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complete rewriting of interface/conversion
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@ -21,7 +21,6 @@ User guide
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.. toctree::
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:maxdepth: 2
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guide/orbital_construction
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guide/conversion
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guide/dftdmft_singleshot
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guide/dftdmft_selfcons
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@ -1,111 +1,237 @@
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.. _conversion:
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Converting DFT data to a hdf archive
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====================================
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Orbital construction and conversion
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===================================
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.. warning::
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TO BE UPDATED!
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The first step for a DMFT calculation is to provide the necessary
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input based on a DFT calculation. We will not review how to do the DFT
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calculation here in this documentation, but refer the user to the
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documentation and tutorials that come with the actual DFT
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package. Here, we will describe how to use output created by Wien2k,
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as well as how to use the light-weight general interface.
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EXPLAIN CONCEPT OF CONVERSION
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Interface with Wien2k
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---------------------
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Wien2k + dmftproj
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-----------------
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We assume that the user has obtained a self-consistent solution of the
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Kohn-Sham equations. We further have to require that the user is
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familiar with the main inout/output files of Wien2k, and how to run
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the DFT code.
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LISTING OF FILES NECESSARY FOR EACH SUBGROUP
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Conversion for the DMFT self-consistency cycle
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""""""""""""""""""""""""""""""""""""""""""""""
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The basic function of the interface to the Wien2k program package is to take
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the output of the program that constructs the projected local orbitals
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(:program:`dmftproj`, for documentation see
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:download:`TutorialDmftproj.pdf <images_scripts/TutorialDmftproj.pdf>`),
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and to store all the necessary information into an hdf5 file. This latter file
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is then used to do the DMFT calculation. The reason for this structure is that
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this enables the user to have everything that is necessary to reproduce the
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calculation in one single hdf5 archive.
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First, we have to write the necessary
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quantities into a file that can be processed further by invoking in a
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shell the command
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`x lapw2 -almd`
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As explained above, this interface produces an hdf5 archive out of the files that
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were written by the band structure package :program:`Wien2k/dmftproj`.
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For this purpose we
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We note that any other flag for lapw2, such as -c or -so (for
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spin-orbit coupling) has to be added also to this line. This creates
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some files that we need for the Wannier orbital construction.
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The orbital construction itself is done by the fortran program
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:program:`dmftproj`. For an extensive manual to this program see
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:download:`TutorialDmftproj.pdf <images_scripts/TutorialDmftproj.pdf>`.
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Here we will only describe only the basic steps.
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Let us take the example of SrVO3, a commonly used
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example for DFT+DMFT calculations. The input file for
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:program:`dmftproj` looks like
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.. literalinclude:: images_scripts/SrVO3.indmftpr
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The first three lines give the number of inequivalent sites, their
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multiplicity (to be in accordance with the Wien2k *struct* file) and
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the maximum orbital quantum number :math:`l_{max}`. In our case our
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struct file contains the atoms in the order Sr, V, O.
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Next we have to
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specify for each of the inequivalent sites, whether we want to treat
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their orbitals as correlated or not. This information is given by the
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following 3 to 5 lines:
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#. We specify which basis set is used (complex or cubic
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harmonics).
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#. The four numbers refer to *s*, *p*, *d*, and *f* electrons,
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resp. Putting 0 means doing nothing, putting 1 will calculate
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**unnormalised** projectors in compliance with the Wien2k
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definition. The important flag is 2, this means to include these
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electrons as correlated electrons, and calculate normalised Wannier
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functions for them. In the example above, you see that only for the
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vanadium *d* we set the flag to 2. If you want to do simply a DMFT
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calculation, then set everything to 0, except one flag 2 for the
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correlated electrons.
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#. In case you have a irrep splitting of the correlated shell, you can
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specify here how many irreps you have. You see that we put 2, since
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eg and t2g symmetries are irreps in this cubic case. If you don't
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want to use this splitting, just put 0.
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#. (optional) If you specifies a number different from 0 in above line, you have
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to tell now, which of the irreps you want to be treated
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correlated. We want to t2g, and not the eg, so we set 0 for eg and
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1 for t2g. Note that the example above is what you need in 99% of
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the cases when you want to treat only t2g electrons. For eg's only
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(e.g. nickelates), you set 10 and 01 in this line.
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#. (optional) If you have specified a correlated shell for this atom,
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you have to tell if spin-orbit coupling should be taken into
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account. 0 means no, 1 is yes.
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These lines have to be repeated for each inequivalent atom.
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The last line gives the energy window, relativ to the Fermi energy,
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that is used for the projective Wannier functions. Note that, in
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accordance with Wien2k, we give energies in Rydberg units!
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After setting up this input file, you run:
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`dmftproj`
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Again, adding possible flags like -so for spin-orbit coupling. This
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program produces the following files (in the following, take *case* as
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the standard Wien2k place holder, to be replaced by the actual working
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directory name):
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* :file:`case.ctqmcout` and :file:`case.symqmc` containing projector
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operators and symmetry operations for orthonormalized Wannier
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orbitals, respectively.
