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Commit 8cc4a62c authored by Berk Onat's avatar Berk Onat
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Data of frame_sequence and single_conf_calc sections are generated in correct order.

parent 488d0409
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parser/parser-amber/AMBERDictionary.py
View file @ 8cc4a62c
......@@ -25,6 +25,7 @@ class MetaInfoMap(dict):
lookupdict=None
subfunction=None
activeSections=None
autoSections=False
def __init__(self, *args, **kwargs):
super(MetaInfoMap, self).__init__(*args, **kwargs)
......@@ -163,6 +164,10 @@ class MapDictionary(dict):
def metaNameConverter(keyName):
newName = keyName.lower().replace(" ", "").replace("-", "")
newName = newName.replace("(", "").replace(")", "")
newName = newName.replace("[", "").replace("]", "")
newName = newName.replace(",", "").replace(".", "")
newName = newName.replace("\\", "").replace("/", "")
return newName
def get_fileListDict():
......@@ -340,9 +345,9 @@ def get_nameListDict(deflist):
'ew_type' : MetaInfoMap(startpage, defaultValue=0),
'dsum_tol' : MetaInfoMap(startpage, defaultValue=1.0E-5),
'rsum_tol' : MetaInfoMap(startpage, defaultValue=5.0E-5),
'mlimit(1)' : MetaInfoMap(startpage),
'mlimit(2)' : MetaInfoMap(startpage),
'mlimit(3)' : MetaInfoMap(startpage),
'mlimit\(1\)' : MetaInfoMap(startpage),
'mlimit\(2\)' : MetaInfoMap(startpage),
'mlimit\(3\)' : MetaInfoMap(startpage),
'ew_coeff' : MetaInfoMap(startpage),
'nbflag' : MetaInfoMap(startpage, defaultValue=1),
'skinnb' : MetaInfoMap(startpage, defaultValue=2.0),
......@@ -514,8 +519,8 @@ def get_nameListDict(deflist):
})
mddatalist = {
'NSTEP' : MetaInfoMap(startpage),
'TIME' : MetaInfoMap(startpage),
'TEMP' : MetaInfoMap(startpage),
'TIME\(PS\)' : MetaInfoMap(startpage),
'TEMP\(K\)' : MetaInfoMap(startpage),
'PRESS' : MetaInfoMap(startpage),
'Etot' : MetaInfoMap(startpage),
'EKtot' : MetaInfoMap(startpage),
......@@ -653,6 +658,27 @@ def get_updateDictionary(self, defname):
'assign' : 'Monte Carlo barostat'}
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_barostat']
),
'x_amber_barostat_target_pressure' : MetaInfoMap(startpage,
depends=[
{'test' : [['imin', '== 0'],
['ntp', '!= 0']],
'value' : 'pres0'}
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_barostat']
),
'x_amber_barostat_tau' : MetaInfoMap(startpage,
depends=[
{'test' : [['imin', '== 0'],
['ntp', '!= 0']],
'value' : 'taup'}
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_barostat']
),
'x_amber_integrator_type' : MetaInfoMap(startpage,
......@@ -663,6 +689,22 @@ def get_updateDictionary(self, defname):
'assign' : 'minimization'}
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_integrator']
),
'x_amber_integrator_dt' : MetaInfoMap(startpage,
depends=[
{'test' : [['imin', '== 0']],
'value' : 'dt'}
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_integrator']
),
'x_amber_number_of_steps_requested' : MetaInfoMap(startpage,
depends=[{'value' : 'nstlim'}],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_integrator']
),
'x_amber_thermostat_type' : MetaInfoMap(startpage,
......@@ -679,8 +721,53 @@ def get_updateDictionary(self, defname):
'assign' : 'RESPA Stochastic Isokinetic Nose-Hoover'}
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_thermostat']
),
'x_amber_thermostat_target_temperature' : MetaInfoMap(startpage,
depends=[
{'test' : [['imin', '== 0'], ['ntt', '> 0']],
'value' : 'temp0'}
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_thermostat']
),
'x_amber_thermostat_tau' : MetaInfoMap(startpage,
depends=[
{'test' : [['imin', '== 0'], ['ntt', '== 1']],
'value' : 'tautp'},
{'test' : [['imin', '== 0'], ['ntt', '== 2']],
'value' : 'tautp'},
{'test' : [['imin', '== 0'], ['ntt', '== 9']],
'value' : 'gamma_ln'},
{'test' : [['imin', '== 0'], ['ntt', '== 10']],
