Commit 0e6743c8 authored by Berk Onat's avatar Berk Onat
Browse files

Removed unnecessary comments in SMs

parent b23cc99a
...@@ -200,9 +200,9 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -200,9 +200,9 @@ class AMBERParser(AmberC.AMBERParserBase):
for fileItem in self.fileDict: for fileItem in self.fileDict:
if (self.fileDict[fileItem].fileSupplied and if (self.fileDict[fileItem].fileSupplied and
self.fileDict[fileItem].activeInfo): self.fileDict[fileItem].activeInfo):
# First check topology file # First, check topology file
topoformat = self.topologyFileHandler(fileItem) topoformat = self.topologyFileHandler(fileItem)
# Second check trajectory file # Second, check trajectory file
trajformat = self.trajectoryFileHandler(fileItem, topoformat) trajformat = self.trajectoryFileHandler(fileItem, topoformat)
if self.topology: if self.topology:
self.topologyTable, self.topologyBonds = self.topology.to_dataframe() self.topologyTable, self.topologyBonds = self.topology.to_dataframe()
...@@ -467,7 +467,6 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -467,7 +467,6 @@ class AMBERParser(AmberC.AMBERParserBase):
section_sampling_Dict = get_updateDictionary(self, 'sampling') section_sampling_Dict = get_updateDictionary(self, 'sampling')
updateDict = { updateDict = {
'startSection' : [['section_sampling_method']], 'startSection' : [['section_sampling_method']],
#'muteSections' : [['section_system']],
'dictionary' : section_sampling_Dict 'dictionary' : section_sampling_Dict
} }
#self.secSamplingGIndex = backend.openSection("section_sampling_method") #self.secSamplingGIndex = backend.openSection("section_sampling_method")
...@@ -492,7 +491,6 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -492,7 +491,6 @@ class AMBERParser(AmberC.AMBERParserBase):
'startSection' : [ 'startSection' : [
['section_topology']], ['section_topology']],
'muteSections' : [['section_sampling_method']], 'muteSections' : [['section_sampling_method']],
#'muteSections' : [['section_method']],
'dictionary' : section_topology_Dict 'dictionary' : section_topology_Dict
} }
self.metaStorage.update(updateDict) self.metaStorage.update(updateDict)
...@@ -604,7 +602,6 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -604,7 +602,6 @@ class AMBERParser(AmberC.AMBERParserBase):
'startSection' : [ 'startSection' : [
['section_energy_van_der_Waals']], ['section_energy_van_der_Waals']],
'muteSections' : [['section_sampling_method']], 'muteSections' : [['section_sampling_method']],
#'muteSections' : [['section_method']],
'dictionary' : section_singlevdw_Dict 'dictionary' : section_singlevdw_Dict
} }
self.secVDWGIndex = backend.superBackend.openSection("section_energy_van_der_Waals") self.secVDWGIndex = backend.superBackend.openSection("section_energy_van_der_Waals")
...@@ -618,7 +615,6 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -618,7 +615,6 @@ class AMBERParser(AmberC.AMBERParserBase):
'startSection' : [ 'startSection' : [
['section_single_configuration_calculation']], ['section_single_configuration_calculation']],
'muteSections' : [['section_sampling_method']], 'muteSections' : [['section_sampling_method']],
#'muteSections' : [['section_method']],
'dictionary' : section_singlecalc_Dict 'dictionary' : section_singlecalc_Dict
} }
self.metaStorage.update(updateDict) self.metaStorage.update(updateDict)
...@@ -905,7 +901,7 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -905,7 +901,7 @@ class AMBERParser(AmberC.AMBERParserBase):
startReStr=r"\s*--{5}--*\s*|\s*Flags:", startReStr=r"\s*--{5}--*\s*|\s*Flags:",
endReStr=r"\s*--{5}--*\s*2\.\s*CONTROL\s*", endReStr=r"\s*--{5}--*\s*2\.\s*CONTROL\s*",
forwardMatch=True, forwardMatch=True,
# subFlags=SM.SubFlags.Unordered, #subFlags=SM.SubFlags.Unordered,
subMatchers=[ subMatchers=[
SM(r"\|\s*Flags\s*:\s*(?P<x_amber_parm_flags>[0-9a-zA-Z]+)?\s*$"), SM(r"\|\s*Flags\s*:\s*(?P<x_amber_parm_flags>[0-9a-zA-Z]+)?\s*$"),
