def write_input(self,
atoms,
properties=None,
system_changes=None,
ghosts=None,
geo_constrain=None,
scaled=False,
velocities=None):
FileIOCalculator.write_input(self, atoms, properties, system_changes)
if geo_constrain is None:
geo_constrain = "relax_geometry" in self.parameters
if scaled is None:
scaled = np.all(atoms.get_pbc())
if velocities is None:
velocities = atoms.has('momenta')
have_lattice_vectors = atoms.pbc.any()
have_k_grid = ('k_grid' in self.parameters
or 'kpts' in self.parameters)
if have_lattice_vectors and not have_k_grid:
raise RuntimeError('Found lattice vectors but no k-grid!')
if not have_lattice_vectors and have_k_grid:
raise RuntimeError('Found k-grid but no lattice vectors!')
write_aims(os.path.join(self.directory, 'geometry.in'),
atoms,
scaled,
geo_constrain,
velocities=velocities,
ghosts=ghosts)
self.write_control(atoms, os.path.join(self.directory, 'control.in'))
self.write_species(atoms, os.path.join(self.directory, 'control.in'))
self.parameters.write(os.path.join(self.directory, 'parameters.ase'))
def calculate(self, atoms):
"""Generate necessary files in the working directory.
If the directory does not exist it will be created.
"""
positions = atoms.get_positions()
have_lattice_vectors = atoms.get_pbc().any()
have_k_grid = self.list_params['k_grid']
if have_lattice_vectors and not have_k_grid:
raise RuntimeError("Found lattice vectors but no k-grid!")
if not have_lattice_vectors and have_k_grid:
raise RuntimeError("Found k-grid but no lattice vectors!")
from ase.io.aims import write_aims
write_aims('geometry.in', atoms)
self.write_control()
self.write_species()
self.run()
self.converged = self.read_convergence()
if not self.converged:
os.system("tail -20 "+self.out)
raise RuntimeError("FHI-aims did not converge!\n"+
"The last lines of output are printed above "+
"and should give an indication why.")
self.set_results(atoms)
def write_input(self, atoms, properties=None, system_changes=None, ghosts=None):
FileIOCalculator.write_input(self, atoms, properties, system_changes)
have_lattice_vectors = atoms.pbc.any()
have_k_grid = ('k_grid' in self.parameters or
'kpts' in self.parameters)
if have_lattice_vectors and not have_k_grid:
raise RuntimeError('Found lattice vectors but no k-grid!')
if not have_lattice_vectors and have_k_grid:
raise RuntimeError('Found k-grid but no lattice vectors!')
write_aims(os.path.join(self.directory, 'geometry.in'), atoms, ghosts)
self.write_control(atoms, os.path.join(self.directory, 'control.in'))
self.write_species(atoms, os.path.join(self.directory, 'control.in'))
self.parameters.write(os.path.join(self.directory, 'parameters.ase'))
ra = options.rotate_around
if (ra > 0 and ra <= natoms):
positions = step.arrays['positions']
origin = positions[ra - 1]
# rotate selected atoms
asekk.rotate_atoms(step,
alpha,
fromto=[a_from, a_to],
axis=options.axis,
origin=origin)
# --- Repetytion ----
if (do_we_repeat):
# multiply by periods
step = step * p
# ----- Write -----
if (options.format == 'xyz'):
write_xyz(sys.stdout, step, comment=comm)
elif (options.format == 'aims'):
write_aims("geometry.in", step)
elif (options.format == 'poscar'):
# print step.get_cell()
step.center()
write_vasp(sys.stdout,
step,
label="POSCAR generated by asm.xyz.py",
direct=False,
sort=False,
vasp5=True)
parser = OptionParser()
parser.add_option("-a", "--lattice", action="store", type="float", default=1.0)
parser.add_option("-p",
"--periods",
action="store",
type="int",
default=[1, 1, 1],
help="repetition of the unit cell",
nargs=3)
parser.add_option("-e",
"--element",
action="store",
type="string",
default='H')
(options, args) = parser.parse_args()
a = options.lattice
p = options.periods
e = options.element
#print a
atoms = FaceCenteredCubic(latticeconstant=a,
directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=p,
symbol=e,
pbc=(1, 1, 1))
write_aims("geometry.in", atoms)
for i in range(3):
l = ls[i].split()
cell[i] = [float(l[0]), float(l[1]), float(l[2])]
atoms.set_cell(cell)
atoms.set_pbc([True, True, True])
elif (iformat == "cube"):
cube = read_cube(sys.argv[num - 1], read_data=True)
atoms = cube[1]
field = cube[0]
print atoms.get_cell()
print len(field), len(field[0]), len(field[0][0])
if (oformat == "geometry.in"):
tmpname = "geometry.in.tmp"
write_aims(tmpname, atoms)
f = open(tmpname, 'r')
print f.read()
f.close()
os.remove(tmpname)
# write_aims("geometry.in", atoms)
# elif(oformat == "cube"):
# write_cube(`,xsf[1],xsf[0])
# elif(oformat == "xsf"):
# write_xsf(sys.stdout,xsf[1],xsf[0])
elif (oformat == "POSCAR"):
write_vasp(ostream,
atoms,
label=options.comment,
direct=False,
