Commit 41936207 authored by Markus Scheidgen's avatar Markus Scheidgen
Browse files

Merge branch 'v1.0.0' into 'dos_notebooks'

# Conflicts:
#   .gitignore
parents be5c0f7c 8366c966
Pipeline #82417 passed with stages
in 22 minutes and 15 seconds
......@@ -31,5 +31,5 @@ setup.json
parser.osio.log
gui/src/metainfo.json
gui/src/searchQuantities.json
gui/src/parserMetadata.json
examples/workdir/
......@@ -69,7 +69,6 @@ RUN python setup.py sdist
RUN cp dist/nomad-lab-*.tar.gz dist/nomad-lab.tar.gz
RUN python -m nomad.cli dev metainfo > gui/src/metainfo.json
RUN python -m nomad.cli dev search-quantities > gui/src/searchQuantities.json
RUN python -m nomad.cli dev parser-metadata > gui/src/parserMetadata.json
RUN python -m nomad.cli dev toolkit-metadata > gui/src/toolkitMetadata.json
WORKDIR /install/docs
RUN make html
......
Subproject commit 1c1dacfde7328e8ec9ca49419fae7d56157d9479
Subproject commit c17dbecac0f395b48fc65b0c7dcc2ba4de1be271
Subproject commit 3e4eb8aac2cf46882569e3823669f894c6890885
Subproject commit e1f873f104d4ce64815636251c8e30971a9fcbda
......@@ -62,7 +62,7 @@ export default function Histogram({
}) {
onClick = onClick || (() => null)
data = data || []
numberOfValues = (numberOfValues && Math.min(data.length, numberOfValues)) || data.length
numberOfValues = numberOfValues || data.length
getValueLabel = getValueLabel || (value => value.name)
title = title || 'Histogram'
......
......@@ -245,9 +245,9 @@ export const domains = ({
searchTabs: ['entries', 'datasets', 'uploads']
},
qcms: {
name: 'Quantum computational data',
name: 'Quantum-computer data',
key: 'qcms',
label: 'Quantum computational material science data',
label: 'Quantum-computer material science data',
about: 'This is computational material science data calculated by quantum computers',
entryLabel: 'calculation',
entryLabelPlural: 'calculations',
......
{
"ABINIT": {
"codeLabel": "ABINIT",
"codeLabelStyle": "all in capitals",
"codeUrl": "https://www.abinit.org/",
"parserDirName": "dependencies/parsers/abinit/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-abinit",
"parserSpecific": "",
"tableOfFiles": "|Input Filename| Description|\n|--- | --- |\n|`*.out` | **Mainfile:** a plain text file w/ **user-defined** name|\n|`*.files`|plain text; user-defined filenames |\n|`*.in`| plain text, input parameters|\n|`*_o_DDB`|binary file, Derivative DataBases of total energy|\n|`*_o_DEN`|binary file, charge density|\n|`*_o_EIG`|text file, eigenvalues|\n|`*_o_WFK`|binary file, wavefunction|\n|`log` | plain text, redirection of screen output (`stdout`)|\n"
},
"Amber": {
"codeLabel": "Amber",
"codeLabelStyle": "only first character in capitals",
"codeUrl": "http://ambermd.org/",
"parserDirName": "dependencies/parsers/amber/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-amber",
"parserSpecific": "The Amber parser supports the SANDER and PMEMD Molecular Dynamics codes.\n",
"tableOfFiles": ""
},
"ASAP": {
"codeLabel": "ASAP",
"codeLabelStyle": "all in capitals",
"codeUrl": "https://wiki.fysik.dtu.dk/asap",
"parserDirName": "dependencies/parsers/asap/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-asap",
"parserSpecific": "",
"tableOfFiles": ""
},
"ATK": {
"codeLabel": "QuantumATK",
"codeLabelStyle": "capitals: Q, A, T, K",
"codeUrl": "https://www.synopsys.com/silicon/quantumatk.html",
"parserDirName": "dependencies/parsers/atk/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-atk",
"parserSpecific": "",
"tableOfFiles": ""
},
"BAND": {
"codeLabel": "BAND",
"codeLabelStyle": "all in capitals",
"codeUrl": "https://www.scm.com/product/band_periodicdft/",
"parserDirName": "dependencies/parsers/band/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-band",
"parserSpecific": "",
"tableOfFiles": ""
},
"BigDFT": {
"codeLabel": "BigDFT",
"codeLabelStyle": "Capitals: B,D,F,T,",
"codeUrl": "http://bigdft.org/",
"parserDirName": "dependencies/parsers/bigdft/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-bigdft",
