Commit b23cc99a authored by Berk Onat's avatar Berk Onat
Browse files

Clean codes from unnecessary comments

parent 1f01ce9e
......@@ -132,12 +132,6 @@ class AMBERParserBase(object):
self.extraDict = get_nameListDict('extra')
self.parserInfo = PARSER_INFO_DEFAULT.copy()
self.metaInfoEnv = get_metaInfo(self)
# self.cachingLevelForMetaName = {
# 'x_amber_trajectory_file_detect': CachingLevel.Cache,
# 'x_amber_geometry_optimization_cdetect': CachingLevel.Cache,
# 'x_amber_section_MD_detect': CachingLevel.Ignore,
# 'x_amber_single_configuration_calculation_detect': CachingLevel.Cache,
# }
self.coverageIgnoreList = [
# ignore empty lines
r"\s*",
......
......@@ -207,7 +207,6 @@ class AMBERParser(AmberC.AMBERParserBase):
if self.topology:
self.topologyTable, self.topologyBonds = self.topology.to_dataframe()
self.topologyDict = self.topologyTable.to_dict(orient='list')
#print(self.atompositions)
self.topologyFormat = topoformat
self.trajectoryFormat = trajformat
#if trajformat or topoformat:
......@@ -397,9 +396,6 @@ class AMBERParser(AmberC.AMBERParserBase):
# write trajectory
#valuesDict = section.simpleValues
# samplingGIndex = backend.openSection("section_sampling_method")
# backend.addValue("sampling_method", sampling_method)
# backend.closeSection("section_sampling_method", samplingGIndex)
frameSequenceGIndex = backend.openSection("section_frame_sequence")
self.metaStorage.updateBackend(backend,
startsection=['section_frame_sequence'],
......@@ -436,7 +432,6 @@ class AMBERParser(AmberC.AMBERParserBase):
if self.fileDict[k].activeInfo:
self.fileDict[k].value = v[-1]
atLeastOneFileExist = True
#backend.superBackend.addValue(k, v[-1])
if atLeastOneFileExist:
self.initializeFileHandlers()
......@@ -457,7 +452,6 @@ class AMBERParser(AmberC.AMBERParserBase):
"""Trigger called when section_method is closed.
"""
# input method
#if gIndex == self.inputMethodIndex:
pass
def onOpen_section_sampling_method(self, backend, gIndex, section):
......@@ -628,11 +622,9 @@ class AMBERParser(AmberC.AMBERParserBase):
'dictionary' : section_singlecalc_Dict
}
self.metaStorage.update(updateDict)
#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", self.secSingleGIndex)
self.onOpen_section_system(backend, None, None)
self.onClose_section_system(backend, None, None)
backend.superBackend.closeSection("section_single_configuration_calculation", self.secSingleGIndex)
......@@ -689,7 +681,6 @@ class AMBERParser(AmberC.AMBERParserBase):
newLine = parser.fIn.readline()
lastLine = ' = '.join([ "%s" % str(line) for line in zip(lastLine, newLine)])
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)}
......@@ -705,13 +696,10 @@ class AMBERParser(AmberC.AMBERParserBase):
else:
matchNameDict[k].value=v
matchNameDict[k].activeInfo=True
#parser.backend.addValue(k, v)
return False
def adHoc_read_namelist_stop_parsing(self, parser, stopOnMatchStr, quitOnMatchStr,
metaNameStart, matchNameList, matchNameDict, onlyCaseSensitive, stopOnFirstLine):
# currentContext = parser.context[len(parser.context) - 1]
# currentMatcherId = currentContext.compiledMatcher.matcher.index.
lastLine = parser.fIn.fInLine
self.firstLine = 0
# Check the captured line has Fortran namelist variables and store them.
......@@ -726,10 +714,7 @@ class AMBERParser(AmberC.AMBERParserBase):
matchNameDict, onlyCaseSensitive,
stopOnFirstLine) is not True:
while True:
# lastLine = parser.fIn.readline()
lastLine = self.peekline(parser)
# self.lastfInLine = lastLine
# self.lastfInMatcher = currentMatcherId
self.firstLine += 1
if not lastLine:
break
......@@ -951,21 +936,6 @@ class AMBERParser(AmberC.AMBERParserBase):
subMatchers=mdoutKeywordsSimpleMatchers
)
########################################
# subMatcher for MD geometry that was used for the finished SCF cycle (see word 'preceding' in the description)
#geometryMDSubMatcher = SM (name = 'GeometryMD',
# startReStr = r"\s*(?:A|Final a)tomic structure \(and velocities\) as used in the preceding time step:",
# sections = ['section_system'],
# subMatchers = [
# SM (r"\s*x \[A\]\s*y \[A\]\s*z \[A\]\s*Atom"),
# SM (startReStr = r"\s*atom\s+(?P<x_fhi_aims_geometry_atom_positions_x__angstrom>[-+0-9.]+)\s+(?P<x_fhi_aims_geometry_atom_positions_y__angstrom>[-+0-9.]+)\s+(?P<x_fhi_aims_geometry_atom_positions_z__angstrom>[-+0-9.]+)\s+(?P<x_fhi_aims_geometry_atom_labels>[a-zA-Z]+)",
# repeats = True,
# subMatchers = [
# SM (r"\s*velocity\s+(?P<x_fhi_aims_geometry_atom_velocity_x__angstrom_ps_1>[-+0-9.]+)\s+(?P<x_fhi_aims_geometry_atom_velocity_y__angstrom_ps_1>[-+0-9.]+)\s+(?P<x_fhi_aims_geometry_atom_velocity_z__angstrom_ps_1>[-+0-9.]+)")
# ])
# ])
########################################
# submatcher for MD
mddataNameList=getList_MetaStrInDict(self.mddataDict)
......
......@@ -249,12 +249,6 @@ class Container(object):
elif "subfunction" in item:
subfunc = item.subfunction
storeValue, updateValue, item = subfunc(item)
#subfunc = item.functionbase
#storeValue, updateValue, item = eval(item.subfunction % item,
# globals(),
# #subfunc.__class__().__dict__
# {k: getattr(subfunc.__class__(), k) for k in dir(subfunc.__class__())}
# )
elif "value" in item:
updateValue = item['value']
if "postfunction" in item:
......@@ -655,9 +649,6 @@ class JsonMetaInfo(object):
if itemname not in nameList:
nameList.append(itemname)
for name in searchList:
#if (('section' in name or
# 'settings' in name or
# 'configuration_core' in name) and
if (set([name]) not in set(nameList) and
self.isparent(name)):
siblings.append(name)
......@@ -728,7 +719,7 @@ if __name__ == "__main__":
for container in run.Containers:
if 'section_topology' in container.Name:
select = container
#select.Color = 4
select.Color = 4
#select.PrintOnlyActive = 1
run.PrintOnlyNames = 1
print(run)
......
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