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Commit 1494b76d authored by Markus Scheidgen's avatar Markus Scheidgen
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Added more parsers to NOMAD

parent 354d933b
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.gitignore
View file @ 1494b76d
......@@ -10,9 +10,7 @@ syntax: glob
*.bk
*.swp
.DS_Store
# logging files
detailed.log
*.annotate
# eclipse conf file
.settings
......@@ -52,3 +50,5 @@ TAGS
lib/
env/
*.egg-info
\ No newline at end of file
parser/parser-gromos/GROMOSDictionary.py → gromosparser/GROMOSDictionary.py
View file @ 1494b76d
# Copyright 2018-2018 Berk Onat
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#
# http://www.apache.org/licenses/LICENSE-2.0
#
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
import setup_paths
import numpy as np
from GROMOSCommon import PARSERNAME, PROGRAMNAME, PARSERTAG
from .GROMOSCommon import PARSERNAME, PROGRAMNAME, PARSERTAG
from nomadcore.smart_parser.SmartParserDictionary import metaNameConverter, metaNameConverter_UnderscoreSpaceDash
from nomadcore.smart_parser.SmartParserDictionary import MetaInfoMap, FileInfoMap, MapDictionary
from nomadcore.smart_parser.SmartParserDictionary import MetaInfoMap, FileInfoMap, MapDictionary
from nomadcore.smart_parser.SmartParserDictionary import getDict_MetaStrInDict, getList_MetaStrInDict, get_unitDict
import nomadcore.md_data_access.MDDataAccess as MDData
......@@ -26,7 +25,7 @@ def get_fileListDict():
Returns:
the list of defaults file namelists
"""
startpage = {
'nameTranslate' : metaNameConverter,
'metaHeader' : PARSERTAG,
......@@ -37,17 +36,17 @@ def get_fileListDict():
'fileInterface' : ["gromosread", "parmed", "mdtraj", "mdanalysis"]
}
namelist = {
'structure' : FileInfoMap(startpage, fileFormat=['.gromostop', '.top'], activeInfo=False,
'structure' : FileInfoMap(startpage, fileFormat=['.gromostop', '.top'], activeInfo=False,
infoPurpose=['topology']),
'input_coord' : FileInfoMap(startpage, fileFormat=['.gromoscnf', '.cnf', '.g96'], activeInfo=False,
infoPurpose=['topology', 'inputcoordinates', 'inputvelocities']),
'output_coord' : FileInfoMap(startpage, fileFormat=['.gromoscnf', '.cnf', '.g96'], activeInfo=False,
infoPurpose=['outputcoordinates', 'outputvelocities']),
'trajectory' : FileInfoMap(startpage, fileFormat=['.gromostrc', '.trc'], activeInfo=False,
'trajectory' : FileInfoMap(startpage, fileFormat=['.gromostrc', '.trc'], activeInfo=False,
infoPurpose=['trajectory', 'unitcell']),
'traj_vel' : FileInfoMap(startpage, fileFormat=['.gromostrv', '.trv'], activeInfo=False,
infoPurpose=['velocities']),
'traj_force' : FileInfoMap(startpage, fileFormat=['.gromostrf', '.trf'], activeInfo=False,
'traj_force' : FileInfoMap(startpage, fileFormat=['.gromostrf', '.trf'], activeInfo=False,
infoPurpose=['forces']),
'output_log' : FileInfoMap(startpage),
'control_input' : FileInfoMap(startpage),
......@@ -62,11 +61,11 @@ def get_nameListDict(deflist):
matchWith parameters:
EOL = End of line
PL = Match with previous line
PL = Match with previous line
PW = Previous word
NW = Next word (until space, comma) (DEFAULT)
UD = until delimeter (can be any string/character)
The text matched inside apostrophe or qoutation is extracted
Returns:
......@@ -83,20 +82,20 @@ def get_nameListDict(deflist):
topocntrllist = {
'MAKE_TOP' : MetaInfoMap(startpage, defaultValue=None, matchWith='EOL',
replaceTag='topology_parameter_files', subFunc=lambda x:
replaceTag='topology_parameter_files', subFunc=lambda x:
', '.join(' '.join(x.strip().split()).replace(
'topology,', '').replace(
'using:', '').replace('Force-field code:', ''