"parserSpecific": "",
"tableOfFiles": ""
},
"CASTEP": {
"codeLabel": "CASTEP",
"codeLabelStyle": "all in capitals",
"codeUrl": "http://www.castep.org/",
"parserDirName": "dependencies/parsers/castep/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-castep",
"parserSpecific": "### CASTEP output examples\n[Note: The list below is much shorter than the existing examples]\nA few output files to test the parser are provided in the directory `castep/test/examples/*/`.\n\n FILE NAME | FILE DESCRIPTION\n __________________|___________________________________________________\n \"Si2.castep_v_1\" --> Single Point Calculation (minimum verbosity)\n \"Si2.castep_v_2\" --> Single Point Calculation (medium verbosity)\n \"Si2.castep_v_3\" --> Single Point Calculation (maximum verbosity)\n\n \"Si2.castep_b_v_1\" --> Band Structure Calculation (minimum verbosity)\n \"Si2.castep_b_v_2\" --> Band Structure Calculation (medium verbosity)\n \"Si2.castep_b_v_3\" --> Band Structure Calculation (maximum verbosity)\n",
"tableOfFiles": ""
},
"Charmm": {
"codeLabel": "CHARMM",
"codeLabelStyle": "all in capitals",
"codeUrl": "https://www.charmm.org/charmm/",
"parserDirName": "dependencies/parsers/charmm/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-charmm",
"tableOfFiles": ""
},
"CP2K": {
"codeLabel": "CP2K",
"codeLabelStyle": "all in capitals",
"codeUrl": "https://www.cp2k.org/",
"parserDirName": "dependencies/parsers/cp2k/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cp2k",
"parserSpecific": "## Usage notes\nThe parser is based on CP2K 2.6.2.\n\nThe CP2K input setting\n[PRINT_LEVEL](https://manual.cp2k.org/trunk/CP2K_INPUT/GLOBAL.html#PRINT_LEVEL)\ncontrols the amount of details that are outputted during the calculation. The\nhigher this setting is, the more can be parsed from the upload.\n\nThe parser will try to find the paths to all the input and output files, but if\nthey are located very deep inside some folder structure or outside the folder\nwhere the output file is, the parser will not be able to locate them. For this\nreason it is recommended to keep the upload structure as flat as possible.\n\nHere is a list of features/fixes that would make the parsing of CP2K results\neasier:\n- The pdb trajectory output doesn't seem to conform to the actual standard as\n the different configurations are separated by the END keyword which is\n supposed to be written only once in the file. The [format\n specification](http://www.wwpdb.org/documentation/file-format) states that\n different configurations should start with MODEL and end with ENDMDL tags.\n- The output file should contain the paths/filenames of different input and\n output files that are accessed during the program run. This data is already\n available for some files (input file, most files produced by MD), but many\n are not mentioned.\n",
"tableOfFiles": ""
},
"CPMD": {
"codeLabel": "CPMD",
"codeLabelStyle": "all in capitals",
"codeUrl": "https://www.cpmd.org/",
"parserDirName": "dependencies/parsers/cpmd/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cpmd",
"parserSpecific": "",
"tableOfFiles": ""
},
"Crystal": {
"codeLabel": "CRYSTAL",
"codeLabelStyle": "all in capitals",
"codeUrl": "https://www.crystal.unito.it/",
"parserDirName": "dependencies/parsers/crystal/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-crystal",
"parserSpecific": "",
"tableOfFiles": ""
},
"DFTb plus": {
"codeLabel": "DFTB+",
"codeLabelStyle": "all in capitals; use + instead of word",
"codeUrl": "http://www.dftbplus.org/",
"parserDirName": "dependencies/parsers/dftbplus/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dftb-plus",
"parserSpecific": "",
"tableOfFiles": ""
},
"DL_POLY": {
"codeLabel": "DL_POLY",
"codeLabelStyle": "all capitals and underscore, not dash (minus)",
"codeUrl": "https://www.scd.stfc.ac.uk/Pages/DL_POLY.aspx",
"parserDirName": "dependencies/parsers/dl-poly/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dl-poly",
