#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 17 16:41:28 2019
@author: michal
"""
import sys
from graphManager import GraphManager
if __name__ == "__main__":
if len(sys.argv) == 1:
print("Usage: graphRemove graphKeys")
elif len(sys.argv) > 1:
sm = GraphManager()
graphKeys = sys.argv[1:]
for g in graphKeys:
sm.deleteGraph(g)
sm.saveGraphs()
else:
print( "cooooo?")
Created on Fri Dec 13 11:15:22 2019
@author: michal
"""
from graphManager import GraphManager
from sremove import SremoveManager
import sys
from os import system
if __name__ == "__main__":
if len(sys.argv) != 2:
print("Usage: graphCancelGraph graphKey")
else:
graphKey = sys.argv[1]
sm = GraphManager()
if not graphKey in sm.graphs:
print("Invalid graph key!")
quit()
graph = sm.graphs[graphKey]
id2remove = []
for node in graph.nodes:
status = graph.nodes[node]["data"].status
if status != "running":
continue
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
if __name__ == "__main__":
if len(sys.argv) < 2:
print("Usage: expandDynamoPMF compileScanScript.sh")
else:
compFile = sys.argv[1]
currentDir = getcwd()
sm = GraphManager()
graph = sm.isGraphHere(currentDir)
if graph:
newGraph = extendDynamoPMF(compFile, graph, currentDir)
sm.buildGraphDirectories(newGraph)
sm.saveGraphs()
print("Created new graph")
else:
print("No graph found in this directory directory")
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 17 16:41:28 2019
@author: michal
"""
import sys
from graphManager import GraphManager
if __name__ == "__main__":
if len(sys.argv) == 1:
print("Usage: graphDelNode nodeId")
elif len(sys.argv) > 1:
sm = GraphManager()
nodeId = sys.argv[1]
graph = sm.isGraphHere(nodeId)
if not graph:
print("Wrong node id")
quit()
successors = list(graph.successors(nodeId))
graph.remove_node(nodeId)
while successors:
node2test = successors.pop()
predecessors = list(graph.predecessors(node2test))
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:
sm.buildGraphDirectories(jobGraph)
sm.saveGraphs()
print("Created new graph")
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 17 17:29:27 2019
@author: michal
"""
import sys
from graphManager import GraphManager
if __name__ == "__main__":
if len(sys.argv) != 3:
print("Usage: graphSave graphKey pickleFile")
else:
sm = GraphManager()
graphKey = sys.argv[1]
pickleFile = sys.argv[2]
sm.saveGraph(graphKey, pickleFile)
if len(sys.argv) == 7:
additionalName = sys.argv[6]
if isfile(whamLog):
tsReactionCoord = getTScoords(whamLog)
else:
tsReactionCoord = float(whamLog)
print("Found reaction coordinate: ", tsReactionCoord)
data = parseFDynamoCompileScript(compileScript)
definedAtoms = data["definedAtoms"]
atoms = atomsFromAtomSelection(definedAtoms)
currentDir = abspath(dirname(compileScript))
graphDir = join(getcwd(), "multiTSsearch-" + method + additionalName)
sm = GraphManager()
graph = sm.isGraphHere(graphDir)
if not graph:
newGraph = jobGraph = buildGraph(tsReactionCoord, atoms, graphDir,
data, currentDir, TSno, method,
basis)
result = sm.addGraph(newGraph, graphDir)
if result:
sm.buildGraphDirectories(newGraph)
sm.saveGraphs()
print("Created new graph")
else:
print("Cannot create more than one graph in the same directory")
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 17 16:41:28 2019
@author: michal
"""
import sys
from graphManager import GraphManager
import pickle
if __name__ == "__main__":
if len(sys.argv) != 3:
print("Usage: graphAdd graphKey pickleFile")
elif len(sys.argv) > 1:
sm = GraphManager()
graphKey = sys.argv[1]
pickleFile = sys.argv[2]
infile = open(pickleFile, 'rb')
graph = pickle.load(infile)
infile.close()
if graphKey in sm.graphs:
print("Graph with this key already exists!")
