def generate_muairss_collection(struct, params):
if params["mu_symbol"] in struct.get_chemical_symbols():
print(
"WARNING: chosen muon symbol conflicts with existing elements in"
" the starting unit cell. This could cause mistakes"
)
# Make a supercell
sm = make_3x3(params["supercell"])
# ASE's make_supercell is weird, avoid if not necessary...
smdiag = np.diag(sm).astype(int)
if np.all(np.diag(smdiag) == sm):
scell0 = struct.repeat(smdiag)
else:
scell0 = make_supercell(struct, sm)
reduced_struct = find_primitive_structure(struct)
print("Generating defect configurations...")
# Seed the random generator
Random.reseed(params["random_seed"])
# Now generate the defect configurations
defect_gen = defectGen(
reduced_struct,
"H",
poisson_r=params["poisson_r"],
vdw_scale=params["vdw_scale"],
)
defect_collection = AtomsCollection(defect_gen)
print("{0} configurations generated".format(len(defect_collection)))
collection = []
for atoms in defect_collection:
# Where's the muon?
# We rely on the fact that it's always put at the first place
mupos = atoms.get_positions()[0]
scell = scell0.copy() + Atoms(
"H", positions=[mupos], masses=[constants.m_mu_amu]
)
# Add castep custom species
csp = scell0.get_chemical_symbols() + [params["mu_symbol"]]
scell.set_array("castep_custom_species", np.array(csp))
scell.set_pbc(params["dftb_pbc"])
collection.append(scell)
return AtomsCollection(collection)
def generate_muairss_collection(struct, params):
if params['mu_symbol'] in struct.get_chemical_symbols():
print('WARNING: chosen muon symbol conflicts with existing elements in'
' the starting unit cell. This could cause mistakes')
# Make a supercell
sm = make_3x3(params['supercell'])
# ASE's make_supercell is weird, avoid if not necessary...
smdiag = np.diag(sm).astype(int)
if np.all(np.diag(smdiag) == sm):
scell0 = struct.repeat(smdiag)
else:
scell0 = make_supercell(struct, sm)
reduced_struct = find_primitive_structure(struct)
print('Generating defect configurations...')
# Now generate the defect configurations
defect_gen = defectGen(reduced_struct,
'H',
poisson_r=params['poisson_r'],
vdw_scale=params['vdw_scale'])
defect_collection = AtomsCollection(defect_gen)
print('{0} configurations generated'.format(len(defect_collection)))
collection = []
for atoms in defect_collection:
# Where's the muon?
# We rely on the fact that it's always put at the first place
mupos = atoms.get_positions()[0]
scell = scell0.copy() + Atoms('H', positions=[mupos])
# Add castep custom species
csp = scell0.get_chemical_symbols() + [params['mu_symbol']]
scell.set_array('castep_custom_species', np.array(csp))
scell.set_pbc(params['dftb_pbc'])
collection.append(scell)
return AtomsCollection(collection)
import sys
import glob
from ase import io, Atoms
from ase.build import make_supercell
from pymuonsuite.utils import make_3x3
from pymuonsuite.schemas import load_input_file, MuAirssSchema
atoms = io.read(sys.argv[1])
if len(sys.argv) > 2:
params = load_input_file(sys.argv[2], MuAirssSchema)
scell = make_3x3(params["supercell"])
atoms = make_supercell(atoms, scell)
for f in glob.glob("muon-airss-out/dftb+/*/geo_end.xyz"):
a = io.read(f)
atoms += Atoms("H", positions=a.get_positions()[-1, None, :])
io.write("merged.cif", atoms)
import sys
import glob
import numpy as np
from ase import io, Atoms
from ase.build import make_supercell
from pymuonsuite.utils import make_3x3
from pymuonsuite.schemas import load_input_file, MuAirssSchema
atoms = io.read(sys.argv[1])
if len(sys.argv) > 2:
params = load_input_file(sys.argv[2], MuAirssSchema)
scell = make_3x3(params['supercell'])
atoms = make_supercell(atoms, scell)
for f in glob.glob('muon-airss-out/dftb+/*/geo_end.xyz'):
a = io.read(f)
atoms += Atoms('H', positions=a.get_positions()[-1, None, :])
io.write('merged.cif', atoms)