def trilayer(doped = None):
a = 5.43
fcc = Lattice([[a/2,a/2,0],[a/2,0,a/2],[0,a/2,a/2]])
trilayer = Structure(fcc,['Si']*2,[[0.00,0.00,0.00],[0.25,0.25,0.25]])
# Make the cell cubic
trilayer.make_supercell([[1,1,-1],[1,-1,1],[-1,1,1]])
trilayer.make_supercell([[1,1,0],[1,-1,0],[0,0,4]])
# Rotate the cell
rt = 0.70710678118654746
symmop = SymmOp.from_rotation_and_translation([[rt,rt,0],[rt,-rt,0],[0,0,1]])
trilayer.apply_operation(symmop)
if doped is not None:
frac_coords = numpy.array([0.5,0.0,0.5])
for i,atom in enumerate(trilayer):
if numpy.linalg.norm(atom.frac_coords-frac_coords) < 0.001:
trilayer.replace(i,doped,frac_coords)
for z in [0.375,0.625]:
for xy in [0.00,0.50]:
trilayer.append('Mn',[xy,xy,z])
return trilayer
def make_InAs001_surface(inas_layers = 4, licras_layers = 4, vacuum_layers = 8):
total_layers = inas_layers + licras_layers + vacuum_layers
err = 1./total_layers/10
a = Length(6.0583, "ang")
fcc_lattice = np.array([[.0,.5,.5],[.5,.0,.5],[.5,.5,.0]])
lattice = Lattice(fcc_lattice * a)
surface = Structure(lattice, ['Li', 'Cr', 'As'], [[0.50,0.50,0.50],[0.00,0.00,0.00],[0.25,0.25,0.25]])
surface.make_supercell([[0,0,1],[1,-1,0],[1,1,-1]])
surface.make_supercell([[1,0,0],[0,1,0],[0,0,total_layers]])
to_remove = []
print (1.*inas_layers / total_layers)
print 1.*(inas_layers+licras_layers)/total_layers
print 1. - 1. / vacuum_layers
print err
for idx,site in enumerate(surface):
if (site.frac_coords[2] - 1.*inas_layers / total_layers) < -err:
if site.specie.symbol == 'Li': to_remove.append(idx)
if site.specie.symbol == 'Cr': surface.replace(idx,Element('In'))
if (site.frac_coords[2] - 1. + 1./vacuum_layers/8.) > -err:
surface.replace(idx,Element('H'))
elif (1.*(inas_layers+licras_layers)/total_layers) - site.frac_coords[2] < err:
to_remove.append(idx)
surface.remove_sites(to_remove)
selective_dynamics = len(surface) * [[True,True,True]]
for idx,site in enumerate(surface):
if (np.linalg.norm(site.frac_coords) < err):
selective_dynamics[idx] = [False,False,False]
return surface.get_sorted_structure(),np.array(selective_dynamics)
def make_trilayer(xyscale = 2, zscale = 4):
a = Length(5.431,"ang")
fcc_lattice = np.array([[.0,.5,.5],[.5,.0,.5],[.5,.5,.0]])
lattice = Lattice(fcc_lattice * a)
trilayer = Structure(lattice, ['Si','Si'], [[0.00,0.00,0.00],[0.25,0.25,0.25]])
trilayer.make_supercell([[0,0,1],[1,-1,0],[1,1,-1]])
trilayer.make_supercell([[xyscale,0,0],[0,xyscale,0],[0,0,zscale]])
# Dope the Ga sites
for idx,site in enumerate(trilayer):
if np.linalg.norm(site.frac_coords - np.array([+.0,+.5,.0])) < 1e-10:
trilayer.replace(idx,Element('Ga'))
if np.linalg.norm(site.frac_coords - np.array([+.5,+.0,.0])) < 1e-10:
trilayer.replace(idx,Element('Ga'))
# Insert the Mn sites
trilayer.append('Mn', [0.0,0.0,zscale*a-a/2], coords_are_cartesian=True)
trilayer.append('Mn', [0,a,zscale*a-a/2], coords_are_cartesian=True)
trilayer.append('Mn', [0.0,0.0,a/2], coords_are_cartesian=True)
trilayer.append('Mn', [0,a,a/2], coords_are_cartesian=True)
return trilayer.get_sorted_structure()
def make_Si001_surface(Si_layers = 4, vacuum_layers = 4):
total_layers = Si_layers + vacuum_layers
a = Length(5.431, "ang")
fcc_lattice = np.array([[.0,.5,.5],[.5,.0,.5],[.5,.5,.0]])
lattice = Lattice(fcc_lattice * a)
surface = Structure(lattice, ['Si','Si'], [[0.00,0.00,0.00],[0.25,0.25,0.25]])
surface.make_supercell([[0,0,1],[1,-1,0],[1,1,-1]])
surface.make_supercell([[2,0,0],[0,2,0],[0,0,total_layers]])
to_remove = []
for idx,site in enumerate(surface):
if (site.frac_coords[2] > 1.0*Si_layers/total_layers):
to_remove.append(idx)
surface.remove_sites(to_remove)
print to_remove
selective_dynamics = len(surface) * [[True,True,True]]
for idx,site in enumerate(surface):
