run_gfn.py

import os
import sys
import subprocess


def ReadXYZ(filename):
    #function reading xyz format
    rfile = open(filename,"r")
    rfilelines = rfile.readlines()
    natoms = int(rfilelines[0])
    geometry = []
    for iatm in range(natoms):
        line = rfilelines[iatm + 2]
        cleanline = line
        for idx in range(250):
            line = cleanline.replace("  "," ")
            cleanline = line
            if not ("  " in cleanline): break
        data = cleanline.split(" ")
        aux = [float(data[1]),float(data[2]),float(data[3])]
        geometry.append(aux)
    return geometry

def run_gfn2(argv):
    #arguments and give them default values
    exe = "./GFN2all_crd_update1.exe"
    geometryfile = ""
    charge = "0"
    Telec = "300"
    solvation = "0"
    solventname = "gas"
    optimisegeometry = "0"
    newgeometryfile = ""
    thermo = "0"
    energythresh = "1.0e-6"
    gradientthresh = "1.0e-3"
    calcdensity = "0"
    densityfile = ""
    electronicreactivity = "0"
    orbitalreactivity = "0"
    KoopmanIP = "0"
    IP = "0"
    EA = "0"
    electronegativity = "0"
    hardness = "0"

    #parse whatever we get
    for iarg in range(1,len(argv)):
        argument = argv[iarg].lower().replace("=","")
        if argument.startswith("geometry") or argument.startswith("geom"):
            geometryfile = argument.replace("geometry","").replace("geom","")
        elif argument.startswith("charge") or argument.startswith("chrg"):
            charge = argument.replace("charge","").replace("chrg","")
        elif argument.startswith("telec") or argument.startswith("telectronic"):
            Telec = argument.replace("telectronic","").replace("telec","")
        elif argument.startswith("usesolv") or argument.startswith("usesolvent"):
            solvation = argument.replace("usesolvent","").replace("usesolv","")
        elif argument.startswith("solvent") or argument.startswith("solventname"):
            solventname = argument.replace("solventname","").replace("solvent","")
        elif argument.startswith("optg") or argument.startswith("optimisegeom") or argument.startswith("optimizegeom") or argument.startswith("optimisegeometry") or argument.startswith("optimizegeometry"):
            optimisegeometry = argument.replace("optg","").replace("optimise","").replace("optimize","").replace("geometry","").replace("geom","")
        elif argument.startswith("newgeom") or argument.startswith("newgeomfile") or argument.startswith("newgeometryfile"):
            newgeometryfile = argument.replace("newgeometryfile","").replace("newgeomfile","").replace("newgeom","")
        elif argument.startswith("dothermo") or argument.startswith("thermo") or argument.startswith("thermodynamics"):
            thermo = argument.replace("dothermo","").replace("thermodynamics","").replace("thermo","")
        elif argument.startswith("ethresh") or argument.startswith("energythresh") or argument.startswith("energythreshold"):
            energythresh = argument.replace("ethresh","").replace("energythreshold","").replace("energythresh","")
        elif argument.startswith("gthresh") or argument.startswith("gradthresh") or argument.startswith("gradientthreshold"):
            gradientthresh = argument.replace("gthresh","").replace("gradientthreshold","").replace("gradthresh","")
        elif argument.startswith("calcdens") or argument.startswith("calcdensity") or argument.startswith("calculatedensity"):
            calcdensity = argument.replace("calcdensity","").replace("calcdens","").replace("calculatedensity","")
        elif argument.startswith("densityfile") or argument.startswith("densfile"):
            calcdensity = argument.replace("densityfile","").replace("densfile","")
        elif argument.startswith("ereact") or argument.startswith("electronicreactivity"):
            electronicreactivity = argument.replace("ereact","").replace("electronicreactivity","")
        elif argument.startswith("oreact") or argument.startswith("orbreact") or argument.startswith("orbitalreactivity"):
            orbitalreactivity = argument.replace("oreact","").replace("orbreact","").replace("orbitalreactivity","")
        elif argument.startswith("koopman") or argument.startswith("ipkoopman") or argument.startswith("koopmanip"):
            KoopmanIP = argument.replace("ip","").replace("koopman","")
        elif argument.startswith("ip") or argument.startswith("ionizationpotential") or argument.startswith("ionisationpotential") or argument.startswith("ipot"):
            IP = argument.replace("ip","").replace("ionizationpotential","").replace("ionisationpotential","").replace("ipot","")
        elif argument.startswith("ea") or argument.startswith("electronaffinity") or argument.startswith("eaffin"):
            EA = argument.replace("ea","").replace("electronaffinity","").replace("eaffin","")
        elif argument.startswith("electronegativity"):
            electronegativity = argument.replace("electronegativity","")
        elif argument.startswith("hardness"):
            hardness = argument.replace("hardness","")

    #ensure consistency
    if geometryfile + "blahblah" == "blahblah":
        print("ERROR: geometry file is needed")
        sys.exit()

    newgeometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","")
    if (newgeometryfile + "blahblah" == "blahblah") and (optimisegeometry == "1"): 
        newgeometryfile = geometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","") + "_opt"

    if (solvation == "1"):
        if (solventname == "water") or (solventname == "h2o") or (solventname == "o"): solventname = "water"
        elif (solventname == "acetone") or (solventname == "cc(o)c"): solventname = "acetone"
        elif (solventname == "acetonitrile") or (solventname == "ch3cn") or (solventname == "ccn"): solventname = "acetonitrile"
        elif (solventname == "aniline") or (solventname == "phnh2") or (solventname == "nc1ccccc1") or (solventname == "c1ccc(cc1)n"): solventname = "aniline"
        elif (solventname == "benzaldehyde") or (solventname == "phcho") or (solventname == "occ1ccccc1") or (solventname == "c1ccc(cc1)co"): solventname = "benzaldehyde"
        elif (solventname == "benzene") or (solventname == "c6h6") or (solventname == "phh") or (solventname == "c1ccccc1"): solventname = "benzene"
        elif (solventname == "dichloromethane") or (solventname == "ch2cl2") or (solventname == "c(cl)cl") or (solventname == "c(cl)(cl)"): solventname = "dichloromethane"
        elif (solventname == "chloroform") or (solventname == "chcl3") or (solventname == "c(cl)(cl)cl") or (solventname == "c(cl)(cl)(cl)"): solventname = "chloroform"
        elif (solventname == "carbon disulfide") or (solventname == "carbondisulfide") or (solventname == "cs2") or (solventname == "scs"): solventname = "carbon disulfide"
        elif (solventname == "dioxane") or (solventname == "o1ccocc1"): solventname = "dioxane"
        elif (solventname == "dmf") or (solventname == "dimethylformamide") or (solventname == "cn(c)co"): solventname = "dmf"
        elif (solventname == "dmso") or (solventname == "dimethylsulfoxide") or (solventname == "cs(o)c") or (solventname == "cs(c)o"): solventname = "dmso"
        elif (solventname == "ethanol") or (solventname == "etoh") or (solventname == "ch3ch2oh") or (solventname == "cco"): solventname = "ethanol"
        elif (solventname == "diethyl ether") or (solventname == "etoet") or (solventname == "ccocc") or (solventname == "ch3ch2och2ch3"): solventname = "diethyl ether"
        elif (solventname == "ethyl acetate") or (solventname == "acoet") or (solventname == "etoac") or (solventname == "ccoc(o)c"): solventname = "ethyl acetate"
        elif (solventname == "furan") or (solventname == "furane"): solventname = "furane"
        elif (solventname == "hexadecane") or (solventname == "c16"): solventname = "hexadecane"
        elif (solventname == "hexane") or (solventname == "cccccc") or (solventname == "c6"): solventname = "hexane"
        elif (solventname == "methanol") or (solventname == "meoh") or (solventname == "co") or (solventname == "ch3oh"): solventname = "methanol"
        elif (solventname == "nitromethane") or (solventname == "meno2") or (solventname == "ch3no2") or (solventname == "cn(o)o"): solventname = "nitromethane"
        elif (solventname == "octanol") or (solventname == "cccccccc") or (solventname == "c8"): solventname = "octanol"
        elif (solventname == "phenol") or (solventname == "phoh") or (solventname == "oc1ccccc1") or (solventname == "c1ccc(cc1)o"): solventname = "phenol"
        elif (solventname == "thf") or (solventname == "tetrahydrofuran"): solventname = "thf"
        elif (solventname == "toluene") or (solventname == "phme") or (solventname == "cc1ccccc1"): solventname = "toluene"
        elif (solventname == "octanol wet") or (solventname == "octanolwet") or (solventname == "wet octanol") or (solventname == "wetoctanol"): solventname = "octanol wet"

    if (densityfile + "blahblah" == "blahblah") and (calcdensity == "1"): 
        densityfile = geometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","") + "_dens"

    def RunQMOptg():
        proc = subprocess.Popen([exe,geometryfile,charge,Telec,solvation,solventname,optimisegeometry,newgeometryfile,thermo,energythresh,gradientthresh,calcdensity,densityfile,electronicreactivity,orbitalreactivity,KoopmanIP,IP,EA,electronegativity,hardness], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
        out,err = proc.communicate()
        return out,err
    out,err = RunQMOptg()

    if err.decode("utf-8") + "blahblah" != "blahblah": print("error:",err)
    else:
        #process data from output file
        outputfile = out.decode("utf-8").split("\n")
        #print(out.decode("utf-8"))
        etotal = 0.0
        gsolvation = 0.0
        fetchvibr = False
        vibrations = []
        fetchthermo = False
        temperature = []
        entropy = []
        enthalpy = []
        gibbs = []
        internalenergy = []
        helmholtz = []
        cp = []
        cv = []
        fetchatomicprops = False
        atmlist = []
        charges = []
        polarisabilities = []
        totalpol = 0.0
        fetchelecreact = False
        fetchorbreact = False
        eFukuiElctrophilie = []
        eFukuiNucleophilie = []
        eFukuiRadical = []
        eSoftnessElctrophilie = []
        eSoftnessNucleophilie = []
        eSoftnessRadical = []
        oFukuiElctrophilie = []
        oFukuiNucleophilie = []
        oFukuiRadical = []
        oSoftnessElctrophilie = []
        oSoftnessNucleophilie = []
        oSoftnessRadical = []
        ipkoopman = 0.0
        ip = 0.0
        ea = 0.0
        eneg = 0.0
        hard = 0.0
        out_dict = {}
        for iline in range(len(outputfile)):
            line = outputfile[iline]
            #check whether array data is available
            if line.startswith(">all vibrational frequencies"): 
                fetchvibr = True
                continue
            elif line.startswith("<all vibrational frequencies"): 
                fetchvibr = False
                continue
            elif line.startswith(">Thermodynamics"): 
                fetchthermo = True
                continue
            elif line.startswith("<Thermodynamics"): 
                fetchthermo = False
                continue
            elif line.startswith(">atom;charge;pol"): 
                fetchatomicprops = True
                continue
            elif line.startswith("<atom;charge;pol"): 
                fetchatomicprops = False
                continue
            elif line.startswith(">Electronic Reactivity indices"): 
                fetchelecreact = True
                continue
            elif line.startswith("<Electronic Reactivity indices"): 
                fetchelecreact = False
                continue
            elif line.startswith(">Orbital Reactivity indices"): 
                fetchorbreact = True
                continue
            elif line.startswith("<Orbital Reactivity indices"): 
                fetchorbreact = False
                continue
            #fetch data
            if line.startswith("Total Energy = "): 
                etotal = float(line.replace("Total Energy = ",""))
                out_dict['etotal']=etotal
            elif line.startswith("Gsolv = "): 
                gsolvation = float(line.replace("Gsolv = ",""))
                out_dict['gsolvation']=gsolvation
            elif "Total Polarizability" in line: 
                totalpol = float(line.replace("Total Polarizability","").replace(" ",""))
                out_dict['totalpol']=totalpol                
            elif line.startswith("Ionization Potential (Koopman):"): 
                ipkoopman = float(line.replace("Ionization Potential (Koopman):","").replace("   eV",""))
                out_dict['ipkoopman']=ipkoopman
            elif line.startswith("Ionization Potential (Definition): "): 
                ip = float(line.replace("Ionization Potential (Definition): ","").replace("   eV",""))
                out_dict['ip']=ip
            elif line.startswith("Electron Affinity (Definition): "): 
                ea = float(line.replace("Electron Affinity (Definition): ","").replace("   eV",""))
                out_dict['ea']=ea
            elif line.startswith("Electronegativity: "): 
                eneg = float(line.replace("Electronegativity: ","").replace("   eV",""))
                out_dict['eneg']=eneg
            elif line.startswith("Hardness: "): 
                hard = float(line.replace("Hardness: ","").replace("   eV",""))
                out_dict['hard']=hard
            elif fetchvibr: 
                vibrations.append(float(line))
                out_dict['vibrations']=vibrations
            elif fetchthermo: 
                data = line.split(";")
                temperature.append(float(data[0]))
                entropy.append(float(data[1]))
                enthalpy.append(float(data[2]))
                gibbs.append(float(data[3]))
                internalenergy.append(float(data[4]))
                helmholtz.append(float(data[5]))
                cp.append(float(data[6]))
                cv.append(float(data[7]))
                out_dict['fetchthermo']={"temperature":temperature,
                "entropy":entropy,
                "enthalpy":enthalpy,
                "gibbs":gibbs,
                "internalenergy":internalenergy,
                "helmholtz":helmholtz,
                "cp":cp,
                "cv":cv
                }
            elif fetchatomicprops:
                data = line.split(";")
                atmlist.append(int(data[0]))
                charges.append(float(data[1]))
                polarisabilities.append(float(data[2]))
                out_dict['fetchatomicprops']={"atmlist":atmlist,
                "charges":charges,
                "polarisabilities":polarisabilities
                }
            elif fetchelecreact:
                data = line.strip().rstrip().replace("  "," ").split(" ")
                eFukuiElctrophilie.append(float(data[0]))
                eFukuiNucleophilie.append(float(data[1]))
                eFukuiRadical.append(float(data[2]))
                eSoftnessElctrophilie.append(float(data[3]))
                eSoftnessNucleophilie.append(float(data[4]))
                eSoftnessRadical.append(float(data[5]))
                out_dict['fetchelecreact']=fetchelecreact
            elif fetchorbreact:
                data = line.strip().rstrip().replace("  "," ").split(" ")
                oFukuiElctrophilie.append(float(data[0]))
                oFukuiNucleophilie.append(float(data[1]))
                oFukuiRadical.append(float(data[2]))
                oSoftnessElctrophilie.append(float(data[3]))
                oSoftnessNucleophilie.append(float(data[4]))
                oSoftnessRadical.append(float(data[5]))
                out_dict['fetchorbreact']=fetchorbreact
        #print(argv)
        #print(out_dict)
        if not newgeometryfile.endswith(".xyz"): 
            newgeometryfile += ".xyz"
        out_dict["xyz"] = ReadXYZ(newgeometryfile)
        return out_dict
        #data collected; if there is a whether, then variable is boolean
        #geometryfile               the geometry of the molecule
        #charge                     the total charge
        #solventname                the name of the solvent
        #optimisegeometry           whether geometry was optimised
        #newgeometryfile            the name of the file containing optimised geometry
        #thermo                     whether thermodynamics was done
        #calcdensity                whether the electronic density was calculated
        #densityfile                the name of the file containing electronic density
        #electronicreactivity       whether electronic reactivity data was calculated
        #orbitalreactivity          whether orbital reacticity data was calculated
        #KoopmanIP                  whether the Koopman ionisation potential was calculated
        #IP                         whether the ionisation potential was calculated
        #EA                         whether electron affinity was calculated
        #electronegativity          whether electronegativity was calculated
        #hardness                   whether hardness was calculated
        #etotal                     the molecule's total energy in Hartree
        #gsolvation                 solvation Gibbs free energy in Hartree
        #vibrations                 array containing vibrational frequencies in cm-1
        #temperature                array containing temperatures
        #entropy                    array containing entropies
        #enthalpy                   array containing enthalpies
        #gibbs                      array containing Gibbs free energies
        #internalenergy             array containing internal energies
        #helmholtz                  array containing Helmholts energies
        #cp                         array containing heat capacities at constant pressure
        #cv                         array containing heat capacities at constant volume
        #atmlist                    list of atoms
        #charges                    partial charges in electrons
        #polarisabilities           atomic polarisabilities in bohr
        #totalpol                   total polarisability in cubic bohr
        #eFukuiElctrophilie         Fukui index for electrophilicity (calculated from charges)
        #eFukuiNucleophilie         Fukui index for nucleophilicity (calculated from charges)
        #eFukuiRadical              Fukui index for radical reactivity (calculated from charges)
        #eSoftnessElctrophilie      softness index for electrophilicity (calculated from charges)
        #eSoftnessNucleophilie      softness index for nucleophilicity (calculated from charges)
        #eSoftnessRadical           softness index for radical reactivity (calculated from charges)
        #oFukuiElctrophilie         Fukui index for electrophilicity (calculated from frontier orbitals)
        #oFukuiNucleophilie         Fukui index for nucleophilicity (calculated from frontier orbitals)
        #oFukuiRadical              Fukui index for radical reactivity (calculated from frontier orbitals)
        #oSoftnessElctrophilie      softness index for electrophilicity (calculated from frontier orbitals)
        #oSoftnessNucleophilie      softness index for nucleophilicity (calculated from frontier orbitals)
        #oSoftnessRadical           softness index for radical reactivity (calculated from frontier orbitals)
        #ipkoopman                  Koopman ionisation potential in eV
        #ip                         ionisation potential in eV
        #ea                         electron affinity in eV
        #eneg                       electronegativity in eV
        #hard                       hardness in eV

if __name__=="__main__":
    out_dict = run_gfn2(sys.argv)

    print(out_dict)