def returnMolecule(self):
lisPos = Find_XYZ(self.targetFile, self.base).gaussian_style()
for elementPos in lisPos:
rawAtom = elementPos.split()
atomType = rawAtom[0]
atomX = float(rawAtom[1])
atomY = float(rawAtom[2])
atomZ = float(rawAtom[3])
self.molecule.addAtom(Atom(atomType, atomX, atomY, atomZ))
return self.molecule
'squaraine-OH-OMe-OH': 34,
'squaraine-OMe-NMe2-H': 40,
'squaraine-OMe-NMe2-O': 41,
'squaraine-OMe-NMe2-OH': 41,
'squaraine-OMe-OMe-H': 36,
'squaraine-OMe-OMe-O': 37,
'squaraine-OMe-OMe-OH': 37,
'stilbene-NMe2-OMe-H': 54,
'stilbene-NMe2-OMe-O': 55,
'stilbene-NMe2-OMe-OH': 55
}
# Description: main function of the script
if (__name__ == "__main__"):
for molecule in list(molecules.keys()):
geomFile = dirGeom + "pre_opt_" + molecule
nameFile = dirOpt + "opt_" + molecule
geom = Find_XYZ(geomFile + ".log",
molecules[molecule]).gaussian_style()
fileToWrite = open(nameFile + ".com", "w")
copyfile(geomFile + ".chk", nameFile + ".chk")
fileToWrite.write(
'{}chk={}.chk \n{}nprocshared=6 \n{}mem=30000mb \n'.format(
"%",
nameFile.split("/")[-1], "%", "%"))
fileToWrite.write(
'#p opt=(ReadFC, gdiis) nosymm output=wfn wb97x/6-31++G**\n\nOptimization of the {}\n\n0 1\n'
.format(nameFile))
for atomCoord in geom:
fileToWrite.write(atomCoord + "\n")
fileToWrite.write("\n\n")
from find_xyz_from_a_log import Find_XYZ
base_name = "BTD-QN"
solvents = {"gas":" ", "water":"scrf=(iefpcm, solvent=Water)"}
methods = ["B3LYP", "CAM-B3LYP", "M062X", "PBE1PBE", "wB97XD"]
td_text = "td=nstates=12"
basis_set = "6-311+G(2d,p)"
text_add_work = "density=current NoSymm"
proc_line = "%nprocshared=6"
mem_line = "%mem=30000MB"
mult = "1"
charge = "0"
text_base = "Calculo TD da "
dir_home = os.getcwd()
for solvent in list(solvents.keys()):
geom_orig = dir_home+"/opt/"+base_name+"_"+solvent+".log"
geom_list = Find_XYZ(geom_orig, 30).gaussian_style()
os.chdir(dir_home+"/"+solvent)
for method in methods:
checkpoint_line = "%chk="+base_name+"_"+solvent+"_"+method+".chk"
file_name=base_name+"_"+solvent+"_"+method+".com"
text = text_base+file_name
file_to_write = open(file_name, "w")
file_to_write.write("{}\n{}\n{}\n".format(checkpoint_line, mem_line, proc_line))
file_to_write.write("#p {}/{} {} {} {}\n\n{}\n\n{} {}\n".format(method, basis_set, td_text, text_add_work, solvents[solvent], text, charge, mult))
for element in geom_list:
file_to_write.write("{}\n".format(element))
file_to_write.write("\n\n")