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
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