def _submit_job(job_name, cpu_num):
js = read_json()
prep = js['job']['prepend']
exe = js['job']['exec']
subprocess.check_output(prep + ' && ' + 'mpirun -n ' + str(cpu_num) + ' ' +
exe.split()[-1],
shell=True,
cwd=job_name)
def write_job_file(node_name,cpu_num,node_num,job_name):
json_f = read_json()
with open('job.sh','w') as f:
f.writelines('#!/bin/bash \n')
f.writelines('#SBATCH -J '+job_name+'\n')
f.writelines('#SBATCH -p '+node_name+' -N '+ str(int(node_num)) +' -n '+str(int(cpu_num))+'\n\n')
f.writelines(json_f['job']['prepend']+'\n')
f.writelines(json_f['job']['exec']+'\n')
def write_file(self,filename='POTCAR'):
json_f = read_json()
potcar_main_dir_path = json_f['potcar_path'][self.functional]
all_pot_file = []
for map in self.sym_potcar_map:
pot_path = path.join(potcar_main_dir_path,map)
if path.isfile(path.join(pot_path,'POTCAR')):
all_pot_file.append(path.join(pot_path,'POTCAR'))
elif path.isfile(path.join(pot_path,'POTCAR.Z')):
all_pot_file.append(path.join(pot_path,'POTCAR.Z'))
else:
from os import listdir
from os.path import isfile, join
possible = [dir for dir in listdir(json_f['potcar_path'][self.functional]) if map.split('_')[0] in dir]
raise FileNotFoundError('Not found supported POTCAR file'
+' you can set sym_potcar_map='+ ','.join(possible))
with open(filename, 'w') as outfile:
for fname in all_pot_file:
outfile.write(zread(fname))