mirror of
https://github.com/triqs/dft_tools
synced 2024-09-12 05:38:31 +02:00
update documentation to use autosummary
* remove manual module reference files * move hdf5 structure reference to guide * fix various doc strings * remove very old update_archive python script for triqs 1.2 * refine main documentation.rst file -> better overview
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@ -1,4 +1,4 @@
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{{ fullname | escape | underline}}
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{{ name | escape | underline}}
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.. automodule:: {{ fullname }}
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@ -76,7 +76,7 @@ html_theme_options = {
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# Toc options
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'collapse_navigation': False,
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'sticky_navigation': True,
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'navigation_depth': 5,
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'navigation_depth': 4,
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'includehidden': True,
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'titles_only': False
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}
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@ -9,7 +9,7 @@ Basic notions
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-------------
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.. toctree::
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:maxdepth: 2
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:maxdepth: 1
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basicnotions/first
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basicnotions/dft_dmft
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@ -23,6 +23,7 @@ Construction of local orbitals from DFT
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:maxdepth: 2
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guide/conversion
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h5structure
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DFT+DMFT
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@ -38,7 +39,7 @@ Advanced Topics
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---------------
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.. toctree::
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:maxdepth: 2
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:maxdepth: 1
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guide/blockstructure
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guide/BasisRotation
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@ -48,7 +49,7 @@ Postprocessing
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--------------
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.. toctree::
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:maxdepth: 2
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:maxdepth: 1
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guide/analysis
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guide/transport
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@ -59,16 +60,18 @@ Reference manual
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This is the reference manual for the python routines.
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.. toctree::
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:maxdepth: 2
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.. autosummary::
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:recursive:
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:toctree: _python_api
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:template: autosummary_module_template.rst
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block_structure
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converters
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sumk_dft
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sumk_dft_tools
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symmetry
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trans_basis
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reference/h5structure
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reference/converters
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reference/sumk_dft
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reference/sumk_dft_tools
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reference/symmetry
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reference/transbasis
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reference/block_structure
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FAQs
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@ -95,6 +95,6 @@ where :file:`hkinputfile` is the name of the input file described
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above. This produces the hdf file that you need for a DMFT calculation.
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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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:py:mod:`Converters <triqs_dft_tools.converters>` section of the reference manual.
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@ -17,10 +17,10 @@ Hubbard-like model Hamiltonian. Resulting in lattice object stored in `SumkDFT`.
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The implementation is presented in `M. Schüler et al. 2018 J. Phys.: Condens.
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Matter 30 475901 <https://doi.org/10.1088/1361-648X/aae80a>`_.
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The interface consists of two parts, :ref:`PLOVASP<refPLOVASP>`, a collection of
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The interface consists of two parts, :py:mod:`PLOVASP<triqs_dft_tools.converters.plovasp>`, a collection of
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python classes and functions converting the raw VASP output to proper projector
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functions, and the python based :ref:`VaspConverter<refVASPconverter>`, which
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creates a h5 archive from the :ref:`PLOVASP<refPLOVASP>` output readable by
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functions, and the python based :py:mod:`VaspConverter<triqs_dft_tools.converters.vasp>`, which
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creates a h5 archive from the :py:mod:`PLOVASP<triqs_dft_tools.converters.plovasp>` output readable by
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`SumkDFT`. Therefore, the conversion consist always of two steps.
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Here, we will present a guide how the interface `can` be used to create input for a DMFT calculation, using SrVO3 as an example. Full examples can be found in the :ref:`tutorial section of DFTTools<tutorials>`.
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@ -134,7 +134,7 @@ described above and it must be chosen independently of the energy range given by
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PLOVASP: converting VASP output
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--------------------------------
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:ref:`PLOVASP<refPLOVASP>` is a collection of python functions and classes, post-processing the raw VASP `LOCPROJ` output creating proper projector functions.
