def test_magnetism_setup():
from jarvis.db.figshare import get_jid_data
from jarvis.core.atoms import get_supercell_dims
atoms = Atoms.from_dict(
get_jid_data(jid="JVASP-78681", dataset="dft_3d")["atoms"]
)
dim = get_supercell_dims(atoms)
print("dim=", dim)
dim = [2, 2, 2]
symm_list, ss = get_unique_magnetic_structures(
atoms, supercell_dim=dim, magnetic_ions=["Mn"]
)
print("dim=", dim, len(symm_list))
assert len(symm_list)==5
assert ss.num_atoms == 16
def basic_data(data={}, source="JARVIS-FF-LAMMPS"):
"""Get basic data for table."""
info = {}
info["id"] = data["jid"]
info["source_folder"] = data["source_folder"]
info["tmp_source_folder"] = "'" + data["source_folder"] + "'"
info["tmp_id"] = "'" + data["jid"] + "'"
ref = data["source_folder"].split("/")[-1].split("@")[1].split("_")[0]
info["ref"] = "'" + ref + "'"
info["jvid"] = get_jvid(ref)
final_atoms = data["bulk_data"]["final_str"]
initial_atoms = data["bulk_data"]["initial_str"]
info["formula"] = final_atoms.composition.reduced_formula
info["tmp_formula"] = "'" + final_atoms.composition.reduced_formula + "'"
info["elements"] = ",".join(final_atoms.uniq_species)
info["tmp_elements"] = "'" + ",".join(final_atoms.uniq_species) + "'"
info["number_uniq_species"] = len(final_atoms.uniq_species)
info["data_source"] = source
info["tmp_data_source"] = "'" + source + "'"
info["pair_style"] = data["bulk_data"]["pair_style"]
info["pair_coeff"] = data["bulk_data"]["pair_coeff"]
# info["pair_coeff"] = (
# '<a href="http://www.ctcms.nist.gov/~knc6/DOWNLOADS/'
# + data["bulk_data"]["pair_coeff"]
# + '.zip">'
# + data["bulk_data"]["pair_coeff"]
# + "</a>"
# )
info["energy_per_atom"] = round(
float(data["bulk_data"]["energy_per_atom"]), 3)
info["pressure"] = round(float(data["bulk_data"]["system_pressure"]), 3)
initial_spg = Spacegroup3D(initial_atoms)
final_spg = Spacegroup3D(final_atoms)
info["initial_spacegroup_number"] = initial_spg.space_group_number
info["initial_spacegroup_symbol"] = initial_spg.space_group_symbol
info["initial_pointgroup_symbol"] = initial_spg.point_group_symbol
info["initial_crystal_system"] = initial_spg.crystal_system
initial_lat_params = initial_atoms.lattice.parameters
info["initial_a"] = round(initial_lat_params[0], 2)
info["initial_b"] = round(initial_lat_params[1], 2)
info["initial_c"] = round(initial_lat_params[2], 2)
info["initial_alpha"] = round(initial_lat_params[3], 2)
info["initial_beta"] = round(initial_lat_params[4], 2)
info["initial_gamma"] = round(initial_lat_params[5], 2)
info["initial_density"] = round(initial_atoms.density, 3)
dim = get_supercell_dims(final_atoms)
info["xyz"] = (
'"' +
str(final_atoms.make_supercell_matrix(dim).get_xyz_string).replace(
"\n", "\\n") + '"')
info["final_str"] = ('"' +
str(final_atoms.get_string()).replace("\n", "\\n") +
'"')
info["initial_str"] = (
'"' + str(initial_atoms.get_string()).replace("\n", "\\n") + '"')
final_lat_params = final_atoms.lattice.parameters
info["final_a"] = round(final_lat_params[0], 2)
info["final_b"] = round(final_lat_params[1], 2)
info["final_c"] = round(final_lat_params[2], 2)
info["final_alpha"] = round(final_lat_params[3], 2)
info["final_beta"] = round(final_lat_params[4], 2)
info["final_gamma"] = round(final_lat_params[5], 2)
