| Name | castep-outputs JSON |
| Version |
0.1.8
JSON |
| download |
| home_page | None |
| Summary | A package for extracting information from castep outputs |
| upload_time | 2025-01-10 13:52:49 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | BSD-3-Clause |
| keywords |
castep
dft
parser
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
castep_outputs
==============
Parser for CASTEP output files
``castep_outputs`` parses the output files of `castep
<https://www.castep.org/>`__ into a standard form and is able to subsequently
dump the processed data into a standard format.
Install
-------
To install ``castep_outputs`` simply run:
::
pip install castep_outputs
To check it is installed run:
::
python -m castep_outputs -h
Dependencies
------------
``castep_outputs`` is designed to have no external dependencies beyond the
standard library, however, it is possible to use either `PyYAML
<https://pypi.org/project/PyYAML/>`__ or `ruamel.yaml
<https://pypi.org/project/ruamel.yaml/>`__ to dump in the YAML format.
Command-line
------------
When run as a commandline tool, it attempts to find all files for the
given seedname, filtered by ``inc`` args (default: all). Explicit
files can be passed using longname arguments. castep_outputs can parse
most human-readable castep outputs including: ``.castep``, ``.cell``,
``.param``, ``.geom``, ``.md``, ``.bands``, ``.hug``, ``.phonon``,
``.phonon_dos``, ``.efield``, ``.xrd_sf``, ``.elf_fmt``,
``.chdiff_fmt``, ``.pot_fmt``, ``.den_fmt``, ``.elastic``, ``.ts``,
``.magres``, ``.tddft``, ``.err``.
to run in basic mode:
::
python -m castep_outputs seedname
Which will attempt to detect all found files and dump a ``.json`` to
stdout, ready for piping.
::
python -m castep_outputs --inc-castep --inc-param seedname
Will parse only the ``seedname.castep`` and ``seedname.param`` files if
found.
::
python -m castep_outputs seedname.castep
Will parse the single named file and again dump a ``.json`` to stdout.
::
python -m castep_outputs --castep seedname.param
Will attempt to parse the file ``seedname.param`` as though it were a
``.castep`` file. While not ordinarily useful it can help with manually renamed
files.
::
python -m castep_outputs -o my_file.yaml -f yaml seedname.castep
Will parse ``seedname.castep``, dump it to ``my_file.yaml`` in ``yaml`` format
using the ``PyYAML`` engine if available and the ``RUAMEL`` engine if not.
As a module
-----------
``import``\ ing ``castep_outputs`` exposes all of the parsers at the
top-level.
The simplest method to use ``castep_outputs`` in a tool is to use the
``parse_single`` method which attempts to determine the parser from the file
extension.
::
from castep_outputs import parse_single
my_dict = parse_single('my_file.castep')
If you need a specific parser rather than determining it by extension
it is possible to pass them as the second argument, or call them
directly.
::
import castep_outputs as co
my_dict = co.parse_single('my_file', co.parse_castep_file)
with open('my_file', 'r', encoding='utf-8') as inp:
my_dict = co.parse_castep_file(inp)
It is recommended that you use ``parse_single`` as it uses special file-handling
to give better diagnostics if it fails. It is possible to enable more detailed
logging via the `logging
<https://docs.python.org/3/library/logging.html#logging.basicConfig>`_ module:
::
import logging
from castep_outputs import parse_single
my_dict = parse_single('my_file', loglevel=logging.INFO)
The available parsing functions are:
- ``parse_bands_file``
- ``parse_castep_file``
- ``parse_cell_file``
- ``parse_cell_param_file``
- ``parse_chdiff_fmt_file``
- ``parse_den_fmt_file``
- ``parse_efield_file``
- ``parse_elastic_file``
- ``parse_elf_fmt_file``
- ``parse_err_file``
- ``parse_geom_file``
- ``parse_hug_file``
- ``parse_magres_file``
- ``parse_md_file``
- ``parse_md_geom_file``
- ``parse_param_file``
- ``parse_phonon_file``
- ``parse_phonon_dos_file``
- ``parse_pot_fmt_file``
- ``parse_tddft_file``
- ``parse_tddft_file``
- ``parse_ts_file``
- ``parse_xrd_sf_file``
Which return processed ``list``\ s of ``dict``\ s of data ready for use
in other applications.
