Last active
January 19, 2020 21:13
-
-
Save Asif-Iqbal-Bhatti/c0bead508582bbddb3665278bd09179b to your computer and use it in GitHub Desktop.
This script creates a number of directories based on POSCARS-* generated from phonopy code
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/usr/bin/env python3.6 | |
#_____________________________________________________________________________ | |
''' | |
USAGE: python3 script to create directories for POSCAR files generated from | |
PHONOPY code. | |
Credit: Asif Iqbal Bhatti | |
DATED: 19-01-2020 | |
''' | |
#_____________________________________________________________________________ | |
import os, sys, scipy | |
import pathlib, subprocess, shutil | |
from os import listdir | |
from os.path import isfile, join | |
import os.path | |
import multiprocessing as mp | |
import fnmatch | |
import time | |
#_____________________________________________________________________________ | |
#os.system("phonopy -d --dim="2 2 2") ## It will call a phonopy code | |
os.system('rm -r disp-*') | |
#_____________________________________________________________________________ | |
def copy_fntn(k): | |
for i in range(1, int(k)+1): | |
shutil.rmtree('disp-'+str(i).zfill(3), ignore_errors=True) #overwrite a directory | |
os.mkdir('disp-'+str(i).zfill(3)) | |
#subprocess.check_call(['mkdir', 'disp-'+str(i).zfill(3)]) | |
#subprocess.check_call('cd disp-'+str(i).zfill(3), shell=True) | |
# print(str(i).zfill(3)) | |
# | |
# The zfill()/rjust() is a function associated with the string object. | |
# 3 is the expected length of the string after padding. | |
# | |
os.system('cp INCAR disp-'+str(i).zfill(3) ) | |
os.system('cp POTCAR disp-'+str(i).zfill(3) ) | |
os.system('cp KPOINTS disp-'+str(i).zfill(3) ) | |
os.system('cp job.sh disp-'+str(i).zfill(3) ) | |
subprocess.call(['cp','-r','POSCAR-'+str(i).zfill(3),'disp-'+str(i).zfill(3)], shell = False) | |
os.chdir('disp-'+str(i).zfill(3)) | |
shutil.copyfile("POSCAR-"+str(i).zfill(3), "POSCAR-"+str(i).zfill(3)+"-disp") | |
#os.system('ls') | |
os.chdir('../') | |
if __name__ == '__main__': | |
print("Number of processors Detected: ", mp.cpu_count()) | |
pool = mp.Pool(4) | |
print("*"*80) | |
if not os.path.exists('POSCAR'): | |
print (' ERROR: POSCAR does not exist here.') | |
sys.exit(0) | |
else: | |
counter=0 | |
mypath = os.getcwd() | |
for entry in os.listdir(mypath): | |
if os.path.isfile(os.path.join(mypath, entry)): | |
if fnmatch.fnmatchcase(entry,'POSCAR-*'): | |
counter+=1 | |
print ("# of POSCAR-* files generated with Phonopy code: ----> {}".format(counter) ) | |
print("*"*80) | |
start_time = time.time() | |
#copy_fntn(counter) | |
#p = mp.Process(target=copy_fntn, args=('9',)) | |
#p.start() | |
#p.join() | |
with pool as p: | |
p.map(copy_fntn, [counter]) | |
end_time = time.time() | |
print("total time taken this loop: ", end_time - start_time) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Please check for your self. I have tried to implement the multiprocessing on the most demanding for loop part but I guess the speed is same.