def opt_and_md(struc='cl20',
file='card.gen',
supercell=[1, 1, 1],
T=3000,
step=20000,
wall=False,
restart=None,
psp=None,
functional='REVPBE',
restart_nve='WAVEFUNCTION COORDINATES LATEST',
ncpu=12):
if file == 'card.gen':
get_structure(struc=struc,
supercell=supercell,
output='dftb',
recover=True,
center=True)
A = read(file)
run_cpmd(A,
res_opt=restart,
res_md=restart_nve,
wall=wall,
psp=psp,
functional=functional,
ncpu=ncpu)
def collect_data(strucs=['cl20mol', 'hmxmol'], T=200, step=20000, np=12):
''' gather datas '''
root = getcwd()
restart_l = 'WAVEFUNCTION COORDINATES VELOCITIES CELL ACCUMULATORS NOSEE NOSEP LATEST'
for s in strucs:
for i in range(5):
dirc = s + '_' + str(i)
system('mkdir ' + dirc)
chdir(dirc)
if i == 0:
system('cp ../*.psp ./')
get_structure(struc=s,
output='dftb',
recover=True,
center=True)
A = read('card.gen')
write_cpmd_inp(A, runtype='wvopt', restart=None)
print('* optimizing wave functions of %s ...' % s)
system('mpirun -n %d cpmd inp-wvopt>wv.out' % np)
write_cpmd_inp(A,
runtype='md',
ensemble='nve',
T=T,
step=step,
restart=restart_l)
else:
system('cp ../' + s + '_' + str(i - 1) + '/*.psp ./')
system('cp ../' + s + '_' + str(i - 1) + '/RESTART.1 ./')
system('cp ../' + s + '_' + str(i - 1) + '/LATEST ./')
write_cpmd_inp(A, runtype='wvopt', restart=restart_l)
print('* optimizing wave functions of %s ...' % s)
system('mpirun -n %d cpmd inp-wvopt>wv.out' % np)
write_cpmd_inp(A,
runtype='md',
ensemble='nvt',
T=T,
step=step,
restart=restart_l)
print('* Car-Parinnello MD simulations ...')
system('mpirun -n %d cpmd inp-nvt>nvt.out' % np)
chdir(root)
if not il == 0:
cell.append([float(l[0]), float(l[1]), float(l[2])])
il += 1
if readlat and il < 2:
if not il == 0:
cell = [[float(l[0]), 0.0, 0.0],
[0.0, float(l[1]) * float(l[0]), 0.0],
[0.0, 0.0, float(l[2]) * float(l[0])]]
il += 1
finp.close()
return cell
if __name__ == '__main__':
from emdk import get_structure, emdk
from ase.io import read, write
from ase import Atoms
from cpmd import write_cpmd_inp
supercell = [1, 1, 1]
struc = 'cl20mol'
get_structure(struc=struc, output='dftb', recover=True, center=True)
# emdk(cardtype='xyz',cardfile='siesta.xyz',
# cell=[[10.0,0.0,0.0],[0.0,10.0,0.0],[0.0,0.0,10.0]],
# output='dftb',
# center='.True.',log='log')
A = read('card.gen')
write_cpmd_inp(A, runtype='md', ensemble='nve')
# write_cpmd_inp(A,runtype='md',ensemble='nvt',restart=True)