def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.Li2O'),
check_for_POTCAR=False)
s1 = p.structure
p = Poscar.from_file(os.path.join(test_dir, 'CONTCAR.Li2O'),
check_for_POTCAR=False)
s2 = p.structure
self.analyzer = RelaxationAnalyzer(s1, s2)
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.Li2O'),
check_for_POTCAR=False)
s1 = p.structure
p = Poscar.from_file(os.path.join(test_dir, 'CONTCAR.Li2O'),
check_for_POTCAR=False)
s2 = p.structure
self.analyzer = RelaxationAnalyzer(s1, s2)
def test_write(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
tempfname = "POSCAR.testing"
poscar.write_file(tempfname)
p = Poscar.from_file(tempfname)
self.assertArrayAlmostEqual(poscar.structure.lattice.abc,
p.structure.lattice.abc, 5)
os.remove(tempfname)
def test_write(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
tempfname = "POSCAR.testing"
poscar.write_file(tempfname)
p = Poscar.from_file(tempfname)
self.assertArrayAlmostEqual(poscar.structure.lattice.abc,
p.structure.lattice.abc, 5)
os.remove(tempfname)
def test_apply_transformation(self):
trans = MagOrderingTransformation({"Fe": 5})
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
s = p.structure
alls = trans.apply_transformation(s, 10)
self.assertEqual(len(alls), 3)
f = SymmetryFinder(alls[0]["structure"], 0.1)
self.assertEqual(f.get_spacegroup_number(), 31)
model = IsingModel(5, 5)
trans = MagOrderingTransformation({"Fe": 5},
energy_model=model)
alls2 = trans.apply_transformation(s, 10)
#Ising model with +J penalizes similar neighbor magmom.
self.assertNotEqual(alls[0]["structure"], alls2[0]["structure"])
self.assertEqual(alls[0]["structure"], alls2[2]["structure"])
from pymatgen.io.smartio import read_structure
s = read_structure(os.path.join(test_dir, 'Li2O.cif'))
#Li2O doesn't have magnetism of course, but this is to test the
# enumeration.
trans = MagOrderingTransformation({"Li+": 1}, max_cell_size=3)
alls = trans.apply_transformation(s, 100)
self.assertEqual(len(alls), 10)
def test_from_md_run(self):
#Parsing from an MD type run with velocities
p = Poscar.from_file(os.path.join(test_dir, "CONTCAR.MD"),
check_for_POTCAR=False)
self.assertAlmostEqual(np.sum(np.array(p.velocities)), 0.0065417961324)
self.assertEqual(p.predictor_corrector[0][0], 1)
self.assertEqual(p.predictor_corrector[1][0], 2)
def test_ferrimagnetic(self):
trans = MagOrderingTransformation({"Fe": 5}, 0.75, max_cell_size=1)
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
s = p.structure
alls = trans.apply_transformation(s, 10)
self.assertEqual(len(alls), 2)
def test_ferrimagnetic(self):
trans = MagOrderingTransformation({"Fe": 5}, 0.75, max_cell_size=1)
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
s = p.structure
alls = trans.apply_transformation(s, 10)
self.assertEqual(len(alls), 2)
def test_init_from_structure(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
struct = poscar.structure
xyz = XYZ(struct)
ans = """24
Fe4 P4 O16
Fe 2.277347 4.550379 2.260125
Fe 2.928536 1.516793 4.639870
Fe 7.483231 4.550379 0.119620
Fe 8.134420 1.516793 2.499364
P 0.985089 1.516793 1.990624
P 4.220794 4.550379 4.370369
P 6.190973 1.516793 0.389120
P 9.426677 4.550379 2.768865
O 0.451582 4.550379 3.365614
O 1.006219 1.516793 3.528306
O 1.725331 0.279529 1.358282
O 1.725331 2.754057 1.358282
O 3.480552 3.313115 3.738027
O 3.480552 5.787643 3.738027
O 4.199665 4.550379 1.148562
O 4.754301 1.516793 0.985870
O 5.657466 4.550379 3.773620
O 6.212102 1.516793 3.610928
O 6.931215 0.279529 1.021463
O 6.931215 2.754057 1.021463
O 8.686436 3.313115 3.401208
O 8.686436 5.787643 3.401208
O 9.405548 4.550379 1.231183
O 9.960184 1.516793 1.393875"""
self.assertEqual(str(xyz), ans)
def test_apply_transformation(self):
p = Poscar.from_file(os.path.join(test_dir, "POSCAR.LiFePO4"), check_for_POTCAR=False)
t = AutoOxiStateDecorationTransformation()
s = t.apply_transformation(p.structure)
expected_oxi = {"Li": 1, "P": 5, "O": -2, "Fe": 2}
for site in s:
self.assertEqual(site.specie.oxi_state, expected_oxi[site.specie.symbol])
def test_get_energy_tersoff(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.Al12O18'),
check_for_POTCAR=False)
structure = p.structure
enrgy = get_energy_tersoff(structure)
self.assertIsInstance(enrgy, float)
print "tersoff energy", enrgy
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
