From c4db7e686716aa16edc362fce68fa22db4607d5b Mon Sep 17 00:00:00 2001 From: Alexander Hampel Date: Tue, 1 Mar 2022 17:51:39 -0500 Subject: [PATCH] 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 --- .../autosummary_module_template.rst | 2 +- doc/conf.py.in | 2 +- doc/documentation.rst | 27 ++-- doc/guide/conv_generalhk.rst | 2 +- doc/guide/conv_vasp.rst | 18 ++- doc/guide/conv_wien2k.rst | 4 +- doc/guide/soc.rst | 2 +- doc/{reference => }/h5structure.rst | 6 +- doc/reference/block_structure.rst | 21 --- doc/reference/converters.rst | 83 ---------- doc/reference/sumk_dft.rst | 8 - doc/reference/sumk_dft_tools.rst | 8 - doc/reference/symmetry.rst | 6 - doc/reference/transbasis.rst | 6 - doc/tutorials.rst | 2 - python/triqs_dft_tools/block_structure.py | 9 +- python/triqs_dft_tools/converters/__init__.py | 3 + .../converters/converter_tools.py | 8 +- python/triqs_dft_tools/converters/elk.py | 3 + .../converters/elktools/__init__.py | 3 + python/triqs_dft_tools/converters/hk.py | 7 +- .../converters/plovasp/__init__.py | 3 + python/triqs_dft_tools/converters/vasp.py | 3 + .../triqs_dft_tools/converters/wannier90.py | 4 +- python/triqs_dft_tools/converters/wien2k.py | 19 ++- python/triqs_dft_tools/sumk_dft.py | 5 +- python/triqs_dft_tools/sumk_dft_tools.py | 4 + python/triqs_dft_tools/symmetry.py | 7 +- python/triqs_dft_tools/trans_basis.py | 25 +++ python/triqs_dft_tools/update_archive.py | 142 ------------------ 30 files changed, 122 insertions(+), 320 deletions(-) rename doc/{reference => }/h5structure.rst (99%) delete mode 100644 doc/reference/block_structure.rst delete mode 100644 doc/reference/converters.rst delete mode 100644 doc/reference/sumk_dft.rst delete mode 100644 doc/reference/sumk_dft_tools.rst delete mode 100644 doc/reference/symmetry.rst delete mode 100644 doc/reference/transbasis.rst delete mode 100644 python/triqs_dft_tools/update_archive.py diff --git a/doc/_templates/autosummary_module_template.rst b/doc/_templates/autosummary_module_template.rst index 737206f84..4d84704b1 100644 --- a/doc/_templates/autosummary_module_template.rst +++ b/doc/_templates/autosummary_module_template.rst @@ -1,4 +1,4 @@ -{{ fullname | escape | underline}} +{{ name | escape | underline}} .. automodule:: {{ fullname }} diff --git a/doc/conf.py.in b/doc/conf.py.in index 670aa3e6f..017200e1f 100644 --- a/doc/conf.py.in +++ b/doc/conf.py.in @@ -76,7 +76,7 @@ html_theme_options = { # Toc options 'collapse_navigation': False, 'sticky_navigation': True, - 'navigation_depth': 5, + 'navigation_depth': 4, 'includehidden': True, 'titles_only': False } diff --git a/doc/documentation.rst b/doc/documentation.rst index 371ff5129..ccaea38d7 100644 --- a/doc/documentation.rst +++ b/doc/documentation.rst @@ -9,7 +9,7 @@ Basic notions ------------- .. toctree:: - :maxdepth: 2 + :maxdepth: 1 basicnotions/first basicnotions/dft_dmft @@ -23,6 +23,7 @@ Construction of local orbitals from DFT :maxdepth: 2 guide/conversion + h5structure DFT+DMFT @@ -38,7 +39,7 @@ Advanced Topics --------------- .. toctree:: - :maxdepth: 2 + :maxdepth: 1 guide/blockstructure guide/BasisRotation @@ -48,7 +49,7 @@ Postprocessing -------------- .. toctree:: - :maxdepth: 2 + :maxdepth: 1 guide/analysis guide/transport @@ -59,16 +60,18 @@ Reference manual This is the reference manual for the python routines. -.. toctree:: - :maxdepth: 2 +.. autosummary:: + :recursive: + :toctree: _python_api + :template: autosummary_module_template.rst + + block_structure + converters + sumk_dft + sumk_dft_tools + symmetry + trans_basis - reference/h5structure - reference/converters - reference/sumk_dft - reference/sumk_dft_tools - reference/symmetry - reference/transbasis - reference/block_structure FAQs diff --git a/doc/guide/conv_generalhk.rst b/doc/guide/conv_generalhk.rst index 5453850d6..3ec40ce34 100644 --- a/doc/guide/conv_generalhk.rst +++ b/doc/guide/conv_generalhk.rst @@ -95,6 +95,6 @@ where :file:`hkinputfile` is the name of the input file described above. This produces the hdf file that you need for a DMFT calculation. For more options