#!/usr/bin/env python
"""
This example shows how to automatize the execution
of ABINIT starting with just the input file "t44.in"
The abinit.files is written with the right
locations for the pseudopotentials and the results
are post-process using the output in NetCDF format
"abinit-o_OUT.nc"
"""
from __future__ import print_function
import os
import shutil
import json
import tempfile
import subprocess
import pychemia
if pychemia.HAS_SCIPY and pychemia.HAS_SCIENTIFIC:
import pychemia.code.abinit
[docs]def test_example2():
"""
Example of a multiple calc :
"""
if not (pychemia.HAS_SCIPY and pychemia.HAS_SCIENTIFIC):
return
path = 'pychemia/test/data'
assert (os.path.isdir(path))
if which('abinit') is None:
print('The executable "abinit" is not in the PATH')
print('Using the results of a previous calc')
check_results(path + os.sep + 'abinit_04')
return
workdir = tempfile.mkdtemp()
print("Work directory: %s" % workdir)
assert (os.path.isfile(path + '/abinit_04/t44.in'))
av = pychemia.code.abinit.InputVariables(path + '/abinit_04/t44.in')
print('Original input:\n%s' % av)
abifiles = pychemia.code.abinit.AbiFiles(workdir)
abifiles.set_input(av)
abifiles.set_psps('LDA', 'FHI')
abifiles.create()
res = []
wf = open(workdir + '/results.json', 'w')
cwd = os.getcwd()
os.chdir(workdir)
for i in range(3):
av.set_value('ecut', av.get_value('ecut') + 3)
print('Computing convergence study with ecut=%f ' % av.get_value('ecut'), end='')
if i > 0:
av.set_value('irdwfk', 1)
av.write(abifiles.get_input_filename())
abifile = open(workdir + '/abinit.files')
logfile = open(workdir + '/abinit.log', 'w')
subprocess.call(['abinit'], stdin=abifile, stdout=logfile)
if os.path.isfile('abinit-o_WFK'):
shutil.copyfile('abinit-o_WFK', 'abinit-i_WFK')
data = pychemia.code.abinit.netcdf2dict(workdir + '/abinit-o_OUT.nc')
os.rename(workdir + '/abinit-o_OUT.nc', '%s/abinit-o_OUT.nc_%d' % (workdir, i))
res.append({'ecut': data['ecut'], 'etotal': data['etotal']})
print('Total energy: %f' % data['etotal'])
os.chdir(cwd)
json.dump(res, wf)
wf.close()
check_results(workdir)
shutil.rmtree(workdir)
[docs]def check_results(workdir):
res = json.load(open(workdir + os.sep + 'results.json'))
assert (res[0]['etotal'] + 4.19954643154 < 1E-6)
assert (res[1]['etotal'] + 4.19954643154 < 1E-6)
assert (res[2]['etotal'] + 4.19954643154 < 1E-6)
[docs]def which(program):
"""
Search for the presence of an executable
Found in: http://stackoverflow.com/questions/377017/test-if-executable-exists-in-python
"""
import os
def is_exe(filep):
return os.path.isfile(filep) and os.access(filep, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
for path in os.environ["PATH"].split(os.pathsep):
exe_file = os.path.join(path, program)
if is_exe(exe_file):
return exe_file
return None
if __name__ == '__main__':
test_example2()