if (site.frac_coords[2] < 0.001):
selective_dynamics[idx] = [False,False,False]
surface.replace(idx,Element('H'))
return surface.get_sorted_structure(),np.array(selective_dynamics)
def test_unique_structure_substitutions(self):
# integration test
# Create a pymatgen structure with 16 sites in a 4x4 square grid
coords = np.array([[0.0, 0.0, 0.0], [0.25, 0.0, 0.0], [0.5, 0., 0.0],
[0.75, 0.0, 0.0], [0.0, 0.25, 0.0],
[0.25, 0.25, 0.0], [0.5, 0.25, 0.0],
[0.75, 0.25, 0.0], [0.0, 0.5,
0.0], [0.25, 0.5, 0.0],
[0.5, 0.5, 0.0], [0.75, 0.5, 0.0], [0.0, 0.75, 0.0],
[0.25, 0.75, 0.0], [0.5, 0.75, 0.0],
[0.75, 0.75, 0.0]])
atom_list = ['Li'] * len(coords)
lattice = Lattice.from_parameters(a=3.0,
b=3.0,
c=3.0,
alpha=90,
beta=90,
gamma=90)
parent_structure = Structure(lattice, atom_list, coords)
parent_structure.replace(0, 'O') # substitute one site with 'O'
ns = unique_structure_substitutions(parent_structure, 'Li', {
'Na': 1,
'Li': 14
})
self.assertEqual(len(ns), 5)
distances = np.array(
sorted([
s.get_distance(
s.indices_from_symbol('O')[0],
s.indices_from_symbol('Na')[0]) for s in ns
]))
np.testing.assert_array_almost_equal(
distances, np.array([0.75, 1.06066, 1.5, 1.677051, 2.12132]))
np.testing.assert_array_equal(
np.array(
sorted([s.number_of_equivalent_configurations for s in ns])),
np.array([1, 2, 4, 4, 4]))
np.testing.assert_array_equal(
np.array(sorted([s.full_configuration_degeneracy for s in ns])),
np.array([1, 2, 4, 4, 4]))
def run_task(self, fw_spec):
atom_style = self.get('atom_style')
start_temp = self.get('start_temp')
end_temp = self.get('end_temp')
nsteps = self.get('nsteps')
spawn = self.get('spawn') or False
production = self.get('production') or False
time_step = self.get('time_step') or 1
vasp_cmd = self.get('vasp_cmd') or ">>vasp_gam<<"
copy_vasp_outputs = self.get('copy_vasp_outputs') or False
user_incar_settings = self.get('user_incar_settings') or {}
user_kpoints_settings = self.get('user_kpoints_settings') or None
db_file = self.get('db_file') or None
transmute = self.get('transmute') or None
pressure_threshold = self.get('pressure_threshold') or 5
max_rescales = self.get('max_rescales') or 6
wall_time = self.get('wall_time') or 19200
copy_calcs = self.get('copy_calcs') or False
calc_home = self.get('calc_home') or '~'
logger.info("PARSING \"lammps.final\" to VASP.")
data = LammpsData.from_file(os.path.join(os.getcwd(),
self.get('final_data')),
atom_style=atom_style,
sort_id=True)
struc = data.structure
structure = Structure(lattice=struc.lattice,
species=[s.specie for s in struc.sites],
coords=[s.coords for s in struc.sites],
coords_are_cartesian=True)
if transmute:
sites = structure.sites
indices = []
for i, s in enumerate(sites):
if s.specie.symbol == transmute[0]:
indices.append(i)
index = random.choice(indices)
structure.replace(
index,
species=transmute[1],
properties={'charge': Specie(transmute[1]).oxi_state})
vasp_input_set = MITMDSet(structure,
start_temp,
end_temp,
nsteps,
time_step,
force_gamma=True,
user_incar_settings=user_incar_settings)
if user_kpoints_settings:
v = vasp_input_set.as_dict()
v.update({"user_kpoints_settings": user_kpoints_settings})
vasp_input_set = vasp_input_set.from_dict(v)
fw = MDFW(structure,
start_temp,
end_temp,
nsteps,
vasp_input_set=vasp_input_set,
vasp_cmd=vasp_cmd,
copy_vasp_outputs=copy_vasp_outputs,
db_file=db_file,
name='MDFW',
wall_time=wall_time)
if spawn:
t = fw.tasks
t.append(
SpawnMDFWTask(pressure_threshold=pressure_threshold,
max_rescales=max_rescales,
wall_time=wall_time,
vasp_cmd=vasp_cmd,
db_file=db_file,
copy_calcs=copy_calcs,
calc_home=calc_home,
spawn_count=1,
production=production))
fw = Firework(tasks=t, name='SpawnMDFW')
return FWAction(detours=fw, stored_data={'LammpsStructure': structure})
