def generateTSsearchFromGuessPCM(slurmFile):
jobGraph = nx.DiGraph()
currentDir = getcwd()
gaussianFile = getGaussianInpFromSlurmFile(slurmFile)
newNode = GaussianNode(gaussianFile, currentDir)
newNode.verification = "Opt"
newNode.slurmFile = slurmFile
jobGraph.add_node(currentDir, data=newNode)
return buildTSsearchGraphPCM(jobGraph, currentDir)
def generateTSsearchFromGuess(slurmFile, functional="B3LYP"):
jobGraph = nx.DiGraph()
currentDir = getcwd()
gaussianFile = getGaussianInpFromSlurmFile(slurmFile)
modredundantSection = getModredundantSection(
join(dirname(slurmFile), gaussianFile))
frozenDists = frozenDistancesFromModredundantSection(modredundantSection)
newNode = GaussianNode(gaussianFile, currentDir)
newNode.verification = "Opt"
newNode.slurmFile = slurmFile
newNode.autorestart = True
jobGraph.add_node(currentDir, data=newNode)
return buildTSsearchGraph(jobGraph, currentDir, functional, frozenDists)
def generateGraph(slurmFile, template):
jobGraph = nx.DiGraph()
currentDir = getcwd()
gaussianFile = getGaussianInpFromSlurmFile(slurmFile)
newNode = GaussianNode(gaussianFile, currentDir)
newNode.verification = "Opt"
newNode.slurmFile = slurmFile
newNode.autorestart = True
jobGraph.add_node(currentDir, data=newNode)
newDir = join(currentDir, "gesp")
newNode = GaussianNode("auto_gesp.inp", newDir)
newNode.verification = "SP"
newNode.routeSection = """%Chk=checkp.chk
%Mem=100GB
#P B3LYP/6-31G(d,p)
# Gfinput Pop=full Density Test iop(6/50=1)
# Units(Ang,Deg) Pop=MK iop(6/33=2) iop(6/42=6)
"""
newNode.additionalSection = "keto.gesp\n\nketo.gesp\n\n"
newNode.gesp = "keto.gesp"
newNode.time = "1:00:00"
newNode.partition = "plgrid-short"
jobGraph.add_node(newDir, data=newNode)
jobGraph.add_edge(currentDir, newDir)
anteDir = join(newDir, "antechamber")
newNode = AntechamberNode("keto.gesp", anteDir)
newNode.partition = "plgrid-short"
jobGraph.add_node(anteDir, data=newNode)
jobGraph.add_edge(newDir, anteDir)
if template != None:
fitDir = join(anteDir, "fit")
newNode = FitNode("keto.mol2", fitDir, template)
newNode.partition = "plgrid-short"
jobGraph.add_node(fitDir, data=newNode)
jobGraph.add_edge(anteDir, fitDir)
return jobGraph
"""
newNode.verification = "SP"
newNode.readResults = True
newNode.processors = 6
newNode.time = "72:00:00"
graph.add_node(newDir, data=newNode)
graph.add_edge(node, newDir)
if __name__ == "__main__":
if len(sys.argv) == 1:
print("Usage: graphDFT-SP slurmFile/nodeKey")
elif len(sys.argv) == 2:
slurmFile = sys.argv[1]
currentDir = getcwd()
gaussianFile = getGaussianInpFromSlurmFile(slurmFile)
gaussianLog = gaussianFile.replace("inp", "log")
sm = GraphManager()
graph = sm.isGraphHere(currentDir)
if not graph:
jobGraph = nx.DiGraph()
newNode = GaussianNode(gaussianFile, currentDir)
newNode.slurmFile = slurmFile
newNode.status = "finished"
jobGraph.add_node(currentDir, data=newNode)
addManySPcorrections(jobGraph, currentDir)
result = sm.addGraph(jobGraph, currentDir)
if result:
"""
from graphManager import GraphManager
import sys
from os.path import basename, dirname, abspath
from parsers import getGaussianInpFromSlurmFile
if __name__ == "__main__":
if len(sys.argv) == 1:
print(
"Usage: graphReplace node slurmFile status [default: waitingForParent]"
)
print("Possible status: waitingForParent, running, finished, examined")
elif len(sys.argv) == 3:
slurmFile = sys.argv[2]
inputFile = getGaussianInpFromSlurmFile(slurmFile)
newNode = dirname(abspath(slurmFile))
slurmFile = basename(slurmFile)
oldNode = sys.argv[1]
sm = GraphManager()
sm.insertPath2node(oldNode, newNode, slurmFile, inputFile)
sm.saveGraphs()
elif len(sys.argv) == 4:
slurmFile = sys.argv[2]
inputFile = getGaussianInpFromSlurmFile(slurmFile)
newNode = dirname(abspath(slurmFile))
slurmFile = basename(slurmFile)
oldNode = sys.argv[1]