def read_struct(filename):
"""
Read lattice and atom positions from the crystal output file after a
SLABCUT run.
"""
with open(filename, "r") as f:
lignes = f.readlines()
sectionCoord = False
sites = list()
for i, ligne in enumerate(lignes):
if "DEFINITION OF THE NEW LATTICE VECTORS" in ligne:
while "LATTICE PARAMETERS (ANGSTROM" not in ligne:
i += 1
ligne = lignes[i]
params = [float(val) for val in lignes[i + 2].split()]
slab_lattice = mg.Lattice.from_lengths_and_angles(
params[0:3], params[3:])
if "COORDINATES OF THE ATOMS BELONGING TO THE SLAB" in ligne:
sectionCoord = True
continue
if sectionCoord:
# on saute la premiere ligne
if "LAB" in ligne:
continue
# si ligne blanche on sort
if ligne.strip() == "":
break
z = int(ligne.split()[1])
valeurs = [float(val) for val in ligne[56:].split()]
sites.append(mg.Site(z, valeurs))
return slab_lattice, sites
def make_hydrogen_capped_cluster_from_cif_3(outfilename, ciffile, numnearest, cappingdistances, bqchargemap, centeratom, sphereradius=6, supercell=6, bondlengthcutoff=2.5):
'''Make hydrogen-capped cluster.
Note: 3 means that this version is trying to accommodate inequivalent sites
Supercell needs to be big enough that all atoms in sphere and neighbors thereof
have full neighbors.'''
print('Importing structure')
struct = mg.Structure.from_file(ciffile)
struct.make_supercell(supercell)
# mol = mg.Molecule(struct.species, struct.cart_coords)
mol = tag_sites_by_equivalency(struct)
center_cluster_on_atom(mol, centeratom) # fixed 3.23.19 to add centeratom arg
remove_oxidation_state_from_species(mol)
print('Finding site inside/outside sphere.')
innersites = mol.get_sites_in_sphere([0, 0, 0], sphereradius)
inner = mg.Molecule.from_sites([s[0] for s in innersites])
neighboringmol = mg.Molecule([], [])
for isite in inner:
print('Checking neighbors of site {}'.format(mol.index(isite)), end='\r')
neighbors = mol.get_neighbors(isite, bondlengthcutoff)
for s, _ in neighbors:
if s not in inner:
if s not in neighboringmol:
neighboringmol.append(s.specie, s.coords)
try:
neighboringmol[neighboringmol.index(s)].innerneighbors.append(isite)
except AttributeError:
neighboringmol[neighboringmol.index(s)].innerneighbors = [isite]
hydrcoords = []
hydrneighbors = []
hydrreplace = []
for ns in neighboringmol:
for n in ns.innerneighbors:
hydrcoords.append(np.mean([ns.coords, n.coords], axis=0)) # create hydrogen halfway along bond
hydrneighbors.append(n) # keep track of neighbor identity
hydrreplace.append(ns) # keep track of identitiy of atom being replaced
hydrsites = [mg.Site('H', c) for c in hydrcoords]
hydr = mg.Molecule.from_sites(hydrsites)
# add hydrogen neighbors and adjust bond lengths accordingly
for hs, hn, hr in zip(hydrsites, hydrneighbors, hydrreplace):
hydr[hydr.index(hs)].innerneighbor = hn
hydr[hydr.index(hs)].replacing = hr
for s in hydr:
adjust_bond_length(s, s.innerneighbor, cappingdistances[str(s.innerneighbor.specie)])
capped = mg.Molecule.from_sites(hydr.sites + inner.sites)
print('Writing capped cluster file: ', '{}.xyz'.format(outfilename))
capped.to('xyz', '{}.xyz'.format(outfilename))
print('Writing bq charge file: ', '{}.bq'.format(outfilename))
totalbqcharge = 0
with open('{}.bq'.format(outfilename), 'w') as file:
for s in hydr:
file.write('Bq {:>15.8f}{:>15.8f}{:>15.8f}{:>10.4f}\n'.format(
*s.coords, bqchargemap[str(s.replacing.specie)][str(s.innerneighbor.specie)]))
totalbqcharge += bqchargemap[str(s.replacing.specie)][str(s.innerneighbor.specie)]
with open('{}.xyz'.format(outfilename), 'r') as file:
oldlines = file.readlines()
oldlines[1] = oldlines[1].strip() + '; Total bqcharge for capped cluster: {}\n'.format(totalbqcharge)
with open('{}.xyz'.format(outfilename), 'w') as file:
for line in oldlines:
file.write(line)
slightly_less_dumb_rename_center_atom('{}.xyz'.format(outfilename))
newLattice = mg.Lattice.from_lengths_and_angles(
(a, b, newc), (90., 90., slab_lattice.gamma))
# --------------------------------------------
# decalage des coordonnees entre 0 et 1 dans (xy)
# conversion de z en coordonnees reduites
# --------------------------------------------
print(args)
newSites = list()
for site in sites:
coords = site.coords
coords[0] += .5
coords[1] += .5
if args.center:
coords[2] = coords[2] / newLattice.c + .5
elif args.bottom:
coords[2] = (coords[2] - zmin) / newLattice.c
else:
coords[2] = coords[2] / newLattice.c
newSites.append(mg.Site(site.specie, coords))
# -----------------------------------
# make a structure and print POSCAR
# -----------------------------------
struct = mg.Structure(newLattice, [site.specie for site in newSites],
[site.coords for site in newSites])
struct.sort()
Poscar(struct).write_file(args.poscar)
print(struct)
def make_hydrogen_capped_cluster_from_cif_old_logic(outfilename, ciffile, numnearest, cappingdistances, bqchargemap, centeratom, sphereradius=6, supercell=6):
'''Make hydrogen-capped cluster.
Supercell needs to be big enough that all atoms in sphere and neighbors thereof
have full neighbors.'''
print('Importing structure')
struct = mg.Structure.from_file(ciffile)
struct.make_supercell(6)
mol = mg.Molecule(struct.species, struct.cart_coords)
center_cluster_on_atom(mol, centeratom) # fixed 3.23.19 to add centeratom arg
print('Finding site inside/outside sphere.')
innersites = mol.get_sites_in_sphere([0, 0, 0], sphereradius)
inner = mg.Molecule.from_sites([s[0] for s in innersites])
SHELLDIST = 4
outersites = mol.get_neighbors_in_shell([0, 0, 0], sphereradius + SHELLDIST / 2, SHELLDIST / 2)
outersiteindices = []
for site, _ in outersites:
outersiteindices.append(mol.index(site))
neighboringsites = []
for osi in outersiteindices:
print('Checking neighbors of site {}'.format(osi), end='\r')
neighbors = get_nearest_sites_by_num_neighbors(mol, mol[osi], numnearest)
for s, _ in neighbors:
if s in inner:
try:
mol[osi].innerneighbors.append(s)
except AttributeError:
mol[osi].innerneighbors = [s]
if osi not in neighboringsites:
neighboringsites.append(osi)
hydrcoords = []
hydrneighbors = []
hydrreplace = []
for ns in neighboringsites:
ocoords = mol[ns].coords
for n in mol[ns].innerneighbors:
hydrcoords.append(np.mean([ocoords, n.coords], axis=0))
hydrneighbors.append(n)
hydrreplace.append(mol[ns])
hydrsites = [mg.Site('H', c) for c in hydrcoords]
hydr = mg.Molecule.from_sites(hydrsites)
# add hydrogen neighbors and adjust bond lengths accordingly
for hs, hn, hr in zip(hydrsites, hydrneighbors, hydrreplace):
hydr[hydr.index(hs)].innerneighbor = hn
hydr[hydr.index(hs)].replacing = hr
for s in hydr:
adjust_bond_length(s, s.innerneighbor, cappingdistances[str(s.innerneighbor.specie)])
capped = mg.Molecule.from_sites(hydr.sites + inner.sites)
print('Writing capped cluster file: ', '{}.xyz'.format(outfilename))
capped.to('xyz', '{}.xyz'.format(outfilename))
print('Writing bq charge file: ', '{}.bq'.format(outfilename))
with open('{}.bq'.format(outfilename), 'w') as file:
for s in hydr:
file.write('Bq {:>15.8f}{:>15.8f}{:>15.8f}{:>10.4f}\n'.format(
*s.coords, bqchargemap[str(s.replacing.specie)]))