"parserSpecific": "",
"tableOfFiles": ""
},
"DMol3": {
"codeLabel": "DMol3 ",
"codeLabelStyle": "Capitals: D, M",
"codeUrl": "http://dmol3.web.psi.ch/",
"parserDirName": "dependencies/parsers/dmol3/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dmol3",
"parserSpecific": "",
"tableOfFiles": ""
},
"eels": {
"codeLabel": "EELSDB",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://eelsdb.eu/",
"parserDirName": "dependencies/parsers/eelsdb/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/eelsdb",
"parserSpecific": "",
"tableOfFiles": ""
},
"elastic": {
"codeLabel": "ElaStic",
"codeLabelStyle": "capitals: E, S. This is part of the exciting project",
"codeUrl": "http://exciting-code.org/elastic",
"parserDirName": "dependencies/parsers/elastic/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-elastic",
"parserSpecific": "",
"tableOfFiles": ""
},
"elk": {
"codeLabel": "Elk",
"codeLabelStyle": "Only E in capitals",
"codeUrl": "http://elk.sourceforge.net/",
"parserDirName": "dependencies/parsers/elk/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-elk",
"parserSpecific": "",
"tableOfFiles": ""
},
"exciting": {
"codeLabel": "exciting",
"codeLabelStyle": "All in LOWER case",
"codeUrl": "http://exciting-code.org/",
"parserDirName": "dependencies/parsers/exciting/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-exciting",
"parserSpecific": "",
"tableOfFiles": "|Input Filename| Description|\n|--- | --- |\n|`INFO.OUT`| mainfile|\n|`BAND-QP.OUT`| |\n|`BANDLINES.OUT`| |\n|`DIELTENS0*.OUT`| |\n|`DIELTENS0_NOSYM*.OUT`| |\n|`EIGVAL.OUT`| |\n|`EPSILON_*FXC*_OC*.OUT `| |\n|`EPSILON_*NLF_FXC*_OC*.OUT`| |\n|`EPSILON_BSE*_SCR*_OC*.OUT`| |\n|`EVALQP.DAT or EVALQP.TXT`| |\n|`EXCITON_BSE*_SCR*_OC*.OUT`| |\n|`FERMISURF.bxsf`| |\n|`GQPOINTS*.OUT`| |\n|`GW_INFO.OUT`| |\n|`INFO_VOL `| |\n|`LOSS_*FXC*_OC*.OUT`| |\n|`LOSS_*NLF_*FXC*_OC*.OUT`| |\n|`QPOINTS.OUT`| |\n|`SIGMA_*FXC*_OC*.OUT`| |\n|`SIGMA_*NLF_FXC*_OC*.OUT `| |\n|`SIGMA_BSE*_SCR*_OC*.OUT `| |\n|`TDOS-QP.OUT` | time dependent DOS|\n|`bandstructure-qp.dat`| |\n|`bandstructure.xml`| (vertexLabGWFile)|\n|`bandstructure.xml`| |\n|`dos.xml`| |\n|`input-gw.xml `| |\n|`input.xml`|(GSFile) |\n|`input.xml`| (XSFile)|\n|`str.out`| |\n"
},
"FHI-aims": {
"codeLabel": "FHI-aims",
"codeLabelStyle": "Capitals: FHI, the rest in lowercase; use dash.",
"codeUrl": "https://aimsclub.fhi-berlin.mpg.de/",
"parserDirName": "dependencies/parsers/fhi-aims/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fhi-aims",
"parserSpecific": "",
"tableOfFiles": "|Input Filename| Description|\n|--- | --- |\n|`<text_file>` | **Mainfile**, plain text file w/arbitrary name, e.g., `<output,control, aims,...>.out` |\n|`control.in` | Runtime information |\n|`geometry.in` | Material's atomic-structure information, |\n|AUX FILES| Description|\n|`<atoml_label>_l_proj_dos.out`| Angular-momentum-resolved DOS @ Fermi Energy|\n|`<atoml_label>_l_proj_dos_raw.out`| Angular-momentum-resolved DOS @ vacuum|\n|`KS_DOS_total.dat`| Kohn-Sham total DOS @ Fermi Energy |\n|`KS_DOS_total_raw.dat`| Kohn-Sham total DOS @ vacuum |\n|`Mulliken.out` **WARNING-->**|Mulliken charge analysis on all atoms. **WARNING** not yet read by NOMAD's parser|\n|`atom_proj_dos_<atom_name><index>_raw.dat` | Atom-projected DOS @ vacuum|\n|`atom_projected_dos_<atom_name><index>.dat` | Atom-projected DOS @ Fermi Energy|\n|`band<spin><segment>.out` | bandstructure file |\n"
},
"fleur": {
"codeLabel": "Fleur",
"codeLabelStyle": "Found: 1) only F in capitals, 2) all in capitals.",
"codeUrl": "https://www.flapw.de/",
"parserDirName": "dependencies/parsers/fleur/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fleur",
"parserSpecific": "",
"tableOfFiles": ""
},
"fplo": {
"codeLabel": "FPLO",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://www.fplo.de/",
"parserDirName": "dependencies/parsers/fplo/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-fplo",
"parserSpecific": "",
"tableOfFiles": ""
},
"GAMESS": {