info["final_density"] = round(final_atoms.density, 3)
info["final_spacegroup_number"] = final_spg.space_group_number
info["final_spacegroup_symbol"] = final_spg.space_group_symbol
info["final_pointgroup_symbol"] = final_spg.point_group_symbol
info["final_crystal_system"] = final_spg.crystal_system
et = ""
# print(data["bulk_data"]["elastic_tensor"]["raw_et_tensor"])
try:
if data["bulk_data"]["elastic_tensor"] != "":
cij = np.round(
(data["bulk_data"]["elastic_tensor"]["raw_et_tensor"]), 2)
et = (
'<cij>"' +
";".join([",".join(map(str, cij[:, i]))
for i in range(0, 6)]) + '"</cij>')
except Exception as exp:
print("Cannot obtain elastic tensor data.", info["source_folder"], exp)
pass
info["elastic_tensor"] = et
vacancy_line = ""
if len(data["vacancy_info"]) != 0:
for i in data["vacancy_info"]:
vacancy_line += i[0] + "," + i[1] + "," + str(round(i[2], 3)) + ";"
info["vacancy_info"] = '"' + vacancy_line + '"'
surf_line = ""
if len(data["surface_info"]) != 0:
for i in data["surface_info"]:
surf_line += i[0] + "," + str(round(i[1], 3)) + ";"
info["surface_info"] = '"' + surf_line + '"'
phonon_band_line = ""
try:
# Band
frequencies = data["band_frequencies"]
distances = data["band_distances"]
labels = data["band_labels"]
label_points = data["band_label_points"]
tmp = ""
for i in range(np.array(frequencies).shape[1]):
tmp += ",".join(map(str, np.array(frequencies)[:, i])) + ";"
phonon_band_line += ("<phonon_bandstructure_distances>'" +
",".join(map(str, distances)) +
"'</phonon_bandstructure_distances>")
phonon_band_line += ("<phonon_bandstructure_frequencies>'" + tmp +
"'</phonon_bandstructure_frequencies>")
phonon_band_line += ("<phonon_bandstructure_labels>'" +
",".join(map(str, labels)) +
"'</phonon_bandstructure_labels>")
phonon_band_line += ("<phonon_bandstructure_label_points>'" +
",".join(map(str, label_points)) +
"'</phonon_bandstructure_label_points>")
except Exception as exp:
print("Cannot obtain phonon band data.", exp)
# Comment until 4 MB text size error
info["phonon_band_line"] = phonon_band_line
phonon_dos_line = ""
try:
freq = data["dos_freq"]
pdos = data["dos_intensity"]
phonon_dos_line += ("<phonon_dos_frequencies>'" +
",".join(map(str, freq)) +
"'</phonon_dos_frequencies>")
phonon_dos_line += ("<phonon_dos_intensity>'" +
",".join(map(str, pdos)) +
"'</phonon_dos_intensity>")
except Exception:
print("Cannot obtain phonon dod data.")
pass
info["phonon_dos_line"] = phonon_dos_line
return info
def from_atoms(
atoms=None,
get_prim=False,
zero_diag=False,
node_atomwise_angle_dist=False,
node_atomwise_rdf=False,
features="basic",
enforce_c_size=10.0,
max_n=100,
max_cut=5.0,
verbose=False,
make_colormap=True,
):
"""
Get Networkx graph. Requires Networkx installation.
Args:
atoms: jarvis.core.Atoms object.
rcut: cut-off after which distance will be set to zero
in the adjacency matrix.
features: Node features.
'atomic_number': graph with atomic numbers only.
'cfid': 438 chemical descriptors from CFID.
'basic':10 features
'atomic_fraction': graph with atomic fractions
in 103 elements.
array: array with CFID chemical descriptor names.
See: jarvis/core/specie.py
enforce_c_size: minimum size of the simulation cell in Angst.
