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 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?")
#!/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:
nodePath = sys.argv[1]
gm = GraphManager()
graph = gm.isGraphHere(nodePath)
if not graph:
print("Invalid path!")
quit()
graph.nodes[nodePath]["data"].status = "waitingForParent"
gm.saveGraphs()
elif len(sys.argv) == 3:
nodePath = sys.argv[1]
status = sys.argv[2]
if not status in [
"waitingForParent", "running", "finished", "examined"
]: