def generateTSsearchDynamo(compFile):
jobGraph = nx.DiGraph()
currentDir = getcwd()
data = parseFDynamoCompileScript(compFile)
newNode = FDynamoNode(data["inputFile"], currentDir)
newNode.coordsIn = data["coordsIn"]
newNode.coordsOut = data["coordsOut"]
newNode.verification = ["Opt", "Freq"]
newNode.slurmFile = None
newNode.autorestart = False
newNode.noOfExcpectedImaginaryFrequetions = 1
newNode.forceField = data["forceField"]
newNode.flexiblePart = data["flexiblePart"]
newNode.sequence = data["sequence"]
newNode.qmSele = data["qmSele"]
newNode.fDynamoPath = data["fDynamoPath"]
newNode.charge = data["charge"]
newNode.method = data["method"]
newNode.additionalKeywords = {"ts_search": "true"}
jobGraph.add_node(currentDir, data=newNode)
# newNode.compileInput()
return buildTSsearchGraphDynamo(jobGraph, currentDir)
def extendDynamoPMF(compFile, jobGraph, currentDir):
startDir = currentDir
data = parseFDynamoCompileScript(compFile)
definedAtoms = data["definedAtoms"]
constraints = data["constraints"]
####################### SCAN FROM TS #########################
scanSteps = 40
reverseScan = join(startDir, "TS1reverseScan")
forwardScan = join(startDir, "TS1forwardScan")
pmfDir = join(startDir, "PMF")
if not reverseScan in jobGraph.nodes:
print("Cannot find directory:")
print(reverseScan)
return jobGraph
if not forwardScan in jobGraph.nodes:
print("Cannot find directory:")
print(forwardScan)
return jobGraph
for crd in glob(join(reverseScan, "seed.-*")):
if "pdb" in crd:
continue
i = int(basename(crd).replace("seed.-", ""))
stepDir = join(pmfDir, "pmfRev" + str(i))
if stepDir in jobGraph.nodes:
continue
else:
print("New PMF step: ", stepDir)
newNode = FDynamoNode("pmfStep.f90", stepDir)
newNode.verification = ["SP"]
newNode.partition = "plgrid"
newNode.time = "72:00:00"
newNode.templateKey = "QMMM_pmf"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = {
"coordScanStart": "",
"definedAtoms": definedAtoms,
"constraints": constraints
}
newNode.coordsIn = "seed.-" + str(i)
newNode.anotherCoordsSource = "seed.-" + str(i)
jobGraph.add_node(stepDir, data=newNode)
jobGraph.add_edge(reverseScan, stepDir)
for crd in glob(join(forwardScan, "seed.+*")):
if "pdb" in crd:
continue
i = int(basename(crd).replace("seed.+", ""))
if i == 0:
continue
stepDir = join(pmfDir, "pmfForw" + str(i))
if stepDir in jobGraph.nodes:
continue
else:
print("New PMF step: ", stepDir)
newNode = FDynamoNode("pmfStep.f90", stepDir)
newNode.verification = ["SP"]
newNode.partition = "plgrid"
newNode.time = "72:00:00"
newNode.templateKey = "QMMM_pmf"
newNode.readInitialScanCoord = True
newNode.anotherCoordsSource = "seed.+" + str(i)
newNode.additionalKeywords = {
"coordScanStart": "",
"definedAtoms": definedAtoms,
"constraints": constraints
}
newNode.coordsIn = "seed.+" + str(i)
jobGraph.add_node(stepDir, data=newNode)
jobGraph.add_edge(forwardScan, stepDir)
return jobGraph
whamLog = sys.argv[1]
compileScript = sys.argv[2]
TSno = int(sys.argv[3])
method = sys.argv[4]
basis = sys.argv[5]
additionalName = ""
if len(sys.argv) == 7:
additionalName = sys.argv[6]
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-" + method + additionalName)
sm = GraphManager()
graph = sm.isGraphHere(graphDir)
if not graph:
newGraph = jobGraph = buildGraph(tsReactionCoord, atoms, graphDir,
data, currentDir, TSno, method,
basis)
result = sm.addGraph(newGraph, graphDir)
def generateTSsearchDynamoPMF(compFile):
jobGraph = nx.DiGraph()
currentDir = getcwd()
rootDir = currentDir
data = parseFDynamoCompileScript(compFile)
