@ Interface with VASP


spinpolarized projectors have not been tested.




A detailed description of the VASP converter tool PLOVasp can be found


in :ref:`plovasp`. Here, a quickstart guide is presented.


in the :ref:`PLOVasp User's Guide <plovasp>`. Here, a quickstart guide is presented.




The VASP interface relies on new options introduced since version


5.4.x. In particular, a new INCARoption `LOCPROJ`


@ 55,11 +55,12 @@ harmonics are:


* `f`states: `fy(3x2y2)`, `fxyz`, `fyz2`, `fz3`,


`fxz2`, `fz(x2y2)`, `fx(x23y2)`.




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 selfconsistent


calculation, then set `ICHARGE = 1` and add the following additional


@ 88,7 +89,7 @@ Postprocessing 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`.





@ 3,35 +3,33 @@


PLOVasp


=======




The general purpose of the PLOVasp tool is to transform


raw, nonnormalized projectors generated by VASP into normalized


projectors corresponding to userdefined projected localized orbitals (PLO).


The PLOs can then be used for DFT+DMFT calculations with or without


charge selfconsistency. 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, nonnormalized


projectors generated by VASP into normalized projectors corresponding to


userdefined projected localized orbitals (PLO). The PLOs can then be used for


DFT+DMFT calculations with or without charge selfconsistency. 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 atomiclike strongly


localized Wannier functions (large energy window) or extended


Wannier functions focusing on selected lowenergy states (small


energy window).


PLOs are determined by the energy window in which the raw projectors are


normalized. This allows to define either atomiclike strongly localized Wannier


functions (large energy window) or extended Wannier functions focusing on


selected lowenergy 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 userdefined input file


whose format is described below.


Projector shells and groups are specified by a userdefined input file whose


format is described below.




Input file format





@ 43,7 +41,7 @@ Parameters (or 'options') are grouped into sections specified as


A PLOVasp input file can contain three types of sections:




#. **[General]**: includes parameters that are independent


of a particular projector set, such as the Fermi level, additional


of a particular projector set, such as the Fermi level, additional


output (e.g. the density of states), etc.


#. **[Group <Ng>]**: describes projector groups, i.e. a set of


projectors sharing the same energy window and normalization type.


@ 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]


"""""""""""""""""


@ 61,24 +59,24 @@ 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`)


is used in VASP to produce `LOCPROJ`.


* **EFERMI** (float): provides the Fermi level. This value overrides


the one extracted from VASP output files.






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 fullfledged 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:


@ 121,18 +119,19 @@ 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 persite (perion) basis. That is, if `NORMION = True` the orthogonality


a persite (perion) 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.








.. _transformation_file:




@ 140,15 +139,29 @@ File of transformation matrices


"""""""""""""""""""""""""""""""




.. warning::


The description below applies only to collinear cases (i.e. without spinorbit


coupling). In this case the matrices are spinindependent.


The description below applies only to collinear cases (i.e., without spinorbit


coupling). In this case, the matrices are spinindependent.




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





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