See `Documentation <https://oerc0122.github.io/castep_outputs/intro.html>`_ for full layout.
Full usage
----------
::
usage: castep_outputs [-h] [-V] [-L {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-o OUTPUT]
[-f {json,ruamel,yaml,pprint,print}] [-t] [-A] [--inc-castep]
[--inc-cell] [--inc-param] [--inc-geom] [--inc-md]
[--inc-bands] [--inc-hug] [--inc-phonon_dos] [--inc-efield]
[--inc-xrd_sf] [--inc-elf_fmt] [--inc-chdiff_fmt]
[--inc-pot_fmt] [--inc-den_fmt] [--inc-elastic] [--inc-ts]
[--inc-magres] [--inc-tddft] [--inc-err] [--inc-phonon]
[--castep [CASTEP ...]] [--cell [CELL ...]]
[--param [PARAM ...]] [--geom [GEOM ...]] [--md [MD ...]]
[--bands [BANDS ...]] [--hug [HUG ...]]
[--phonon_dos [PHONON_DOS ...]] [--efield [EFIELD ...]]
[--xrd_sf [XRD_SF ...]] [--elf_fmt [ELF_FMT ...]]
[--chdiff_fmt [CHDIFF_FMT ...]] [--pot_fmt [POT_FMT ...]]
[--den_fmt [DEN_FMT ...]] [--elastic [ELASTIC ...]]
[--ts [TS ...]] [--magres [MAGRES ...]] [--tddft [TDDFT ...]]
[--err [ERR ...]] [--phonon [PHONON ...]]
...
Attempts to find all files for seedname, filtered by `inc` args (default: all).
Explicit files can be passed using longname arguments. castep_outputs can parse most
human-readable castep outputs including: .castep, .cell, .param, .geom, .md, .bands,
.hug, .phonon_dos, .efield, .xrd_sf, .elf_fmt, .chdiff_fmt, .pot_fmt, .den_fmt,
.elastic, .ts, .magres, .tddft, .err, .phonon
positional arguments:
seedname Seed name for data
options:
-h, --help show this help message and exit
-V, --version show program's version number and exit
-L {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Verbose output
-o OUTPUT, --output OUTPUT
File to write output, default: screen
-f {json,ruamel,yaml,pprint,print}, --out-format {json,ruamel,yaml,pprint,print}
Output format
-t, --testing Set testing mode to produce flat outputs
-A, --inc-all Extract all available information
--inc-castep Extract .castep information
--inc-cell Extract .cell information
--inc-param Extract .param information
--inc-geom Extract .geom information
--inc-md Extract .md information
--inc-bands Extract .bands information
--inc-hug Extract .hug information
--inc-phonon_dos Extract .phonon_dos information
--inc-efield Extract .efield information
--inc-xrd_sf Extract .xrd_sf information
--inc-elf_fmt Extract .elf_fmt information
--inc-chdiff_fmt Extract .chdiff_fmt information
--inc-pot_fmt Extract .pot_fmt information
--inc-den_fmt Extract .den_fmt information
--inc-elastic Extract .elastic information
--inc-ts Extract .ts information
--inc-magres Extract .magres information
--inc-tddft Extract .tddft information
--inc-err Extract .err information
--inc-phonon Extract .phonon information
--castep [CASTEP ...]
Extract from CASTEP as .castep type
--cell [CELL ...] Extract from CELL as .cell type
--param [PARAM ...] Extract from PARAM as .param type
--geom [GEOM ...] Extract from GEOM as .geom type
--md [MD ...] Extract from MD as .md type
--bands [BANDS ...] Extract from BANDS as .bands type
--hug [HUG ...] Extract from HUG as .hug type
--phonon_dos [PHONON_DOS ...]