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* :file:`case.parproj` and :file:`case.sympar` containing projector
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operators and symmetry operations for uncorrelated states,
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respectively. These files are needed for projected
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density-of-states or spectral-function calculations in
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post-processing only.
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* :file:`case.oubwin` needed for the charge desity recalculation in
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the case of fully self-consistent DFT+DMFT run (see below).
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Now we convert these files into an hdf5 file that can be used for the
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DMFT calculations. For this purpose we
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use the python module :class:`Wien2kConverter`. It is initialised as::
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from pytriqs.applications.dft.converters.wien2k_converter import *
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Converter = Wien2kConverter(filename = material_of_interest)
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Converter = Wien2kConverter(filename = case)
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The only necessary parameter to this construction is the parameter `filename`.
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It has to be the root of the files produces by dmftproj. For example, if you did a
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calculation for TiO, the :program:`Wien2k` naming convention is that all files are called
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:file:`TiO.*`, so you would give `filename = "TiO"`. The constructor opens
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an hdf5 archive, named :file:`material_of_interest.h5`, where all the data is stored.
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It has to be the root of the files produces by dmftproj. For our
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example, the :program:`Wien2k` naming convention is that all files are
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called the same, for instance
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:file:`SrVO3.*`, so you would give `filename = "SrVO3"`. The constructor opens
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an hdf5 archive, named :file:`case.h5`, where all the data is
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stored. For other parameters of the constructor please visit the
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:ref:`refconverters` section of the reference manual.
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These are the parameters to the Constructor:
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========================= ============================ ===========================================================================
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Name Type, Default Meaning
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========================= ============================ ===========================================================================
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filename String Material being studied, corresponding to the :program:`Wien2k` file names.
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The constructor stores the data in the hdf5 archive :file:`material_of_interest.h5`.
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dft_subgrp String, dft_input hdf5 subgroup containing required DFT data
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symmcorr_subgrp String, dft_symmcorr_input hdf5 subgroup containing all necessary data to apply
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the symmetry operations in the DMFT loop
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repacking Boolean, False Does the hdf5 file already exist and should the :program:`h5repack` be
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invoked to ensures a minimal archive file size?
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Note that the :program:`h5repack` must be in your path variable!
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========================= ============================ ===========================================================================
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After initialising the interface module, we can now convert the input text files into the
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hdf5 archive by::
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After initialising the interface module, we can now convert the input
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text files to the hdf5 archive by::
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Converter.convert_dft_input()
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This reads all the data, and stores it in the subgroup `dft_subgrp`, as discussed above.
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In this step, the files :file:`material_of_interest.ctqmcout` and :file:`material_of_interest.symqmc`
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This reads all the data, and stores it in the file :file:`case.h5`.
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In this step, the files :file:`case.ctqmcout` and
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:file:`case.symqmc`
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have to be present in the working directory.
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After this step, all the necessary information for the DMFT loop is stored in the hdf5 archive, where
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the string variable `Converter.hdf_file` gives the file name of the archive.
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You can now proceed with :ref:`DFTDMFTmain`.
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After this step, all the necessary information for the DMFT loop is
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stored in the hdf5 archive, where the string variable
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`Converter.hdf_filename` gives the file name of the archive.
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A general H(k)
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--------------
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LISTING OF FILES NECESSARY, NAME OF CONVERTER
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You have now everything for performing a DMFT calculation, and you can
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proceed with :ref:`singleshot`.
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Data for post-processing
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------------------------
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""""""""""""""""""""""""
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In order to calculate some properties using the DMFT self energy, several other routines are
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used in order to convert the necessary input from :program:`Wien2k/dmftproj`. For instance, for
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calculating the partial density of states or partial charges consistent with the definition
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of :program:`Wien2k`, you have to use::
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In case you want to do post-processing of your data using the module
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:class:`SumkDFTTools`, some more files
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have to be converted to the hdf5 archive. For instance, for
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calculating the partial density of states or partial charges
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consistent with the definition of :program:`Wien2k`, you have to invoke::
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Converter.convert_parproj_input()
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This reads the files :file:`material_of_interest.parproj` and :file:`material_of_interest.sympar`.
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Again, there are two optional parameters
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This reads and converts the files :file:`case.parproj` and
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:file:`case.sympar`.
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========================= ============================ ===========================================================================
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Name Type, Default Meaning
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========================= ============================ ===========================================================================
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parproj_subgrp String, dft_parproj_input hdf5 subgroup containing partial projectors data.
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symmpar_subgrp String, dft_symmpar_input hdf5 subgroup containing symmetry operations data.
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========================= ============================ ===========================================================================
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If you want to plot band structures, one has to do the
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following. First, one has to do the Wien2k calculation on the given
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:math:`\mathbf{k}`-path, and run :program:`dmftproj` on that path:
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| `x lapw1 -band`
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| `x lapw2 -band -almd`
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| `dmftproj -band`
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Another routine of the class allows to read the input for plotting the momentum-resolved
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spectral function. It is done by::
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Again, maybe with the optional additional extra flags according to
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Wien2k. Now we use a routine of the converter module allows to read
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and convert the input for :class:`SumkDFTTools`::
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Converter.convert_bands_input()
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After having converted this input, you can further proceed with the
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:ref:`analysis`. For more options on the converter module, please have
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a look at the :ref:`refconverters` section of the reference manual.