scanLen = "73"
########## INITIAL SCAN ###########################
definedAtoms = data["definedAtoms"]
constraints = data["constraints"]
newNode = FDynamoNode(data["inputFile"], currentDir)
newNode.coordsIn = data["coordsIn"]
newNode.coordsOut = "seed.+"+scanLen
newNode.verification = [ "SP" ]
newNode.slurmFile = None
newNode.autorestart = False
newNode.readInitialScanCoord = True
# newNode.noOfExcpectedImaginaryFrequetions = 1
newNode.forceField = data["forceField"]
newNode.flexiblePart = data["flexiblePart"]
newNode.sequence = data["sequence"]
newNode.qmSele = data["qmSele"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.fDynamoPath = data["fDynamoPath"]
newNode.charge = data["charge"]
newNode.method = data["method"]
newNode.additionalKeywords = { "scanDir" : "+", "coordScanStart" : "" , "gradientTolerance" : "1.0",
"iterNo" : scanLen, "definedAtoms" : definedAtoms, "constraints" : constraints }
jobGraph.add_node( currentDir , data = newNode )
newNode.generateInput()
# newNode.compileInput()
iterNo = 7
forwardScan = currentDir
for i in range(iterNo):
#opt i
iOptDir = join(rootDir, "optI_"+str(i))
newNode = FDynamoNode("optStep.f90", iOptDir)
newNode.verification = ["Opt"]
newNode.partition = "plgrid-short"
newNode.time = "1:00:00"
newNode.templateKey = "QMMM_opt_mopac_no_hess"
newNode.coordsIn = "coordsIn.crd"
newNode.coordsOut = "coordsOut.crd"
newNode.additionalKeywords = { "gradientTolerance" : "0.1"}
jobGraph.add_node(iOptDir, data = newNode)
jobGraph.add_edge( forwardScan, iOptDir)
#scan back
reverseScan = join(rootDir, "reverseScan_"+str(i))
newNode = FDynamoNode("scan.f90", reverseScan)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = { "scanDir" : "-", "coordScanStart" : "" , "gradientTolerance" : "1.0",
"iterNo" : scanLen, "definedAtoms" : definedAtoms, "constraints" : constraints}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "seed.-"+scanLen
jobGraph.add_node(reverseScan, data = newNode)
jobGraph.add_edge( iOptDir, reverseScan)
#opt s
sOptDir = join(rootDir, "optS_"+str(i))
newNode = FDynamoNode("optStep.f90", sOptDir)
newNode.verification = ["Opt"]
newNode.partition = "plgrid-short"
newNode.time = "1:00:00"
newNode.templateKey = "QMMM_opt_mopac_no_hess"
newNode.coordsIn = "coordsIn.crd"
newNode.coordsOut = "coordsOut.crd"
newNode.additionalKeywords = { "gradientTolerance" : "0.1"}
jobGraph.add_node(sOptDir, data = newNode)
jobGraph.add_edge( reverseScan, sOptDir)
if i == iterNo -1:
break
#scan to I
forwardScan = join(rootDir, "forwardScan_"+str(i))
newNode = FDynamoNode("scan.f90", forwardScan)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = { "scanDir" : "+", "coordScanStart" : "" , "gradientTolerance" : "1.0",
"iterNo" : scanLen, "definedAtoms" : definedAtoms, "constraints" : constraints}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "seed.+"+scanLen
jobGraph.add_node(forwardScan, data = newNode)
jobGraph.add_edge( sOptDir, forwardScan)
return jobGraph
def generateGraph(topologyFile, forcefield, compileScript, coordinates):
jobGraph = nx.DiGraph()
rootDir = getcwd()
notSolventNo = getNumberOfNotSolventRes(topologyFile)
data = parseFDynamoCompileScript(compileScript)
newNode = JobNode(None, rootDir)
newNode.status = "finished"
jobGraph.add_node(rootDir, data = newNode)
for crd in coordinates:
coolDirName = join( rootDir, basename(crd).replace(".", "_") )
makedirs(coolDirName)
copyfile( join( rootDir, basename(topologyFile) ), join(coolDirName, basename(topologyFile)) )
