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docs (conversion): update VASP-conversion documentation

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Oleg E. Peil 2018-08-01 16:59:47 +02:00 committed by Manuel
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doc/guide/conversion.rst
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@ -23,8 +23,8 @@ Conversion for the DMFT self-consistency cycle
First, we have to write the necessary
quantities into a file that can be processed further by invoking in a
shell the command
shell the command
`x lapw2 -almd`
We note that any other flag for lapw2, such as -c or -so (for
@ -38,7 +38,7 @@ Here we will only describe the basic steps.
Let us take the compound SrVO3, a commonly used
example for DFT+DMFT calculations. The input file for
:program:`dmftproj` looks like
:program:`dmftproj` looks like
.. literalinclude:: images_scripts/SrVO3.indmftpr
@ -90,18 +90,18 @@ After setting up this input file, you run:
Again, adding possible flags like -so for spin-orbit coupling. This
program produces the following files (in the following, take *case* as
the standard Wien2k place holder, to be replaced by the actual working
directory name):
directory name):
* :file:`case.ctqmcout` and :file:`case.symqmc` containing projector
operators and symmetry operations for orthonormalized Wannier
orbitals, respectively.
orbitals, respectively.
* :file:`case.parproj` and :file:`case.sympar` containing projector
operators and symmetry operations for uncorrelated states,
respectively. These files are needed for projected
density-of-states or spectral-function calculations in
post-processing only.
post-processing only.
* :file:`case.oubwin` needed for the charge density recalculation in
the case of fully self-consistent DFT+DMFT run (see below).
the case of fully self-consistent DFT+DMFT run (see below).
Now we convert these files into an hdf5 file that can be used for the
DMFT calculations. For this purpose we
@ -124,9 +124,9 @@ text files to the hdf5 archive by::
Converter.convert_dft_input()
This reads all the data, and stores it in the file :file:`case.h5`.
This reads all the data, and stores it in the file :file:`case.h5`.
In this step, the files :file:`case.ctqmcout` and
:file:`case.symqmc`
:file:`case.symqmc`
have to be present in the working directory.
After this step, all the necessary information for the DMFT loop is
@ -157,7 +157,7 @@ This reads and converts the files :file:`case.parproj` and
If you want to plot band structures, one has to do the
following. First, one has to do the Wien2k calculation on the given
:math:`\mathbf{k}`-path, and run :program:`dmftproj` on that path:
| `x lapw1 -band`
| `x lapw2 -band -almd`
| `dmftproj -band`
@ -168,7 +168,7 @@ Wien2k. Now we use a routine of the converter module allows to read
and convert the input for :class:`SumkDFTTools <dft.sumk_dft_tools.SumkDFTTools>`::
Converter.convert_bands_input()
After having converted this input, you can further proceed with the
:ref:`analysis`. For more options on the converter module, please have
a look at the :ref:`refconverters` section of the reference manual.
@ -180,7 +180,7 @@ For the transport calculations, the situation is a bit more involved,
since we need also the :program:`optics` package of Wien2k. Please
look at the section on :ref:`Transport` to see how to do the necessary
steps, including the conversion.
Interface with VASP
---------------------
@ -189,54 +189,98 @@ Interface with VASP
yet publicly released. The documentation may, thus, be subject to changes
before the final release.
Note that this VASP interface relies on new options introduced since version
5.4.x.
*Limitations of the alpha-version:*
Additionally, the interface only works correctly if the k-point symmetries
are turned off during the VASP run (ISYM=-1).
* The interface works correctly only if the k-point symmetries
are turned off during the VASP run (ISYM=-1).
The output of raw (non-normalized) projectors is controlled by an INCAR option
LOCPROJ whose complete syntax is described in the VASP documentaion.
* Generation of projectors for k-point lines (option `Lines` in KPOINTS)
needed for Bloch spectral function calculations is not possible at the moment.
The definition of a projector set starts with specifying which sites
and which local states we are going to project onto.