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:py:mod:`PLOVASP<triqs_dft_tools.converters.plovasp>` is a collection of python functions and classes, post-processing the raw VASP `LOCPROJ` output creating proper projector functions.
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The following VASP files are used by PLOVASP:
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* PROJCAR, LOCPROJ: raw projectors generated by VASP-PLO interface
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@ -176,12 +176,12 @@ or embedded in a python script as::
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# Generate and store PLOs
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plo_converter.generate_and_output_as_text('plo.cfg', vasp_dir='./')
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This will create the xml files `vasp.ctrl` and `vasp.pg1` containing the orthonormalized projector functions readable by the :ref:`VaspConverter<refVASPconverter>`. Moreover, `PLOVASP` will output important information of the orthonormalization process, such as the density matrix of the correlated shell and the local Hamiltonian.
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This will create the xml files `vasp.ctrl` and `vasp.pg1` containing the orthonormalized projector functions readable by the :py:mod:`VaspConverter<triqs_dft_tools.converters.vasp>`. Moreover, :py:mod:`PLOVASP<triqs_dft_tools.converters.plovasp>` will output important information of the orthonormalization process, such as the density matrix of the correlated shell and the local Hamiltonian.
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Running the VASP converter
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-------------------------------------
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The actual conversion to a h5-file is performed with the orthonormalized projector functions readable by the :ref:`VaspConverter<refVASPconverter>` in the same fashion as with the other `DFTTools` converters::
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The actual conversion to a h5-file is performed with the orthonormalized projector functions readable by the :py:mod:`VaspConverter<triqs_dft_tools.converters.vasp>` in the same fashion as with the other `DFTTools` converters::
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from triqs_dft_tools.converters.vasp import *
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Converter = VaspConverter(filename = 'vasp')
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@ -394,12 +394,14 @@ in the header. One can either copy the Fermi energy manually there after a succe
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VASP run, or modify the VASP source code slightly, by replacing the following line in
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`locproj.F` (around line 695):
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::
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< WRITE(99,'(4I6," # of spin, # of k-points, # of bands, # of proj" )') NS,NK,NB,NF
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---
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> WRITE(99,'(4I6,F12.7," # of spin, # of k-points, # of bands, # of proj, Efermi" )') W%WDES%NCDIJ,NK,NB,NF,EFERMI
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Now one needs to pass additionally the variable `EFERMI` to the function, by changing (at arount line 560):
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::
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< SUBROUTINE LPRJ_WRITE(IU6,IU0,W)
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---
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> SUBROUTINE LPRJ_WRITE(IU6,IU0,W,EFERMI)
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@ -408,6 +410,7 @@ Now one needs to pass additionally the variable `EFERMI` to the function, by cha
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Next, we need to pass this option when calling from `electron.F` and `main.F`
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(just search for LPRJ_WRITE in the files) and change all occurences as follows:
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::
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< CALL LPRJ_WRITE(IO%IU6, IO%IU0, W)
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---
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> CALL LPRJ_WRITE(IO%IU6, IO%IU0, W, EFERMI)
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@ -424,13 +427,16 @@ Furthermore, there is a bug in `fileio.F` around line 1710 where VASP tries to
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print "reading the density matrix from Gamma". This should be done only by the
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master node, and VASP gets stuck sometimes. Adding a
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::
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IF (IO%IU0>=0) THEN
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...
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ENDIF
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statement resolves this issue. A similar problem occurs, when VASP writes the
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`OSZICAR` file and a buffer is stuck. Adding a `flush` to the buffer in
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`electron.F` around line 580 after
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::
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CALL STOP_TIMING("G",IO%IU6,"DOS")
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flush(17)
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print *, ' '
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@ -128,7 +128,7 @@ example, the :program:`Wien2k` naming convention is that all files have the
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same name, but different extensions, :file:`case.*`. The constructor opens
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an hdf5 archive, named :file:`case.h5`, where all relevant data will be
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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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:py:mod:`Converters <triqs_dft_tools.converters>` section of the reference manual.
