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}