"""
if get_prim:
atoms = atoms.get_primitive_atoms
dim = get_supercell_dims(atoms=atoms, enforce_c_size=enforce_c_size)
atoms = atoms.make_supercell(dim)
adj = np.array(atoms.raw_distance_matrix.copy())
# zero out edges with bond length greater than threshold
adj[adj >= max_cut] = 0
if zero_diag:
np.fill_diagonal(adj, 0.0)
nodes = np.arange(atoms.num_atoms)
if features == "atomic_number":
node_attributes = np.array(
[[np.array(Specie(i).Z)] for i in atoms.elements],
dtype="float",
)
if features == "atomic_fraction":
node_attributes = []
fracs = atoms.composition.atomic_fraction_array
for i in fracs:
node_attributes.append(np.array([float(i)]))
node_attributes = np.array(node_attributes)
elif features == "basic":
feats = [
"Z",
"coulmn",
"row",
"X",
"atom_rad",
"nsvalence",
"npvalence",
"ndvalence",
"nfvalence",
"first_ion_en",
"elec_aff",
]
node_attributes = []
for i in atoms.elements:
tmp = []
for j in feats:
tmp.append(Specie(i).element_property(j))
node_attributes.append(tmp)
node_attributes = np.array(node_attributes, dtype="float")
elif features == "cfid":
node_attributes = np.array(
[np.array(Specie(i).get_descrp_arr) for i in atoms.elements],
dtype="float",
)
elif isinstance(features, list):
node_attributes = []
for i in atoms.elements:
tmp = []
for j in features:
tmp.append(Specie(i).element_property(j))
node_attributes.append(tmp)
node_attributes = np.array(node_attributes, dtype="float")
else:
print("Please check the input options.")
if node_atomwise_rdf or node_atomwise_angle_dist:
nbr = NeighborsAnalysis(atoms,
max_n=max_n,
verbose=verbose,
max_cut=max_cut)
if node_atomwise_rdf:
node_attributes = np.concatenate(
(node_attributes, nbr.atomwise_radial_dist()), axis=1)
node_attributes = np.array(node_attributes, dtype="float")
if node_atomwise_angle_dist:
node_attributes = np.concatenate(
(node_attributes, nbr.atomwise_angle_dist()), axis=1)
node_attributes = np.array(node_attributes, dtype="float")
# construct edge list
uv = []
edge_features = []
for ii, i in enumerate(atoms.elements):
for jj, j in enumerate(atoms.elements):
bondlength = adj[ii, jj]
if bondlength > 0:
uv.append((ii, jj))
edge_features.append(bondlength)
edge_attributes = edge_features
if make_colormap:
sps = atoms.uniq_species
color_dict = random_colors(number_of_colors=len(sps))
new_colors = {}
for i, j in color_dict.items():
new_colors[sps[i]] = j
color_map = []
for ii, i in enumerate(atoms.elements):
color_map.append(new_colors[i])
return Graph(
nodes=nodes,
edges=uv,
node_attributes=np.array(node_attributes),
edge_attributes=np.array(edge_attributes),
color_map=color_map,
)
def test_basic_atoms():
box = [[2.715, 2.715, 0], [0, 2.715, 2.715], [2.715, 0, 2.715]]
coords = [[0, 0, 0], [0.25, 0.2, 0.25]]
elements = ["Si", "Si"]
Si = Atoms(lattice_mat=box, coords=coords, elements=elements)
dim = get_supercell_dims(Si)
