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Commit 8a593d5f authored by Carl Poelking's avatar Carl Poelking
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Setup.

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README.md 0 → 100644
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# DL_POLY Parser
This is the parser for [DL_POLY](http://www.scd.stfc.ac.uk//research/app/44516.aspx).
It is part of the [NOMAD Laboratory](http://nomad-lab.eu).
The official version lives at
git@gitlab.mpcdf.mpg.de:nomad-lab/parser-dl_poly.git
you can browse it at
https://gitlab.mpcdf.mpg.de/nomad-lab/parser-dl_poly
It relies on having the nomad-meta-info and the python common repositories one level higher.
The simplest way to have this is to check out nomad-lab-base recursively:
git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
then this will be in parsers/dl_poly.
parser/parser-dl_poly/SimpleDL_POLYParser.py 0 → 100644
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import setup_paths
import numpy as np
import math
from nomadcore.simple_parser import mainFunction
from nomadcore.simple_parser import SimpleMatcher as SM
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.caching_backend import CachingLevel
import re, os, sys, json, logging
class DL_POLYParserContext(object):
def __init__(self):
self.cell = []
return
def onClose_section_run(self, backend, gIndex, section):
print "<onClose_section_run>"
return
def onClose_section_method(self, backend, gIndex, section):
print "<onClose_section_method>"
return
def onClose_section_system_description(self, backend, gIndex, section):
print "<onClose_section_system_description>"
return
def onClose_dl_poly_section_md_molecule_type(self, backend, gIndex, section):
print "<onClose_molecule_type>"
return
def test_adhoc(parser):
return None
for i in range(10):
ln = parser.fIn.readline()
print ln
parser.fIn.pushbackLine(ln)
#print len(parser.backend.openSections)
return None
mainFileDescription = SM(name = 'root',
weak = True,
startReStr = "",
subMatchers = [
SM(name = 'newRun',
startReStr = r" \*\* DL_POLY \*\* authors: i.t.todorov & w.smith \** P \**",
repeats = False,
required = True,
forwardMatch = True,
adHoc = test_adhoc,
sections = ['section_run'],
subMatchers = [
SM(name = 'progHeader',
startReStr = r" \*\* DL_POLY \*\* authors: i.t.todorov & w.smith \** P \**",
subMatchers = [
SM(r"\s*\*\*\s*\*\* version: (?P<program_version>[0-9a-zA-Z_.]*) / \s* (?P<dl_poly_program_version_date>[\w]*\s*[\w]*)\s*\** O \**"),
SM(r"\s*\** when publishing research data obtained using (?P<program_name>[0-9a-zA-Z_.]*) \**"),
SM(r"\s*\**\s*(?P<dl_poly_system_description>[0-9a-zA-Z_()]*)\s*\**")
]),
SM(name = 'mdParams',
startReStr = r"\s*SIMULATION CONTROL PARAMETERS\s*",
required = True,
sections = ['section_method'],
subMatchers = [
SM(r"\s*simulation temperature \(K\)\s*(?P<dl_poly_thermostat_temperature>[-+0-9.eEdD]*)\s*"),
SM(r"\s*equilibration period \(steps\)\s*(?P<dl_poly_step_number_equilibration>[0-9]*)\s*"),
SM(r"\s*selected number of timesteps\s*(?P<dl_poly_step_number>[0-9]*)\s*")