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After initializing the interface module, we can now convert the input
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text files to the hdf5 archive by::
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@ -181,7 +181,7 @@ and convert the input for :class:`SumkDFTTools <dft.sumk_dft_tools.SumkDFTTools>
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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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a look at the :py:mod:`Converters <triqs_dft_tools.converters>` section of the reference manual.
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Data for transport calculations
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-------------------------------
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@ -39,7 +39,7 @@ Note that in presence of SOC, it is not possible to project only onto the :math:
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Treatment of SOC in Elk
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-------------------------
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First, a Elk calculation including SOC has to be performed. For details, we refer the reader to the SOC Elk examples in Elk's example directory and `Elk manual <https//elk.sourceforge.net/elk.pdf>`_ for further information about the input flags. Then the projectors can be generated using the ``wanproj`` input flag in the same format as in :ref:`conv_elk`. Like in Wien2k, you cannot project only onto the :math:`t_{2g}` subshell because it is not an irreducible representation in SOC calculations.
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First, a Elk calculation including SOC has to be performed. For details, we refer the reader to the SOC Elk examples in Elk's example directory and `Elk manual <https//elk.sourceforge.net/elk.pdf>`_ for further information about the input flags. Then the projectors can be generated using the ``wanproj`` input flag in the same format as in :ref:`convElk`. Like in Wien2k, you cannot project only onto the :math:`t_{2g}` subshell because it is not an irreducible representation in SOC calculations.
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After generating the projectors
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-------------------------------
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@ -1,9 +1,9 @@
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.. _hdfstructure:
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hdf5 structure
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==============
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standardized hdf5 structure
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===========================
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All the data is stored using the hdf5 standard, as described also in the
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All the DFT input data is stored using the hdf5 standard, as described also in the
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documentation of the TRIQS package itself. In order to do a DMFT calculation,
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using input from DFT applications, a converter is needed on order to provide
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the necessary data in the hdf5 format.
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@ -1,21 +0,0 @@
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Block Structure
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===============
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The `BlockStructure` class allows to change and manipulate
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Green functions structures and mappings from sumk to solver.
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The block structure can also be written to and read from HDF files.
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.. warning::
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Do not write the individual elements of this class to a HDF file,
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as they belong together and changing one without the other can
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result in unexpected results. Always write the BlockStructure
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object as a whole.
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Writing the sumk_to_solver and solver_to_sumk elements
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individually is not implemented.
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.. autoclass:: triqs_dft_tools.block_structure.BlockStructure
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:members:
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:show-inheritance:
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@ -1,83 +0,0 @@
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.. _refconverters:
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Converters
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==========
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Wien2k Converter
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----------------
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.. autoclass:: triqs_dft_tools.converters.wien2k.Wien2kConverter
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:members:
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:special-members:
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:show-inheritance:
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H(k) Converter
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--------------
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.. autoclass:: triqs_dft_tools.converters.hk.HkConverter
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:members:
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:special-members:
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Wannier90 Converter
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-------------------
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.. autoclass:: triqs_dft_tools.converters.wannier90.Wannier90Converter
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:members:
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:special-members:
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PLOVASP
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----------
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.. _refPLOVASP:
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PLOVASP reference, the classes / functions are sorted the way the converter uses them.
