def opt(ncpu=20,T=2500,us='F',tstep=2001,dt=1.0,gen='poscar.gen'):
if exists('siesta.MDE') or exists('siesta.MD_CAR'):
system('rm siesta.MDE siesta.MD_CAR')
A = read(gen,index=-1)
A = press_mol(A)
print('\n- running siesta opt ...')
siesta_opt(A,ncpu=ncpu,us=us)
def pm(gen='md.traj', index=-1):
''' pressMol '''
A = read(gen, index=index)
cell = A.get_cell()
print(cell)
A = press_mol(A)
A.write('poscar.gen')
del A
#!/usr/bin/env python
from irff.molecule import packmol, press_mol
from ase.io import read,write
from ase.io.trajectory import TrajectoryWriter
from ase import Atoms
# packmol(strucs=['cl20mol','hmxmol','co2','CO','no2','NO','h2o'],
# supercell=[2,2,2],
# w=True)
A = read('siesta.traj',index=-1)
A = press_mol(A,inbox=False)
A.write('pos.gen')