self.struct = poscar.structure
self.mitparamset = MITVaspInputSet()
self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False)
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MPVaspInputSet()
self.userparamset = MPVaspInputSet(
user_incar_settings={'MAGMOM': {
"Fe": 10,
"S": -5,
"Mn3+": 100
}})
self.mitggaparam = MITGGAVaspInputSet()
self.mpstaticparamset = MPStaticVaspInputSet()
self.mpnscfparamsetu = MPNonSCFVaspInputSet({"NBANDS": 50},
mode="Uniform")
self.mpnscfparamsetl = MPNonSCFVaspInputSet({"NBANDS": 60},
mode="Line")
self.mphseparamset = MPHSEVaspInputSet()
self.mpbshseparamsetl = MPBSHSEVaspInputSet(mode="Line")
self.mpbshseparamsetu = MPBSHSEVaspInputSet(
mode="Uniform", added_kpoints=[[0.5, 0.5, 0.0]])
self.mpdielparamset = MPStaticDielectricDFPTVaspInputSet()
def test_init_from_structure(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
struct = poscar.structure
xyz = XYZ(struct)
ans = """24
Fe4 P4 O16
Fe 2.277347 4.550379 2.260125
Fe 2.928536 1.516793 4.639870
Fe 7.483231 4.550379 0.119620
Fe 8.134420 1.516793 2.499364
P 0.985089 1.516793 1.990624
P 4.220794 4.550379 4.370369
P 6.190973 1.516793 0.389120
P 9.426677 4.550379 2.768865
O 0.451582 4.550379 3.365614
O 1.006219 1.516793 3.528306
O 1.725331 0.279529 1.358282
O 1.725331 2.754057 1.358282
O 3.480552 3.313115 3.738027
O 3.480552 5.787643 3.738027
O 4.199665 4.550379 1.148562
O 4.754301 1.516793 0.985870
O 5.657466 4.550379 3.773620
O 6.212102 1.516793 3.610928
O 6.931215 0.279529 1.021463
O 6.931215 2.754057 1.021463
O 8.686436 3.313115 3.401208
O 8.686436 5.787643 3.401208
O 9.405548 4.550379 1.231183
O 9.960184 1.516793 1.393875"""
self.assertEqual(str(xyz), ans)
def test_get_structure(self):
if not aio.ase_loaded:
raise SkipTest("ASE not present. Skipping...")
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
atoms = aio.AseAtomsAdaptor.get_atoms(p.structure)
self.assertEqual(aio.AseAtomsAdaptor.get_structure(atoms).formula,
"Fe4 P4 O16")
def test_from_md_run(self):
#Parsing from an MD type run with velocities
p = Poscar.from_file(os.path.join(test_dir, "CONTCAR.MD"),
check_for_POTCAR=False)
self.assertAlmostEqual(np.sum(np.array(p.velocities)), 0.0065417961324)
self.assertEqual(p.predictor_corrector[0][0], 1)
self.assertEqual(p.predictor_corrector[1][0], 2)
def test_apply_transformation(self):
enum_trans = EnumerateStructureTransformation(refine_structure=True)
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
struct = p.structure
expected_ans = [1, 3, 1]
for i, frac in enumerate([0.25, 0.5, 0.75]):
trans = SubstitutionTransformation({'Fe': {'Fe': frac}})
s = trans.apply_transformation(struct)
oxitrans = OxidationStateDecorationTransformation({'Li': 1,
'Fe': 2,
'P': 5,
'O': -2})
s = oxitrans.apply_transformation(s)
alls = enum_trans.apply_transformation(s, 100)
self.assertEquals(len(alls), expected_ans[i])
self.assertIsInstance(trans.apply_transformation(s), Structure)
for s in alls:
self.assertIn("energy", s)
#make sure it works for non-oxidation state decorated structure
trans = SubstitutionTransformation({'Fe': {'Fe': 0.5}})
s = trans.apply_transformation(struct)
alls = enum_trans.apply_transformation(s, 100)
self.assertEquals(len(alls), 3)
self.assertIsInstance(trans.apply_transformation(s), Structure)
for s in alls:
self.assertNotIn("energy", s)
def run_task(self, fw_spec):
chgcar_start = False
# read the VaspInput from the previous run
poscar = Poscar.from_file(zpath('POSCAR'))
incar = Incar.from_file(zpath('INCAR'))
# figure out what GGA+U values to use and override them
# LDAU values to use
mpvis = MPVaspInputSet()
ggau_incar = mpvis.get_incar(poscar.structure).to_dict
incar_updates = {k: ggau_incar[k] for k in ggau_incar.keys() if 'LDAU' in k}
for k in ggau_incar:
# update any parameters not set explicitly in previous INCAR
if k not in incar and k in ggau_incar:
incar_updates[k] = ggau_incar[k]
incar.update(incar_updates) # override the +U keys
# start from the CHGCAR of previous run
if os.path.exists('CHGCAR'):
incar['ICHARG'] = 1
chgcar_start = True
# write back the new INCAR to the current directory
incar.write_file('INCAR')
return FWAction(stored_data={'chgcar_start': chgcar_start})
def test_get_structure(self):
if not aio.ase_loaded:
raise SkipTest("ASE not present. Skipping...")