).strip().split()[:-1]) if x is not None else None),
'Force-field code' : MetaInfoMap(startpage, defaultValue=None,
subFunc=lambda x: 'Gromos-'+x if x is not None else None),
'topology type' : MetaInfoMap(startpage, defaultValue=None,
'topology type' : MetaInfoMap(startpage, defaultValue=None,
activeInfo=False, matchWith='PW'),
'using atomistic' : MetaInfoMap(startpage, defaultValue=None,
replaceTag='topology_parameters', subFunc=lambda x:
'using atomistic' : MetaInfoMap(startpage, defaultValue=None,
replaceTag='topology_parameters', subFunc=lambda x:
'Atomistic' if x is not None else None),
'using coarse-grained' : MetaInfoMap(startpage, defaultValue=None,
replaceTag='topology_parameters', subFunc=lambda x:
replaceTag='topology_parameters', subFunc=lambda x:
'Coarse-Grained' if x is not None else None),
'RESNAME' : MetaInfoMap(startpage, defaultValue=None, matchWith='EOL',
subFunc=lambda x: ', '.join(' '.join(x.strip().split()
......@@ -104,7 +103,7 @@ def get_nameListDict(deflist):
'RESNAME', '').strip().split()
) if x is not None else None),
'atom types' : MetaInfoMap(startpage, defaultValue=None, matchWith='PW',
replaceTag='number_of_atom_types', matchAlso="ATOMTYPENAME",
replaceTag='number_of_atom_types', matchAlso="ATOMTYPENAME",
subFunc=lambda x: ' '.join(x.strip().split()
).replace('END', '').replace('ATOMTYPENAME', ''
) if x is not None else None),
......@@ -116,30 +115,30 @@ def get_nameListDict(deflist):
matchAlso="LJEXCEPTIONS", subFunc=lambda x: ' '.join(x.strip().split()
).replace('END', '').replace('LJEXCEPTIONS', ''
) if x is not None else None),
'bonds from BONDH block added to CONSTRAINT' : MetaInfoMap(startpage,
'bonds from BONDH block added to CONSTRAINT' : MetaInfoMap(startpage,
defaultValue=None, matchWith='PW', replaceTag='number of H bonds at CONSTRAINT',
matchAlso="END", subFunc=lambda x: ' '.join(x.strip().split()
).replace('END', '') if x is not None else None),
'bonds from BOND block added to CONSTRAINT' : MetaInfoMap(startpage,
defaultValue=None, matchWith='PW',
replaceTag='number of bonds at CONSTRAINT', matchAlso="END"),
'bondangles containing hydrogens' : MetaInfoMap(startpage,
'bonds from BOND block added to CONSTRAINT' : MetaInfoMap(startpage,
defaultValue=None, matchWith='PW',
replaceTag='number of bonds at CONSTRAINT', matchAlso="END"),
'bondangles containing hydrogens' : MetaInfoMap(startpage,
defaultValue=None, matchAlso="BONDANGLE"),
'bondangles not containing hydrogens' : MetaInfoMap(startpage,
'bondangles not containing hydrogens' : MetaInfoMap(startpage,
defaultValue=None, matchAlso="BONDANGLE"),
'improper dihedrals not containing hydrogens' : MetaInfoMap(startpage,
'improper dihedrals not containing hydrogens' : MetaInfoMap(startpage,
defaultValue=None, matchAlso="IMPDIHEDRAL"),
'improper dihedrals containing hydrogens' : MetaInfoMap(startpage,
'improper dihedrals containing hydrogens' : MetaInfoMap(startpage,
defaultValue=None, matchAlso="IMPDIHEDRAL"),
'propdihedrals not containing hydrogens' : MetaInfoMap(startpage,
'propdihedrals not containing hydrogens' : MetaInfoMap(startpage,
defaultValue=None, matchAlso="DIHEDRAL",
replaceTag='dihedrals not containing hydrogens'),
'propdihedrals containing hydrogens' : MetaInfoMap(startpage,
'propdihedrals containing hydrogens' : MetaInfoMap(startpage,
defaultValue=None, matchAlso="DIHEDRAL",
replaceTag='dihedrals containing hydrogens'),
'crossdihedrals not containing hydrogens' : MetaInfoMap(startpage,
'crossdihedrals not containing hydrogens' : MetaInfoMap(startpage,
defaultValue=None, matchAlso="CROSSDIHEDRAL"),
'crossdihedrals containing hydrogens' : MetaInfoMap(startpage,