of this converter, have a look at the -:ref:`refconverters` section of the reference manual. +:py:mod:`Converters ` section of the reference manual. diff --git a/doc/guide/conv_vasp.rst b/doc/guide/conv_vasp.rst index 1a039180b..f563e6aa5 100644 --- a/doc/guide/conv_vasp.rst +++ b/doc/guide/conv_vasp.rst @@ -17,10 +17,10 @@ Hubbard-like model Hamiltonian. Resulting in lattice object stored in `SumkDFT`. The implementation is presented in `M. Schüler et al. 2018 J. Phys.: Condens. Matter 30 475901 `_. -The interface consists of two parts, :ref:`PLOVASP`, a collection of +The interface consists of two parts, :py:mod:`PLOVASP`, a collection of python classes and functions converting the raw VASP output to proper projector -functions, and the python based :ref:`VaspConverter`, which -creates a h5 archive from the :ref:`PLOVASP` output readable by +functions, and the python based :py:mod:`VaspConverter`, which +creates a h5 archive from the :py:mod:`PLOVASP` output readable by `SumkDFT`. Therefore, the conversion consist always of two steps. 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`. @@ -134,7 +134,7 @@ described above and it must be chosen independently of the energy range given by PLOVASP: converting VASP output -------------------------------- -:ref:`PLOVASP` is a collection of python functions and classes, post-processing the raw VASP `LOCPROJ` output creating proper projector functions. +:py:mod:`PLOVASP` is a collection of python functions and classes, post-processing the raw VASP `LOCPROJ` output creating proper projector functions. The following VASP files are used by PLOVASP: * PROJCAR, LOCPROJ: raw projectors generated by VASP-PLO interface @@ -176,12 +176,12 @@ or embedded in a python script as:: # Generate and store PLOs plo_converter.generate_and_output_as_text('plo.cfg', vasp_dir='./') -This will create the xml files `vasp.ctrl` and `vasp.pg1` containing the orthonormalized projector functions readable by the :ref:`VaspConverter`. Moreover, `PLOVASP` will output important information of the orthonormalization process, such as the density matrix of the correlated shell and the local Hamiltonian. +This will create the xml files `vasp.ctrl` and `vasp.pg1` containing the orthonormalized projector functions readable by the :py:mod:`VaspConverter`. Moreover, :py:mod:`PLOVASP` will output important information of the orthonormalization process, such as the density matrix of the correlated shell and the local Hamiltonian. Running the VASP converter ------------------------------------- -The actual conversion to a h5-file is performed with the orthonormalized projector functions readable by the :ref:`VaspConverter` in the same fashion as with the other `DFTTools` converters:: +The actual conversion to a h5-file is performed with the orthonormalized projector functions readable by the :py:mod:`VaspConverter` in the same fashion as with the other `DFTTools` converters:: from triqs_dft_tools.converters.vasp import * Converter = VaspConverter(filename = 'vasp') @@ -394,12 +394,14 @@ in the header. One can either copy the Fermi energy manually there after a succe VASP run, or modify the VASP source code slightly, by replacing the following line in `locproj.F` (around line 695): :: + < WRITE(99,'(4I6," # of spin, # of k-points, # of bands, # of proj" )') NS,NK,NB,NF --- > WRITE(99,'(4I6,F12.7," # of spin, # of k-points, # of bands, # of proj, Efermi" )') W%WDES%NCDIJ,NK,NB,NF,EFERMI Now one needs to pass additionally the variable `EFERMI` to the function, by changing (at arount line 560): :: + < SUBROUTINE LPRJ_WRITE(IU6,IU0,W) --- > SUBROUTINE LPRJ_WRITE(IU6,IU0,W,EFERMI) @@ -408,6 +410,7 @@ Now one needs to pass additionally the variable `EFERMI` to the function, by cha Next, we need to pass this option when calling from `electron.F` and `main.F` (just search for LPRJ_WRITE in the files) and change all occurences as follows: :: + < CALL LPRJ_WRITE(IO%IU6, IO%IU0, W) --- > CALL LPRJ_WRITE(IO%IU6, IO%IU0, W, EFERMI) @@ -424,13 +427,16 @@ Furthermore, there is a bug in `fileio.F` around