quit()
sm.graphs[graphKey] = graph
sm.saveGraphs()
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 14 10:27:35 2020
@author: michal
"""
from graphManager import GraphManager
import sys
if __name__ == "__main__":
if len(sys.argv) != 2:
print("Usage: graphRunNode nodePath")
else:
nodePath = sys.argv[1]
gm = GraphManager()
graph = gm.isGraphHere(nodePath)
if not graph:
print("Invalid path!")
quit()
graph.nodes[nodePath]["data"].run()
gm.saveGraphs()
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 17 16:57:10 2019
@author: michal
"""
from graphManager import GraphManager
import sys
if __name__ == "__main__":
if len(sys.argv) == 1:
sm = GraphManager()
sm.printStatus()
elif len(sys.argv) == 2:
sm = GraphManager()
sm.printStatus(True)
elif len(sys.argv) == 3:
graphKey = sys.argv[2]
sm = GraphManager()
sm.printStatus(True, graphKey)
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 21 14:22:30 2019
@author: michal
"""
from graphManager import GraphManager
import sys
if __name__ == "__main__":
if len(sys.argv) == 1:
print("Usage: graphPrintNodeAttry nodePath")
elif len(sys.argv) == 2:
node = sys.argv[1]
sm = GraphManager()
sm.printNodeAttributes(node)
else:
print("Cooo?")
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]
status = sys.argv[3]
sm = GraphManager()
sm.insertPath2node(oldNode, newNode, slurmFile, inputFile, status)
sm.saveGraphs()
def addTSsearch (jobGraph, rootDir, currentDir, baseData, initialGeom, index):
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"
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)
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"
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" , "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)
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"
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" , "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)
if len(sys.argv) < 4:
print("Usage: graphTSsearchWHAM wham.log/RC compileScanScript.sh numberOfTS2find addName")
else:
whamLog = sys.argv[1]
compileScript = sys.argv[2]
TSno = int(sys.argv[3])
addName = ""
if len(sys.argv) > 4:
addName = sys.argv[4]
if isfile(whamLog):
tsReactionCoord = getTScoords(whamLog)
else:
tsReactionCoord = float(whamLog)
print("Found reaction coordinate: ", tsReactionCoord)
data = parseFDynamoCompileScript(compileScript)
definedAtoms = data["definedAtoms"]
atoms = atomsFromAtomSelection( definedAtoms)
currentDir = abspath(dirname(compileScript))
graphDir = join( getcwd(), "multiTSsearch"+addName )
sm = GraphManager()
graph = sm.isGraphHere(graphDir)
if not graph:
newGraph = jobGraph = buildGraph(tsReactionCoord, atoms, graphDir, data, currentDir, TSno)
result = sm.addGraph(newGraph, graphDir)
if result:
sm.buildGraphDirectories(newGraph)
sm.saveGraphs()
print("Created new graph")
else:
print("Cannot create more than one graph in the same directory")
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 17 23:27:46 2019
@author: michal
"""
from graphManager import GraphManager
import sys
if __name__ == "__main__":
if len(sys.argv) != 2:
print("Usage: graphRestart node")
else:
sm = GraphManager()
path = sys.argv[-1]
sm.restartNode(path)
sm.saveGraphs()
if __name__ == "__main__":
if len(sys.argv) == 1:
print(
"Usage: graphAdd parentNode 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.addNewNode(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]
status = sys.argv[3]
sm = GraphManager()
sm.addNewNode(oldNode, newNode, slurmFile, inputFile, status)
sm.saveGraphs()
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 17 23:24:04 2019
@author: michal
"""
from graphManager import GraphManager
import sys
if __name__ == "__main__":
if len(sys.argv) < 2:
print("Usage: graphResults graphKey force[optional]")
elif len(sys.argv) == 2:
graphKey = sys.argv[1]
sm = GraphManager()
sm.printResults(graphKey)
sm.saveGraphs()
else:
graphKey = sys.argv[1]
sm = GraphManager()
sm.printResults(graphKey, True)
sm.saveGraphs()