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.. automodule:: triqs_dft_tools.converters.plovasp.converter
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:members: generate_and_output_as_text
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.. automodule:: triqs_dft_tools.converters.plovasp.inpconf
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:members: ConfigParameters
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.. automodule:: triqs_dft_tools.converters.plovasp.vaspio
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:members: VaspData, Plocar, Poscar, Kpoints, Eigenval, Doscar, read_symmcar
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.. automodule:: triqs_dft_tools.converters.plovasp.elstruct
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:members: ElectronicStructure
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.. automodule:: triqs_dft_tools.converters.plovasp.plotools
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:members:
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.. automodule:: triqs_dft_tools.converters.plovasp.proj_shell
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:members:
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.. automodule:: triqs_dft_tools.converters.plovasp.proj_group
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:members:
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VASP Converter
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-------------------
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.. _refVASPconverter:
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.. autoclass:: triqs_dft_tools.converters.vasp.VaspConverter
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:members:
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:special-members:
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Elk Converter
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-------------------
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.. _refElkconverter:
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.. autoclass:: triqs_dft_tools.converters.elk.ElkConverter
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:members:
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:special-members:
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Elk Tools
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-------------------
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.. _refElkTools:
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.. autoclass:: triqs_dft_tools.converters.elktools.ElkConverterTools
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:members:
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:special-members:
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.. autoclass:: triqs_dft_tools.converters.elktools.readElkfiles
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:members:
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:special-members:
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Converter Tools
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---------------
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.. autoclass:: triqs_dft_tools.converters.converter_tools.ConverterTools
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:members:
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:special-members:
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@ -1,8 +0,0 @@
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SumK DFT
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========
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.. autoclass:: triqs_dft_tools.sumk_dft.SumkDFT
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:members:
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:special-members:
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:show-inheritance:
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@ -1,8 +0,0 @@
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SumK DFT Tools
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==============
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.. autoclass:: triqs_dft_tools.sumk_dft_tools.SumkDFTTools
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:members:
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:special-members:
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:show-inheritance:
|
@ -1,6 +0,0 @@
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Symmetry
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========
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.. autoclass:: triqs_dft_tools.Symmetry
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:members:
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:special-members:
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@ -1,6 +0,0 @@
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TransBasis
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==========
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.. autoclass:: triqs_dft_tools.trans_basis.TransBasis
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:members:
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:special-members:
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@ -1,5 +1,3 @@
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.. module:: triqs_dft_tools
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.. _tutorials:
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Tutorials
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|
@ -21,7 +21,9 @@
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# TRIQS. If not, see <http://www.gnu.org/licenses/>.
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#
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##########################################################################
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"""
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Block structure class and helper functions
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"""
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import copy
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import numpy as np
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@ -38,6 +40,11 @@ class BlockStructure(object):
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This class contains information about the structure of the solver
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and sumk Green functions and the mapping between them.
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Do not write the individual elements of this class to a HDF file,
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as they belong together and changing one without the other can
|
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result in unexpected results. Always write the BlockStructure
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object as a whole.
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Parameters
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----------
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gf_struct_sumk : list of list of tuple
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|
@ -19,6 +19,9 @@
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# TRIQS. If not, see <http://www.gnu.org/licenses/>.
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#
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||||
##########################################################################
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"""
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module containing all available converters for DFTTools
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"""
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from .wien2k import Wien2kConverter
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from .hk import HkConverter
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|
@ -19,6 +19,10 @@
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# TRIQS. If not, see <http://www.gnu.org/licenses/>.
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#
|
||||
##########################################################################
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||||
"""
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Converter helper module
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"""
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import triqs.utility.mpi as mpi
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class ConverterTools:
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@ -59,7 +63,7 @@ class ConverterTools:
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Note
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----
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Should only be used before the first invokation of HDFArchive in the program,
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Should only be used before the first invokation of HDFArchive in the program,
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otherwise the hdf5 linking will be broken.
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||||
"""
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@ -92,7 +96,7 @@ class ConverterTools:
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Number of inequivalent shells.
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corr_to_inequiv : list
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Mapping between correlated shell index and inequivalent shell index.
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corr_to_inequiv(i_corr_shells) = i_inequiv_shells
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corr_to_inequiv(i_corr_shells) = i_inequiv_shells
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inequiv_to_corr : list
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Mapping between inequivalent shell index and correlated shell index.
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inequiv_to_corr(i_inequiv_shells) = i_corr_shells
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|
@ -19,6 +19,9 @@
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# TRIQS. If not, see <http://www.gnu.org/licenses/>.