assert dim == [3, 3, 3]
polar = Si.check_polar
Si.props = ["a", "a"]
vac_pad = VacuumPadding(Si)
den_2d = round(vac_pad.get_effective_2d_slab().density, 2)
den_0d = round(vac_pad.get_effective_molecule().density, 2)
den_lll_red = round(Si.get_lll_reduced_structure().density, 2)
strng = Si.get_string()
scell_nat = Si.make_supercell([2, 2, 2]).num_atoms
scell_nat2 = Si.make_supercell_matrix([[2, 0, 0], [0, 2, 0],
[0, 0, 2]]).num_atoms
# print("scell_nat,scell_nat2", scell_nat, scell_nat2)
# print(Si.make_supercell([2, 2, 2]))
# print()
# print(Si.make_supercell_matrix([[2, 0, 0], [0, 2, 0], [0, 0, 2]]))
com = round(Si.get_center_of_mass()[0], 3)
rem = (Si.make_supercell([2, 2, 2]).remove_site_by_index(site=0)).num_atoms
prim = Si.get_primitive_atoms
print(prim.cart_coords)
assert round(prim.cart_coords[0][0], 2) == round(4.37815150, 2)
# print ('raw_distance_matrix', prim.raw_distance_matrix)
# print ('raw_distance_matrix', Si.raw_distance_matrix)
# print ('distance_matrix', Si.pymatgen_converter().distance_matrix)
assert round(prim.raw_distance_matrix[0][1],
2) == round(4.42386329832851, 2)
print(prim.raw_angle_matrix)
d = Si.to_dict()
new_at = Atoms.from_dict(d)
angs_a = d["angles"][0]
Si_2_den = Atoms(
lattice_mat=d["lattice_mat"],
coords=d["coords"],
elements=d["elements"],
).density
Si_xyz = Si.get_xyz_string
Si.write_xyz(filename="atoms.xyz")
tmp = Atoms.from_xyz(filename="atoms.xyz")
cmd = 'rm atoms.xyz'
os.system(cmd)
Si.center_around_origin()
# print ('scell_nat', Si_2)
assert (
round(Si.volume, 2),
Si.atomic_numbers,
Si.num_atoms,
Si.frac_coords[0][0],
Si.cart_coords[0][0],
round(Si.density, 2),
Si.spacegroup(),
Si.pymatgen_converter() != {},
polar,
Si.props[0],
den_2d,
den_0d,
round(Si.packing_fraction, 2),
Si.composition.to_dict(),
strng != "",
den_lll_red,
scell_nat,
com,
rem,
angs_a,
round(Si_2_den, 2),
) == (
40.03,
[14, 14],
2,
0,
0.0,
2.33,
"C2/m (12)",
True,
False,
"a",
0.35,
0.01,
0.28,
{
"Si": 2
},
True,
2.33,
16,
0.679,
15,
60.0,
2.33,
)
cc = Si.center()
cc = Si.center(axis=[0, 0, 1])
m1 = Atoms.from_dict(get_jid_data("JVASP-6640")["atoms"])
assert m1.check_polar == True
print("Strain test")
print(m1)
m1.apply_strain(0.1)
print(m1)
assert m1.lattice_mat[2][2] == 32.8717576
m1.apply_strain([0, 0, 0.1])
assert m1.lattice_mat[2][2] == 36.158933360000006
filename = "atoms.cif"
m1.write_cif(filename)
a = Atoms.from_cif(filename)
filename = "POSCAR"
m1.write_poscar(filename)
m2 = Atoms.from_poscar(filename)
filename = "atoms.xyz"
m1.write_xyz(filename)
m3 = Atoms.from_xyz(filename)
cmd = "rm atoms.xyz POSCAR atoms.cif"
os.system(cmd)
def all_props_eam_alloy(
self,
atoms=None,
ff_path="",
lammps_cmd="",
enforce_conventional_structure=True,
enforce_c_size=0,
extend=1,
):
"""
Provide generic function for LAMMPS calculations using eam/alloy.
Must provide Atoms class and path to force-field.