move( join( rootDir, basename(crd) ), join(coolDirName, basename(crd)) )
coolNode = AmberNode("amber.slurm", coolDirName, coolDirName, basename(topologyFile), basename(crd))
coolNode.runType = "standardCooling"
coolNode.time = "1:00:00"
coolNode.partition = "plgrid-short"
coolNode.processors = 8
jobGraph.add_node( coolDirName, data = coolNode )
jobGraph.add_edge(rootDir, coolDirName)
optimDir = join( coolDirName, "MM_opt")
optimNode = AmberNode("amber.slurm", optimDir, optimDir, topologyFile)
optimNode.NoSolventResidues = notSolventNo
optimNode.runType = "standardOptimization"
optimNode.time = "1:00:00"
optimNode.partition = "plgrid-short"
jobGraph.add_node( optimDir, data = optimNode )
jobGraph.add_edge( coolDirName, optimDir)
qmmmSetupDirName = join( coolDirName, "QMMM_setup")
qmmmSetupNode = QMMMsetupNode("qmmmSetup.slurm", qmmmSetupDirName, basename(topologyFile), "cooled.nc")
jobGraph.add_node( qmmmSetupDirName, data = qmmmSetupNode )
jobGraph.add_edge( optimDir, qmmmSetupDirName)
qmmmOptDir = join(qmmmSetupDirName, "opt")
makedirs(qmmmOptDir)
copyfile( join( rootDir, basename(forcefield) ), join(qmmmOptDir, basename(forcefield)) )
definedAtoms = data["definedAtoms"]
constraints = data["constraints"]
qmmmOptNode = FDynamoNode(data["inputFile"], qmmmOptDir)
qmmmOptNode.coordsIn = "coordsIn.crd"
qmmmOptNode.coordsOut = "coordsOut.crd"
qmmmOptNode.verification = [ "Opt" ]
qmmmOptNode.slurmFile = None
qmmmOptNode.autorestart = False
qmmmOptNode.forceField = data["forceField"]
qmmmOptNode.flexiblePart = data["flexiblePart"]
qmmmOptNode.sequence = data["sequence"]
qmmmOptNode.qmSele = data["qmSele"]
qmmmOptNode.templateKey = "QMMM_opt_mopac_no_hess"
qmmmOptNode.fDynamoPath = data["fDynamoPath"]
qmmmOptNode.charge = data["charge"]
qmmmOptNode.method = data["method"]
jobGraph.add_node( qmmmOptDir, data = qmmmOptNode )
jobGraph.add_edge( qmmmSetupDirName, qmmmOptDir)
qmmmScanDir = join(qmmmSetupDirName, "scan")
qmmmScanNode = FDynamoNode("scan.f90", qmmmScanDir)
qmmmScanNode.verification = [ "scan1D" ]
qmmmScanNode.readInitialScanCoord = True
qmmmScanNode.templateKey = "QMMM_scan1D_mopac"
qmmmScanNode.additionalKeywords = { "scanDir" : "+", "coordScanStart" : "" ,
"iterNo" : "80", "definedAtoms" : definedAtoms, "constraints" : constraints }
jobGraph.add_node( qmmmScanDir, data = qmmmScanNode )
jobGraph.add_edge( qmmmOptDir, qmmmScanDir)
qmmmTSoptDir = join(qmmmSetupDirName, "ts_search")
qmmmTSoptNode = FDynamoNode("tsSearch.f90", qmmmTSoptDir)
qmmmTSoptNode.verification = ["Opt" , "Freq"]
qmmmTSoptNode.noOfExcpectedImaginaryFrequetions = 1
qmmmTSoptNode.templateKey = "QMMM_opt_mopac"
qmmmTSoptNode.additionalKeywords = { "ts_search" : "true" }
qmmmTSoptNode.coordsIn = "coordsStart.crd"
qmmmTSoptNode.coordsOut = "coordsDone.crd"
jobGraph.add_node( qmmmTSoptDir, data = qmmmTSoptNode )
jobGraph.add_edge( qmmmScanDir, qmmmTSoptDir)
return jobGraph
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 generateTSsearchDynamoPMF(compFile):
jobGraph = nx.DiGraph()
currentDir = getcwd()
rootDir = currentDir
data = parseFDynamoCompileScript(compFile)
########## INITIAL SCAN ###########################
definedAtoms = data["definedAtoms"]
constraints = data["constraints"]
newNode = FDynamoNode(data["inputFile"], currentDir)
newNode.coordsIn = data["coordsIn"]
newNode.verification = [ "scan1D" ]
newNode.slurmFile = None
newNode.autorestart = False
newNode.readInitialScanCoord = True
# newNode.noOfExcpectedImaginaryFrequetions = 1
newNode.forceField = data["forceField"]
