def __init__(self, inputFile, path):
JobNode.__init__(self, inputFile, path)
self.dftValue = None
self.semiEmpiricalValue = None
self.reactionCoordinate = None
self.diff = None
def __init__(self,
inputFile,
path,
mdDirectory,
topologyFile,
coordinatesIn=None):
JobNode.__init__(self, inputFile, path)
self.time = None
self.partition = None
self.processors = 24
self.mdDirectory = mdDirectory
self.topology = topologyFile
self.coordsIn = coordinatesIn
self.coordsOut = None
self.NoSolventResidues = None
self.runType = None
self.nsOfSimulation = None
self.templateDict = {
"standardOptimization": "standardOptimization.slurm",
"standardHeating": "standardHeating.slurm",
"standardMD": "standardMD.slurm",
"standardCooling": "standardCooling.slurm"
}
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 __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 __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 __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