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The optional parameter that controls where the data is stored is `bands_subgrp`,
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with the default value `dft_bands_input`. Note however that you need to run "dmftproj -band" to produce the
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necessary outband file. The casename.indmftpr file needs an additional line with E_fermi
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(obtainable from casename.qtl).
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Data for transport calculations
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"""""""""""""""""""""""""""""""
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After having converted this input, you can further proceed with the :ref:`analysis`.
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For the transport calculations, the situation is a bit more involved,
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since we need also the :program:`optics` package of Wien2k. Please
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look at the section on :ref:`Transport` to see how to do the necessary
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steps, including the conversion.
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A general H(k)
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--------------
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In addition to the more complicated Wien2k converter,
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:program:`dft_tools` contains also a light converter. It takes only
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one inputfile, and creates the necessary hdf outputfile for
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the DMFT calculation. The header of this input file has to have the
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following format:
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.. literalinclude:: images_scripts/case.hk
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The lines of this header define
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#. Number of :math:`\mathbf{k}`-points used in the calculation
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#. Electron density for setting the chemical potential
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#. Number of correlated atoms in the unit cell
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#. The next line contains four numbers: index of the atom, index
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of the correlated shell, :math:`l` quantum number, dimension
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of this shell. Repeat this line for each correlated atom.
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#. The last line contains several numbers: the number of irreducible
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representations, and then the dimensions of the irreps. One
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possibility is as the example above, another one would be 2
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2 3. Thiw would mean, 2 irreps (eg and t2g), of dimension 2 and 3,
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resp.
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After these header lines, the file has to contain the hamiltonian
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matrix in orbital space. The standard convention is that you give for
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each
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:math:`\mathbf{k}`-point first the matrix of the real part, then the
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matrix of the imaginary part, and then move on to the next
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:math:`\mathbf{k}`-point.
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The converter itself is used as::
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from pytriqs.applications.dft.converters.hk_converter import *
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Converter = HkConverter(filename = hkinputfile)
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Converter.convert_dft_input()
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where :file:`hkinputfile` is the name of the input file described
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above. This produces the hdf file that you need, and you cna proceed
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with the
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For more options of this converter, have a look at the
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:ref:`refconverters` section of the reference manual.
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MPI issues
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----------
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The interface package is written such that all the operations are done only on the master node.
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The broadcasting to the nodes has to be done by hand. The :class:`SumkDFT`, described in the
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following section, takes care of this automatically.
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The interface packages are written such that all the file operations
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are done only on the master node. In general, the philosophy of the
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package is that whenever you read in something from the archive
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yourself, you have to *manually* broadcast it to the nodes. An
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exception to this rule is when you use routines from :class:`SumkDFT`
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or :class:`SumkDFTTools`, where the broadcasting is done for you.
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Interfaces to other packages
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----------------------------
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@ -113,4 +239,5 @@ Interfaces to other packages
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Because of the modular structure, it is straight forward to extend the TRIQS package
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in order to work with other band-structure codes. The only necessary requirement is that
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the interface module produces an hdf5 archive, that stores all the data in the specified
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form. For the details of what data is stored in detail, see the reference manual.
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form. For the details of what data is stored in detail, see the
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:ref:`hdfstructure` part of the reference manual.
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17
doc/guide/images_scripts/SrVO3.indmftpr
Normal file
17
doc/guide/images_scripts/SrVO3.indmftpr
Normal file
@ -0,0 +1,17 @@
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3 ! Nsort
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1 1 3 ! Mult(Nsort)
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3 ! lmax
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complex ! choice of angular harmonics
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1 0 0 0 ! l included for each sort
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0 0 0 0 ! If split into ireps, gives number of ireps. for a given orbital (otherwise 0)
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cubic ! choice of angular harmonics
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1 1 2 0 ! l included for each sort
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0 0 2 0 ! If split into ireps, gives number of ireps. for a given orbital (otherwise 0)
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01 !
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0 ! SO flag
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complex ! choice of angular harmonics
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1 1 0 0 ! l included for each sort
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0 0 0 0 ! If split into ireps, gives number of ireps. for a given orbital (otherwise 0)
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-0.11 0.14
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5
doc/guide/images_scripts/case.hk
Normal file
5
doc/guide/images_scripts/case.hk
Normal file
@ -0,0 +1,5 @@
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64 ! number of k-points
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1.0 ! Electron density
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1 ! number of correlated atoms
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1 1 2 5 ! iatom, isort, l, dimension
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1 5 ! # of ireps, dimension of irep
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@ -1,19 +0,0 @@
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.. _orbital_construction:
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Orbital construction
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====================
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.. warning::
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TO BE UPDATED!
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dmftproj
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--------
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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`.
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Wannier90
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---------
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.. warning::
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IN PROGRESS!
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@ -1,3 +1,5 @@
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.. _refconverters:
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Converters
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==========
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@ -1,3 +1,5 @@
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.. _hdfstructure:
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hdf5 structure
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==============
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