Extract from PHONON_DOS as .phonon_dos type
--efield [EFIELD ...]
Extract from EFIELD as .efield type
--xrd_sf [XRD_SF ...]
Extract from XRD_SF as .xrd_sf type
--elf_fmt [ELF_FMT ...]
Extract from ELF_FMT as .elf_fmt type
--chdiff_fmt [CHDIFF_FMT ...]
Extract from CHDIFF_FMT as .chdiff_fmt type
--pot_fmt [POT_FMT ...]
Extract from POT_FMT as .pot_fmt type
--den_fmt [DEN_FMT ...]
Extract from DEN_FMT as .den_fmt type
--elastic [ELASTIC ...]
Extract from ELASTIC as .elastic type
--ts [TS ...] Extract from TS as .ts type
--magres [MAGRES ...]
Extract from MAGRES as .magres type
--tddft [TDDFT ...] Extract from TDDFT as .tddft type
--err [ERR ...] Extract from ERR as .err type
--phonon [PHONON ...]
Extract from PHONON as .phonon type
Current Parsers:
- ``.bands``
- ``.castep``
- ``.cell``
- ``.chdiff_fmt``
- ``.den_fmt``
- ``.efield``
- ``.elastic``
- ``.elf_fmt``
- ``.err``
- ``.geom``
- ``.hug``
- ``.magres``
- ``.md``
- ``.param``
- ``.phonon``
- ``.phonon_dos``
- ``.pot_fmt``
- ``.tddft``
- ``.ts``
- ``.xrd_sf``
Current dumpers:
- ``json``
- ``ruamel.yaml``
- ``pyyaml``
- ``print``
- ``pprint``
Raw data
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"description": "castep_outputs\n==============\n\nParser for CASTEP output files\n\n``castep_outputs`` parses the output files of `castep\n<https://www.castep.org/>`__ into a standard form and is able to subsequently\ndump the processed data into a standard format.\n\nInstall\n-------\n\nTo install ``castep_outputs`` simply run:\n\n::\n\n pip install castep_outputs\n\nTo check it is installed run:\n\n::\n\n python -m castep_outputs -h\n\nDependencies\n------------\n\n``castep_outputs`` is designed to have no external dependencies beyond the\nstandard library, however, it is possible to use either `PyYAML\n<https://pypi.org/project/PyYAML/>`__ or `ruamel.yaml\n<https://pypi.org/project/ruamel.yaml/>`__ to dump in the YAML format.\n\nCommand-line\n------------\n\nWhen run as a commandline tool, it attempts to find all files for the\ngiven seedname, filtered by ``inc`` args (default: all). Explicit\nfiles can be passed using longname arguments. castep_outputs can parse\nmost human-readable castep outputs including: ``.castep``, ``.cell``,\n``.param``, ``.geom``, ``.md``, ``.bands``, ``.hug``, ``.phonon``,\n``.phonon_dos``, ``.efield``, ``.xrd_sf``, ``.elf_fmt``,\n``.chdiff_fmt``, ``.pot_fmt``, ``.den_fmt``, ``.elastic``, ``.ts``,\n``.magres``, ``.tddft``, ``.err``.\n\nto run in basic mode:\n\n::\n\n python -m castep_outputs seedname\n\nWhich will attempt to detect all found files and dump a ``.json`` to\nstdout, ready for piping.\n\n::\n\n python -m castep_outputs --inc-castep --inc-param seedname\n\nWill parse only the ``seedname.castep`` and ``seedname.param`` files if\nfound.\n\n::\n\n python -m castep_outputs seedname.castep\n\nWill parse the single named file and again dump a ``.json`` to stdout.\n\n::\n\n python -m castep_outputs --castep seedname.param\n\nWill attempt to parse the file ``seedname.param`` as though it were a\n``.castep`` file. While not ordinarily useful it can help with manually renamed\nfiles.