diff --git a/parser/parser-amber/AMBERCommon.py b/parser/parser-amber/AMBERCommon.py
index 37532a973a518a03ad01f4b7c569f48d58dd933f..ef9141fb201d34aae614b87ba116b908e415f6c3 100644
--- a/parser/parser-amber/AMBERCommon.py
+++ b/parser/parser-amber/AMBERCommon.py
@@ -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*",
diff --git a/parser/parser-amber/AMBERParser.py b/parser/parser-amber/AMBERParser.py
index 5ea9cae71ec223a556ac612156f356dd7fe25ff6..6730b734961ae9335070686a61d1ecbfa1fb70bb 100644
--- a/parser/parser-amber/AMBERParser.py
+++ b/parser/parser-amber/AMBERParser.py
@@ -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)
diff --git a/parser/parser-amber/MetaInfoStorage.py b/parser/parser-amber/MetaInfoStorage.py
index a7ffd62455f664170155088777ca393634f14cc5..b8504cf4785e03c4755782a18b9968cdd4643dbf 100644
--- a/parser/parser-amber/MetaInfoStorage.py
+++ b/parser/parser-amber/MetaInfoStorage.py
@@ -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)