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#
|
||||
##########################################################################
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||||
"""
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Elk converter
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"""
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from types import *
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import numpy
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|
@ -19,6 +19,9 @@
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# TRIQS. If not, see <http://www.gnu.org/licenses/>.
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#
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||||
##########################################################################
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"""
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elk converter tools for file I/O
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"""
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from .readElkfiles import readElkfiles
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from .elk_converter_tools import ElkConverterTools
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|
@ -19,6 +19,9 @@
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# TRIQS. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
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||||
##########################################################################
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"""
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General H(k) converter
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"""
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from types import *
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import numpy
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@ -69,14 +72,14 @@ class HkConverter(ConverterTools):
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def convert_dft_input(self, first_real_part_matrix=True, only_upper_triangle=False, weights_in_file=False):
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"""
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Reads the appropriate files and stores the data for the dft_subgrp in the hdf5 archive.
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||||
Reads the appropriate files and stores the data for the dft_subgrp in the hdf5 archive.
|
||||
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||||
Parameters
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||||
----------
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first_real_part_matrix : boolean, optional
|
||||
Should all the real components for given k be read in first, followed by the imaginary parts?
|
||||
only_upper_triangle : boolean, optional
|
||||
Should only the upper triangular part of H(k) be read in?
|
||||
Should only the upper triangular part of H(k) be read in?
|
||||
weights_in_file : boolean, optional
|
||||
Are the k-point weights to be read in?
|
||||
|
||||
|
@ -22,5 +22,8 @@
|
||||
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
################################################################################
|
||||
"""
|
||||
plovasp module for I/O operations in the Vasp converter
|
||||
"""
|
||||
|
||||
__all__ = []
|
||||
|
@ -23,6 +23,9 @@
|
||||
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
################################################################################
|
||||
"""
|
||||
Vasp converter
|
||||
"""
|
||||
|
||||
from types import *
|
||||
import numpy
|
||||
|
@ -45,7 +45,9 @@
|
||||
# can cause a problem in creating the udis_mat in read_wannier90data
|
||||
# - add_lambda does not work for multiple impurities
|
||||
###
|
||||
|
||||
"""
|
||||
Wannier90 converter
|
||||
"""
|
||||
|
||||
import numpy
|
||||
import os.path
|
||||
|
@ -19,6 +19,9 @@
|
||||
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
##########################################################################
|
||||
"""
|
||||
Wien2k converter
|
||||
"""
|
||||
|
||||
from types import *
|
||||
import numpy
|
||||
@ -99,7 +102,7 @@ class Wien2kConverter(ConverterTools):
|
||||
- symmcorr_subgrp
|
||||
- misc_subgrp
|
||||
|
||||
in the hdf5 archive.
|
||||
in the hdf5 archive.
|
||||
|
||||
"""
|
||||
|
||||
@ -277,12 +280,12 @@ class Wien2kConverter(ConverterTools):
|
||||
|
||||
def convert_parproj_input(self):
|
||||
"""
|
||||
Reads the appropriate files and stores the data for the
|
||||
Reads the appropriate files and stores the data for the
|
||||
|
||||
- parproj_subgrp
|
||||
- symmpar_subgrp
|
||||
|
||||
in the hdf5 archive.
|
||||
in the hdf5 archive.
|
||||
|
||||
"""
|
||||
|
||||
@ -382,7 +385,7 @@ class Wien2kConverter(ConverterTools):
|
||||
|
||||
def convert_bands_input(self):
|
||||
"""
|
||||
Reads the appropriate files and stores the data for the bands_subgrp in the hdf5 archive.
|
||||
Reads the appropriate files and stores the data for the bands_subgrp in the hdf5 archive.
|
||||
|
||||
"""
|
||||
|
||||
@ -496,7 +499,7 @@ class Wien2kConverter(ConverterTools):
|
||||
- symmetries from :file:`case.outputs`,
|
||||
|
||||
if those Wien2k files are present and stores the data in the hdf5 archive.