]),
# Open system
# ... open topology
# ... ... store <numberofmoleculetypes>
# ... ... open molecule type id1
# ... ... open molecule type ...
SM(name = 'mdSystem',
startReStr = r"\s*SYSTEM SPECIFICATION\s*",
required = True,
sections = ['section_system_description'],
subMatchers = [
SM(name = 'mdTopology',
startReStr = r"\s*number of molecular types\s*[0-9]*\s*",
required = True,
forwardMatch = True,
sections = ['dl_poly_section_md_topology'],
subMatchers = [
SM(r"\s*number of molecular types\s*(?P<dl_poly_md_molecular_types>[0-9]*)"),
SM(name = 'mdTopologyMolecule',
startReStr = r"\s*molecular species type\s*[0-9]*\s*",
repeats = True,
required = True,
forwardMatch = True,
sections = ['dl_poly_section_md_molecule_type'],
subMatchers = [
SM(r"\s*molecular species type\s*(?P<dl_poly_md_molecule_type_id>[0-9]*)\s*"),
SM(r"\s*name of species:\s*(?P<dl_poly_md_molecule_type_name>[\w]* [\w]*)\s*")
])
])
#SM(r"\s*number of molecular types\s*(?P<dl_poly_molecular_types_number>[0-9]*)\s*"),
#SM(name = 'mdTopologyMolecule',
#startReStr = r"\s*molecular species type\s*[0-9]*\s*",
#repeats = True,
#required = True,
#sections = ['dl_poly_section_molecule_types'],
#subMatchers = [\
#])
])
])
])
"""
mainFileDescription = SM(name = 'root',
weak = True,
startReStr = "",
subMatchers = [
SM(name = "newRun",
startReStr = r"",
#repeats = True,
required = True,
forwardMatch = True,
sections = ["section_run"],
subMatchers = [
SM(startReStr = "Number of k-points\s*",
forwardMatch = True,
sections = ["section_system_description"],
subMatchers = [
SM(startReStr = "Number of k-points\s*",
forwardMatch = True,
sections = ["section_single_configuration_calculation"],
subMatchers = [
SM(startReStr = "Number of k-points\s*",
forwardMatch = True,
sections = ["section_eigenvalues_group"],
subMatchers = [
SM(startReStr = "Number of k-points\s*",
sections = ["section_eigenvalues"],
forwardMatch = True,
subMatchers = [
SM(startReStr = "K\-point\s*[0-9]+\s*",
sections = ["dl_poly_section_k_points"],
forwardMatch = True,
repeats = True,
subMatchers = [
SM(r"K\-point\s*[0-9]+\s*(?P<dl_poly_store_k_points> [-\d\.]+\s+[-\d\.]+\s+[-\d\.]+)",
repeats = True),
SM(name = 'Eigen',
startReStr = r"Spin component\s*[0-9]+\s*",
sections = ['dl_poly_section_eigenvalues'],
repeats = True,
subMatchers = [
SM(r"\s*(?P<dl_poly_store_eigenvalues> [-\d\.]+)",
repeats = True)
]), # CLOSING dl_poly_section_eigenvalues
]), # CLOSING dl_poly_section_k_points
]), # CLOSING section_eigenvalues
]), # CLOSING section_eigenvalues_group
]), # CLOSING section_single_configuration_calculation
]), # CLOSING section_system_description
]), # CLOSING SM newRun
])
"""
# THIS PARSER
parserInfo = {'name':'dl_poly-parser', 'version': '0.0'}
# LOAD METADATA
metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/dl_poly.nomadmetainfo.json"))
metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
# CUSTOMIZE CACHING
cachingLevelForMetaName = {}
if __name__ == "__main__":
mainFunction(mainFileDescription,
metaInfoEnv,
parserInfo,
superContext = DL_POLYParserContext(),
cachingLevelForMetaName = cachingLevelForMetaName,
onClose = {},
defaultSectionCachingLevel = False)
parser/parser-dl_poly/setup_paths.py 0 → 100644
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import sys, os, os.path
baseDir = os.path.dirname(os.path.abspath(__file__))
commonDir = os.path.normpath(os.path.join(baseDir,"../../../../python-common/common/python"))
if not commonDir in sys.path:
sys.path.insert(0, commonDir)
src/main/scala/eu/nomad_lab/parsers/DL_POLYParser.scala 0 → 100644
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package eu.nomad_lab.parsers
import eu.nomad_lab.DefaultPythonInterpreter
import org.{json4s => jn}
object DLPOLYParser extends SimpleExternalParserGenerator(
name = "DLPOLYParser",
parserInfo = jn.JObject(
("name" -> jn.JString("DLPOLYParser")) ::
("version" -> jn.JString("1.0")) :: Nil),
mainFileTypes = Seq("text/.*"),
mainFileRe = """ DL_POLY """.r,
cmd = Seq(DefaultPythonInterpreter.python2Exe(), "${envDir}/parsers/dl_poly/parser/parser-dl_poly/SimpleDL_POLYParser.py",
"--uri", "${mainFileUri}", "${mainFilePath}"),
resList = Seq(
"parser-dl_poly/SimpleDL_POLYParser.py",
"parser-dl_poly/setup_paths.py",
"nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json",
"nomad_meta_info/dl_poly.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
"parser-dl_poly" -> "parsers/dl_poly/parser/parser-dl_poly",
"nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info"
) ++ DefaultPythonInterpreter.commonDirMapping()
)
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test/examples/dl-poly-test1/CONFIG 0 → 100644
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SODIUM CHLORIDE WITH (27000 IONS)
restart scale
temperature 500.0
equilibration steps 200
steps 200
timestep 0.001
#scale 5
cutoff 12.0
rvdw 12.0
ewald precision 1d-6
#ensemble nvt hoover 0.02
ensemble nvt berendsen 0.01
print every 10
stats every 10
collect
job time 100
close time 10
finish
test/examples/dl-poly-test1/FIELD 0 → 100644
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SODIUM CHLORIDE WITH EWALD SUM (27000 IONS)
units internal
molecular types 1
SODIUM CHLORIDE
nummols 27
atoms 1000
Na+ 22.9898 1.0 500
Cl- 35.453 -1.0 500
finish
vdw 3
Na+ Na+ bhm 2544.35 3.1545 2.3400 1.0117e+4 4.8177e+3
Na+ Cl- bhm 2035.48 3.1545 2.7550 6.7448e+4 8.3708e+4
Cl- Cl- bhm 1526.61 3.1545 3.1700 6.9857e+5 1.4032e+6
close
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test/examples/dl-poly-test1/README.md 0 → 100644
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sample files to test the parser: "TEST1" from the DL_POLY data repository
test/examples/dl-poly-test1/STATIS 0 → 100644
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SODIUM CHLORIDE WITH EWALD SUM (27000 IONS)
ENERGY UNITS = DL_POLY Internal UNITS
0 0.000000E+00 38
-9.624952E+08 5.000000E+02 -9.793315E+08 1.042706E+08 -1.083602E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -9.992985E+08
0.000000E+00 1.440824E+08 -9.393424E+08 1.083425E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.257424E+00 0.000000E+00 0.000000E+00 -6.163359E+00
8.198487E-01 -3.929859E-01 8.198487E-01 -5.716668E+00 1.300186E+00
-3.929859E-01 1.300186E+00 -6.892246E+00
10 1.000000E-02 38
-9.626103E+08 5.076689E+02 -9.797048E+08 1.039151E+08 -1.083620E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -9.999714E+08
0.000000E+00 1.462723E+08 -9.371709E+08 1.083443E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.352262E+00 5.419631E-03 3.505213E-03 -6.361781E+00
8.513704E-01 -5.041795E-01 8.513704E-01 -5.817797E+00 1.218538E+00
-5.041795E-01 1.218538E+00 -6.877209E+00
20 2.000000E-02 38
-9.631545E+08 5.195889E+02 -9.806504E+08 1.031115E+08 -1.083762E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.001938E+09
0.000000E+00 1.513418E+08 -9.322434E+08 1.083585E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.594081E+00 2.145847E-02 1.382840E-02 -6.851638E+00
9.713287E-01 -7.485644E-01 9.713287E-01 -6.018311E+00 1.033642E+00
-7.485644E-01 1.033642E+00 -6.912295E+00
30 3.000000E-02 38
-9.640164E+08 5.245942E+02 -9.816808E+08 1.024376E+08 -1.084118E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.004220E+09
0.000000E+00 1.559409E+08 -9.280002E+08 1.083941E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.835630E+00 4.714687E-02 3.029612E-02 -7.323061E+00
1.108741E+00 -1.013488E+00 1.108741E+00 -6.192257E+00 7.786746E-01
-1.013488E+00 7.786746E-01 -6.991572E+00
40 4.000000E-02 38
-9.649123E+08 5.226264E+02 -9.825104E+08 1.021763E+08 -1.084687E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.005929E+09
0.000000E+00 1.582463E+08 -9.262627E+08 1.084509E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.973794E+00 8.063239E-02 5.188191E-02 -7.549815E+00
1.219861E+00 -1.234591E+00 1.219861E+00 -6.300432E+00 4.853114E-01
-1.234591E+00 4.853114E-01 -7.071134E+00
50 5.000000E-02 38
