def __init__(self, inputFile, path):
JobNode.__init__(self, inputFile, path)
self.logFile = "a.log"
self.verification = []
self.templateKey = ""
self.additionalKeywords = {}
self.templateDict = {
"QMMM_opt_mopac": ["QMMM_opt.f90", "panadero.f90"],
"QMMM_opt_mopac_no_hess": ["QMMM_opt_noHess.f90"],
"QMMM_opt_mopac_no_hess_restr": ["QMMM_opt_noHess_restr.f90"],
"QMMM_irc_mopac": ["IRC.f90", "mep_project.f90"],
"QMMM_scan1D_mopac": ["scan1D.f90"],
"QMMM_pmf": ["pmf.f90"],
"QMMM_sp": ["SP.f90"],
"QMMM_opt_gaussian": [
"QMMM_opt_Gauss.f90", "panadero.f90", "keep_log",
"with_gaussian.f90"
],
"QMMM_irc_gaussian": [
"IRC_Gauss.f90", "mep_project.f90", "keep_log",
"with_gaussian.f90"
],
"QMMM_sp_gaussian":
["SP_Gauss.f90", "keep_log", "with_gaussian.f90"]
}
self.noOfExcpectedImaginaryFrequetions = -1
self.processors = 1
self.time = "1:00:00"
self.partition = "plgrid-short"
self.getCoordsFromParent = True
self.readResults = False
self.results = []
self.software = "fDynamo"
self.structure2dump = ""
self.forceField = ""
self.flexiblePart = ""
self.sequence = ""
self.qmSele = ""
self.fDynamoPath = ""
self.charge = None
self.method = ""
self.coordsIn = ""
self.coordsOut = ""
self.anotherCoordsSource = ""
self.copyHessian = False
self.readInitialScanCoord = False
self.measureRCinOutput = False
self.QMenergy = None
self.PotentialEnergy = None
self.moduleAddLines = ""
def __init__(self, inputFile, path, topology, coordinates):
JobNode.__init__(self, inputFile, path)
self.topology = topology
self.coordsIn = coordinates
self.partition = "plgrid-short"
self.time = "0:15:00"
self.coordsOut = "test.crd"
self.flexiblePart = "in20.f90"
self.sequence = "test.seq"
def buildGraph( rc, definedAtoms, dir2start, dynamoData, dynamoFilesDir, tsNo ):
jobGraph = nx.DiGraph()
dynamoData["filesDir"] = dynamoFilesDir
newNode = JobNode(None, dir2start)
newNode.status = "finished"
jobGraph.add_node(dir2start, data = newNode)
bestStr = findNstrClosest2rc( rc, tsNo, definedAtoms )
for i, structure in enumerate( bestStr ):
print("Structure for TS search ", structure.dcd, structure.frame)
newDir = join( dir2start, "TS_"+str(i) )
addTSsearch(jobGraph, dir2start, newDir, dynamoData, structure, i )
return jobGraph
def __init__(self, inputFile, path):
JobNode.__init__(self, inputFile, path)
self.routeSection = None
self.additionalSection = None
self.skipParentAdditionalSection = True
self.logFile = self.inputFile.split(".")[0] + ".log"
self.verification = None
self.noOfExcpectedImaginaryFrequetions = -1
self.processors = 24
self.time = "72:00:00"
self.partition = "plgrid"
self.chk = "checkp.chk"
self.getCoordsFromParent = True
self.readResults = False
self.copyChk = False
self.results = []
self.software = "Gaussian"
self.structure2dump = ""
def buildGraph(rc, definedAtoms, dir2start, dynamoData, dynamoFilesDir, tsNo,
method, basis):
jobGraph = nx.DiGraph()
dynamoData["filesDir"] = dynamoFilesDir
# dynamoData["fDynamoPath"] = "/net/people/plgglanow/fortranPackages/AMBER-g09/AMBER-dynamo/makefile"
gaussianFlexibleSele = rewriteFlexibleSeleFile(
join(dynamoFilesDir, dynamoData["flexiblePart"]))
newNode = JobNode(None, dir2start)
newNode.status = "finished"
jobGraph.add_node(dir2start, data=newNode)
bestStr = findNstrClosest2rc(rc, tsNo, definedAtoms)
for i, structure in enumerate(bestStr):
print("Structure for TS search ", structure.dcd, structure.frame)
newDir = join(dir2start, "TS_" + str(i))
addTSsearch(jobGraph, dir2start, newDir, dynamoData, structure, i,
method, basis, gaussianFlexibleSele)
return jobGraph
def __init__(self, inputFile, path, topologyFile, mdDir):
JobNode.__init__(self, inputFile, path)
self.topology = topologyFile
self.mdDir = mdDir
def __init__(self, inputFile, path, pmfOutputs):
JobNode.__init__(self,inputFile, path)
self.pmfOutputs = pmfOutputs
self.time = "00:20:00"
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 __init__(self, inputFile, path):
JobNode.__init__(self,inputFile, path)
def __init__(self, inputFile, path, templateXyz):
JobNode.__init__(self,inputFile, path)
self.templateAbs = abspath(templateXyz)
self.templateBase = join(self.path, "reindexed_" + basename(self.templateAbs) )
self.time = "0:10:00"
def __init__(self, inputFile, path, whamLog):
JobNode.__init__(self, inputFile, path)
self.whamLog = abspath(whamLog)
self.scanOk = True