line 1710 where VASP tries to print "reading the density matrix from Gamma". This should be done only by the master node, and VASP gets stuck sometimes. Adding a :: + IF (IO%IU0>=0) THEN ... ENDIF + statement resolves this issue. A similar problem occurs, when VASP writes the `OSZICAR` file and a buffer is stuck. Adding a `flush` to the buffer in `electron.F` around line 580 after :: + CALL STOP_TIMING("G",IO%IU6,"DOS") flush(17) print *, ' ' diff --git a/doc/guide/conv_wien2k.rst b/doc/guide/conv_wien2k.rst index 895bdaa0b..a93ede33a 100644 --- a/doc/guide/conv_wien2k.rst +++ b/doc/guide/conv_wien2k.rst @@ -128,7 +128,7 @@ example, the :program:`Wien2k` naming convention is that all files have the same name, but different extensions, :file:`case.*`. The constructor opens an hdf5 archive, named :file:`case.h5`, where all relevant data will be stored. For other parameters of the constructor please visit the -:ref:`refconverters` section of the reference manual. +:py:mod:`Converters ` section of the reference manual. After initializing the interface module, we can now convert the input text files to the hdf5 archive by:: @@ -181,7 +181,7 @@ and convert the input for :class:`SumkDFTTools 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. +a look at the :py:mod:`Converters ` section of the reference manual. Data for transport calculations ------------------------------- diff --git a/doc/guide/soc.rst b/doc/guide/soc.rst index 56a43f222..a0cf39e7f 100644 --- a/doc/guide/soc.rst +++ b/doc/guide/soc.rst @@ -39,7 +39,7 @@ Note that in presence of SOC, it is not possible to project only onto the :math: Treatment of SOC in Elk ------------------------- -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 `_ 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. +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 `_ 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. After generating the projectors ------------------------------- diff --git a/doc/reference/h5structure.rst b/doc/h5structure.rst similarity index 99% rename from doc/reference/h5structure.rst rename to doc/h5structure.rst index 215dd2015..af01c191d 100644 --- a/doc/reference/h5structure.rst +++ b/doc/h5structure.rst @@ -1,9 +1,9 @@ .. _hdfstructure: -hdf5 structure -============== +standardized hdf5 structure +=========================== -All the data is stored using the hdf5 standard, as described also in the +All the DFT input data is stored using the hdf5 standard, as described also in the documentation of the TRIQS package itself. In order to do a DMFT calculation, using input from DFT applications, a converter is needed on order to provide the necessary data in the hdf5 format. diff --git a/doc/reference/block_structure.rst b/doc/reference/block_structure.rst deleted file mode 100644 index 1fe1bebbb..000000000 --- a/doc/reference/block_structure.rst +++ /dev/null @@ -1,21 +0,0 @@ -Block Structure -=============== - -The `BlockStructure` class allows to change and manipulate -Green functions structures and mappings from sumk to solver. - -The block structure can also be written to and read from HDF files. - -.. warning:: - - Do not write the individual elements of this class to a HDF file, - as they belong together and changing one without the other can - result in unexpected results. Always write the BlockStructure - object as a whole. - - Writing the sumk_to_solver and solver_to_sumk elements - individually is not implemented. - -.. autoclass:: triqs_dft_tools.block_structure.BlockStructure - :members: - :show-inheritance: diff --git a/doc/reference/converters.rst b/doc/reference/converters.rst deleted file mode 100644 index 3dd802155..000000000 --- a/doc/reference/converters.rst +++ /dev/null @@ -1,83 +0,0 @@ -.. _refconverters: - -Converters -========== - -Wien2k Converter ----------------- -.. autoclass:: triqs_dft_tools.converters.wien2k.Wien2kConverter - :members: - :special-members: - :show-inheritance: - -H(k) Converter --------------- -.. autoclass:: triqs_dft_tools.converters.hk.HkConverter - :members: - :special-members: - -Wannier90 Converter -------------------- -.. autoclass:: triqs_dft_tools.converters.wannier90.Wannier90Converter - :members: - :special-members: - -PLOVASP ----------- -.. _refPLOVASP: - -PLOVASP reference, the classes / functions are sorted the way the converter uses them. - -.. automodule:: triqs_dft_tools.converters.plovasp.converter - :members: generate_and_output_as_text - -.. automodule:: triqs_dft_tools.converters.plovasp.inpconf - :members: ConfigParameters - -.. automodule:: triqs_dft_tools.converters.plovasp.vaspio - :members: VaspData, Plocar, Poscar, Kpoints, Eigenval, Doscar, read_symmcar - -.. automodule:: triqs_dft_tools.converters.plovasp.elstruct - :members: ElectronicStructure - -.. automodule:: triqs_dft_tools.converters.plovasp.plotools - :members: - -.. automodule:: triqs_dft_tools.converters.plovasp.proj_shell - :members: - -.. automodule:: triqs_dft_tools.converters.plovasp.proj_group - :members: - - -VASP Converter -------------------- -.. _refVASPconverter: -.. autoclass:: triqs_dft_tools.converters.vasp.VaspConverter - :members: - :special-members: - - -Elk Converter -------------------- -.. _refElkconverter: -.. autoclass:: triqs_dft_tools.converters.elk.ElkConverter - :members: - :special-members: - -Elk Tools -------------------- -.. _refElkTools: -.. autoclass:: triqs_dft_tools.converters.elktools.ElkConverterTools - :members: - :special-members: - -.. autoclass:: triqs_dft_tools.converters.elktools.readElkfiles - :members: - :special-members: - -Converter Tools ---------------- -.. autoclass:: triqs_dft_tools.converters.converter_tools.ConverterTools - :members: - :special-members: diff --git a/doc/reference/sumk_dft.rst b/doc/reference/sumk_dft.rst deleted file mode 100644 index 3c28ecd7a..000000000 --- a/doc/reference/sumk_dft.rst +++ /dev/null @@ -1,8 +0,0 @@ -SumK DFT -======== - - -.. autoclass:: triqs_dft_tools.sumk_dft.SumkDFT - :members: - :special-members: - :show-inheritance: diff --git a/doc/reference/sumk_dft_tools.rst b/doc/reference/sumk_dft_tools.rst deleted file mode 100644 index f0ad0fda1..000000000 --- a/doc/reference/sumk_dft_tools.rst +++ /dev/null @@ -1,8 +0,0 @@ -SumK DFT Tools -============== - - -.. autoclass:: triqs_dft_tools.sumk_dft_tools.SumkDFTTools - :members: - :special-members: - :show-inheritance: diff --git a/doc/reference/symmetry.rst b/doc/reference/symmetry.rst deleted file mode 100644 index 597f84fc6..000000000 --- a/doc/reference/symmetry.rst +++ /dev/null @@ -1,6 +0,0 @@ -Symmetry -======== - -.. autoclass:: triqs_dft_tools.Symmetry - :members: - :special-members: diff --git a/doc/reference/transbasis.rst b/doc/reference/transbasis.rst deleted file mode 100644 index 670126c49..000000000 --- a/doc/reference/transbasis.rst +++ /dev/null @@ -1,6 +0,0 @@ -TransBasis -========== - -.. autoclass:: triqs_dft_tools.trans_basis.TransBasis - :members: - :special-members: diff --git a/doc/tutorials.rst b/doc/tutorials.rst index bf1d4dd02..a45567527 100644 --- a/doc/tutorials.rst +++ b/doc/tutorials.rst @@ -1,5 +1,3 @@ -.. module:: triqs_dft_tools - .. _tutorials: Tutorials diff --git a/python/triqs_dft_tools/block_structure.py b/python/triqs_dft_tools/block_structure.py index e7274b60d..d0babdf5f 100644 --- a/python/triqs_dft_tools/block_structure.py +++ b/python/triqs_dft_tools/block_structure.py @@ -21,7 +21,9 @@ # TRIQS. If not, see . # ########################################################################## - +""" +Block structure class and helper functions +""" import copy import numpy as np @@ -38,6 +40,11 @@ class BlockStructure(object): This class contains information about the structure of the solver and sumk Green functions and the mapping between them. + Do not write the individual elements of this class to a HDF file, + as they belong together and changing one without the other can + result in unexpected results. Always write the BlockStructure + object as a whole. + Parameters ---------- gf_struct_sumk : list of list of tuple diff --git a/python/triqs_dft_tools/converters/__init__.py