def siesta_md(atoms=None,
gen='poscar.gen',
ncpu=4,
supercell=[1, 1, 1],
dt=0.5,
P=0.0,
T=None,
tstep=5000,
opt='Verlet',
us='F',
FreeAtoms=None):
if exists('siesta.MDE') or exists('siesta.MD_CAR'):
system('rm siesta.MDE siesta.MD_CAR')
if atoms is None:
atoms = read(gen)
write_siesta_in(atoms,
coord='cart',
md=True,
opt=opt,
xcf='VDW',
xca='DRSLL',
dt=dt,
T=T,
P=P,
tstep=tstep,
us=us,
FreeAtoms=FreeAtoms) # for MD
run_siesta(ncpu=ncpu)
images = siesta_traj(batch=tstep)
return images
def siesta_opt(atoms,
label='siesta',
ncpu=4,
supercell=[1, 1, 1],
VariableCell='true',
xcf='VDW',
xca='DRSLL',
basistype='DZP',
dt=0.5,
T=None,
tstep=5000,
us='F',
P=0.0,
coord='cart'):
write_siesta_in(atoms,
coord=coord,
VariableCell=VariableCell,
md=False,
opt='CG',
P=P,
xcf=xcf,
xca=xca,
basistype=basistype,
us=us) # for MD
run_siesta(ncpu=ncpu)
images = siesta_traj(label=label)
return images
def single_point(atoms,
xcf='VDW',
xca='DRSLL',
basistype='DZP',
val={
'C': 4.0,
'H': 1.0,
'O': 6.0,
'N': 5.0,
'F': 7.0,
'Al': 3.0
},
cpu=4):
if isfile('siesta.out'):
system('rm siesta.*')
write_siesta_in(atoms,
coord='cart',
md=True,
opt='SinglePoint',
xcf=xcf,
xca=xca,
basistype=basistype,
us=False) # for MD
system('mpirun -n %d siesta<in.fdf>siesta.out' % cpu)
natom = len(atoms)
atom_name = atoms.get_chemical_symbols()
spec = []
for sp in atom_name:
if sp not in spec:
spec.append(sp)
e, f, p, q = get_siesta_info(natom,
spec,
atom_name,
val=val,
label='siesta')
atoms.set_initial_charges(charges=q[-1])
calc = SinglePointCalculator(atoms, energy=e, stress=p[-1])
atoms.set_calculator(calc)
return atoms
def single_point(atoms, cpu=4):
if isfile('siesta.out'):
system('rm siesta.*')
write_siesta_in(atoms,
coord='cart',
md=True,
opt='SinglePoint',
xcf='VDW',
xca='DRSLL',
us=False) # for MD
system('mpirun -n %d siesta<in.fdf>siesta.out' % cpu)
with open('siesta.out', 'r') as fs:
for line in fs.readlines():
if line.startswith('siesta: E_KS(eV)'):
e = float(line.split()[-1])
break
calc = SinglePointCalculator(atoms, energy=e)
atoms.set_calculator(calc)
return atoms
x1 = xd[0] * a[0] + xd[1] * b[0] + xd[2] * c[0]
x2 = xd[0] * a[1] + xd[1] * b[1] + xd[2] * c[1]
x3 = xd[0] * a[2] + xd[1] * b[2] + xd[2] * c[2]
x.append([x1, x2, x3])
il += 1
xs.append(x)
A = Atoms(atom_name, x, cell=[a, b, c], pbc=[True, True, True])
A.set_calculator(calc)
# A._calc.results['energy'] =
his.write(atoms=A)
cell = np.array([a, b, c])
his.close()
if __name__ == '__main__':
from emdk import get_structure, emdk
from ase.io import read, write
from ase import Atoms
from siesta import write_siesta_in
supercell = [1, 1, 1]
struc = 'cl20'
get_structure(struc=struc, output='dftb', recover=True, center=True)
A = read('card.gen')
write_siesta_in(A, coord='zmatrix', fac=1.20)
