def addTSsearch(jobGraph, rootDir, currentDir, baseData, initialGeom, index,
method, basis, gaussianFelxSele):
newNode = FDynamoNode("tsSearch.f90", currentDir)
newNode.verification = ["Opt", "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 1
newNode.templateKey = "QMMM_opt_mopac"
newNode.additionalKeywords = {"ts_search": "true"}
newNode.coordsIn = "coordsIn.crd"
gaussianTime = "72:00:00"
if not isdir(currentDir):
makedirs(currentDir)
saveCrdFromDCD(join(currentDir, "coordsIn.crd"), initialGeom)
newNode.coordsOut = "coordsDone.crd"
newNode.getCoordsFromParent = False
newNode.fDynamoPath = baseData["fDynamoPath"]
newNode.charge = baseData["charge"]
newNode.method = baseData["method"]
newNode.forceField = data["forceField"]
copyfile(join(baseData["filesDir"], baseData["forceField"]),
join(currentDir, newNode.forceField))
newNode.flexiblePart = data["flexiblePart"]
copyfile(join(baseData["filesDir"], baseData["flexiblePart"]),
join(currentDir, newNode.flexiblePart))
newNode.sequence = data["sequence"]
copyfile(join(baseData["filesDir"], baseData["sequence"]),
join(currentDir, newNode.sequence))
newNode.qmSele = data["qmSele"]
jobGraph.add_node(currentDir, data=newNode)
jobGraph.add_edge(rootDir, currentDir)
am1Dir = currentDir
########################################################
currentDir = join(currentDir, "ts_gaussian")
if not isdir(currentDir):
makedirs(currentDir)
newNode = FDynamoNode("tsSearch", currentDir)
newNode.verification = ["Opt", "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 1
newNode.templateKey = "QMMM_opt_gaussian"
newNode.fDynamoPath = "/net/people/plgglanow/fortranPackages/AMBER-g09/AMBER-dynamo/makefile"
newNode.additionalKeywords = {
"ts_search": "true",
"method": method,
"basis": basis,
"multiplicity": 1,
"otherOptions": ""
}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
newNode.flexiblePart = basename(gaussianFelxSele)
copyfile(gaussianFelxSele, join(currentDir, newNode.flexiblePart))
newNode.processors = 24
newNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
newNode.partition = "plgrid"
newNode.time = gaussianTime
jobGraph.add_node(currentDir, data=newNode)
jobGraph.add_edge(am1Dir, currentDir)
########################################################
newDir = join(am1Dir, "irc_reverse")
newNode = FDynamoNode("irc_reverse.f90", newDir)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_irc_mopac"
newNode.additionalKeywords = {"IRC_dir": "-1"}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
jobGraph.add_node(newDir, data=newNode)
jobGraph.add_edge(am1Dir, newDir)
########################################################
optDir = join(newDir, "opt")
newNode = FDynamoNode("opt.f90", optDir)
newNode.verification = ["Opt", "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 0
newNode.templateKey = "QMMM_opt_mopac"
newNode.additionalKeywords = {
"ts_search": "false",
"definedAtoms": baseData["definedAtoms"]
}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone" + str(index) + ".crd"
newNode.measureRCinOutput = True
jobGraph.add_node(optDir, data=newNode)
jobGraph.add_edge(newDir, optDir)
########################################################
optDirGaussian = join(newDir, "optGaussian")
if not isdir(optDirGaussian):
makedirs(optDirGaussian)
newNode = FDynamoNode("opt.f90", optDirGaussian)
newNode.verification = ["Opt", "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 0
newNode.templateKey = "QMMM_opt_gaussian"
newNode.fDynamoPath = "/net/people/plgglanow/fortranPackages/AMBER-g09/AMBER-dynamo/makefile"
newNode.additionalKeywords = {
"ts_search": "false",
"definedAtoms": baseData["definedAtoms"],
"method": method,
"basis": basis,
"multiplicity": 1,
"otherOptions": ""
}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone" + str(index) + ".crd"
newNode.flexiblePart = basename(gaussianFelxSele)
copyfile(gaussianFelxSele, join(optDirGaussian, newNode.flexiblePart))
newNode.measureRCinOutput = True
newNode.processors = 24
newNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
newNode.partition = "plgrid"
newNode.time = gaussianTime
jobGraph.add_node(optDirGaussian, data=newNode)
jobGraph.add_edge(optDir, optDirGaussian)
########################################################
newDir = join(am1Dir, "irc_forward")
newNode = FDynamoNode("irc_forward.f90", newDir)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_irc_mopac"
newNode.additionalKeywords = {"IRC_dir": "1"}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
jobGraph.add_node(newDir, data=newNode)
jobGraph.add_edge(am1Dir, newDir)
########################################################
optDir = join(newDir, "opt")
newNode = FDynamoNode("opt.f90", optDir)
newNode.verification = ["Opt", "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 0
newNode.templateKey = "QMMM_opt_mopac"
newNode.additionalKeywords = {
"ts_search": "false",
"definedAtoms": baseData["definedAtoms"]
}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone" + str(index) + ".crd"
newNode.measureRCinOutput = True
jobGraph.add_node(optDir, data=newNode)
jobGraph.add_edge(newDir, optDir)
########################################################
optDirGaussian = join(optDir, "optGaussian")
if not isdir(optDirGaussian):
makedirs(optDirGaussian)
newNode = FDynamoNode("opt.f90", optDirGaussian)
newNode.verification = ["Opt", "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 0
newNode.templateKey = "QMMM_opt_gaussian"
newNode.fDynamoPath = "/net/people/plgglanow/fortranPackages/AMBER-g09/AMBER-dynamo/makefile"
newNode.additionalKeywords = {
"ts_search": "false",
"definedAtoms": baseData["definedAtoms"],
"method": method,
"basis": basis,
"multiplicity": 1,
"otherOptions": ""
}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone" + str(index) + ".crd"
newNode.measureRCinOutput = True
newNode.processors = 24
newNode.flexiblePart = basename(gaussianFelxSele)
copyfile(gaussianFelxSele, join(optDirGaussian, newNode.flexiblePart))
newNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
newNode.partition = "plgrid"
newNode.time = gaussianTime
jobGraph.add_node(optDirGaussian, data=newNode)
jobGraph.add_edge(optDir, optDirGaussian)
def addTSsearch (jobGraph, rootDir, currentDir, baseData, initialGeom, index):
newNode = FDynamoNode("tsSearch.f90", currentDir)
newNode.verification = ["Opt" , "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 1
newNode.templateKey = "QMMM_opt_mopac"
newNode.additionalKeywords = { "ts_search" : "true" }
newNode.coordsIn = "coordsIn.crd"
makedirs(currentDir)
saveCrdFromDCD( join(currentDir, "coordsIn.crd"), initialGeom )
newNode.coordsOut = "coordsDone.crd"
newNode.getCoordsFromParent = False
newNode.fDynamoPath = baseData["fDynamoPath"]
newNode.charge = baseData["charge"]
newNode.method = baseData["method"]
newNode.forceField = data["forceField"]
copyfile( join(baseData["filesDir"], baseData["forceField"]), join(currentDir, newNode.forceField) )
newNode.flexiblePart = data["flexiblePart"]
copyfile( join(baseData["filesDir"], baseData["flexiblePart"]), join(currentDir, newNode.flexiblePart) )
newNode.sequence = data["sequence"]
copyfile( join(baseData["filesDir"], baseData["sequence"]), join(currentDir, newNode.sequence) )
newNode.qmSele = data["qmSele"]
jobGraph.add_node(currentDir, data = newNode)
jobGraph.add_edge(rootDir, currentDir)
newDir = join(currentDir, "irc_reverse")
newNode = FDynamoNode("irc_reverse.f90", newDir)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_irc_mopac"
newNode.additionalKeywords = { "IRC_dir" : "-1" }
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
jobGraph.add_node(newDir, data = newNode)
jobGraph.add_edge(currentDir, newDir)
optDir = join(newDir, "opt")
newNode = FDynamoNode("opt.f90", optDir)
newNode.verification = ["Opt", "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 0
newNode.templateKey = "QMMM_opt_mopac"
newNode.additionalKeywords = { "ts_search" : "false" , "definedAtoms" : baseData["definedAtoms"]}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone"+str(index)+".crd"
newNode.measureRCinOutput = True
jobGraph.add_node(optDir, data = newNode)
jobGraph.add_edge( newDir, optDir)
newDir = join(currentDir, "irc_forward")
newNode = FDynamoNode("irc_forward.f90", newDir)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_irc_mopac"
newNode.additionalKeywords = { "IRC_dir" : "1" }
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
jobGraph.add_node(newDir, data = newNode)
jobGraph.add_edge(currentDir, newDir)
optDir = join(newDir, "opt")
newNode = FDynamoNode("opt.f90", optDir)
newNode.verification = ["Opt", "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 0
newNode.templateKey = "QMMM_opt_mopac"
newNode.additionalKeywords = { "ts_search" : "false" , "definedAtoms" : baseData["definedAtoms"]}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone"+str(index)+".crd"
newNode.measureRCinOutput = True
jobGraph.add_node(optDir, data = newNode)
jobGraph.add_edge( newDir, optDir)
if len(sys.argv) < 4:
print("Usage: graphTSsearchWHAM wham.log/RC compileScanScript.sh numberOfTS2find addName")
else:
whamLog = sys.argv[1]
compileScript = sys.argv[2]
TSno = int(sys.argv[3])
addName = ""
if len(sys.argv) > 4:
addName = sys.argv[4]
if isfile(whamLog):
tsReactionCoord = getTScoords(whamLog)
else:
tsReactionCoord = float(whamLog)
print("Found reaction coordinate: ", tsReactionCoord)
data = parseFDynamoCompileScript(compileScript)
definedAtoms = data["definedAtoms"]
atoms = atomsFromAtomSelection( definedAtoms)
currentDir = abspath(dirname(compileScript))
graphDir = join( getcwd(), "multiTSsearch"+addName )
sm = GraphManager()
graph = sm.isGraphHere(graphDir)
if not graph:
newGraph = jobGraph = buildGraph(tsReactionCoord, atoms, graphDir, data, currentDir, TSno)
result = sm.addGraph(newGraph, graphDir)
if result:
sm.buildGraphDirectories(newGraph)
sm.saveGraphs()
print("Created new graph")
else:
print("Cannot create more than one graph in the same directory")