|
||||
This function is automatically called by :meth:`convert_dft_input <triqs_dft_tools.converters.wien2k.Wien2kConverter.convert_dft_input>`.
|
||||
This function is automatically called by :meth:`convert_dft_input <triqs_dft_tools.converters.wien2k.Wien2kConverter.convert_dft_input>`.
|
||||
|
||||
"""
|
||||
|
||||
@ -619,7 +622,7 @@ class Wien2kConverter(ConverterTools):
|
||||
ar[self.misc_subgrp][it] = locals()[it]
|
||||
|
||||
def convert_transport_input(self):
|
||||
"""
|
||||
"""
|
||||
Reads the necessary information for transport calculations on:
|
||||
|
||||
- the optical band window and the velocity matrix elements from :file:`case.pmat`
|
||||
@ -712,10 +715,10 @@ class Wien2kConverter(ConverterTools):
|
||||
Parameters
|
||||
----------
|
||||
orbits : list of dicts
|
||||
This is either shells or corr_shells depending on whether the symmetry
|
||||
This is either shells or corr_shells depending on whether the symmetry
|
||||
information is for correlated shells or partial projectors.
|
||||
symm_file : string
|
||||
Name of the file containing symmetry data.
|
||||
Name of the file containing symmetry data.
|
||||
This is case.symqmc for correlated shells and case.sympar for partial projectors.
|
||||
symm_subgrp : string, optional
|
||||
Name of subgroup storing symmetry data.
|
||||
|
@ -20,6 +20,9 @@
|
||||
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
##########################################################################
|
||||
"""
|
||||
General SumK class and helper functions for combining ab-initio code and triqs
|
||||
"""
|
||||
|
||||
from types import *
|
||||
import numpy
|
||||
@ -2215,7 +2218,7 @@ class SumkDFT(object):
|
||||
valim = deltaN[spn[ispn]][ik][inu, imu].imag
|
||||
f.write(" %.14f %.14f"%(valre, valim))
|
||||
f.write("\n")
|
||||
|
||||
|
||||
elif dm_type == 'qe':
|
||||
assert self.SP == 0, "Spin-polarized density matrix is not implemented"
|
||||
|
||||
|
@ -18,6 +18,10 @@
|
||||
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
##########################################################################
|
||||
"""
|
||||
Extension to the SumkDFT class with some analyiss tools
|
||||
"""
|
||||
|
||||
import sys
|
||||
from types import *
|
||||
import numpy
|
||||
|
@ -19,6 +19,9 @@
|
||||
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
##########################################################################
|
||||
"""
|
||||
module for the symmetry operations in k sums
|
||||
"""
|
||||
|
||||
import copy
|
||||
import numpy
|
||||
@ -85,12 +88,12 @@ class Symmetry:
|
||||
|
||||
def symmetrize(self, obj):
|
||||
"""
|
||||
Symmetrizes a given object.
|
||||
Symmetrizes a given object.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
obj : list
|
||||
object to symmetrize. It has to be given as list, where its length is determined by the number
|
||||
object to symmetrize. It has to be given as list, where its length is determined by the number
|
||||
of equivalent members of the object. Two types of objects are supported:
|
||||
|
||||
- BlockGf : list of Green's functions,
|
||||
|
@ -1,3 +1,28 @@
|
||||
##########################################################################
|
||||
#
|
||||
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
|
||||
#
|
||||
# Copyright (C) 2011 by M. Aichhorn, L. Pourovskii, V. Vildosola
|
||||
#
|
||||
# TRIQS is free software: you can redistribute it and/or modify it under the
|
||||
# terms of the GNU General Public License as published by the Free Software
|
||||
# Foundation, either version 3 of the License, or (at your option) any later
|
||||
# version.
|
||||
#
|
||||
# TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
|
||||
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
|
||||
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
|
||||
# details.
|
||||
#
|
||||
# You should have received a copy of the GNU General Public License along with
|
||||
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
##########################################################################
|
||||
"""
|
||||
Module for orbital basis transformations
|
||||
"""
|
||||
|
||||
|
||||
from triqs_dft_tools.sumk_dft import *
|
||||
from triqs_dft_tools.converters import Wien2kConverter
|
||||
from triqs.gf import *
|
||||
|
@ -1,142 +0,0 @@
|
||||
from h5 import HDFArchive
|
||||
import h5py
|
||||
import sys
|
||||
import numpy
|
||||
import subprocess
|
||||
|
||||
if len(sys.argv) < 2:
|
||||
print("Usage: python update_archive.py old_archive [v1.0|v1.2]")
|
||||
sys.exit()
|
||||
|
||||
print("""
|
||||
This script is an attempt to update your archive to TRIQS 1.2.
|
||||
Please keep a copy of your old archive as this script is
|
||||
** not guaranteed ** to work for your archive.
|
||||
If you encounter any problem please report it on github!
|
||||
""")
|
||||
|
||||
|
||||
def convert_shells(shells):
|
||||
shell_entries = ['atom', 'sort', 'l', 'dim']
|
||||
return [{name: int(val) for name, val in zip(shell_entries, shells[ish])} for ish in range(len(shells))]
|
||||
|
||||
|
||||
def convert_corr_shells(corr_shells):
|
||||
corr_shell_entries = ['atom', 'sort', 'l', 'dim', 'SO', 'irep']
|
||||
return [{name: int(val) for name, val in zip(corr_shell_entries, corr_shells[icrsh])} for icrsh in range(len(corr_shells))]
|
||||
|
||||
|
||||
def det_shell_equivalence(corr_shells):
|
||||
corr_to_inequiv = [0 for i in range(len(corr_shells))]
|
||||
inequiv_to_corr = [0]
|
||||
n_inequiv_shells = 1
|
||||
|
||||
if len(corr_shells) > 1:
|
||||
inequiv_sort = [corr_shells[0]['sort']]
|
||||
inequiv_l = [corr_shells[0]['l']]
|
||||
for i in range(len(corr_shells) - 1):
|
||||
is_equiv = False
|
||||
for j in range(n_inequiv_shells):
|
||||
if (inequiv_sort[j] == corr_shells[i + 1]['sort']) and (inequiv_l[j] == corr_shells[i + 1]['l']):
|
||||
is_equiv = True
|
||||
corr_to_inequiv[i + 1] = j
|
||||
if is_equiv == False:
|
||||
corr_to_inequiv[i + 1] = n_inequiv_shells
|
||||
n_inequiv_shells += 1
|
||||
inequiv_sort.append(corr_shells[i + 1]['sort'])
|
||||
inequiv_l.append(corr_shells[i + 1]['l'])
|
||||
inequiv_to_corr.append(i + 1)
|
||||
|
||||
return n_inequiv_shells, corr_to_inequiv, inequiv_to_corr
|
||||
|
||||
|
||||
### Main ###
|
||||
|
||||
filename = sys.argv[1]
|
||||
if len(sys.argv) > 2:
|
||||
from_v = sys.argv[2]
|
||||
else: # Assume updating an old v1.0 script