This information is provided by option LOCPROJ
* The interface currently supports only collinear-magnetism calculation
(this implis no spin-orbit coupling) and
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.
The VASP interface relies on new options introduced since version
5.4.x. In particular, a new INCAR-option `LOCPROJ`
and new `LORBIT` modes 13 and 14 have been added.
Option `LOCPROJ` selects a set of localized projectors that will
be written to file `LOCPROJ` after a successful VASP run.
A projector set is specified by site indices,
labels of the target local states, and projector type:
| `LOCPROJ = <sites> : <shells> : <projector type>`
where `<sites>` represents a list of site indices separated by spaces,
with the indices corresponding to the site position in the POSCAR file;
`<shells>` specifies local states (e.g. :math:`s`, :math:`p`, :math:`d`,
:math:`d_{x^2-y^2}`, etc.);
`<shells>` specifies local states (see below);
`<projector type>` chooses a particular type of the local basis function.
The recommended projector type is `Pr 2`.
Some projector types also require parameters `EMIN`, `EMAX` in INCAR to
be set to define an (approximate) energy window corresponding to the
valence states.
The allowed labels of the local states defined in terms of cubic
harmonics are:
When either a self-consistent (`ICHARG < 10`) or a non-self-consistent
(`ICHARG >= 10`) calculation is done VASP produces file `LOCPROJ` which
will serve as the main input for the conversion routine.
* Entire shells: `s`, `p`, `d`, `f`
* `p`-states: `py`, `pz`, `px`
* `d`-states: `dxy`, `dyz`, `dz2`, `dxz`, `dx2-y2`
* `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 example, in case of SrVO3 one may first want to perform a self-consistent
calculation, then set `ICHARGE = 1` and add the following additional
lines into INCAR (provided that V is the second ion in POSCAR):
| `EMIN = 3.0`
| `EMAX = 8.0`
| `LORBIT = 14`
| `LOCPROJ = 2 : d : Pr 2`
The energy range does not have to be precise. Important is that it has a large
overlap with valence bands and no overlap with semi-core or high unoccupied states.
Conversion for the DMFT self-consistency cycle
""""""""""""""""""""""""""""""""""""""""""""""
In order to use the projectors generated by VASP for defining an
impurity problem they must be processed, i.e. normalized, possibly
transformed, and then converted to a format suitable for DFT_tools scripts.
The projectors generated by VASP require certain post-processing before
they can be used for DMFT calculations. The most important step is to normalize
them within an energy window that selects band states relevant for the impurity
problem. Note that this energy window is different from the one described above
and it must be chosen independently of the energy
range given by `EMIN, EMAX` in INCAR.
Currently, it is necessary to add the Fermi energy by hand as the fifth value
in the first line of the LOCPROJ file before the next steps can be executed.
Post-processing of `LOCPROJ` data is generally done as follows:
The processing of projectors is performed by the program :program:`plovasp`
invoked as
#. Prepare an input file `<name>.cfg` (e.g., `plo.cfg`) that describes the definition
of your impurity problem (more details below).
| `plovasp <plo.cfg>`
#. Extract the value of the Fermi level from OUTCAR and paste at the end of
the first line of LOCPROJ.
where `<plo.cfg>` is a input file controlling the conversion of projectors.
#. Run :program:`plovasp` with the input file as an argument, e.g.:
The format of input file `<plo.cfg>` is described in details in
| `plovasp plo.cfg`
This requires that the TRIQS paths are set correctly (see Installation
of TRIQS).
If everything goes right one gets files `<name>.ctrl` and `<name>.pg1`.
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
of SrVO3:
@ -252,12 +296,12 @@ parameters are required
orbitals must be present in `LOCPROJ`.
- **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
only three :math:`t_{2g}` orbitals out of five `d` orbitals given by
only three :math:`t_{2g}` orbitals out of five `d` orbitals given by
:math:`l = 2`.
