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complete rewriting of interface/conversion

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doc/documentation.rst
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@ -21,7 +21,6 @@ User guide
.. toctree::
:maxdepth: 2
guide/orbital_construction
guide/conversion
guide/dftdmft_singleshot
guide/dftdmft_selfcons

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doc/guide/conversion.rst
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.. _conversion:
Converting DFT data to a hdf archive
====================================
Orbital construction and conversion
===================================
.. warning::
TO BE UPDATED!
The first step for a DMFT calculation is to provide the necessary
input based on a DFT calculation. We will not review how to do the DFT
calculation here in this documentation, but refer the user to the
documentation and tutorials that come with the actual DFT
package. Here, we will describe how to use output created by Wien2k,
as well as how to use the light-weight general interface.
EXPLAIN CONCEPT OF CONVERSION
Interface with Wien2k
---------------------
Wien2k + dmftproj
-----------------
We assume that the user has obtained a self-consistent solution of the
Kohn-Sham equations. We further have to require that the user is
familiar with the main inout/output files of Wien2k, and how to run
the DFT code.
LISTING OF FILES NECESSARY FOR EACH SUBGROUP
Conversion for the DMFT self-consistency cycle
""""""""""""""""""""""""""""""""""""""""""""""
The basic function of the interface to the Wien2k program package is to take
the output of the program that constructs the projected local orbitals
(:program:`dmftproj`, for documentation see
:download:`TutorialDmftproj.pdf <images_scripts/TutorialDmftproj.pdf>`),
and to store all the necessary information into an hdf5 file. This latter file
is then used to do the DMFT calculation. The reason for this structure is that
this enables the user to have everything that is necessary to reproduce the
calculation in one single hdf5 archive.
First, we have to write the necessary
quantities into a file that can be processed further by invoking in a
shell the command
`x lapw2 -almd`
As explained above, this interface produces an hdf5 archive out of the files that
were written by the band structure package :program:`Wien2k/dmftproj`.
For this purpose we
We note that any other flag for lapw2, such as -c or -so (for
spin-orbit coupling) has to be added also to this line. This creates
some files that we need for the Wannier orbital construction.
The orbital construction itself is done by the fortran program
:program:`dmftproj`. For an extensive manual to this program see
:download:`TutorialDmftproj.pdf <images_scripts/TutorialDmftproj.pdf>`.
Here we will only describe only the basic steps.
Let us take the example of SrVO3, a commonly used
example for DFT+DMFT calculations. The input file for
:program:`dmftproj` looks like
.. literalinclude:: images_scripts/SrVO3.indmftpr
The first three lines give the number of inequivalent sites, their
multiplicity (to be in accordance with the Wien2k *struct* file) and
the maximum orbital quantum number :math:`l_{max}`. In our case our
struct file contains the atoms in the order Sr, V, O.
Next we have to
specify for each of the inequivalent sites, whether we want to treat
their orbitals as correlated or not. This information is given by the
following 3 to 5 lines:
#. We specify which basis set is used (complex or cubic
harmonics).
#. The four numbers refer to *s*, *p*, *d*, and *f* electrons,
resp. Putting 0 means doing nothing, putting 1 will calculate
**unnormalised** projectors in compliance with the Wien2k
definition. The important flag is 2, this means to include these
electrons as correlated electrons, and calculate normalised Wannier
functions for them. In the example above, you see that only for the
vanadium *d* we set the flag to 2. If you want to do simply a DMFT
calculation, then set everything to 0, except one flag 2 for the
correlated electrons.
#. In case you have a irrep splitting of the correlated shell, you can
specify here how many irreps you have. You see that we put 2, since
eg and t2g symmetries are irreps in this cubic case. If you don't
want to use this splitting, just put 0.
#. (optional) If you specifies a number different from 0 in above line, you have
to tell now, which of the irreps you want to be treated
correlated. We want to t2g, and not the eg, so we set 0 for eg and
1 for t2g. Note that the example above is what you need in 99% of
the cases when you want to treat only t2g electrons. For eg's only
(e.g. nickelates), you set 10 and 01 in this line.
#. (optional) If you have specified a correlated shell for this atom,
you have to tell if spin-orbit coupling should be taken into
account. 0 means no, 1 is yes.
These lines have to be repeated for each inequivalent atom.
The last line gives the energy window, relativ to the Fermi energy,
that is used for the projective Wannier functions. Note that, in
accordance with Wien2k, we give energies in Rydberg units!
After setting up this input file, you run:
`dmftproj`
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):
* :file:`case.ctqmcout` and :file:`case.symqmc` containing projector
operators and symmetry operations for orthonormalized Wannier
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.
* :file:`case.oubwin` needed for the charge desity recalculation in
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
use the python module :class:`Wien2kConverter`. It is initialised as::
from pytriqs.applications.dft.converters.wien2k_converter import *
Converter = Wien2kConverter(filename = material_of_interest)
Converter = Wien2kConverter(filename = case)
The only necessary parameter to this construction is the parameter `filename`.
It has to be the root of the files produces by dmftproj. For example, if you did a
calculation for TiO, the :program:`Wien2k` naming convention is that all files are called
:file:`TiO.*`, so you would give `filename = "TiO"`. The constructor opens
an hdf5 archive, named :file:`material_of_interest.h5`, where all the data is stored.
It has to be the root of the files produces by dmftproj. For our
example, the :program:`Wien2k` naming convention is that all files are
called the same, for instance
:file:`SrVO3.*`, so you would give `filename = "SrVO3"`. The constructor opens
an hdf5 archive, named :file:`case.h5`, where all the data is
stored. For other parameters of the constructor please visit the
:ref:`refconverters` section of the reference manual.
These are the parameters to the Constructor:
========================= ============================ ===========================================================================
Name Type, Default Meaning