'crossdihedrals containing hydrogens' : MetaInfoMap(startpage,
defaultValue=None, matchAlso="CROSSDIHEDRAL"),
'atoms' : MetaInfoMap(startpage, defaultValue=None, matchAlso="SOLVENT",
replaceTag='number of solvent atoms'),
......@@ -157,16 +156,16 @@ def get_nameListDict(deflist):
}
ffcntrllist = {
'bond angle \(cosine\) interaction' : MetaInfoMap(startpage, defaultValue=None,
'bond angle \(cosine\) interaction' : MetaInfoMap(startpage, defaultValue=None,
matchAlso="FORCEFIELD", replaceTag='bond angle interaction in force field',
subFunc=lambda x: 'Yes' if x is not None else None),
'improper-dihedral-interaction' : MetaInfoMap(startpage, defaultValue=None,
'improper-dihedral-interaction' : MetaInfoMap(startpage, defaultValue=None,
matchAlso="FORCEFIELD", replaceTag='improper dihedral interaction in force field',
subFunc=lambda x: 'Yes' if x is not None else None),
'propdihedral_interaction' : MetaInfoMap(startpage, defaultValue=None,
'propdihedral_interaction' : MetaInfoMap(startpage, defaultValue=None,
matchAlso="FORCEFIELD", replaceTag='dihedral interaction in force field',
subFunc=lambda x: 'Yes' if x is not None else None),
'crossdihedral interaction' : MetaInfoMap(startpage, defaultValue=None,
'crossdihedral interaction' : MetaInfoMap(startpage, defaultValue=None,
matchAlso="FORCEFIELD", replaceTag='cross dihedral interaction in force field',
subFunc=lambda x: 'Yes' if x is not None else None),
'nonbonded force' : MetaInfoMap(startpage, defaultValue=None, matchWith='EOL',
......@@ -174,10 +173,10 @@ def get_nameListDict(deflist):
subFunc=lambda x: ', '.join(x.strip().split()) if x is not None else None),
'Pairlist Algorithm' : MetaInfoMap(startpage, defaultValue=None, matchWith='EOL',
subFunc=lambda x: ' '.join(x.strip().split()) if x is not None else None),
'boundary' : MetaInfoMap(startpage, defaultValue=None, matchWith='EOL',
'boundary' : MetaInfoMap(startpage, defaultValue=None, matchWith='EOL',
replaceTag='periodic boundary conditions',
subFunc=lambda x: ' '.join(x.strip().split()) if x is not None else None),
'virial' : MetaInfoMap(startpage, defaultValue=None, matchWith='EOL',
'virial' : MetaInfoMap(startpage, defaultValue=None, matchWith='EOL',
subFunc=lambda x: ' '.join(x.strip().split()) if x is not None else None),
'cutoff ' : MetaInfoMap(startpage, defaultValue=None, matchAlso='pairlist creation',
replaceTag='cutoff type'),
......@@ -432,7 +431,7 @@ def set_Dictionaries(self):
self.stepcontrolDict = {
'logsteps' : None,
'nextlogsteps' : None,
'trajsteps' : None,
'trajsteps' : None,
'velsteps' : None,
'forcesteps' : None,
'steps' : None,
......@@ -450,12 +449,12 @@ def set_Dictionaries(self):
'mddata' : self.mddataDict,
'extra' : self.extraDict,
}
self.sectionDict = {
'section' : {
"metaNameTag" : ['input_output_files',
'control_parameters'],
"listTypStr" : 'type_section',
"repeatingSection" : False,
self.sectionDict = {
'section' : {
"metaNameTag" : ['input_output_files',
'control_parameters'],
"listTypStr" : 'type_section',
"repeatingSection" : False,
"supraNames" : ["section_run"]
}
}
......@@ -477,7 +476,7 @@ def get_updateDictionary(self, defname):
if(st is not None and isinstance(st, str)):
if("[" in st or "(" in st):
val.append(list(storedtext))
if val:
if val:
return False, np.linalg.norm(np.asarray(val)), itemdict
else:
return False, itemdict["value"], itemdict
......@@ -492,27 +491,27 @@ def get_updateDictionary(self, defname):
# ---------------------------------------------------------------
# Definitions of meta data values for section_sampling_method
# ---------------------------------------------------------------
sampling = {