SM(r"\s*getting\s*new\s*box\s*info\s*from\s*(?:bottom\s*of\s*|netcdf)(?P<x_amber_mdin_finline>[0-9a-zA-Z]+)\s*(file)?\s*", SM(r"\s*getting\s*new\s*box\s*info\s*from\s*(?:bottom\s*of\s*|netcdf)(?P<x_amber_mdin_finline>[0-9a-zA-Z]+)\s*(file)?\s*",
...@@ -932,7 +928,7 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -932,7 +928,7 @@ class AMBERParser(AmberC.AMBERParserBase):
mdoutSubMatcher = SM(name='mdoutKeywords', mdoutSubMatcher = SM(name='mdoutKeywords',
startReStr=r"\s*General\s*flags:", startReStr=r"\s*General\s*flags:",
forwardMatch=True, forwardMatch=True,
# subFlags=SM.SubFlags.Unordered, #subFlags=SM.SubFlags.Unordered,
subMatchers=mdoutKeywordsSimpleMatchers subMatchers=mdoutKeywordsSimpleMatchers
) )
...@@ -940,20 +936,15 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -940,20 +936,15 @@ class AMBERParser(AmberC.AMBERParserBase):
# submatcher for MD # submatcher for MD
mddataNameList=getList_MetaStrInDict(self.mddataDict) mddataNameList=getList_MetaStrInDict(self.mddataDict)
MDSubMatcher = SM(name='MDStep', MDSubMatcher = SM(name='MDStep',
# startReStr=r"\s*(?:NSTEP\s*=|NSTEP\s*ENERGY\s*RMS)",
startReStr=r"\s*(?:NSTEP\s*=|NSTEP\s*ENERGY\s*RMS\s*)", 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)", #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, forwardMatch=True,
subMatchers=[ subMatchers=[
# SM(startReStr=(r"\s*(?:" +
SM(startReStr=(r"\s*(?:(?:" + SM(startReStr=(r"\s*(?:(?:" +
'|'.join(["%s" % (cName) for cName in mddataNameList]) + '|'.join(["%s" % (cName) for cName in mddataNameList]) +
"AMBER)\s*=\s*|NSTEP\s*ENERGY\s*RMS\s*)(?:'|\")?" + "AMBER)\s*=\s*|NSTEP\s*ENERGY\s*RMS\s*)(?:'|\")?" +
"(?P<x_amber_mdin_finline>[\-+0-9.:a-zA-Z]+)(?:'|\")?\s*,?"), "(?P<x_amber_mdin_finline>[\-+0-9.:a-zA-Z]+)(?:'|\")?\s*,?"),
# endReStr=r"\s*(?:FINAL\s*RESULTS|A\sV\sE\sR\sA\sG\sE\sS\s*O\sV\sE\sR)", #endReStr=r"\s*(?:FINAL\s*RESULTS|A\sV\sE\sR\sA\sG\sE\sS\s*O\sV\sE\sR)",
coverageIgnore=True, coverageIgnore=True,
adHoc=lambda p: adHoc=lambda p:
self.adHoc_read_namelist_stop_parsing(p, self.adHoc_read_namelist_stop_parsing(p,
...@@ -965,7 +956,6 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -965,7 +956,6 @@ class AMBERParser(AmberC.AMBERParserBase):
onlyCaseSensitive=True, onlyCaseSensitive=True,
stopOnFirstLine=False) stopOnFirstLine=False)
) )
#geometryMDSubMatcher
]) ])
######################################## ########################################
...@@ -1008,19 +998,14 @@ class AMBERParser(AmberC.AMBERParserBase): ...@@ -1008,19 +998,14 @@ class AMBERParser(AmberC.AMBERParserBase):
SM(name='SingleConfigurationCalculationWithSystemDescription', SM(name='SingleConfigurationCalculationWithSystemDescription',
startReStr=r"\s*4\.\s*RESULTS", 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)", endReStr=r"\s*(?:FINAL\s*RESULTS|A\sV\sE\sR\sA\sG\sE\sS\s*O\sV\sE\sR)",
#repeats=True,
forwardMatch=True, forwardMatch=True,
#sections=['section_single_configuration_calculation'],
subMatchers=[ subMatchers=[
# the actual section for a single configuration calculation starts here # the actual section for a single configuration calculation starts here
SM(name='SingleConfigurationCalculation', SM(name='SingleConfigurationCalculation',
startReStr=r"\s*(?:NSTEP\s*=|NSTEP\s*ENERGY\s*RMS\s*)", 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)", #endReStr=r"\s*(?:FINAL\s*RESULTS|A\sV\sE\sR\sA\sG\sE\sS\s*O\sV\sE\sR)",
repeats=True, repeats=True,
forwardMatch=True, forwardMatch=True,
#sections=['section_system', 'section_single_configuration_calculation'],
#sections = ['section_method','section_single_configuration_calculation'],
#sections=['section_single_configuration_calculation', 'section_system'],
sections=['section_single_configuration_calculation'], sections=['section_single_configuration_calculation'],
subMatchers=[ subMatchers=[
# MD # MD
......
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