|
||||
from_v = 'v1.0'
|
||||
A = h5py.File(filename)
|
||||
|
||||
# Rename groups
|
||||
old_to_new = {'SumK_LDA': 'dft_input', 'SumK_LDA_ParProj': 'dft_parproj_input',
|
||||
'SymmCorr': 'dft_symmcorr_input', 'SymmPar': 'dft_symmpar_input', 'SumK_LDA_Bands': 'dft_bands_input'}
|
||||
|
||||
for old, new in old_to_new.items():
|
||||
if old not in list(A.keys()):
|
||||
continue
|
||||
print("Changing %s to %s ..." % (old, new))
|
||||
A.copy(old, new)
|
||||
del(A[old])
|
||||
|
||||
# Move output items from dft_input to user_data
|
||||
move_to_output = ['chemical_potential', 'dc_imp', 'dc_energ']
|
||||
for obj in move_to_output:
|
||||
if obj in list(A['dft_input'].keys()):
|
||||
if 'user_data' not in A:
|
||||
A.create_group('user_data')
|
||||
print("Moving %s to user_data ..." % obj)
|
||||
A.copy('dft_input/' + obj, 'user_data/' + obj)
|
||||
del(A['dft_input'][obj])
|
||||
# Delete obsolete quantities
|
||||
to_delete = ['gf_struct_solver', 'map_inv', 'map', 'deg_shells', 'h_field']
|
||||
for obj in to_delete:
|
||||
if obj in list(A['dft_input'].keys()):
|
||||
del(A['dft_input'][obj])
|
||||
|
||||
if from_v == 'v1.0':
|
||||
# Update shells and corr_shells to list of dicts
|
||||
shells_old = HDFArchive(filename, 'r')['dft_input']['shells']
|
||||
corr_shells_old = HDFArchive(filename, 'r')['dft_input']['corr_shells']
|
||||
shells = convert_shells(shells_old)
|
||||
corr_shells = convert_corr_shells(corr_shells_old)
|
||||
del(A['dft_input']['shells'])
|
||||
del(A['dft_input']['corr_shells'])
|
||||
A.close()
|
||||
# Need to use HDFArchive for the following
|
||||
HDFArchive(filename, 'a')['dft_input']['shells'] = shells
|
||||
HDFArchive(filename, 'a')['dft_input']['corr_shells'] = corr_shells
|
||||
A = h5py.File(filename)
|
||||
|
||||
# Add shell equivalency quantities
|
||||
if 'n_inequiv_shells' not in A['dft_input']:
|
||||
equiv_shell_info = det_shell_equivalence(corr_shells)
|
||||
A['dft_input']['n_inequiv_shells'] = equiv_shell_info[0]
|
||||
A['dft_input']['corr_to_inequiv'] = equiv_shell_info[1]
|
||||
A['dft_input']['inequiv_to_corr'] = equiv_shell_info[2]
|
||||
|
||||
# Rename variables
|
||||
groups = ['dft_symmcorr_input', 'dft_symmpar_input']
|
||||
for group in groups:
|
||||
if group not in list(A.keys()):
|
||||
continue
|
||||
if 'n_s' not in A[group]:
|
||||
continue
|
||||
print("Changing n_s to n_symm ...")
|
||||
A[group].move('n_s', 'n_symm')
|
||||
# Convert orbits to list of dicts
|
||||
orbits_old = HDFArchive(filename, 'r')[group]['orbits']
|
||||
orbits = convert_corr_shells(orbits_old)
|
||||
del(A[group]['orbits'])
|
||||
A.close()
|
||||
HDFArchive(filename, 'a')[group]['orbits'] = orbits
|
||||
A = h5py.File(filename)
|
||||
|
||||
groups = ['dft_parproj_input']
|
||||
for group in groups:
|
||||
if group not in list(A.keys()):
|
||||
continue
|
||||
if 'proj_mat_pc' not in A[group]:
|
||||
continue
|
||||
print("Changing proj_mat_pc to proj_mat_all ...")
|
||||
A[group].move('proj_mat_pc', 'proj_mat_all')
|
||||
|
||||
A.close()
|
||||
|
||||
# Repack to reclaim disk space
|
||||
retcode = subprocess.call(["h5repack", "-i%s" % filename, "-otemphgfrt.h5"])
|
||||
if retcode != 0:
|
||||
print("h5repack failed!")
|
||||
else:
|
||||
subprocess.call(["mv", "-f", "temphgfrt.h5", "%s" % filename])
|
Loading…
Reference in New Issue
Block a user