newNode.flexiblePart = data["flexiblePart"]
newNode.sequence = data["sequence"]
newNode.qmSele = data["qmSele"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.fDynamoPath = data["fDynamoPath"]
newNode.charge = data["charge"]
newNode.method = data["method"]
newNode.additionalKeywords = { "scanDir" : "+", "coordScanStart" : "" , "gradientTolerance" : "1.0",
"iterNo" : "80", "definedAtoms" : definedAtoms, "constraints" : constraints }
jobGraph.add_node( currentDir , data = newNode )
newNode.generateInput()
# newNode.compileInput()
################## TS SEARCH #####################################
startDir, currentDir = currentDir, join(currentDir, "ts_search")
newNode = FDynamoNode("tsSearch.f90", currentDir)
newNode.verification = ["Opt" , "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 1
newNode.templateKey = "QMMM_opt_mopac"
newNode.additionalKeywords = { "ts_search" : "true" }
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
jobGraph.add_node(currentDir, data = newNode)
jobGraph.add_edge(startDir, currentDir)
tsFoundDir = currentDir
stepOptDir = join(currentDir, "tsTightOpt")
newNode = FDynamoNode("optStep.f90", stepOptDir)
newNode.verification = ["Opt"]
newNode.partition = "plgrid-short"
newNode.time = "1:00:00"
newNode.templateKey = "QMMM_opt_mopac_no_hess_restr"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = { "coordScanStart" : "" , "definedAtoms" : definedAtoms, "constraints" : constraints, "gradientTolerance" : "0.1"}
jobGraph.add_node(stepOptDir, data = newNode)
jobGraph.add_edge( tsFoundDir, stepOptDir)
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" }
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
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" }
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
jobGraph.add_node(optDir, data = newNode)
jobGraph.add_edge( newDir, optDir)
####################### SCAN FROM TS #########################
reverseScan = join(startDir, "TS1reverseScan1")
newNode = FDynamoNode("scan.f90", reverseScan)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = { "scanDir" : "-", "coordScanStart" : "" , "gradientTolerance" : "0.1",
"iterNo" : str(15), "definedAtoms" : definedAtoms, "constraints" : constraints}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "seed.-15"
jobGraph.add_node(reverseScan, data = newNode)
jobGraph.add_edge( stepOptDir, reverseScan)
reverseScan2 = join(startDir, "TS1reverseScan2")
newNode = FDynamoNode("scan.f90", reverseScan2)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = { "scanDir" : "-", "coordScanStart" : "" , "gradientTolerance" : "0.1",
"iterNo" : str(16), "definedAtoms" : definedAtoms, "constraints" : constraints}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "seed.-16"
jobGraph.add_node(reverseScan2, data = newNode)
jobGraph.add_edge( reverseScan, reverseScan2)
reverseScan3 = join(startDir, "TS1reverseScan3")
newNode = FDynamoNode("scan.f90", reverseScan3)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = { "scanDir" : "-", "coordScanStart" : "" , "gradientTolerance" : "0.1",
"iterNo" : str(11), "definedAtoms" : definedAtoms, "constraints" : constraints}
newNode.coordsIn = "coordsStart.crd"
jobGraph.add_node(reverseScan3, data = newNode)
jobGraph.add_edge( reverseScan2, reverseScan3)
forwardScan = join(startDir, "TS1forwardScan1")
newNode = FDynamoNode("scan.f90", forwardScan)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = { "scanDir" : "+", "coordScanStart" : "" , "gradientTolerance" : "0.1",