========================= ============================ ===========================================================================
filename String Material being studied, corresponding to the :program:`Wien2k` file names.
The constructor stores the data in the hdf5 archive :file:`material_of_interest.h5`.
dft_subgrp String, dft_input hdf5 subgroup containing required DFT data
symmcorr_subgrp String, dft_symmcorr_input hdf5 subgroup containing all necessary data to apply
the symmetry operations in the DMFT loop
repacking Boolean, False Does the hdf5 file already exist and should the :program:`h5repack` be
invoked to ensures a minimal archive file size?
Note that the :program:`h5repack` must be in your path variable!
========================= ============================ ===========================================================================
After initialising the interface module, we can now convert the input text files into the
hdf5 archive by::
After initialising the interface module, we can now convert the input
text files to the hdf5 archive by::
Converter.convert_dft_input()
This reads all the data, and stores it in the subgroup `dft_subgrp`, as discussed above.
In this step, the files :file:`material_of_interest.ctqmcout` and :file:`material_of_interest.symqmc`
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`
have to be present in the working directory.
After this step, all the necessary information for the DMFT loop is stored in the hdf5 archive, where
the string variable `Converter.hdf_file` gives the file name of the archive.
You can now proceed with :ref:`DFTDMFTmain`.
After this step, all the necessary information for the DMFT loop is
stored in the hdf5 archive, where the string variable
`Converter.hdf_filename` gives the file name of the archive.
A general H(k)
--------------
LISTING OF FILES NECESSARY, NAME OF CONVERTER
You have now everything for performing a DMFT calculation, and you can
proceed with :ref:`singleshot`.
Data for post-processing
------------------------
""""""""""""""""""""""""
In order to calculate some properties using the DMFT self energy, several other routines are
used in order to convert the necessary input from :program:`Wien2k/dmftproj`. For instance, for
calculating the partial density of states or partial charges consistent with the definition
of :program:`Wien2k`, you have to use::
In case you want to do post-processing of your data using the module
:class:`SumkDFTTools`, some more files
have to be converted to the hdf5 archive. For instance, for
calculating the partial density of states or partial charges
consistent with the definition of :program:`Wien2k`, you have to invoke::
Converter.convert_parproj_input()
This reads the files :file:`material_of_interest.parproj` and :file:`material_of_interest.sympar`.
Again, there are two optional parameters
This reads and converts the files :file:`case.parproj` and
:file:`case.sympar`.
========================= ============================ ===========================================================================
Name Type, Default Meaning
========================= ============================ ===========================================================================
parproj_subgrp String, dft_parproj_input hdf5 subgroup containing partial projectors data.
symmpar_subgrp String, dft_symmpar_input hdf5 subgroup containing symmetry operations data.
========================= ============================ ===========================================================================
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`
Another routine of the class allows to read the input for plotting the momentum-resolved
spectral function. It is done by::
Again, maybe with the optional additional extra flags according to
Wien2k. Now we use a routine of the converter module allows to read
and convert the input for :class:`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.
The optional parameter that controls where the data is stored is `bands_subgrp`,
with the default value `dft_bands_input`. Note however that you need to run "dmftproj -band" to produce the
necessary outband file. The casename.indmftpr file needs an additional line with E_fermi
(obtainable from casename.qtl).
Data for transport calculations
"""""""""""""""""""""""""""""""
After having converted this input, you can further proceed with the :ref:`analysis`.
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.
A general H(k)
--------------
In addition to the more complicated Wien2k converter,
:program:`dft_tools` contains also a light converter. It takes only
one inputfile, and creates the necessary hdf outputfile for
the DMFT calculation. The header of this input file has to have the
following format:
.. 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 correlated atoms in the unit cell
#. The next line contains four numbers: index of the atom, index
of the correlated shell, :math:`l` quantum number, dimension
of this shell. Repeat this line for each correlated atom.
#. 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
2 3. Thiw would mean, 2 irreps (eg and t2g), of dimension 2 and 3,
resp.
After these header lines, the file has to contain the hamiltonian
matrix in orbital space. The standard convention is that you give for
each
:math:`\mathbf{k}`-point first the matrix of the real part, then the
matrix of the imaginary part, and then move on to the next
:math:`\mathbf{k}`-point.
The converter itself is used as::
from pytriqs.applications.dft.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, and you cna proceed
with the
For more options of this converter, have a look at the
:ref:`refconverters` section of the reference manual.
MPI issues
----------
The interface package is written such that all the operations are done only on the master node.
The broadcasting to the nodes has to be done by hand. The :class:`SumkDFT`, described in the
following section, takes care of this automatically.
The interface packages are written such that all the file operations
are done only on the master node. In general, the philosophy of the
package is that whenever you read in something from the archive
yourself, you have to *manually* broadcast it to the nodes. An
exception to this rule is when you use routines from :class:`SumkDFT`
or :class:`SumkDFTTools`, where the broadcasting is done for you.
Interfaces to other packages
----------------------------
@ -113,4 +239,5 @@ Interfaces to other packages
Because of the modular structure, it is straight forward to extend the TRIQS package
in order to work with other band-structure codes. The only necessary requirement is that
the interface module produces an hdf5 archive, that stores all the data in the specified
form. For the details of what data is stored in detail, see the reference manual.
form. For the details of what data is stored in detail, see the
:ref:`hdfstructure` part of the reference manual.