sampling = {
#'ensemble_type' : MetaInfoMap(startpage, activeInfo=True,
# depends=[
# {'test' : [['DYNA', ' is not None'],
# {'test' : [['DYNA', ' is not None'],
# ['FIRSTT', ' in [\"tcouple\",'
# '\"rescale\",'
# '\"reassign\",'
# '\"andersen\",'
# '\"langevin\"]'],
# '\"langevin\"]'],
# ['barostat', ' in [\"berendsen\",'
# '\"langevin\"]']],
# '\"langevin\"]']],
# 'assign' : 'NPT'},
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' in [\"langevin\"]'],
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' in [\"langevin\"]'],
# ['thermostat', ' not in [\"tcouple\",'
# '\"rescale\",'
# '\"reassign\",'
# '\"andersen\"]'],
# ['barostat', ' is None']],
# 'assign' : 'Langevin'},
# {'test' : [['minimization', ' is None'],
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' in [\"tcouple\",'
# '\"rescale\",'
# '\"reassign\",'
......@@ -521,16 +520,16 @@ def get_updateDictionary(self, defname):
# 'assign' : 'NVT'},
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' is None'],
# ['barostat', ' is None']],
# ['barostat', ' is None']],
# 'assign' : 'NVE'},
# {'test' : [['minimization', ' is not None']],
# {'test' : [['minimization', ' is not None']],
# 'assign' : 'minimization'},
# ],
# lookupdict=self.extraDict
# ),
'sampling_method' : MetaInfoMap(startpage, activeInfo=True,
'sampling_method' : MetaInfoMap(startpage, activeInfo=True,
depends=[
{'test' : [['MINI', ' is not None']],
{'test' : [['MINI', ' is not None']],
'assign' : 'geometry_optimization'},
{'test' : [['DYNA', ' is not None']],
'assign' : 'molecular_dynamics'}
......@@ -551,22 +550,22 @@ def get_updateDictionary(self, defname):
'geometry_optimization_method' : MetaInfoMap(startpage,
depends=[
{'test' : [['MINI',' is not None'],
['MINI', ' in [\"SD\",\"sd\"]']],
['MINI', ' in [\"SD\",\"sd\"]']],
'assign' : 'SD'},
{'test' : [['MINI',' is not None'],
['MINI', ' in [\"ABNR\",\"abnr\"]']],
['MINI', ' in [\"ABNR\",\"abnr\"]']],
'assign' : 'Adopted Basis Newton-Raphson'},
{'test' : [['MINI',' is not None'],
['MINI', ' in [\"NRAP\",\"nrap\"]']],
['MINI', ' in [\"NRAP\",\"nrap\"]']],
'assign' : 'Newton-Raphson'},
{'test' : [['MINI',' is not None'],
['MINI', ' in [\"POWELL\",\"powell\"]']],
['MINI', ' in [\"POWELL\",\"powell\"]']],
'assign' : 'Powell'},
{'test' : [['MINI',' is not None'],
['MINI', ' in [\"POWE\",\"powe\"]']],
['MINI', ' in [\"POWE\",\"powe\"]']],
'assign' : 'Powell'},
{'test' : [['MINI',' is not None'],
['MINI', ' in [\"TNPACK\",\"tnpack\"]']],
['MINI', ' in [\"TNPACK\",\"tnpack\"]']],
'assign' : 'Truncated Newton Method'},
{'test' : [['MINI',' is not None'],
['MINI', ' not in [\"SD\",\"sd\",'
......@@ -574,7 +573,7 @@ def get_updateDictionary(self, defname):
'\"NRAP\",\"nrap\",'
'\"POWE\",\"powe\",'
'\"POWELL\",\"powell\",'
'\"TNPACK\",\"tnpack\"]']],
'\"TNPACK\",\"tnpack\"]']],
'assign' : 'CG'},
],
lookupdict=self.cntrlDict,
......@@ -583,12 +582,12 @@ def get_updateDictionary(self, defname):
# 'geometry_optimization_threshold_force' : MetaInfoMap(startpage),
#'x_gromos_barostat_type' : MetaInfoMap(startpage,
# depends=[
# {'test' : [['minimization', ' is None'],
# {'test' : [['minimization', ' is None'],
# ['barostat', '== \"berendsen\"']],
# 'assign' : 'Berendsen'},
# {'test' : [['minimization', ' is None'],
# {'test' : [['minimization', ' is None'],
# ['barostat', '== \"langevin\"']],
# 'assign' : 'Nose-Hoover Langevin'}
# 'assign' : 'Nose-Hoover Langevin'}
# ],
# lookupdict=self.extraDict,
# #autoSections=True,
......@@ -598,7 +597,7 @@ def get_updateDictionary(self, defname):
#'x_gromos_barostat_target_pressure' : MetaInfoMap(startpage,