"codeLabel": "GAMESS",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://www.msg.chem.iastate.edu/",
"parserDirName": "dependencies/parsers/gamess/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gamess",
"parserSpecific": "",
"tableOfFiles": ""
},
"Gaussian": {
"codeLabel": "Gaussian",
"codeLabelStyle": "Capitals: G",
"codeUrl": "http://gaussian.com",
"parserDirName": "dependencies/parsers/gaussian/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gaussian",
"parserSpecific": "",
"tableOfFiles": ""
},
"GPAW": {
"codeLabel": "GPAW",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://wiki.fysik.dtu.dk/gpaw/",
"parserDirName": "dependencies/parsers/gpaw/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gpaw",
"parserSpecific": "",
"tableOfFiles": ""
},
"Gromacs": {
"codeLabel": "GROMACS",
"codeLabelStyle": "All in capitals",
"codeUrl": "http://www.gromacs.org/",
"parserDirName": "dependencies/parsers/gromacs/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gromacs",
"parserSpecific": "",
"tableOfFiles": ""
},
"Gromos": {
"codeLabel": "GROMOS",
"codeLabelStyle": "All in capitals",
"codeUrl": "http://www.gromos.net/",
"parserDirName": "dependencies/parsers/gromos/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gromos",
"parserSpecific": "",
"tableOfFiles": ""
},
"gulp": {
"codeLabel": "GULP",
"codeLabelStyle": "All in capitals",
"codeUrl": "http://gulp.curtin.edu.au/gulp/",
"parserDirName": "dependencies/parsers/gulp/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-gulp",
"parserSpecific": "",
"tableOfFiles": ""
},
"lammps": {
"codeLabel": "LAMMPS",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://lammps.sandia.gov/",
"parserDirName": "dependencies/parsers/lammps/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lammps",
"tableOfFiles": ""
},
"libAtoms": {
"codeLabel": "libAtoms",
"codeLabelStyle": "Capitals: A",
"codeUrl": "http://libatoms.github.io/",
"parserDirName": "dependencies/parsers/lib-atoms/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-lib-atoms",
"parserSpecific": "",
"tableOfFiles": ""
},
"MOLCAS": {
"codeLabel": "Molcas",
"codeLabelStyle": "Capitals: M; also seen all in capitals",
"codeUrl": "http://molcas.org/",
"parserDirName": "dependencies/parsers/molcas/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-molcas",
"parserSpecific": "",
"tableOfFiles": ""
},
"MOPAC": {
"codeLabel": "MOPAC",
"codeLabelStyle": "All in capitals",
"codeUrl": "http://openmopac.net/",
"parserDirName": "dependencies/parsers/mopac/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-mopac",
"parserSpecific": "",
"tableOfFiles": ""
},
"mpes": {
"codeLabel": "APTFIM",
"codeLabelStyle": "all in capitals",
"codeUrl": "??",
"parserDirName": "dependencies/parsers/aptfim/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/mkuehbac/parser-aptfim",
"parserSpecific": "",
"tableOfFiles": ""
},
"Namd": {
"codeLabel": "NAMD",
"codeLabelStyle": "All in capitals",
"codeUrl": "http://www.ks.uiuc.edu/Research/namd/",
"parserDirName": "dependencies/parsers/namd/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-namd",
"parserSpecific": "",
"tableOfFiles": ""
},
"NWChem": {
"codeLabel": "NWChem",
"codeLabelStyle": "Capitals: N, W, C",
"codeUrl": "https://nwchemgit.github.io/",
"parserDirName": "dependencies/parsers/nwchem/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-nwchem",
"parserSpecific": "",
"tableOfFiles": ""
},
"Octopus": {
"codeLabel": "Octopus",
"codeLabelStyle": "Capitals: O",
"codeUrl": "https://octopus-code.org/",
"parserDirName": "dependencies/parsers/octopus/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-octopus",
"parserSpecific": "",
"tableOfFiles": "|Input Filename| Description|\n|--- | --- |\n|`<text_file>` | **Mainfile:** a plain text file w/arbitrary name|\n|`exec/` | Subdir for runtime information |\n|`exec/parser.log` | Input variables (user-defined & default values) |\n|`inp`| input file|\n|`parse.log`| **Warining** : probably obsolete|\n|`restart/`| Data to restart a calculation, e.g., `restart/gs/` is for ground-state|\n|`static/` | Subdir to report static part of a calculation|\n|`static/eigenvalues`| |\n|`static/info` | General info on static part|\n"
