def __init__(self, outFile, fchkFile): self.outFile = outFile self.outPath = os.path.abspath(outFile) print self.outPath self.fchkFile = fchkFile self.fchkpath = os.path.abspath(fchkFile) self.lines = op.read_lines(self.outPath)
parser.add_option("-n", "--multiplicity", dest="multi", help="multiplicity of the computation (default: 1)", default = "1") parser.add_option("-z", "--otheroption", dest="other", help="Any other option that should be added", default = " ") (options, args) = parser.parse_args() input_irc = options.filenameIRC input_sp = options.input_sp proc_num = options.proc_num mem_num = options.mem_num sp_folder = options.folder scf = options.scf multi = options.multi charge = options.charge other = options.other filelines = op.read_lines(input_irc) theory = sp.get_level_of_theory(filelines) basis = sp.get_basis(filelines) if not os.path.isdir(sp_folder): os.makedirs(sp_folder) os.chdir(sp_folder) f = open(input_sp,'w') if not os.path.isdir("CHK"): os.makedirs("CHK") xyz_list = get_xyz(filelines)
) (options, args) = parser.parse_args() outfile = options.filename proc_num = options.proc_num mem_num = options.mem_num checkfile = options.check dirrection = options.dirrection points = options.points step = options.step irc_folder = options.folder force = options.force other = options.other filelines = op.read_lines(outfile) theory = sp.get_level_of_theory(filelines) basis = sp.get_basis(filelines) charge = sp.get_charge(filelines) multi = sp.get_multiplicity(filelines) xyz = sp.get_last_xyz(filelines) os.chdir("../") if not os.path.isdir(irc_folder): os.makedirs(irc_folder) os.chdir(irc_folder) inputfile = "input_" + dirrection.split()[0] + ".dat" f = open(inputfile, "w") f.write("%Nproc=" + proc_num + "\n")
#! /usr/bin/python import sys, os import operations as op import singlePoint as sp from optparse import OptionParser rev = sys.argv[1] forw = sys.argv[2] irc_rev_lines = op.read_lines(rev) irc_forw_lines = op.read_lines(forw) f = open('output.log', 'w') for line in irc_rev_lines: f.write(line) for line in irc_forw_lines: f.write(line) f.close()
def __init__(self, outfile): self.outfile = outfile self.outpath = os.path.abspath(outfile) self.lines = op.read_lines(outfile)
def EA(self, outfile_an): an_lines = op.read_lines(outfile_an) ea = irclib.get_EA(self.lines,an_lines) return {"Reaction Coordinate": self.rxCoord(), "EA":ea}
def IP(self, outfile_cat): cat_lines = op.read_lines(outfile_cat) ip = irclib.get_IP(self.lines,cat_lines) return {"Reaction Coordinate": self.rxCoord(), "IP":ip}