Args:
atoms : Atoms object
ff_path : inter-atomic potential path
lammps_cmd : LAMMPS executable path
enforce_conventional_structure :
whether to enforce conventional cell
enforce_c_size : minimum cell-sizes
extend : used for round-off during making supercells
"""
if enforce_conventional_structure:
atoms = Spacegroup3D(atoms).conventional_standard_structure
if enforce_c_size is not None:
dim = get_supercell_dims(atoms, enforce_c_size=enforce_c_size)
atoms = atoms.make_supercell([dim[0], dim[1], dim[2]])
self.pair_style = "eam/alloy"
self.pair_coeff = ff_path
parameters = {
"pair_style": self.pair_style,
"atom_style": "charge",
"pair_coeff": self.pair_coeff,
}
parameters["control_file"] = "inelast.mod"
en, final_str, forces = LammpsJob(
atoms=atoms,
jobname="ELASTIC",
parameters=parameters,
lammps_cmd=lammps_cmd,
).runjob()
print("en, final_str, forces", en, final_str, forces)
indices = symmetrically_distinct_miller_indices(max_index=1,
cvn_atoms=atoms)
for i in indices:
surf = Surface(atoms=final_str, indices=i).make_surface()
jobname = str("Surf-") + str("_".join(map(str, i)))
en2, final_str2, forces2 = LammpsJob(
atoms=surf,
jobname=jobname,
parameters=parameters,
lammps_cmd=lammps_cmd,
).runjob()
# sys.exit()
v = Vacancy(atoms=final_str).generate_defects(enforce_c_size=5)
print("vacs=", v)
for i, ii in enumerate(v):
jobname = (str("symbol-") + str(ii._symbol) + str("-") +
str("Wycoff-") + str(ii._wyckoff_multiplicity))
print("ii._defect_structure", ii._atoms)
en2, final_str2, forces2 = LammpsJob(
atoms=ii._defect_structure,
jobname=jobname,
parameters=parameters,
lammps_cmd=lammps_cmd,
).runjob()
self.phonons(atoms=atoms, lammps_cmd=lammps_cmd, parameters=parameters)
def phonons(self,
atoms=None,
lammps_cmd="",
enforce_c_size=15.0,
parameters={}):
"""Make Phonon calculation setup."""
from phonopy import Phonopy
from phonopy.file_IO import (
# parse_FORCE_CONSTANTS,
write_FORCE_CONSTANTS, )
bulk = atoms.phonopy_converter()
dim = get_supercell_dims(atoms, enforce_c_size=enforce_c_size)
atoms = atoms.make_supercell([dim[0], dim[1], dim[2]])
Poscar(atoms).write_file("POSCAR")
atoms = atoms.make_supercell_matrix([dim[0], dim[1], dim[2]])
Poscar(atoms).write_file("POSCAR-Super.vasp")
phonon = Phonopy(bulk,
[[dim[0], 0, 0], [0, dim[1], 0], [0, 0, dim[2]]])
print("[Phonopy] Atomic displacements1:", bulk)
print("[Phonopy] Atomic displacements2:", phonon, dim[0], dim[1],
dim[2])
phonon.generate_displacements(distance=0.03)
disps = phonon.get_displacements()
print("[Phonopy] Atomic displacements3:", disps)
for d in disps:
print("[Phonopy]", d[0], d[1:])
supercells = phonon.get_supercells_with_displacements()
# Force calculations by calculator
set_of_forces = []
disp = 0
from ase import Atoms as AseAtoms
for scell in supercells:
ase_atoms = AseAtoms(
symbols=scell.get_chemical_symbols(),
scaled_positions=scell.get_scaled_positions(),
cell=scell.get_cell(),
pbc=True,
)
j_atoms = ase_to_atoms(ase_atoms)
disp = disp + 1
parameters["control_file"] = "run0.mod"
a, b, forces = LammpsJob(
atoms=j_atoms,
lammps_cmd=lammps_cmd,
parameters=parameters,
jobname="disp-" + str(disp),
).runjob()
print("forces=", forces)
drift_force = forces.sum(axis=0)
print("drift forces=", drift_force)
# Simple translational invariance
for force in forces:
force -= drift_force / forces.shape[0]
set_of_forces.append(forces)
phonon.produce_force_constants(forces=set_of_forces)
write_FORCE_CONSTANTS(phonon.get_force_constants(),
filename="FORCE_CONSTANTS")
print()
print("[Phonopy] Phonon frequencies at Gamma:")