| 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) < 8:
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| 6 | sys.stderr.write("Usage: "+sys.argv[0]+" <source file> <steps> <basis> <theory> <server> <port> <workdir> <energyfile> <conformationfile>\n")
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| 7 | sys.exit(255)
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| 8 |
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| 9 | order=4
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| 10 | sourcefile=sys.argv[1]
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| 11 | steps=int(sys.argv[2])
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| 12 | basis=sys.argv[3]
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| 13 | theory=sys.argv[4]
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| 14 | serveraddress=sys.argv[5]
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| 15 | serverport=sys.argv[6]
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| 16 | workdir=sys.argv[7]
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| 17 | energyfile=sys.argv[8]
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| 18 | conformationfile=""
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| 19 | if len(sys.argv) >= 9:
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| 20 | conformationfile=sys.argv[9]
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| 21 |
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| 22 | # ========================== Stored Session BEGIN ==========================
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| 23 | pyMoleCuilder.MoleculeLoad(sourcefile)
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| 24 | pyMoleCuilder.ParserSetParserParameters(set_parser_parameters="mpqc", parser_parameters="basis="+basis+";theory="+theory+";do_gradient=no;")
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| 25 | energies={}
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| 26 | stepwidth=int(360/steps)
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| 27 | for step in range(0,360,stepwidth):
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| 28 | pyMoleCuilder.wait()
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| 29 | # calculate energy
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| 30 | pyMoleCuilder.SelectionAllAtoms()
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| 31 | pyMoleCuilder.FragmentationFragmentation(fragment_molecule="BondFragment", distance="3", order=str(order), DoSaturate="1", ExcludeHydrogen="1", output_types="", max_meshwidth="0", grid_level="5", inter_order="0", DoCyclesFull="0", parse_state_files="0")
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| 32 | pyMoleCuilder.FragmentationFragmentationAutomation(server_address=serveraddress, server_port=serverport, fragment_executable="", max_meshwidth="0", grid_level="5", near_field_cells="3", interpolation_degree="3", DoLongrange="0", DoValenceOnly="0", DoPrintDebug="0", DoSmearElectronicCharges="0", UseImplicitCharges="0")
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| 33 | pyMoleCuilder.FragmentationAnalyseFragmentationResults(store_grids="0", fragment_prefix="BondFragment", UseImplicitCharges="0")
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| 34 | # extract energy and place in hash map
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| 35 | pyMoleCuilder.wait()
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| 36 | with open(workdir+"/BondFragment_Energy.dat", 'rb') as csvfile:
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| 37 | energyreader = csv.reader(csvfile, delimiter='\t', quotechar='|')
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| 38 | for row in energyreader:
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| 39 | if (row[0]==str(order)):
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| 40 | energies[step]=row[1]
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| 41 | break
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| 42 | # select bond
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| 43 | pyMoleCuilder.SelectionClearAllAtoms()
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| 44 | pyMoleCuilder.SelectionAtomById("0")
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| 45 | pyMoleCuilder.SelectionAtomById("1")
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| 46 | # advance to next time step
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| 47 | pyMoleCuilder.WorldStepWorldTime("1")
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| 48 | # rotate bond
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| 49 | pyMoleCuilder.MoleculeRotateAroundBond(str(stepwidth), "1")
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| 50 | # output all
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| 51 | pyMoleCuilder.ParserSetOutputFormats("tremolo")
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| 52 | pyMoleCuilder.ParserSetTremoloAtomdata(set_tremolo_atomdata="Id type x=3 u=3 F=3 neighbors=4", reset="1")
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| 53 | if len(conformationfile) != 0:
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| 54 | pyMoleCuilder.WorldOutputAs(conformationfile)
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| 55 | # save energies as csv
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| 56 | with open(energyfile, 'wb') as csvfile:
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| 57 | energywriter = csv.writer(csvfile, delimiter=',', quotechar='|', quoting=csv.QUOTE_MINIMAL)
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| 58 | energywriter.writerow(["step", "energy"])
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| 59 | for key in sorted(energies.keys()):
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| 60 | energywriter.writerow([str(key), str(energies[key])])
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| 61 | # =========================== Stored Session END ===========================
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| 62 |
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| 63 | sys.exit(0)
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