def buildGraph(whamLog, compileScript, method, basis, structures, sourceDir, graphDir, dftTime, minRC, maxRC):
jobGraph = nx.DiGraph()
# currentDir = getcwd()
data = parseFDynamoCompileScript(compileScript)
definedAtoms = data["definedAtoms"]
gaussianFlexibleSele = rewriteFlexibleSeleFile( join(sourceDir, data["flexiblePart"]) )
########## ROOT NODE ###########################
rootNode = FDynamoNode(None, graphDir)
rootNode.status = "finished"
if not isdir(graphDir):
makedirs(graphDir)
rootNode.fDynamoPath = data["fDynamoPath"]
rootNode.charge = data["charge"]
rootNode.method = data["method"]
rootNode.forceField = data["forceField"]
copyfile( join(sourceDir, data["forceField"]), join(graphDir, rootNode.forceField) )
rootNode.flexiblePart = data["flexiblePart"]
copyfile( join(sourceDir, data["flexiblePart"]), join(graphDir, rootNode.flexiblePart) )
rootNode.sequence = data["sequence"]
copyfile( join(sourceDir, data["sequence"]), join(graphDir, rootNode.sequence) )
rootNode.qmSele = data["qmSele"]
rootNode.additionalKeywords["definedAtoms"] = definedAtoms
jobGraph.add_node(graphDir, data = rootNode)
########### SPLINE NODE ####################
splineDir = join( graphDir, "spline" )
splineNode = SplineNode(None, splineDir, whamLog )
jobGraph.add_node( splineDir, data= splineNode )
################## SP DFT + SP SEMIEMPIRICAL #####################################
RCstructList = []
for struct in structures:
RC = rootNode.measureRC(struct)
print(struct, RC)
if RC < minRC or RC > maxRC:
continue
RCstructList.append( (RC, struct) )
RCstructList.sort()
for i, rcStruct in enumerate(RCstructList):
struct = rcStruct[1]
dirNo = str(i)
dirname = join( graphDir, dirNo )
dftDir = join(dirname, method)
semiEmpDir = join(dirname, data["method"])
if not isdir(dftDir):
makedirs(dftDir)
if not isdir(semiEmpDir):
makedirs(semiEmpDir)
dftNode = FDynamoNode("DFT-SP-"+dirNo, dftDir)
dftNode.verification = ["SP"]
dftNode.templateKey = "QMMM_sp_gaussian"
dftNode.fDynamoPath = "/net/people/plgglanow/fortranPackages/AMBER-g09/AMBER-dynamo/makefile"
# if structNo >= 35:
# dftNode.additionalKeywords = { "method" : method, "basis" : basis , "multiplicity" : 1 , "definedAtoms" : data["definedAtoms"] , "otherOptions" : "SCF=(QC,direct,conver=6)" }
# else:
dftNode.additionalKeywords = { "method" : method, "basis" : basis , "multiplicity" : 1 , "definedAtoms" : data["definedAtoms"] , "otherOptions" : "SCF=(direct)" }
# dftNode.additionalKeywords = { "method" : method, "basis" : basis , "multiplicity" : 1 , "definedAtoms" : data["definedAtoms"] , "otherOptions" : "SCF=direct" }
dftNode.coordsIn = "coordsStart.crd"
copyfile(struct, join( dftNode.path, dftNode.coordsIn ))
dftNode.coordsOut = "coordsDone.crd"
dftNode.flexiblePart = basename(gaussianFlexibleSele)
copyfile( gaussianFlexibleSele, join(dftDir, dftNode.flexiblePart) )
dftNode.processors = 24
dftNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
dftNode.partition = "plgrid"
dftNode.time = dftTime
dftNode.getCoordsFromParent = False
jobGraph.add_node(dftDir, data = dftNode)
jobGraph.add_edge(graphDir, dftDir)
semiNode = FDynamoNode("SemiEmp-SP-"+dirNo, semiEmpDir)
semiNode.verification = ["SP"]
semiNode.templateKey = "QMMM_sp"
semiNode.coordsIn = "coordsStart.crd"
semiNode.coordsOut = "coordsDone.crd"
copyfile(struct, join( semiNode.path, semiNode.coordsIn ))
semiNode.partition = "plgrid-short"
semiNode.time = "0:10:00"
semiNode.getCoordsFromParent = False
jobGraph.add_node(semiEmpDir, data = semiNode)
jobGraph.add_edge( graphDir, semiEmpDir )
splineDiff = SplineDiffNode("diff", dirname)
jobGraph.add_node(dirname, data = splineDiff)
jobGraph.add_edge( dftDir, dirname )
jobGraph.add_edge( semiEmpDir, dirname )
jobGraph.add_edge( dirname, splineDir )
return jobGraph
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")