# depends=[
# {'test' : [['TARGET PRESSURE', ' is not None']],
# 'value' : 'TARGET PRESSURE'}
# 'value' : 'TARGET PRESSURE'}
# ],
# lookupdict=self.cntrlDict,
# valtype='float',
......@@ -611,9 +610,9 @@ def get_updateDictionary(self, defname):
#'x_gromos_barostat_tau' : MetaInfoMap(startpage,
# depends=[
# {'test' : [['LANGEVIN OSCILLATION PERIOD', ' is not None']],
# 'value' : 'LANGEVIN OSCILLATION PERIOD'},
# 'value' : 'LANGEVIN OSCILLATION PERIOD'},
# {'test' : [['BERENDSEN RELAXATION TIME', ' is not None']],
# 'value' : 'BERENDSEN RELAXATION TIME'}
# 'value' : 'BERENDSEN RELAXATION TIME'}
# ],
# lookupdict=self.cntrlDict,
# valtype='float',
......@@ -626,7 +625,7 @@ def get_updateDictionary(self, defname):
#'x_gromos_integrator_type' : MetaInfoMap(startpage,
# depends=[
# {'test' : [['integrator', ' is not None']],
# 'value' : 'integrator'},
# 'value' : 'integrator'},
# {'test' : [['thermostat', ' == \"langevin\"']],
# 'assign' : 'Langevin'}
# ],
......@@ -659,21 +658,21 @@ def get_updateDictionary(self, defname):
),
#'x_gromos_thermostat_type' : MetaInfoMap(startpage,
# depends=[
# {'test' : [['minimization', ' is None'],
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' == \"tcouple\"']],
# 'assign' : 'Berendsen'},
# {'test' : [['minimization', ' is None'],
# 'assign' : 'Berendsen'},
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' == \"rescale\"']],
# 'assign' : 'Velocity Rescaling'},
# {'test' : [['minimization', ' is None'],
# 'assign' : 'Velocity Rescaling'},
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' == \"reassign\"']],
# 'assign' : 'Velocity Reassigning'},
# {'test' : [['minimization', ' is None'],
# 'assign' : 'Velocity Reassigning'},
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' == \"andersen\"']],
# 'assign' : 'Andersen'},
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' == \"langevin\"']],
# 'assign' : 'Nose-Hoover Langevin'},
# 'assign' : 'Andersen'},
# {'test' : [['minimization', ' is None'],
# ['thermostat', ' == \"langevin\"']],
# 'assign' : 'Nose-Hoover Langevin'},
# ],
# lookupdict=self.extraDict,
# #autoSections=True,
......@@ -734,7 +733,7 @@ def get_updateDictionary(self, defname):
# ------------------------------------------------------------
# Definitions for section_single_configuration_calculation
# ------------------------------------------------------------
singleconfcalc = {
singleconfcalc = {
#'atom_forces_type' : MetaInfoMap(startpage,
# depends=[{'assign' : 'Force Field'}],
# lookupdict=self.mddataDict
......@@ -786,7 +785,7 @@ def get_updateDictionary(self, defname):
'time_single_configuration_calculation_wall_start' : MetaInfoMap(startpage),
'stress_tensor_kind' : MetaInfoMap(startpage,
depends=[
{'test' : [['MINI', ' is not None']],
{'test' : [['MINI', ' is not None']],
'assign' : 'geometry_optimization'},
{'test' : [['DYNA', ' is not None']],
'assign' : 'molecular_dynamics'}
......@@ -822,7 +821,7 @@ def get_updateDictionary(self, defname):
#autoSections=True,
activeInfo=True,
activeSections=['section_restricted_uri'],
subfunction={
subfunction={
'function' : self.parameter_file_name,
'supportDict' : self.fileDict,
},
......@@ -852,11 +851,11 @@ def get_updateDictionary(self, defname):
activeSections=['section_restricted_uri']
),
}
# ------------------------------------------
# Definitions for section_frame_sequence
# ------------------------------------------
frameseq = {
frameseq = {
#'frame_sequence_conserved_quantity_frames' : MetaInfoMap(startpage,
# depends=[{'store' : 'TS'}],
# valtype='int',
......@@ -953,7 +952,7 @@ def get_updateDictionary(self, defname):