},
"ONETEP": {
"codeLabel": "ONETEP",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://www.onetep.org/",
"parserDirName": "dependencies/parsers/onetep/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-onetep",
"parserSpecific": "",
"tableOfFiles": ""
},
"OpenKIM": {
"codeLabel": "openKIM",
"codeLabelStyle": "Capitals: K,I,M",
"codeUrl": "https://openkim.org/",
"parserDirName": "dependencies/parsers/openkim/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-openkim",
"parserSpecific": "",
"tableOfFiles": ""
},
"ORCA": {
"codeLabel": "ORCA",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://www.faccts.de/orca/",
"parserDirName": "dependencies/parsers/orca/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-orca",
"parserSpecific": "",
"tableOfFiles": ""
},
"Phonopy": {
"codeLabel": "Phonopy",
"codeLabelStyle": "Capitals: P",
"codeUrl": "https://phonopy.github.io/phonopy/",
"parserDirName": "dependencies/parsers/phonopy/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-phonopy",
"parserSpecific": "",
"tableOfFiles": ""
},
"qbox": {
"codeLabel": "Qbox",
"codeLabelStyle": "Capitals: Q",
"codeUrl": "http://qboxcode.org/",
"parserDirName": "dependencies/parsers/qbox/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-qbox",
"parserSpecific": "",
"tableOfFiles": ""
},
"Quantum Espresso": {
"codeLabel": "QUANTUM ESPRESSO",
"codeLabelStyle": "All in capitals, separated by space",
"codeUrl": "http://www.quantum-espresso.org/",
"parserDirName": "dependencies/parsers/quantum-espresso/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-quantum-espresso",
"parserSpecific": "",
"tableOfFiles": "|Filename| Description|\n|---|---|\n|`<text_file>`|**Mainfile:** a plain text file w/arbitrary name. \\\nOne of the top lines must contain '`Program PWSCF.*starts`', \\\nwhere '`.*`' means an arbitrary number '`*`' of arbitrary \\\ncharacters '`.`'|\"\n"
},
"Siesta": {
"codeLabel": "SIESTA",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://departments.icmab.es/leem/siesta/",
"parserDirName": "dependencies/parsers/siesta/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-siesta",
"parserSpecific": "",
"tableOfFiles": ""
},
"TINKER": {
"codeLabel": "Tinker",
"codeLabelStyle": "Capitals: T",
"codeUrl": "https://dasher.wustl.edu/tinker/",
"parserDirName": "dependencies/parsers/tinker/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-tinker",
"parserSpecific": "",
"tableOfFiles": ""
},
"turbomole": {
"codeLabel": "TURBOMOLE",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://www.turbomole.org/",
"parserDirName": "dependencies/parsers/turbomole/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-turbomole",
"parserSpecific": "",
"tableOfFiles": ""
},
"VASP": {
"codeLabel": "VASP",
"codeLabelStyle": "All in capitals",
"codeUrl": "https://www.vasp.at/",
"parserDirName": "dependencies/parsers/vasp/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-vasp",
"parserSpecific": "",
"tableOfFiles": "|Input Filename| Description|\n|--- | --- |\n|`vasprun.xml` | **Mainfile** in plain-text (structured) XML format |\n|`OUTCAR` | plain-text (semi-structured) file, VAPS's detailed output. Read by NOMAD only as fallback to parse `outcar` data |\n"
},
"WIEN2k": {
"codeLabel": "WIEN2k",
"codeLabelStyle": "All in capitals, except k",
"codeUrl": "http://www.wien2k.at/",
"parserDirName": "dependencies/parsers/wien2k/",
"parserGitUrl": "https://gitlab.mpcdf.mpg.de/nomad-lab/parser-wien2k",
"parserSpecific": "",
"tableOfFiles": ""
}
}
......@@ -1607,6 +1607,32 @@ class section_energy_van_der_Waals(MSection):
a_legacy=LegacyDefinition(name='energy_van_der_Waals'))
class section_energy_contribution(MSection):
'''
Section describing the contributions to the total energy.
