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 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