depends=[{'store' : 'TIME'}],
valtype='float',
unitdict=self.unitDict,
unit='nano-second',
unit='nano-second',
# Calculates in AKMA units including inputs but prints in picoseconds.
lookupdict=self.mddataDict
),
......@@ -1152,7 +1151,7 @@ def get_updateDictionary(self, defname):
#'previous_sequence_ref' : MetaInfoMap(startpage)
}
frameseqend = {
frameseqend = {
#'number_of_conserved_quantity_evaluations_in_sequence' : MetaInfoMap(startpage,
# activeInfo=True,
# value=(lambda x: np.array(x['val']).flatten().shape[0] if(
......@@ -1342,7 +1341,7 @@ def get_updateDictionary(self, defname):
'system_name' : MetaInfoMap(startpage,
activeInfo=True,
activeSections=['section_system'],
subfunction={
subfunction={
'function' : MDData.MDDataConverter.topology_system_name,
'supportDict' : self.topoDict,
},
......@@ -1469,7 +1468,7 @@ def get_updateDictionary(self, defname):
'number_of_atoms_per_molecule_interaction' : MetaInfoMap(startpage),
'number_of_molecule_interactions' : MetaInfoMap(startpage)
}
# section_atom_in_molecule of section_molecule_type
atom_in_mol = {
'atom_in_molecule_charge' : MetaInfoMap(startpage),
......
parser/parser-gromos/GROMOSParser.py → gromosparser/GROMOSParser.py
View file @ 1494b76d
# Copyright 2018-2018 Berk Onat
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#
# http://www.apache.org/licenses/LICENSE-2.0
#
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
......@@ -15,7 +15,6 @@
from builtins import map
from builtins import range
from builtins import object
import setup_paths
import numpy as np
import nomadcore.ActivateLogging
from nomadcore.caching_backend import CachingLevel
......@@ -24,9 +23,9 @@ from nomadcore.smart_parser import SmartParserCommon as SmartParser
from nomadcore.smart_parser.SmartParserCommon import get_metaInfo, conv_str, conv_int, conv_float, open_section
from nomadcore.smart_parser.SmartParserDictionary import getList_MetaStrInDict, getDict_MetaStrInDict
from nomadcore.smart_parser.SmartParserDictionary import isMetaStrInDict, setMetaStrInDict, copyMetaDictToDict
from GROMOSDictionary import get_updateDictionary, set_Dictionaries
from GROMOSCommon import PARSERNAME, PROGRAMNAME, PARSERVERSION, PARSERTAG, LOGGER
from GROMOSCommon import PARSER_INFO_DEFAULT, META_INFO_PATH, set_excludeList, set_includeList
from .GROMOSDictionary import get_updateDictionary, set_Dictionaries
from .GROMOSCommon import PARSERNAME, PROGRAMNAME, PARSERVERSION, PARSERTAG, LOGGER
from .GROMOSCommon import PARSER_INFO_DEFAULT, META_INFO_PATH, set_excludeList, set_includeList
from nomadcore.md_data_access import MDDataAccess as MDDA
import argparse
import logging
......@@ -47,7 +46,7 @@ TEXTCHARS = bytearray({7,8,9,10,12,13,27} | set(range(0x20, 0x100)) - {0x7f})
def is_file_binary(fName, checkBytes=None):
if checkBytes is None:
checkBytes = 1024
checkBytes = 1024
with open(fName, 'rb') as fin:
testin = fin.read(checkBytes)
if is_binary_string(testin):
......@@ -77,7 +76,7 @@ class GROMOSParser(SmartParser.ParserBase):
}
SmartParser.ParserBase.__init__(
self, re_program_name=re.compile(r"\s*"+PROGRAMNAME+"$"),
parsertag=PARSERTAG, metainfopath=META_INFO_PATH,
parsertag=PARSERTAG, metainfopath=META_INFO_PATH,
parserinfodef=PARSER_INFO_DEFAULT, recorderOn=True)
set_Dictionaries(self)
......@@ -95,27 +94,27 @@ class GROMOSParser(SmartParser.ParserBase):
metaInfo = self.metaInfoEnv.infoKinds[name]
if (name.startswith(PARSERTAG + '_mdin_') and
metaInfo.kindStr == "type_document_content" and
(PARSERTAG + "_mdin_method" in metaInfo.superNames or