'value' : 'gamma_ln'},
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_thermostat']
),
'x_amber_langevin_gamma' : MetaInfoMap(startpage,
depends=[
{'test' : [['imin', '== 0'], ['ntt', '== 3']],
'value' : 'gamma_ln'}
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_thermostat']
),
'x_amber_periodicity_type' : MetaInfoMap(startpage,
depends=[
{'test' : [['ntb', '== 0']],
'assign' : 'no periodic boundaries'},
{'test' : [['ntb', '> 0']],
'assign' : 'periodic boundaries'}
],
lookupdict=self.cntrlDict,
#autoSections=True,
activeSections=['settings_thermostat']
)
}
singleconfcalc = {
......@@ -689,10 +776,11 @@ def get_updateDictionary(self, defname):
# lookupdict=self.mddataDict
# ),
'energy_correction_entropy' : MetaInfoMap(startpage),
'energy_current' : MetaInfoMap(startpage,
depends=[{'value' : 'Etot'}],
lookupdict=self.mddataDict
),
#'energy_current' : MetaInfoMap(startpage,
# depends=[{'value' : 'EPtot'}],
# lookupdict=self.mddataDict
# ),
'energy_current' : MetaInfoMap(startpage),
'energy_electrostatic' : MetaInfoMap(startpage,
depends=[{'value' : 'EELEC'}],
lookupdict=self.mddataDict
......@@ -700,7 +788,7 @@ def get_updateDictionary(self, defname):
'energy_free_per_atom' : MetaInfoMap(startpage),
'energy_free' : MetaInfoMap(startpage),
'energy_method_current' : MetaInfoMap(startpage,
depends=[{'assign' : 'Amber Force Field'}],
depends=[{'assign' : 'Force Field'}],
lookupdict=self.mddataDict
),
'energy_T0_per_atom' : MetaInfoMap(startpage),
......@@ -710,7 +798,6 @@ def get_updateDictionary(self, defname):
depends=[{'value' : 'Etot'}],
lookupdict=self.mddataDict
),
'energy_type_van_der_Waals' : MetaInfoMap(startpage),
'hessian_matrix' : MetaInfoMap(startpage),
'single_configuration_calculation_converged' : MetaInfoMap(startpage),
'single_configuration_calculation_to_system_ref' : MetaInfoMap(startpage),
......@@ -725,6 +812,15 @@ def get_updateDictionary(self, defname):
'stress_tensor_kind' : MetaInfoMap(startpage),
'stress_tensor_value' : MetaInfoMap(startpage)
}
singlevdw = {
'energy_van_der_Waals_value' : MetaInfoMap(startpage,
depends=[{'value' : 'VDWAALS'}],
lookupdict=self.mddataDict,
#autoSections=True,
activeSections=['section_energy_van_der_Waals']
),
}
frameseq = {
'frame_sequence_conserved_quantity_frames' : MetaInfoMap(startpage,
......@@ -772,11 +868,11 @@ def get_updateDictionary(self, defname):
),
'frame_sequence_temperature_stats' : MetaInfoMap(startpage),
'frame_sequence_temperature' : MetaInfoMap(startpage,
depends=[{'store' : 'TEMP'}],
depends=[{'store' : 'TEMP\(K\)'}],
lookupdict=self.mddataDict
),
'frame_sequence_time' : MetaInfoMap(startpage,
depends=[{'store' : 'TIME'}],
depends=[{'store' : 'TIME\(PS\)'}],
lookupdict=self.mddataDict
),
'x_amber_frame_sequence_volume_frames' : MetaInfoMap(startpage,
......@@ -796,13 +892,51 @@ def get_updateDictionary(self, defname):
lookupdict=self.mddataDict
),
'frame_sequence_to_sampling_ref' : MetaInfoMap(startpage),
'geometry_optimization_converged' : MetaInfoMap(startpage),
'number_of_conserved_quantity_evaluations_in_sequence' : MetaInfoMap(startpage),
'number_of_frames_in_sequence' : MetaInfoMap(startpage),
'number_of_kinetic_energies_in_sequence' : MetaInfoMap(startpage),
'number_of_potential_energies_in_sequence' : MetaInfoMap(startpage),
'number_of_pressure_evaluations_in_sequence' : MetaInfoMap(startpage),
'number_of_temperatures_in_sequence' : MetaInfoMap(startpage),
'geometry_optimization_converged' : MetaInfoMap(startpage,
value=self.minConverged
),
'number_of_conserved_quantity_evaluations_in_sequence' : MetaInfoMap(startpage,
value=len([
item for item in self.metaStorage.fetchAttr(
{'frame_sequence_conserved_quantity_frames' : None}
)['frame_sequence_conserved_quantity_frames']
])
),
'number_of_frames_in_sequence' : MetaInfoMap(startpage,
value=len([
item for item in self.metaStorage.fetchAttr(