"iterNo" : str(15), "definedAtoms" : definedAtoms, "constraints" : constraints}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "seed.+15"
jobGraph.add_node(forwardScan, data = newNode)
jobGraph.add_edge( stepOptDir, forwardScan)
forwardScan2 = join(startDir, "TS1forwardScan2")
newNode = FDynamoNode("scan.f90", forwardScan2)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = { "scanDir" : "+", "coordScanStart" : "" , "gradientTolerance" : "0.1",
"iterNo" : str(16), "definedAtoms" : definedAtoms, "constraints" : constraints}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "seed.+16"
jobGraph.add_node(forwardScan2, data = newNode)
jobGraph.add_edge( forwardScan, forwardScan2)
forwardScan3 = join(startDir, "TS1forwardScan3")
newNode = FDynamoNode("scan.f90", forwardScan3)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = { "scanDir" : "+", "coordScanStart" : "" , "gradientTolerance" : "0.1",
"iterNo" : str(11), "definedAtoms" : definedAtoms, "constraints" : constraints}
newNode.coordsIn = "coordsStart.crd"
jobGraph.add_node(forwardScan3, data = newNode)
jobGraph.add_edge( forwardScan2, forwardScan3)
return jobGraph
def generateTSsearchDynamoPMF(compFile, onlyPrepare, onlyRun, runDFT):
jobGraph = nx.DiGraph()
currentDir = getcwd()
rootDir = currentDir
data = parseFDynamoCompileScript(compFile)
########## INITIAL SCAN ###########################
definedAtoms = data["definedAtoms"]
constraints = data["constraints"]
newNode = FDynamoNode(data["inputFile"], currentDir)
newNode.coordsIn = data["coordsIn"]
newNode.verification = ["scan1D"]
newNode.slurmFile = None
newNode.autorestart = False
newNode.readInitialScanCoord = True
# newNode.noOfExcpectedImaginaryFrequetions = 1
newNode.forceField = data["forceField"]
newNode.flexiblePart = data["flexiblePart"]
newNode.sequence = data["sequence"]
newNode.qmSele = data["qmSele"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.fDynamoPath = data["fDynamoPath"]
newNode.charge = data["charge"]
newNode.method = data["method"]
newNode.additionalKeywords = {
"scanDir": "+",
"coordScanStart": "",
"iterNo": "80",
"definedAtoms": definedAtoms,
"constraints": constraints
}
if not onlyRun:
jobGraph.add_node(currentDir, data=newNode)
newNode.generateInput()
# newNode.compileInput()
################## TS SEARCH #####################################
startDir, currentDir = currentDir, join(currentDir, "ts_search")
newNode = FDynamoNode("tsSearch.f90", currentDir)
newNode.verification = ["Opt", "Freq"]
newNode.noOfExcpectedImaginaryFrequetions = 1
newNode.templateKey = "QMMM_opt_mopac"
newNode.additionalKeywords = {"ts_search": "true"}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
if not onlyRun:
jobGraph.add_node(currentDir, data=newNode)
jobGraph.add_edge(startDir, currentDir)
tsFoundDir = currentDir
if runDFT:
gaussianFlexibleSele = rewriteFlexibleSeleFile(
join(rootDir, data["flexiblePart"]))
tsGaussianDir = join(tsFoundDir, "b3lyp")
if not isdir(tsGaussianDir):
makedirs(tsGaussianDir)
newNode = FDynamoNode("tsSearch", tsGaussianDir)
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": "B3LYP",
"basis": "6-31G(d,p)",
"multiplicity": 1,
"otherOptions": ""
}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
newNode.flexiblePart = basename(gaussianFlexibleSele)
newNode.partition = "plgrid-gpu\n#SBATCH --gres=gpu:1\n#SBATCH -A plgksdhphdgpu"
copyfile(gaussianFlexibleSele, join(tsGaussianDir,
newNode.flexiblePart))
newNode.processors = 24
newNode.time = "30:00:00"
newNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
