| 1 | import pyMoleCuilder
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| 2 | import os, sys, csv
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| 3 |
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| 4 | # check arguments
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| 5 | if len(sys.argv) < 6:
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| 6 | sys.stderr.write("Usage: "+sys.argv[0]+" <source file> <steps> <server> <port> <workdir> <energyfile> <conformationfile>\n")
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| 7 | sys.exit(255)
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| 8 |
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| 9 | sourcefile=sys.argv[1]
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| 10 | steps=int(sys.argv[2])
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| 11 | serveraddress=sys.argv[3]
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| 12 | serverport=sys.argv[4]
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| 13 | workdir=sys.argv[5]
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| 14 | energyfile=sys.argv[6]
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| 15 | conformationfile=""
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| 16 | if len(sys.argv) >= 7:
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| 17 | conformationfile=sys.argv[7]
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| 18 |
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| 19 | # ========================== Stored Session BEGIN ==========================
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| 20 | pyMoleCuilder.MoleculeLoad(sourcefile)
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| 21 | pyMoleCuilder.ParserSetParserParameters("mpqc", "basis=6-31G;theory=MBPT2;")
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| 22 | energies={}
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| 23 | stepwidth=int(360/steps)
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| 24 | for step in range(0,360,stepwidth):
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| 25 | pyMoleCuilder.wait()
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| 26 | # select bond
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| 27 | pyMoleCuilder.SelectionClearAllAtoms()
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| 28 | pyMoleCuilder.SelectionAtomByElement("C")
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| 29 | # advance to next time step
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| 30 | pyMoleCuilder.WorldStepWorldTime("1")
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| 31 | # rotate bond
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| 32 | pyMoleCuilder.MoleculeRotateAroundBond(str(stepwidth), "1")
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| 33 | # calculate energy
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| 34 | pyMoleCuilder.SelectionAllAtoms()
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| 35 | pyMoleCuilder.FragmentationFragmentation("BondFragment", "3", "2", "1", "1", "", "0", "5", "0", "0", "0")
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| 36 | pyMoleCuilder.FragmentationFragmentationAutomation(serveraddress, serverport, "", "0", "5", "3", "3", "0", "0", "0", "0", "0")
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| 37 | pyMoleCuilder.FragmentationAnalyseFragmentationResults("0", "BondFragment", "0")
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| 38 | # extract energy and place in hash map
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| 39 | pyMoleCuilder.wait()
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| 40 | with open(workdir+"/BondFragment_Energy.dat", 'rb') as csvfile:
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| 41 | energyreader = csv.reader(csvfile, delimiter='\t', quotechar='|')
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| 42 | for row in energyreader:
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| 43 | if (row[0]=="2"):
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| 44 | energies[step]=row[1]
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| 45 | break
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| 46 | # output all
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| 47 | if len(conformationfile) != 0:
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| 48 | pyMoleCuilder.WorldOutputAs(conformationfile)
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| 49 | # save energies as csv
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| 50 | with open(energyfile, 'wb') as csvfile:
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| 51 | energywriter = csv.writer(csvfile, delimiter=',', quotechar='|', quoting=csv.QUOTE_MINIMAL)
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| 52 | energywriter.writerow(["step", "energy"])
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| 53 | for key in sorted(energies.keys()):
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| 54 | energywriter.writerow([str(key), str(energies[key])])
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| 55 | # =========================== Stored Session END ===========================
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| 56 |
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| 57 | sys.exit(0)
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