def convertors(b): #toGeo(b, b.name+'.geo') toGeo(b, 'geo') toXyz(b, b.name+'.xyz') toGjf(b, b.name+'.gjf') toPdb(b, b.name+'.pdb') toReaxLammps(b)
def main(): """get qm info """ if len(sys.argv) < 2: print("g03.py logfile") else: for i in sys.argv[1:]: geo = i.split(".")[0] # get configuration a = G03LogConf(i) # get charge and energy (HF and Zero) b = G03tools(i) # parse the configuration to standard format c = a.parser() hf, zpe = b.getEnergy() o = open("qm_ener.dat", "w") o.write("%-15s HF %.8f\n" % (geo, hf)) o.write("%-15s ZPE %.8f\n" % (geo, zpe)) o.close() charges = b.getMullikenCharge() o = open("qm_mulliken_charge.dat", "w") for j in charges: o.write("%-15s%6s%6s%12s # %s\n" % (geo, "1", j[0], j[2], j[1])) o.close() charges = b.getESPCharge() o = open("qm_esp_charge.dat", "w") for j in charges: o.write("%-15s%6s%6s%12s # %s\n" % (geo, "1", j[0], j[2], j[1])) o.close() # freq calculation if quit normally if a.stat == 1: method = " ".join([j.strip() for j in c.methods]) tokens = method.strip().split() for n in range(len(tokens)): if "opt" in tokens[n]: tokens[n] = "freq" elif "geo" in tokens[n]: tokens[n] = '' c.methods = [" ".join(tokens)] c.options = ["%mem=800MB"] toGjf(c, "freq.gjf") else: runfile = os.path.join(os.getcwd(), i) print("Warning: unfinished calculation!: %s" % runfile) method = " ".join([j.strip() for j in c.methods]) tokens = method.strip().split() for n in range(len(tokens)): if "geo" in tokens[n]: tokens[n] = '' c.methods = [" ".join(tokens)] toGjf(c, "conti.gjf")
def main(): """get qm info """ if len(sys.argv) < 2: print "g03.py logfile" else: for i in sys.argv[1:]: geo = i.split(".")[0] # get configuration a = G03LogConf(i) # get charge and energy (HF and Zero) b = G03tools(i) # parse the configuration to standard format c = a.parser() hf, zpe = b.getEnergy() o = open("qm_ener.dat", "w") o.write("%-15s HF %.8f\n"%(geo, hf)) o.write("%-15s ZPE %.8f\n"%(geo, zpe)) o.close() charges = b.getCharge() o = open("qm_charge.dat", "w") for j in charges: o.write("%-15s%6s%6s%12s # %s\n"%( geo, "1", j[0], j[2], j[1])) o.close() # freq calculation if quit normally if a.stat == 1: method = " ".join([j.strip() for j in c.methods]) tokens = method.strip().split() for n in range(len(tokens)): if "opt" in tokens[n]: tokens[n] = "freq" elif "geo" in tokens[n]: tokens[n] = '' c.methods = [" ".join(tokens)] c.options = ["%mem=800MB"] toGjf(c, "freq.gjf") else: runfile = os.path.join(os.getcwd(), i) print "Warning: unfinished calculation!: %s"%runfile method = " ".join([j.strip() for j in c.methods]) tokens = method.strip().split() for n in range(len(tokens)): if "geo" in tokens[n]: tokens[n] = '' c.methods = [" ".join(tokens)] toGjf(c, "conti.gjf")
""" read the geo file and output to data (LAMMPS), geo and xyz file. """ import sys, os from mytype import System, Molecule, Atom from g03 import G03Gjf from output_conf import toXyz, toGeo, toGjf usage = """gau2xyz g03logfiles""" if len(sys.argv) < 2: print usage else: for i in sys.argv[1:]: outfile = i.split(".")[0] if os.path.exists(i): a = G03Gjf(i) b = a.parser() b.geotag = "BIOGRF 200" toXyz(b, outfile + ".xyz") toGeo(b, outfile + ".geo") toGjf(b, outfile + ".gjf.bak") else: print "missing file %s" % i
""" read the geo file and output to data (LAMMPS), geo and xyz file. """ import sys, os from mytype import System, Molecule, Atom from g03 import G03Gjf from output_conf import toXyz, toGeo, toGjf usage = """gau2xyz g03logfiles""" if len(sys.argv) < 2: print usage else: for i in sys.argv[1:]: outfile = i.split(".")[0] if os.path.exists(i): a = G03Gjf(i) b = a.parser() b.geotag = "BIOGRF 200" toXyz(b, outfile+".xyz") toGeo(b, outfile+".geo") toGjf(b, outfile+".gjf.bak") else: print "missing file %s"%i