{'frame_sequence_potential_energy_frames' : None}
)['frame_sequence_potential_energy_frames']
])
),
'number_of_kinetic_energies_in_sequence' : MetaInfoMap(startpage,
value=len([
item for item in self.metaStorage.fetchAttr(
{'frame_sequence_kinetic_energy_frames' : None}
)['frame_sequence_kinetic_energy_frames']
])
),
'number_of_potential_energies_in_sequence' : MetaInfoMap(startpage,
value=len([
item for item in self.metaStorage.fetchAttr(
{'frame_sequence_potential_energy_frames' : None}
)['frame_sequence_potential_energy_frames']
])
),
'number_of_pressure_evaluations_in_sequence' : MetaInfoMap(startpage,
value=len([
item for item in self.metaStorage.fetchAttr(
{'frame_sequence_pressure_frames' : None}
)['frame_sequence_pressure_frames']
])
),
'number_of_temperatures_in_sequence' : MetaInfoMap(startpage,
value=len([
item for item in self.metaStorage.fetchAttr(
{'frame_sequence_temperature_frames' : None}
)['frame_sequence_temperature_frames']
])
),
'previous_sequence_ref' : MetaInfoMap(startpage)
}
......@@ -893,6 +1027,8 @@ def get_updateDictionary(self, defname):
dictionary = interaction
elif defname == 'sampling':
dictionary = sampling
elif defname == 'singlevdw':
dictionary = singlevdw
else:
dictionary = singleconfcalclist
return MapDictionary(dictionary)
......@@ -907,6 +1043,7 @@ def set_excludeList(self):
'x_amber_mdin_verbatim_writeout',
'x_amber_dumm_text',
'x_amber_dummy',
'x_amber_mdin_wt'
]
excludelist.extend(['x_amber_mdin_file_%s' % fileNL.lower() for fileNL in self.fileDict.keys()])
excludelist.extend(['x_amber_mdin_%s' % cntrlNL.lower() for cntrlNL in self.cntrlDict.keys()])
......@@ -920,9 +1057,7 @@ def set_includeList():
Returns:
the list of names
"""
includelist = [
'x_amber_mdin_wt'
]
includelist = []
return includelist
def getList_MetaStrInDict(sourceDict):
......@@ -940,8 +1075,8 @@ def getDict_MetaStrInDict(sourceDict):
used as the keywords in the parsing.
"""
newDict = {}
for item in sourceDict:
newDict.update({sourceDict[item].matchStr : sourceDict[item]})
for key, value in sourceDict.items():
newDict.update({sourceDict[key].matchStr : key})
return newDict
parser/parser-amber/AMBERParser.py
View file @ 8cc4a62c
......@@ -7,7 +7,7 @@ import nomadcore.ActivateLogging
from nomadcore.caching_backend import CachingLevel
from nomadcore.simple_parser import AncillaryParser, mainFunction, ParsingContext
from nomadcore.simple_parser import SimpleMatcher as SM
from AMBERDictionary import set_excludeList, set_includeList, get_updateDictionary, getList_MetaStrInDict
from AMBERDictionary import set_excludeList, set_includeList, get_updateDictionary, getList_MetaStrInDict, getDict_MetaStrInDict
import AMBERCommon as AmberC
import trajectory_reader as TrajRead
import logging
......@@ -37,7 +37,6 @@ class AMBERParser(AmberC.AMBERParserBase):
def __init__(self):
# dictionary of energy values, which are tracked between SCF iterations and written after convergence
self.totalEnergyList = {
'electronic_kinetic_energy': None,
'energy_electrostatic': None,
'energy_total_T0_per_atom': None,
'energy_free_per_atom': None,
......@@ -49,8 +48,9 @@ class AMBERParser(AmberC.AMBERParserBase):
'x_amber_trajectory_file_detect': CachingLevel.Cache,
'x_amber_geometry_optimization_cdetect': CachingLevel.Cache,
'x_amber_mdin_finline': CachingLevel.Ignore,
'x_amber_mdin_wt': CachingLevel.Ignore,
'x_amber_single_configuration_calculation_detect': CachingLevel.Cache,
'x_amber_single_configuration_calculation': CachingLevel.Cache,
#'x_amber_single_configuration_calculation': CachingLevel.Cache,
}
for name in self.metaInfoEnv.infoKinds:
metaInfo = self.metaInfoEnv.infoKinds[name]
......@@ -82,9 +82,11 @@ class AMBERParser(AmberC.AMBERParserBase):
This allows a consistent setting and resetting of the variables,
when the parsing starts and when a section_run closes.