jobGraph.add_node(tsGaussianDir, data=newNode)
jobGraph.add_edge(tsFoundDir, tsGaussianDir)
spDir = join(tsGaussianDir, "SP")
dftNode = FDynamoNode("DFT-SP-", spDir)
dftNode.verification = ["SP"]
dftNode.templateKey = "QMMM_sp_gaussian"
dftNode.additionalKeywords = {
"method": "B3LYP",
"basis": "6-311++G(2d,2p)",
"multiplicity": 1,
"otherOptions": ""
}
dftNode.coordsIn = "coordsStart.crd"
dftNode.coordsOut = "coordsDone.crd"
dftNode.flexiblePart = basename(gaussianFlexibleSele)
dftNode.processors = 24
dftNode.time = "30:00:00"
dftNode.partition = "plgrid-gpu\n#SBATCH --gres=gpu:1\n#SBATCH -A plgksdhphdgpu"
dftNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
jobGraph.add_node(spDir, data=dftNode)
jobGraph.add_edge(tsGaussianDir, spDir)
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"
if not onlyRun:
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"}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
if not onlyRun:
jobGraph.add_node(optDir, data=newNode)
jobGraph.add_edge(newDir, optDir)
if runDFT:
tsGaussianDir = join(optDir, "b3lyp")
if not isdir(tsGaussianDir):
makedirs(tsGaussianDir)
newNode = FDynamoNode("opt", tsGaussianDir)
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",
"method": "B3LYP",
"basis": "6-31G(d,p)",
"multiplicity": 1,
"otherOptions": ""
}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
newNode.flexiblePart = basename(gaussianFlexibleSele)
copyfile(gaussianFlexibleSele, join(tsGaussianDir,
newNode.flexiblePart))
newNode.processors = 24
newNode.time = "30:00:00"
newNode.partition = "plgrid-gpu\n#SBATCH --gres=gpu:1\n#SBATCH -A plgksdhphdgpu"
newNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
jobGraph.add_node(tsGaussianDir, data=newNode)
jobGraph.add_edge(optDir, tsGaussianDir)
spDir = join(tsGaussianDir, "SP")
dftNode = FDynamoNode("DFT-SP-", spDir)
dftNode.verification = ["SP"]
dftNode.templateKey = "QMMM_sp_gaussian"
dftNode.additionalKeywords = {
"method": "B3LYP",
"basis": "6-311++G(2d,2p)",
"multiplicity": 1,
"otherOptions": ""
}
dftNode.coordsIn = "coordsStart.crd"
dftNode.coordsOut = "coordsDone.crd"
dftNode.flexiblePart = basename(gaussianFlexibleSele)
dftNode.processors = 24
dftNode.time = "30:00:00"
dftNode.partition = "plgrid-gpu\n#SBATCH --gres=gpu:1\n#SBATCH -A plgksdhphdgpu"
dftNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
jobGraph.add_node(spDir, data=dftNode)
jobGraph.add_edge(tsGaussianDir, spDir)
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"
if not onlyRun:
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"}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
if not onlyRun:
jobGraph.add_node(optDir, data=newNode)
jobGraph.add_edge(newDir, optDir)
if runDFT:
tsGaussianDir = join(optDir, "b3lyp")
if not isdir(tsGaussianDir):
makedirs(tsGaussianDir)
newNode = FDynamoNode("opt", tsGaussianDir)
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",
"method": "B3LYP",
"basis": "6-31G(d,p)",
"multiplicity": 1,
"otherOptions": ""
}
newNode.coordsIn = "coordsStart.crd"
newNode.coordsOut = "coordsDone.crd"
newNode.flexiblePart = basename(gaussianFlexibleSele)
copyfile(gaussianFlexibleSele, join(tsGaussianDir,
newNode.flexiblePart))
newNode.processors = 24
newNode.time = "30:00:00"
newNode.partition = "plgrid-gpu\n#SBATCH --gres=gpu:1\n#SBATCH -A plgksdhphdgpu"
newNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
jobGraph.add_node(tsGaussianDir, data=newNode)
jobGraph.add_edge(optDir, tsGaussianDir)
spDir = join(tsGaussianDir, "SP")