PARSERTAG + "_mdin_run" in metaInfo.superNames or
(PARSERTAG + "_mdin_method" in metaInfo.superNames or
PARSERTAG + "_mdin_run" in metaInfo.superNames or
PARSERTAG + "_mdin_system" in metaInfo.superNames) or
name.startswith(PARSERTAG + '_parm_') and
metaInfo.kindStr == "type_document_content" and
(PARSERTAG + "_mdin_method" in metaInfo.superNames or
(PARSERTAG + "_mdin_method" in metaInfo.superNames or
PARSERTAG + "_mdin_run" in metaInfo.superNames or
PARSERTAG + "_mdin_system" in metaInfo.superNames) or
#name.startswith(PARSERTAG + '_mdin_file_') and
name.startswith(PARSERTAG + '_inout_file_') or
#metaInfo.kindStr == "type_document_content" and
#(PARSERTAG + "_section_input_output_files" in metaInfo.superNames or
#(PARSERTAG + "_section_input_output_files" in metaInfo.superNames or
# "section_run" in metaInfo.superNames) or
name.startswith(PARSERTAG + '_inout_control_') or
#(PARSERTAG + "_section_control_parameters" in metaInfo.superNames) or
#(PARSERTAG + "_section_control_parameters" in metaInfo.superNames) or
#name.startswith(PARSERTAG + '_mdin_') and
#(PARSERTAG + "_section_control_parameters" in metaInfo.superNames) or
name.startswith(PARSERTAG + '_mdout_') or
name.startswith(PARSERTAG + '_mdout_') and
#metaInfo.kindStr == "type_document_content" and
(PARSERTAG + "_mdout_method" in metaInfo.superNames or
(PARSERTAG + "_mdout_method" in metaInfo.superNames or
PARSERTAG + "_mdout_system" in metaInfo.superNames or
"section_run" in metaInfo.superNames or
PARSERTAG + "_mdout_single_configuration_calculation" in metaInfo.superNames)
......@@ -258,8 +257,8 @@ class GROMOSParser(SmartParser.ParserBase):
def onClose_section_run(self, backend, gIndex, section):
"""Trigger called when section_run is closed.
Write the keywords from control parametres and
the GROMOS output from the parsed log output,
Write the keywords from control parametres and
the GROMOS output from the parsed log output,
which belong to settings_run.
Variables are reset to ensure clean start for new run.
"""
......@@ -272,7 +271,7 @@ class GROMOSParser(SmartParser.ParserBase):
'dictionary' : section_frameseq_Dict
}
self.metaStorage.update(updateFrameDict)
self.metaStorage.updateBackend(backend.superBackend,
self.metaStorage.updateBackend(backend.superBackend,
startsection=['section_frame_sequence'],
autoopenclose=False)
backend.addValue("frame_sequence_to_sampling_ref", self.secSamplingGIndex)
......@@ -306,14 +305,14 @@ class GROMOSParser(SmartParser.ParserBase):
Determine whether topology, trajectory and input coordinate files are
supplied to the parser
Initiates topology and trajectory file handles.
Captures topology, atomic positions, atom labels, lattice vectors and
stores them before section_system and
Captures topology, atomic positions, atom labels, lattice vectors and
stores them before section_system and
section_single_configuration_calculation are encountered.
"""
# Checking whether topology, input
# Checking whether topology, input
# coordinates and trajectory files exist
fileList=None
fKey = PARSERTAG + '_inout_file_'
......@@ -345,7 +344,7 @@ class GROMOSParser(SmartParser.ParserBase):
'dictionary' : section_control_Dict
}
self.metaStorage.update(updateDict)
self.metaStorage.updateBackend(backend.superBackend,
self.metaStorage.updateBackend(backend.superBackend,
startsection=[PARSERTAG+'_section_control_parameters'],
autoopenclose=False)
......@@ -426,7 +425,7 @@ class GROMOSParser(SmartParser.ParserBase):
'dictionary' : restrictionsDict