'''
m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_energy_contribution'))
energy_contibution_kind = Quantity(
type=str,
shape=[],
description='''
The kind of the energy contribution. Can be one of bond, pair, coulomb, etc.
''',
a_legacy=LegacyDefinition(name='energy_contibution_kind'))
energy_contribution_value = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule',
description='''
Value of the energy contribution.
''',
categories=[energy_component, energy_value],
a_legacy=LegacyDefinition(name='energy_contribution_value'))
class section_frame_sequence_user_quantity(MSection):
'''
Section collecting some user-defined quantities evaluated along a sequence of frame.
......@@ -4460,6 +4486,42 @@ class section_single_configuration_calculation(MSection):
''',
a_legacy=LegacyDefinition(name='zero_point_method'))
enthalpy = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='joule',
description='''
Value of the calculated enthalpy i.e. energy_total + pressure * volume.
''',
categories=[energy_component, energy_value],
a_legacy=LegacyDefinition(name='energy_enthalpy'))
pressure = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='pascal',
description='''
Value of the pressure of the system.
''',
a_legacy=LegacyDefinition(name='pressure'))
temperature = Quantity(
type=np.dtype(np.float64),
shape=[],
unit='kelvin',
description='''
Value of the temperature of the system.
''',
a_legacy=LegacyDefinition(name='temperature'))
time_step = Quantity(
type=int,
shape=[],
description='''
The number of time steps with respect to the start of the calculation.
''',
a_legacy=LegacyDefinition(name='time_step'))
section_atom_projected_dos = SubSection(
sub_section=SectionProxy('section_atom_projected_dos'),
repeats=True,
......@@ -4505,6 +4567,11 @@ class section_single_configuration_calculation(MSection):
repeats=True,
a_legacy=LegacyDefinition(name='section_energy_van_der_Waals'))
section_energy_contribution = SubSection(
sub_section=SectionProxy('section_energy_contribution'),
repeats=True,
a_legacy=LegacyDefinition(name='section_energy_contribution'))
section_k_band_normalized = SubSection(
sub_section=SectionProxy('section_k_band_normalized'),
repeats=True,
......@@ -5579,20 +5646,20 @@ class section_XC_functionals(MSection):
a_legacy=LegacyDefinition(name='XC_functional_weight'))
class Relaxation(MSection):
class GeometryOptimization(MSection):
'''
Section containing the results of a relaxation workflow.
Section containing the results of a geometry_optimization workflow.
'''
m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_relaxation'))
m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_geometry_optimization'))
relaxation_type = Quantity(
geometry_optimization_type = Quantity(
type=str,
shape=[],
description='''
The type of relaxation ionic, cell_shape, cell_volume.
The type of geometry optimization can either be ionic, cell_shape, cell_volume.
''',
a_legacy=LegacyDefinition(name='relaxation_type')
a_legacy=LegacyDefinition(name='geometry_optimization_type')
)
input_energy_difference_tolerance = Quantity(
......@@ -5618,7 +5685,7 @@ class Relaxation(MSection):
shape=[],
unit='joule',
description='''
The difference in the energy between the last two steps during relaxation.
The difference in the energy between the last two steps during optimization.
''',
a_legacy=LegacyDefinition(name='final_energy_difference'),
a_search=Search())
......@@ -5628,35 +5695,17 @@ class Relaxation(MSection):
shape=[],
unit='newton',
description='''
The maximum net force in the last relaxation step.
The maximum net force in the last optimization step.
''',