-9.656544E+08 5.173328E+02 -9.830743E+08 1.022979E+08 -1.085372E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.006793E+09
0.000000E+00 1.582559E+08 -9.269387E+08 1.085195E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.994541E+00 1.194661E-01 7.748287E-02 -7.521299E+00
1.280982E+00 -1.410322E+00 1.280982E+00 -6.371240E+00 1.891122E-01
-1.410322E+00 1.891122E-01 -7.091085E+00
60 6.000000E-02 38
-9.661930E+08 5.122594E+02 -9.834421E+08 1.026085E+08 -1.086051E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.007034E+09
0.000000E+00 1.570201E+08 -9.288518E+08 1.085872E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.943869E+00 1.609918E-01 1.060787E-01 -7.375436E+00
1.282175E+00 -1.544601E+00 1.282175E+00 -6.430392E+00 -5.897526E-02
-1.544601E+00 -5.897526E-02 -7.025780E+00
70 7.000000E-02 38
-9.665910E+08 5.097623E+02 -9.837560E+08 1.028750E+08 -1.086631E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.007110E+09
0.000000E+00 1.558872E+08 -9.305646E+08 1.086452E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.889196E+00 2.027365E-01 1.367718E-01 -7.255856E+00
1.235167E+00 -1.613792E+00 1.235167E+00 -6.502671E+00 -2.134163E-01
-1.613792E+00 -2.134163E-01 -6.909061E+00
80 8.000000E-02 38
-9.669511E+08 5.097717E+02 -9.841164E+08 1.029816E+08 -1.087098E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.007370E+09
0.000000E+00 1.555866E+08 -9.313318E+08 1.086918E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.872120E+00 2.427728E-01 1.687885E-01 -7.214110E+00
1.167832E+00 -1.600735E+00 1.167832E+00 -6.601666E+00 -2.657989E-01
-1.600735E+00 -2.657989E-01 -6.800586E+00
90 9.000000E-02 38
-9.673342E+08 5.106233E+02 -9.845282E+08 1.029671E+08 -1.087495E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.007860E+09
0.000000E+00 1.559641E+08 -9.313509E+08 1.087315E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.890266E+00 2.799410E-01 2.014910E-01 -7.222967E+00
1.106951E+00 -1.525848E+00 1.106951E+00 -6.709154E+00 -2.388554E-01
-1.525848E+00 -2.388554E-01 -6.738676E+00
100 1.000000E-01 38
-9.677418E+08 5.109726E+02 -9.849475E+08 1.029212E+08 -1.087869E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.008442E+09
0.000000E+00 1.565137E+08 -9.311742E+08 1.087688E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.920078E+00 3.138344E-01 2.344029E-01 -7.243727E+00
1.063387E+00 -1.420093E+00 1.063387E+00 -6.781669E+00 -1.639152E-01
-1.420093E+00 -1.639152E-01 -6.734838E+00
110 1.100000E-01 38
-9.681430E+08 5.103870E+02 -9.853290E+08 1.028983E+08 -1.088227E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.008978E+09
0.000000E+00 1.568772E+08 -9.311680E+08 1.088045E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.942917E+00 3.446241E-01 2.672191E-01 -7.252346E+00
1.035282E+00 -1.287127E+00 1.035282E+00 -6.787045E+00 -8.031188E-02
-1.287127E+00 -8.031188E-02 -6.789361E+00
120 1.200000E-01 38
-9.685063E+08 5.090360E+02 -9.856468E+08 1.029026E+08 -1.088549E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.009400E+09
0.000000E+00 1.569620E+08 -9.314037E+08 1.088366E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.952877E+00 3.728662E-01 2.997684E-01 -7.240149E+00
1.017532E+00 -1.115659E+00 1.017532E+00 -6.730815E+00 -3.064078E-02
-1.115659E+00 -3.064078E-02 -6.887667E+00
130 1.300000E-01 38
-9.688019E+08 5.068498E+02 -9.858688E+08 1.029458E+08 -1.088815E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.009657E+09
0.000000E+00 1.567006E+08 -9.319279E+08 1.088629E+09 0.000000E+00
0.000000E+00 0.000000E+00 0.000000E+00 9.638822E+05 0.000000E+00
0.000000E+00 0.000000E+00 9.000000E+01 9.000000E+01 9.000000E+01
0.000000E+00 -6.946410E+00 3.993638E-01 3.319403E-01 -7.214991E+00
1.004592E+00 -9.138909E-01 1.004592E+00 -6.635016E+00 -3.671107E-02
-9.138909E-01 -3.671107E-02 -6.989224E+00
140 1.400000E-01 38
-9.690078E+08 5.044996E+02 -9.859956E+08 1.030120E+08 -1.089008E+09
0.000000E+00 0.000000E+00 0.000000E+00 0.000000E+00 -1.009762E+09
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