"""
self.secMethodIndex = None
self.secSystemDescriptionIndex = None
self.samplingGIndex = None
self.secMethodGIndex = None
self.secSystemGIndex = None
self.secSamplingGIndex = None
self.secSingleGIndex = None
self.secVDWGIndex = None
self.inputMethodIndex = None
self.mainMethodIndex = None
self.mainCalcIndex = None
......@@ -101,7 +103,7 @@ class AMBERParser(AmberC.AMBERParserBase):
# start with -1 since zeroth iteration is the initialization
self.mdIterNr = -1
self.singleConfCalcs = []
self.minConvergence = None
self.minConverged = None
self.parsedLogFile = False
self.LogSuperContext = None
self.forces_raw = []
......@@ -192,16 +194,6 @@ class AMBERParser(AmberC.AMBERParserBase):
#else:
# return False
#def compile_traj_parser(self):
# """Instantiate superContext and construct parser for MD trajactory file.
# """
# self.trajSuperContext = AMBERmdcrdParser.AMBERmdcrdParserContext(False)
# self.trajParser = AncillaryParser(
# fileDescription = AMBERmdcrdParser.build_AMBERmdcrdFileSimpleMatcher(),
# parser = self.parser,
# cachingLevelForMetaName = AMBERmdcrdParser.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.Ignore),
# superContext = self.trajSuperContext)
def onClose_section_run(self, backend, gIndex, section):
"""Trigger called when section_run is closed.
......@@ -253,7 +245,7 @@ class AMBERParser(AmberC.AMBERParserBase):
self.metaStorage.updateBackend(backend,
startsection=['section_frame_sequence'],
autoopenclose=False)
backend.addValue("frame_sequence_to_sampling_ref", self.samplingGIndex)
backend.addValue("frame_sequence_to_sampling_ref", self.secSamplingGIndex)
backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs))
backend.closeSection("section_frame_sequence", frameSequenceGIndex)
......@@ -264,15 +256,6 @@ class AMBERParser(AmberC.AMBERParserBase):
# """
# self.MD = True
# def check_file_exist(self, k, v, filePath, fileList):
# if k.startswith('x_amber_mdin_file_') and
# :
#
# file_name = os.path.normpath(os.path.join(filePath, v[-1]))
# = os.path.isfile(file_name)
# if self.topoFound:
# self.topoFileName = file_name
def onClose_x_amber_section_input_output_files(self, backend, gIndex, section):
"""Trigger called when x_amber_section_input_output_files is closed.
......@@ -304,7 +287,7 @@ class AMBERParser(AmberC.AMBERParserBase):
def onOpen_section_method(self, backend, gIndex, section):
# keep track of the latest method section
self.secMethodIndex = gIndex
self.secMethodGIndex = gIndex
if self.inputMethodIndex is None:
self.inputMethodIndex = gIndex
else:
......@@ -361,28 +344,53 @@ class AMBERParser(AmberC.AMBERParserBase):
if int(v[-1]) == 1:
self.MD = False
def onOpen_section_system(self, backend, gIndex, section):
# keep track of the latest system description section
self.secSystemDescriptionIndex = gIndex
def onOpen_section_sampling_method(self, backend, gIndex, section):
# keep track of the latest sampling description section
self.secSamplingGIndex = gIndex
def onClose_section_system(self, backend, gIndex, section):
"""Trigger called when section_system is closed.
def onClose_section_sampling_method(self, backend, gIndex, section):
"""Trigger called when section_sampling_method is closed.
Writes atomic positions, atom labels and lattice vectors.
Writes sampling method details for minimization and molecular dynamics.
"""
# check if control keywords were found
# check control keywords were found throguh dictionary support
section_sampling_Dict = get_updateDictionary(self, 'sampling')
updateDict = {
'startSection' : [['section_sampling_method']],
#'muteSections' : [['section_system']],
'dictionary' : section_sampling_Dict
}
self.samplingGIndex = backend.openSection("section_sampling_method")
#self.secSamplingGIndex = backend.openSection("section_sampling_method")
self.metaStorage.update(updateDict)
self.metaStorage.updateBackend(backend,
startsection=['section_sampling_method'],
autoopenclose=False)
backend.closeSection("section_sampling_method", self.samplingGIndex)
#backend.closeSection("section_sampling_method", self.secSamplingGIndex)
def onOpen_section_system(self, backend, gIndex, section):
# keep track of the latest system description section
self.secSystemGIndex = gIndex
def onClose_section_system(self, backend, gIndex, section):
"""Trigger called when section_system is closed.
Writes atomic positions, atom labels and lattice vectors.
"""
# check if control keywords were found
#section_sampling_Dict = get_updateDictionary(self, 'sampling')
#updateDict = {
# 'startSection' : [['section_sampling_method']],
# #'muteSections' : [['section_system']],
# 'dictionary' : section_sampling_Dict
# }
#self.secSamplingGIndex = backend.openSection("section_sampling_method")
#self.metaStorage.update(updateDict)
#self.metaStorage.updateBackend(backend,
# startsection=['section_sampling_method'],
# autoopenclose=False)
#backend.closeSection("section_sampling_method", self.secSamplingGIndex)
#self.secMethodGIndex = backend.openSection("section_method")
#backend.closeSection("section_method", self.secMethodGIndex)
counter = 0
......@@ -401,10 +409,6 @@ class AMBERParser(AmberC.AMBERParserBase):
# # default writeout
# else:
backend.superBackend.addValue(k, v[-1])
if k.startswith('x_amber_mdin_imin'):
# print("-----IMIN----",k,v)
if int(v[-1]) == 1:
self.MD = False
# Write atomic geometry in the case of MD
# if not self.MD:
......@@ -457,9 +461,10 @@ class AMBERParser(AmberC.AMBERParserBase):
def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
# write the references to section_method and section_system
backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemDescriptionIndex)
backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodGIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemGIndex)
self.singleConfCalcs.append(gIndex)
self.secSingleGIndex = backend.superBackend.openSection("section_single_configuration_calculation")
def onClose_section_single_configuration_calculation(self, backend, gIndex, section):
"""Trigger called when section_single_configuration_calculation is closed.
......@@ -489,46 +494,62 @@ class AMBERParser(AmberC.AMBERParserBase):
# if self.forces_raw:
# # need to transpose array since its shape is [number_of_atoms,3] in the metadata
# backend.addArrayValues('atom_forces_free_raw', np.transpose(np.asarray(self.forces_raw)))
# get reference to current section_single_configuration_calculation if trajectory was found in there
# if self.trajFound:
# self.trajRefSingleConfigurationCalculation = gIndex
# self.trajFound = False
self.lastCalculationGIndex = gIndex
exclude_list = set_excludeList(self)
include_list = set_includeList()
#for name in self.metaInfoEnv.infoKinds:
# if name.startswith('x_fhi_aims_mdin_'):
# if name.startswith('x_amber_mdin_'):
# exclude_list.append(name)
# write settings of aims output from the parsed mdin
for k,v in section.simpleValues.items():
if (k.startswith('x_amber_section_single_') or
k.startswith('x_amber_mdout_')):
if k in exclude_list and k not in include_list:
continue
# default writeout
else:
backend.superBackend.addValue(k, v[-1])
backend.superBackend.addValue(k, v[-1])
# if k in exclude_list and k not in include_list:
# continue
# # default writeout
# else:
# backend.superBackend.addValue(k, v[-1])
# get reference to current section_single_configuration_calculation if trajectory was found in there
if self.atompositions is not None:
self.trajRefSingleConfigurationCalculation = gIndex
print(self.atompositions)
self.atompositions = self.trajectory.iread()
section_frameseq_Dict = get_updateDictionary(self, 'frameseq')
section_singlecalc_Dict = get_updateDictionary(self, 'singleconfcalc')
section_frameseq_single_Dict = section_frameseq_Dict
section_frameseq_single_Dict.update(section_singlecalc_Dict)
updateDict = {
updateFrameDict = {
'startSection' : [
['section_single_configuration_calculation'],
['section_frame_sequence']],
'muteSections' : [['section_method']],
'dictionary' : section_frameseq_single_Dict
'dictionary' : section_frameseq_Dict
}
self.metaStorage.update(updateFrameDict)
section_singlevdw_Dict = get_updateDictionary(self, 'singlevdw')
updateDictVDW = {
'startSection' : [
['section_energy_van_der_Waals']],
#'muteSections' : [['section_method']],
'dictionary' : section_singlevdw_Dict
}
self.secVDWGIndex = backend.superBackend.openSection("section_energy_van_der_Waals")
self.metaStorage.update(updateDictVDW)
self.metaStorage.updateBackend(backend.superBackend,
startsection=['section_energy_van_der_Waals'],
autoopenclose=False)
backend.superBackend.closeSection("section_energy_van_der_Waals", self.secVDWGIndex)
section_singlecalc_Dict = get_updateDictionary(self, 'singleconfcalc')
updateDict = {
'startSection' : [
['section_single_configuration_calculation']],
#'muteSections' : [['section_method']],
'dictionary' : section_singlecalc_Dict
}
self.metaStorage.update(updateDict)
singleGIndex = backend.openSection("section_single_configuration_calculation")
self.metaStorage.updateBackend(backend,
#self.secSingleGIndex = backend.openSection("section_single_configuration_calculation")
self.metaStorage.updateBackend(backend.superBackend,
startsection=['section_single_configuration_calculation'],
autoopenclose=False)
backend.closeSection("section_single_configuration_calculation", singleGIndex)
#backend.closeSection("section_single_configuration_calculation", self.secSingleGIndex)
backend.superBackend.closeSection("section_single_configuration_calculation", self.secSingleGIndex)
def setStartingPointCalculation(self, parser):
backend = parser.backend
......@@ -560,8 +581,8 @@ class AMBERParser(AmberC.AMBERParserBase):
if self.MD is not True:
newLine = parser.fIn.readline()
lastLine = ' = '.join([ "%s" % str(line) for line in zip(lastLine, newLine)])
for cName in matchNameList:
key = metaNameStart + cName.lower().replace(" ", "").replace("-", "")
for cName, key in getDict_MetaStrInDict(matchNameDict).items():
#key = metaNameStart + cName.lower().replace(" ", "").replace("-", "")
reDict={key:value for value in
re.compile(r"(?:\s%s|^%s|,%s)\s*=\s*(?:'|\")?(?P<%s>[\-+0-9.a-zA-Z:]+)(?:'|\")?\s*,?"
% (cName, cName, cName, key)).findall(lastLine)}
......@@ -846,6 +867,8 @@ class AMBERParser(AmberC.AMBERParserBase):
startReStr=r"\s*(?:NSTEP\s*=|NSTEP\s*ENERGY\s*RMS\s*)",
# endReStr=r"\s*(?:FINAL\s*RESULTS|A\sV\sE\sR\sA\sG\sE\sS\s*O\sV\sE\sR)",
# sections=['x_amber_section_single_configuration_calculation'],
#sections = ['section_method','section_single_configuration_calculation'],
#sections=['section_single_configuration_calculation', 'section_system'],
forwardMatch=True,
subMatchers=[
# SM(startReStr=(r"\s*(?:" +
......@@ -893,10 +916,10 @@ class AMBERParser(AmberC.AMBERParserBase):
subFlags=SM.SubFlags.Unordered,
subMatchers=fileNameListGroupSubMatcher
), # END SectionMethod
SM(name='SectionTopology',
SM(name='SectionMethod',
startReStr=r"\s*Here\s*is\s*the\s*input\s*file:",
forwardMatch=True,
sections=['section_system'],
sections=['section_sampling_method'],
subMatchers=[
# parse verbatim writeout of mdin file
mdinSubMatcher,
......@@ -904,14 +927,13 @@ class AMBERParser(AmberC.AMBERParserBase):
parmSubMatcher,
# parse control settings writeout of Amber
mdoutSubMatcher
# parse geometry writeout of Amber
#geometryInSubMatcher
]), # END SectionMethod
SM(name='SingleConfigurationCalculationWithSystemDescription',
startReStr=r"\s*4\.\s*RESULTS",
endReStr=r"\s*(?:FINAL\s*RESULTS|A\sV\sE\sR\sA\sG\sE\sS\s*O\sV\sE\sR)",
#repeats=True,
forwardMatch=True,