For the conversion to a h5 file we use on the python level (in analogy to the Wien2kConverter)::
The conversion to a h5-file is performed in the same way as for Wien2TRIQS::
from triqs_dft_tools.converters.vasp_converter import *
Converter = VaspConverter(filename = filename)
@ -265,12 +309,15 @@ For the conversion to a h5 file we use on the python level (in analogy to the Wi
As usual, the resulting h5-file can then be used with the SumkDFT class.
Note that the automatic detection of the correct blockstructure might fail for VASP inputs.
This can be circumvented by increase the :class:`SumkDFT <dft.sumk_dft.SumkDFT>` threshold to e.g.::
Note that the automatic detection of the correct block structure might
fail for VASP inputs.
This can be circumvented by setting a bigger value of the threshold in
:class:`SumkDFT <dft.sumk_dft.SumkDFT>`, e.g.::
SK.analyse_block_structure(threshold = 1e-4)
However, only do this after a careful study of the density matrix and the dos in the wannier basis.
However, do this only after a careful study of the density matrix and
the projected DOS in the localized basis.
A general H(k)
--------------
@ -285,7 +332,7 @@ input file):
.. literalinclude:: images_scripts/case.hk
The lines of this header define
#. Number of :math:`\mathbf{k}`-points used in the calculation
#. Electron density for setting the chemical potential
#. Number of total atomic shells in the hamiltonian matrix. In short,
@ -325,7 +372,7 @@ The lines of this header define
as `4 2 1 3`. We have 4 atoms, since the first number runs from 1 to 4,
but only two inequivalent atoms, since the second number runs
only form 1 to 2.
Note that the total dimension of the hamiltonian matrices that are
read in is the sum of all shell dimensions that you specified. For
example number 4 given above we have a dimension of 5+5+3+3=16. It is important
@ -333,8 +380,8 @@ The lines of this header define
the order of the orbitals in the hamiltonian matrix. In the last
example case above the code assumes that matrix index 1 to 5
belongs to the first d shell, 6 to 10 to the second, 11 to 13 to
the first p shell, and 14 to 16 the second p shell.
the first p shell, and 14 to 16 the second p shell.
#. Number of correlated shells in the hamiltonian matrix, in the same
spirit as line 3.
@ -345,7 +392,7 @@ The lines of this header define
parameters are not used at the moment in the code, and only kept
for compatibility reasons. In our example file we use only the
d-shell as correlated, that is why we have only one line here.
#. The last line contains several numbers: the number of irreducible
representations, and then the dimensions of the irreps. One
possibility is as the example above, another one would be 2
@ -362,7 +409,7 @@ The converter itself is used as::
from triqs_dft_tools.converters.hk_converter import *
Converter = HkConverter(filename = hkinputfile)
Converter.convert_dft_input()
where :file:`hkinputfile` is the name of the input file described
above. This produces the hdf file that you need for a DMFT calculation.
@ -415,7 +462,7 @@ Currently implemented options are:
:math:`n_{k_x} \times n_{k_y} \times n_{k_z}`;
specify ``0`` followed by the three grid dimensions,
like in the example above
* :math:`\Gamma`-centered uniform grid with dimensions
* :math:`\Gamma`-centered uniform grid with dimensions
automatically determined by the converter (from the number of
:math:`\mathbf{R}` vectors found in :file:`seedname_hr.dat`);
just specify ``-1``
@ -440,7 +487,7 @@ When reading the hoppings :math:`\langle w_i | H(\mathbf{R}) | w_j \rangle`
(where :math:`w_i` is the :math:`i`-th MLWF), the converter also assumes that
the first indices correspond to the correlated shells (in our example,
the V-t\ :sub:`2g` shells). Therefore, the MLWFs corresponding to the
uncorrelated shells (if present) must be listed **after** those of the
uncorrelated shells (if present) must be listed **after** those of the
correlated shells.
With the :program:`wannier90` code, this can be achieved by listing the
projections for the uncorrelated shells after those for the correlated shells.
@ -484,7 +531,7 @@ The current implementation of the Wannier90 Converter has some limitations:
* ``proj_mat_all`` are not used, so there are no projectors onto the
uncorrelated orbitals for now.
MPI issues
----------