b/python/triqs_dft_tools/converters/__init__.py index 32131913b..658242ba0 100644 --- a/python/triqs_dft_tools/converters/__init__.py +++ b/python/triqs_dft_tools/converters/__init__.py @@ -19,6 +19,9 @@ # TRIQS. If not, see . # ########################################################################## +""" +module containing all available converters for DFTTools +""" from .wien2k import Wien2kConverter from .hk import HkConverter diff --git a/python/triqs_dft_tools/converters/converter_tools.py b/python/triqs_dft_tools/converters/converter_tools.py index 2d393c755..89cc2351c 100644 --- a/python/triqs_dft_tools/converters/converter_tools.py +++ b/python/triqs_dft_tools/converters/converter_tools.py @@ -19,6 +19,10 @@ # TRIQS. If not, see . # ########################################################################## +""" +Converter helper module +""" + import triqs.utility.mpi as mpi class ConverterTools: @@ -59,7 +63,7 @@ def repack(self): Note ---- - Should only be used before the first invokation of HDFArchive in the program, + Should only be used before the first invokation of HDFArchive in the program, otherwise the hdf5 linking will be broken. """ @@ -92,7 +96,7 @@ def det_shell_equivalence(self, corr_shells): Number of inequivalent shells. corr_to_inequiv : list Mapping between correlated shell index and inequivalent shell index. - corr_to_inequiv(i_corr_shells) = i_inequiv_shells + corr_to_inequiv(i_corr_shells) = i_inequiv_shells inequiv_to_corr : list Mapping between inequivalent shell index and correlated shell index. inequiv_to_corr(i_inequiv_shells) = i_corr_shells diff --git a/python/triqs_dft_tools/converters/elk.py b/python/triqs_dft_tools/converters/elk.py index 0b62a9b32..39b67e0aa 100644 --- a/python/triqs_dft_tools/converters/elk.py +++ b/python/triqs_dft_tools/converters/elk.py @@ -19,6 +19,9 @@ # TRIQS. If not, see . # ########################################################################## +""" +Elk converter +""" from types import * import numpy diff --git a/python/triqs_dft_tools/converters/elktools/__init__.py b/python/triqs_dft_tools/converters/elktools/__init__.py index 282313172..583b4fc65 100644 --- a/python/triqs_dft_tools/converters/elktools/__init__.py +++ b/python/triqs_dft_tools/converters/elktools/__init__.py @@ -19,6 +19,9 @@ # TRIQS. If not, see . # ########################################################################## +""" +elk converter tools for file I/O +""" from .readElkfiles import readElkfiles from .elk_converter_tools import ElkConverterTools diff --git a/python/triqs_dft_tools/converters/hk.py b/python/triqs_dft_tools/converters/hk.py index 0984a7b4b..02a881ae0 100644 --- a/python/triqs_dft_tools/converters/hk.py +++ b/python/triqs_dft_tools/converters/hk.py @@ -19,6 +19,9 @@ # TRIQS. If not, see . # ########################################################################## +""" +General H(k) converter +""" from types import * import numpy @@ -69,14 +72,14 @@ def __init__(self, filename, hdf_filename=None, dft_subgrp='dft_input', symmcorr def convert_dft_input(self, first_real_part_matrix=True, only_upper_triangle=False, weights_in_file=False): """ - Reads the appropriate files and stores the data for the dft_subgrp in the hdf5 archive. + Reads the appropriate files and stores the data for the dft_subgrp in the hdf5 archive. Parameters ---------- 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? diff --git a/python/triqs_dft_tools/converters/plovasp/__init__.py b/python/triqs_dft_tools/converters/plovasp/__init__.py index d6a0c54a9..3eb6c0ec3 100644 --- a/python/triqs_dft_tools/converters/plovasp/__init__.py +++ b/python/triqs_dft_tools/converters/plovasp/__init__.py @@ -22,5 +22,8 @@ # TRIQS. If not, see . # ################################################################################ +""" +plovasp module for I/O operations in the Vasp converter +""" __all__ = [] diff --git a/python/triqs_dft_tools/converters/vasp.py b/python/triqs_dft_tools/converters/vasp.py index d3aca83bb..5b5fa4788 100644 --- a/python/triqs_dft_tools/converters/vasp.py +++ b/python/triqs_dft_tools/converters/vasp.py @@ -23,6 +23,9 @@ # TRIQS. If not, see . # ################################################################################ +""" +Vasp converter +""" from types import * import numpy diff --git a/python/triqs_dft_tools/converters/wannier90.py b/python/triqs_dft_tools/converters/wannier90.py index 107f00785..2650d9aed 100644 --- a/python/triqs_dft_tools/converters/wannier90.py +++ b/python/triqs_dft_tools/converters/wannier90.py @@ -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 diff --git a/python/triqs_dft_tools/converters/wien2k.py b/python/triqs_dft_tools/converters/wien2k.py index b45ffa72c..3025ef5b7 100644 --- a/python/triqs_dft_tools/converters/wien2k.py +++ b/python/triqs_dft_tools/converters/wien2k.py @@ -19,6 +19,9 @@ # TRIQS. If not, see . # ########################################################################## +""" +Wien2k converter +""" from types import * import numpy @@ -99,7 +102,7 @@ def convert_dft_input(self): - symmcorr_subgrp - misc_subgrp - in the hdf5 archive. + in the hdf5 archive. """ @@ -277,12 +280,12 @@ def convert_dft_input(self): 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 @@ def convert_parproj_input(self): 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 @@ def convert_misc_input(self): - 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 `. + This function is automatically called by :meth:`convert_dft_input `. """ @@ -619,7 +622,7 @@ def convert_misc_input(self): 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 @@ def convert_symmetry_input(self, orbits, symm_file, symm_subgrp, SO, SP): 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. diff --git a/python/triqs_dft_tools/sumk_dft.py b/python/triqs_dft_tools/sumk_dft.py index 7f7347612..18f96da90 100644 --- a/python/triqs_dft_tools/sumk_dft.py +++ b/python/triqs_dft_tools/sumk_dft.py @@ -20,6 +20,9 @@ # TRIQS. If not, see . # ########################################################################## +""" +General SumK class and helper functions for combining ab-initio code and triqs +""" from types import * import numpy @@ -2215,7 +2218,7 @@ def calc_density_correction(self, filename=None, dm_type='wien2k', spinave=False 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" diff --git a/python/triqs_dft_tools/sumk_dft_tools.py b/python/triqs_dft_tools/sumk_dft_tools.py index d1c640dba..acf9e1c30 100644 --- a/python/triqs_dft_tools/sumk_dft_tools.py +++ b/python/triqs_dft_tools/sumk_dft_tools.py @@ -18,6 +18,10 @@ # TRIQS. If not, see . # ########################################################################## +""" +Extension to the SumkDFT class with some analyiss tools +""" + import sys from types import * import numpy diff --git a/python/triqs_dft_tools/symmetry.py b/python/triqs_dft_tools/symmetry.py index 56df919df..b021ec004 100644 --- a/python/triqs_dft_tools/symmetry.py +++ b/python/triqs_dft_tools/symmetry.py @@ -19,6 +19,9 @@ # TRIQS. If not, see . # ########################################################################## +""" +module for the symmetry operations in k sums +""" import copy import numpy @@ -85,12 +88,12 @@ def __init__(self, hdf_file, subgroup=None): 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, diff --git a/python/triqs_dft_tools/trans_basis.py b/python/triqs_dft_tools/trans_basis.py index baaa5857c..75dc0bf49 100644 --- a/python/triqs_dft_tools/trans_basis.py +++ b/python/triqs_dft_tools/trans_basis.py @@ -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 . +# +########################################################################## +""" +Module for orbital basis transformations +""" + + from triqs_dft_tools.sumk_dft import * from triqs_dft_tools.converters import Wien2kConverter from triqs.gf import * diff --git a/python/triqs_dft_tools/update_archive.py b/python/triqs_dft_tools/update_archive.py deleted file mode 100644 index cc9db916f..000000000 --- a/python/triqs_dft_tools/update_archive.py +++ /dev/null @@ -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])