\n\n::\n\n python -m castep_outputs -o my_file.yaml -f yaml seedname.castep\n\nWill parse ``seedname.castep``, dump it to ``my_file.yaml`` in ``yaml`` format\nusing the ``PyYAML`` engine if available and the ``RUAMEL`` engine if not.\n\nAs a module\n-----------\n\n``import``\\ ing ``castep_outputs`` exposes all of the parsers at the\ntop-level.\n\nThe simplest method to use ``castep_outputs`` in a tool is to use the\n``parse_single`` method which attempts to determine the parser from the file\nextension.\n\n::\n\n from castep_outputs import parse_single\n\n my_dict = parse_single('my_file.castep')\n\nIf you need a specific parser rather than determining it by extension\nit is possible to pass them as the second argument, or call them\ndirectly.\n\n::\n\n import castep_outputs as co\n\n my_dict = co.parse_single('my_file', co.parse_castep_file)\n\n with open('my_file', 'r', encoding='utf-8') as inp:\n my_dict = co.parse_castep_file(inp)\n\nIt is recommended that you use ``parse_single`` as it uses special file-handling\nto give better diagnostics if it fails. It is possible to enable more detailed\nlogging via the `logging\n<https://docs.python.org/3/library/logging.html#logging.basicConfig>`_ module:\n\n::\n\n import logging\n from castep_outputs import parse_single\n\n my_dict = parse_single('my_file', loglevel=logging.INFO)\n\nThe available parsing functions are:\n\n- ``parse_bands_file``\n- ``parse_castep_file``\n- ``parse_cell_file``\n- ``parse_cell_param_file``\n- ``parse_chdiff_fmt_file``\n- ``parse_den_fmt_file``\n- ``parse_efield_file``\n- ``parse_elastic_file``\n- ``parse_elf_fmt_file``\n- ``parse_err_file``\n- ``parse_geom_file``\n- ``parse_hug_file``\n- ``parse_magres_file``\n- ``parse_md_file``\n- ``parse_md_geom_file``\n- ``parse_param_file``\n- ``parse_phonon_file``\n- ``parse_phonon_dos_file``\n- ``parse_pot_fmt_file``\n- ``parse_tddft_file``\n- ``parse_tddft_file``\n- ``parse_ts_file``\n- ``parse_xrd_sf_file``\n\nWhich return processed ``list``\\ s of ``dict``\\ s of data ready for use\nin other applications.\n\nSee `Documentation <https://oerc0122.github.io/castep_outputs/intro.html>`_ for full layout.\n\nFull usage\n----------\n\n::\n\n usage: castep_outputs [-h] [-V] [-L {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-o OUTPUT]\n [-f {json,ruamel,yaml,pprint,print}] [-t] [-A] [--inc-castep]\n [--inc-cell] [--inc-param] [--inc-geom] [--inc-md]\n [--inc-bands] [--inc-hug] [--inc-phonon_dos] [--inc-efield]\n [--inc-xrd_sf] [--inc-elf_fmt] [--inc-chdiff_fmt]\n [--inc-pot_fmt] [--inc-den_fmt] [--inc-elastic] [--inc-ts]\n [--inc-magres] [--inc-tddft] [--inc-err] [--inc-phonon]\n [--castep [CASTEP ...]] [--cell [CELL ...]]\n [--param [PARAM ...]] [--geom [GEOM ...]] [--md [MD ...]]\n [--bands [BANDS ...]] [--hug [HUG ...]]\n [--phonon_dos [PHONON_DOS ...]] [--efield [EFIELD ...]]\n [--xrd_sf [XRD_SF ...]] [--elf_fmt [ELF_FMT ...]]\n [--chdiff_fmt [CHDIFF_FMT ...]] [--pot_fmt [POT_FMT ...]]\n [--den_fmt [DEN_FMT ...]] [--elastic [ELASTIC ...]]\n [--ts [TS ...]] [--magres [MAGRES ...]] [--tddft [TDDFT ...]]\n [--err [ERR ...]] [--phonon [PHONON ...]]\n ...\n\n Attempts to find all files for seedname, filtered by `inc` args (default: all).