From 8eae4ba58ad44cbe332cbcdd5f22975820a54d0f Mon Sep 17 00:00:00 2001
From: Berk Onat <b.onat@warwick.ac.uk>
Date: Fri, 30 Mar 2018 20:28:14 +0100
Subject: [PATCH] Fixed meta info update for input output files.
---
parser/parser-tinker/TINKERParser.py | 52 ++++++++++++----------------
1 file changed, 22 insertions(+), 30 deletions(-)
diff --git a/parser/parser-tinker/TINKERParser.py b/parser/parser-tinker/TINKERParser.py
index 4f943da..2df2403 100644
--- a/parser/parser-tinker/TINKERParser.py
+++ b/parser/parser-tinker/TINKERParser.py
@@ -278,7 +278,7 @@ class TINKERParser(SmartParser.ParserBase):
self.metaStorage.reset({'startSection' : [['section_run']]})
self.reset_values()
- def tinker_input_output_files(self, backend, gIndex, section):
+ def tinker_input_output_files(self, backend, gIndex, section, call_level):
"""Called with onClose_x_tinker_section_control_parameters to setup
topology and trajectory inputs/outputs
@@ -316,16 +316,6 @@ class TINKERParser(SmartParser.ParserBase):
#inputOK = self.findInputCmdFileAndRead(parser)
- section_control_Dict = {}
- section_control_Dict.update(self.cntrlDict)
- updateDict = {
- 'startSection' : [[PARSERTAG+'_section_control_parameters']],
- 'dictionary' : section_control_Dict
- }
- self.metaStorage.update(updateDict)
- self.metaStorage.updateBackend(backend.superBackend,
- startsection=[PARSERTAG+'_section_control_parameters'],
- autoopenclose=False)
# Here we update topology info
# Check if topology files can be loaded
@@ -404,16 +394,6 @@ class TINKERParser(SmartParser.ParserBase):
trajDone = True
self.newTraj = True
- if atLeastOneFileExist:
- updateDict = {
- 'startSection' : [[PARSERTAG+'_section_input_output_files']],
- 'dictionary' : self.fileDict
- }
- self.metaStorage.update(updateDict)
- self.metaStorage.updateBackend(backend.superBackend,
- startsection=[PARSERTAG+'_section_input_output_files'],
- autoopenclose=False)
-
if self.newTopo:
if topoDone and atLeastOneFileExist:
self.MDData.initializeTopologyFileHandlers(self)
@@ -453,6 +433,7 @@ class TINKERParser(SmartParser.ParserBase):
#self.MDcurrentstep = int(self.MDiter)
#self.stepcontrolDict.update({"MDcurrentstep" : int(self.MDcurrentstep)})
#pass
+ return atLeastOneFileExist
def onOpen_x_tinker_section_control_parameters(self, backend, gIndex, section):
# keep track of the latest section
@@ -460,6 +441,8 @@ class TINKERParser(SmartParser.ParserBase):
self.inputControlIndex = gIndex
def onClose_x_tinker_section_control_parameters(self, backend, gIndex, section):
+ # Find input and output files. Read input control parameters
+ atLeastOneFileExist = self.tinker_input_output_files(backend, gIndex, section, "control")
section_control_Dict = {}
section_control_Dict.update(self.mdcntrlDict)
section_control_Dict.update(self.filecntrlDict)
@@ -473,8 +456,17 @@ class TINKERParser(SmartParser.ParserBase):
startsection=[PARSERTAG+'_section_control_parameters'],
autoopenclose=False)
- # Find input and output files. Read input control parameters
- self.tinker_input_output_files(backend, gIndex, section)
+ #if atLeastOneFileExist:
+ # secIOGIndex = backend.openSection(PARSERTAG+'_section_input_output_files')
+ # updateFileDict = {
+ # 'startSection' : [[PARSERTAG+'_section_input_output_files']],
+ # 'dictionary' : self.fileDict
+ # }
+ # self.metaStorage.update(updateFileDict)
+ # self.metaStorage.updateBackend(backend.superBackend,
+ # startsection=[PARSERTAG+'_section_input_output_files'],
+ # autoopenclose=False)
+ # backend.closeSection(PARSERTAG+'_section_input_output_files', secIOGIndex)
# TINKER prints the initial and final energies to the log file.
if self.MDcurrentstep < 0:
@@ -912,7 +904,7 @@ class TINKERParser(SmartParser.ParserBase):
trajfile = filetrajs[self.MDcurrentstep]
if trajfile is not None:
rtn = setMetaStrInDict(self, 'filecntrlDict', 'archive file', trajfile)
- self.tinker_input_output_files(backend, gIndex, section)
+ self.tinker_input_output_files(backend, gIndex, section, "traj")
self.onOpen_section_system(backend, None, None)
self.onClose_section_system(backend, None, None)
@@ -1937,13 +1929,13 @@ class TINKERParser(SmartParser.ParserBase):
"tablestartsat" : r"\s*(?:QN|TN|CG|VM)\s*Iter",
"tableendsat" : r"^\s*$",
"lineFilter" : {
- 'QN Iter' : 'ITER',
- 'TN Iter' : 'ITER',
- 'VM Iter' : 'ITER',
- 'CG Iter' : 'ITER',
+ 'QN Iter' : 'ITER1',
+ 'TN Iter' : 'ITER2',
+ 'VM Iter' : 'ITER3',
+ 'CG Iter' : 'ITER4',
'F Value' : 'FVALUE',
- 'G RMS' : 'GRMS',
- 'RMS G' : 'GRMS',
+ 'G RMS' : 'GRMS1',
+ 'RMS G' : 'GRMS2',
'F Move' : 'FMove',
'X Move' : 'XMove',
'FG Call' : 'FGCall'
--
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