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ioMOD.py
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ioMOD.py
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#!/usr/bin/env python3
from contextlib import contextmanager
import os
# Globals
CWD = os.getcwd()
### Context manager for changing the current working directory ###
@contextmanager
def cd(newdir):
prevdir = os.getcwd()
os.chdir(os.path.expanduser(newdir))
try:
yield
finally:
os.chdir(prevdir)
### Function to extract parameters from params file ###
def getparams(paramsFile):
with open(paramsFile, 'r') as inp:
for line in inp:
data = line.split()
if not line.startswith("#"):
if line.startswith("state1_xyz"):
state1File = data[2]
elif line.startswith("state2_xyz"):
state2File = data[2]
elif line.startswith("basename1"):
base1File = data[2]
elif line.startswith("basename2"):
base2File = data[2]
elif line.startswith("dir_name1"):
dir1 = data[2]
elif line.startswith("dir_name2"):
dir2 = data[2]
elif line.startswith("head_file1"):
h1File = data[2]
elif line.startswith("head_file2"):
h2File = data[2]
elif line.startswith("allxyz_file"):
allxyzFile = data[2]
elif line.startswith("nAtoms"):
nAtoms = int(data[2])
elif line.startswith("nPoints"):
nPoints = int(data[2])
elif line.startswith("nProcs"):
nProcs = int(data[2])
params = [state1File, state2File, base1File, base2File, dir1, dir2,
h1File, h2File, allxyzFile, nAtoms, nPoints, nProcs]
return params
def createinps(data):
nPoints = data[0]
baseName = data[1]
DIR = data[2]
allInp = []
n = 1
if not os.path.exists(DIR):
os.makedirs(DIR)
while n <= nPoints:
number = str(n)
number = number.rjust(3,'0')
writeFile = baseName + "." + number + ".inp"
allInp.append(writeFile)
with cd(DIR):
with open(writeFile, 'w') as output:
title = "# ORCA PES calculation step "+ number+ "\n"
output.write(title)
n += 1
return allInp
### Function to create the inputs and write the headers ###
def write(dataFile):
wFile = str(dataFile[0])
inpLines = str(dataFile[1])
DIR = str(dataFile[2])
# Enter DIR and write to file
with cd(DIR):
with open(wFile,'a') as output:
output.write(inpLines)
return
### Extract coordinates from file
def extcoord(inFile):
allCoord = []
with open(inFile,'r') as file:
lines = file.readlines()
del lines[0]
del lines[0]
for line in lines:
line = line.split()
allCoord.append([str(line[0]), float(line[1]), float(line[2]), float(line[3])])
return allCoord