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@ -0,0 +1,17 @@
3 ! Nsort
1 1 3 ! Mult(Nsort)
3 ! lmax
complex ! choice of angular harmonics
1 0 0 0 ! l included for each sort
0 0 0 0 ! If split into ireps, gives number of ireps. for a given orbital (otherwise 0)
cubic ! choice of angular harmonics
1 1 2 0 ! l included for each sort
0 0 2 0 ! If split into ireps, gives number of ireps. for a given orbital (otherwise 0)
01 !
0 ! SO flag
complex ! choice of angular harmonics
1 1 0 0 ! l included for each sort
0 0 0 0 ! If split into ireps, gives number of ireps. for a given orbital (otherwise 0)
-0.11 0.14

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@ -0,0 +1,5 @@
64 ! number of k-points
1.0 ! Electron density
1 ! number of correlated atoms
1 1 2 5 ! iatom, isort, l, dimension
1 5 ! # of ireps, dimension of irep

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.. _orbital_construction:
Orbital construction
====================
.. warning::
TO BE UPDATED!
dmftproj
--------
The dft_tools package comes with a converter to use `Wien2k <http://www.wien2k.at>`_ band structure calculations as input for the DMFT part of the calculation, through the construction of projective Wannier functions. The first step is done by the program :program:`dmftproj`, producing text output files. In the second step, this ouput is read and converted into the hdf5 format, using the python module :class:`Wien2kConverter`.
Wannier90
---------
.. warning::
IN PROGRESS!

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.. _refconverters:
Converters
==========

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.. _hdfstructure:
hdf5 structure
==============