dftNode = FDynamoNode("DFT-SP-", spDir)
dftNode.verification = ["SP"]
dftNode.templateKey = "QMMM_sp_gaussian"
dftNode.additionalKeywords = {
"method": "B3LYP",
"basis": "6-311++G(2d,2p)",
"multiplicity": 1,
"otherOptions": ""
}
dftNode.coordsIn = "coordsStart.crd"
dftNode.coordsOut = "coordsDone.crd"
dftNode.flexiblePart = basename(gaussianFlexibleSele)
dftNode.processors = 24
dftNode.time = "30:00:00"
dftNode.partition = "plgrid-gpu\n#SBATCH --gres=gpu:1\n#SBATCH -A plgksdhphdgpu"
dftNode.moduleAddLines = "module add plgrid/apps/gaussian/g16.B.01"
jobGraph.add_node(spDir, data=dftNode)
jobGraph.add_edge(tsGaussianDir, spDir)
####################### SCAN FROM TS #########################
scanSteps = 40
reverseScan = join(startDir, "TS1reverseScan")
newNode = FDynamoNode("scan.f90", reverseScan)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = {
"scanDir": "-",
"coordScanStart": "",
"iterNo": str(scanSteps),
"definedAtoms": definedAtoms,
"constraints": constraints
}
newNode.coordsIn = "coordsStart.crd"
jobGraph.add_node(reverseScan, data=newNode)
if onlyRun:
newNode.forceField = data["forceField"]
newNode.flexiblePart = data["flexiblePart"]
newNode.sequence = data["sequence"]
newNode.qmSele = data["qmSele"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.fDynamoPath = data["fDynamoPath"]
newNode.charge = data["charge"]
newNode.method = data["method"]
newNode.status = "examined"
else:
jobGraph.add_edge(tsFoundDir, reverseScan)
if not onlyPrepare:
pmfDir = join(startDir, "PMF")
for i in range(scanSteps + 1):
stepDir = join(pmfDir, "pmfRev" + str(i))
newNode = FDynamoNode("pmfStep.f90", stepDir)
newNode.verification = ["SP"]
newNode.partition = "plgrid"
newNode.time = "72:00:00"
newNode.templateKey = "QMMM_pmf"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = {
"coordScanStart": "",
"definedAtoms": definedAtoms,
"constraints": constraints
}
newNode.coordsIn = "seed.-" + str(i)
newNode.anotherCoordsSource = "seed.-" + str(i)
jobGraph.add_node(stepDir, data=newNode)
jobGraph.add_edge(reverseScan, stepDir)
forwardScan = join(startDir, "TS1forwardScan")
newNode = FDynamoNode("scan.f90", forwardScan)
newNode.verification = ["SP"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.readInitialScanCoord = True
newNode.additionalKeywords = {
"scanDir": "+",
"coordScanStart": "",
"iterNo": str(scanSteps),
"definedAtoms": definedAtoms,
"constraints": constraints
}
newNode.coordsIn = "coordsStart.crd"
jobGraph.add_node(forwardScan, data=newNode)
if onlyRun:
newNode.forceField = data["forceField"]
newNode.flexiblePart = data["flexiblePart"]
newNode.sequence = data["sequence"]
newNode.qmSele = data["qmSele"]
newNode.templateKey = "QMMM_scan1D_mopac"
newNode.fDynamoPath = data["fDynamoPath"]
newNode.charge = data["charge"]
newNode.method = data["method"]
newNode.status = "examined"
else:
jobGraph.add_edge(tsFoundDir, forwardScan)
if not onlyPrepare:
for i in range(1, scanSteps + 1):
stepDir = join(pmfDir, "pmfForw" + str(i))
newNode = FDynamoNode("pmfStep.f90", stepDir)
newNode.verification = ["SP"]
newNode.partition = "plgrid"
newNode.time = "72:00:00"
newNode.templateKey = "QMMM_pmf"
newNode.readInitialScanCoord = True
newNode.anotherCoordsSource = "seed.+" + str(i)
newNode.additionalKeywords = {
"coordScanStart": "",
"definedAtoms": definedAtoms,
"constraints": constraints
}
newNode.coordsIn = "seed.+" + str(i)
jobGraph.add_node(stepDir, data=newNode)
jobGraph.add_edge(forwardScan, stepDir)
return jobGraph
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")