\n Explicit files can be passed using longname arguments. castep_outputs can parse most\n human-readable castep outputs including: .castep, .cell, .param, .geom, .md, .bands,\n .hug, .phonon_dos, .efield, .xrd_sf, .elf_fmt, .chdiff_fmt, .pot_fmt, .den_fmt,\n .elastic, .ts, .magres, .tddft, .err, .phonon\n\n positional arguments:\n seedname Seed name for data\n\n options:\n -h, --help show this help message and exit\n -V, --version show program's version number and exit\n -L {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --log {DEBUG,INFO,WARNING,ERROR,CRITICAL}\n Verbose output\n -o OUTPUT, --output OUTPUT\n File to write output, default: screen\n -f {json,ruamel,yaml,pprint,print}, --out-format {json,ruamel,yaml,pprint,print}\n Output format\n -t, --testing Set testing mode to produce flat outputs\n -A, --inc-all Extract all available information\n --inc-castep Extract .castep information\n --inc-cell Extract .cell information\n --inc-param Extract .param information\n --inc-geom Extract .geom information\n --inc-md Extract .md information\n --inc-bands Extract .bands information\n --inc-hug Extract .hug information\n --inc-phonon_dos Extract .phonon_dos information\n --inc-efield Extract .efield information\n --inc-xrd_sf Extract .xrd_sf information\n --inc-elf_fmt Extract .elf_fmt information\n --inc-chdiff_fmt Extract .chdiff_fmt information\n --inc-pot_fmt Extract .pot_fmt information\n --inc-den_fmt Extract .den_fmt information\n --inc-elastic Extract .elastic information\n --inc-ts Extract .ts information\n --inc-magres Extract .magres information\n --inc-tddft Extract .tddft information\n --inc-err Extract .err information\n --inc-phonon Extract .phonon information\n --castep [CASTEP ...]\n Extract from CASTEP as .castep type\n --cell [CELL ...] Extract from CELL as .cell type\n --param [PARAM ...] Extract from PARAM as .param type\n --geom [GEOM ...] Extract from GEOM as .geom type\n --md [MD ...] Extract from MD as .md type\n --bands [BANDS ...] Extract from BANDS as .bands type\n --hug [HUG ...] Extract from HUG as .hug type\n --phonon_dos [PHONON_DOS ...]\n Extract from PHONON_DOS as .phonon_dos type\n --efield [EFIELD ...]\n Extract from EFIELD as .efield type\n --xrd_sf [XRD_SF ...]\n Extract from XRD_SF as .xrd_sf type\n --elf_fmt [ELF_FMT ...]\n Extract from ELF_FMT as .elf_fmt type\n --chdiff_fmt [CHDIFF_FMT ...]\n Extract from CHDIFF_FMT as .chdiff_fmt type\n --pot_fmt [POT_FMT ...]\n Extract from POT_FMT as .pot_fmt type\n --den_fmt [DEN_FMT ...]\n Extract from DEN_FMT as .den_fmt type\n --elastic [ELASTIC ...]\n Extract from ELASTIC as .elastic type\n --ts [TS ...] Extract from TS as .ts type\n --magres [MAGRES ...]\n Extract from MAGRES as .magres type\n --tddft [TDDFT ...] Extract from TDDFT as .tddft type\n --err [ERR ...] Extract from ERR as .err type\n --phonon [PHONON ...]\n Extract from PHONON as .phonon type\n\nCurrent Parsers:\n\n- ``.bands``\n- ``.castep``\n- ``.cell``\n- ``.chdiff_fmt``\n- ``.den_fmt``\n- ``.efield``\n- ``.elastic``\n- ``.elf_fmt``\n- ``.err``\n- ``.geom``\n- ``.hug``\n- ``.magres``\n- ``.md``\n- ``.param``\n- ``.phonon``\n- ``.phonon_dos``\n- ``.pot_fmt``\n- ``.tddft``\n- ``.ts``\n- ``.xrd_sf``\n\nCurrent dumpers:\n\n- ``json``\n- ``ruamel.yaml``\n- ``pyyaml``\n- ``print``\n- ``pprint``\n",
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