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
atoms = aio.AseAtomsAdaptor.get_atoms(p.structure)
self.assertEqual(
aio.AseAtomsAdaptor.get_structure(atoms).formula, "Fe4 P4 O16")
def parse_vasp(groupdireclist, args):
data_to_csv = []
default_energies = not (args.get_energies or args.ion_list or args.ion_avg_list)
templatestructure = []
if args.template:
for (parent, subdirs, files) in os.walk(args.strtemp[0]):
if 'POSCAR' in files:
filepath = glob.glob(os.path.join(parent,"POSCAR"))
poscarfile = Poscar.from_file(filepath[0])
templatestructure = poscarfile.structure
if args.get_energies or default_energies:
for d in groupdireclist:
groupdata= get_energies(d, args.reanalyze, args.verbose,
args.detailed, args.sort[0],args.formulaunit,args.debug,args.hull,args.threshold, args, templatestructure)
data_to_csv.extend(groupdata)
output_CSV(data_to_csv,args)
def test_apply_transformations_best_first(self):
p = Poscar.from_file(os.path.join(test_dir, "POSCAR.LiFePO4"), check_for_POTCAR=False)
t1 = OxidationStateDecorationTransformation({"Li": 1, "Fe": 2, "P": 5, "O": -2})
s = t1.apply_transformation(p.structure)
t = PartialRemoveSpecieTransformation("Li+", 0.5, PartialRemoveSpecieTransformation.ALGO_BEST_FIRST)
self.assertEqual(len(t.apply_transformation(s)), 26)
def run_task(self, fw_spec):
chgcar_start = False
# read the VaspInput from the previous run
poscar = Poscar.from_file(zpath('POSCAR'))
incar = Incar.from_file(zpath('INCAR'))
# figure out what GGA+U values to use and override them
# LDAU values to use
mpvis = MPVaspInputSet()
ggau_incar = mpvis.get_incar(poscar.structure).to_dict
incar_updates = {
k: ggau_incar[k]
for k in ggau_incar.keys() if 'LDAU' in k
}
for k in ggau_incar:
# update any parameters not set explicitly in previous INCAR
if k not in incar and k in ggau_incar:
incar_updates[k] = ggau_incar[k]
incar.update(incar_updates) # override the +U keys
# start from the CHGCAR of previous run
if os.path.exists('CHGCAR'):
incar['ICHARG'] = 1
chgcar_start = True
# write back the new INCAR to the current directory
incar.write_file('INCAR')
return FWAction(stored_data={'chgcar_start': chgcar_start})
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 4, 4]])
self.assertEqual(kpoints.style, "Monkhorst")
kpoints = Kpoints.automatic_density(poscar.structure, 500, True)
self.assertEqual(kpoints.style, "Gamma")
kpoints = Kpoints.automatic_density_by_vol(poscar.structure, 1000)
self.assertEqual(kpoints.kpts, [[6, 11, 13]])
self.assertEqual(kpoints.style, "Gamma")
s = poscar.structure
s.make_supercell(3)
kpoints = Kpoints.automatic_density(s, 500)
self.assertEqual(kpoints.kpts, [[1, 1, 1]])
self.assertEqual(kpoints.style, "Gamma")
def test_apply_transformation(self):
enum_trans = EnumerateStructureTransformation(refine_structure=True)
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
struct = p.structure
expected_ans = [1, 3, 1]
for i, frac in enumerate([0.25, 0.5, 0.75]):
trans = SubstitutionTransformation({'Fe': {'Fe': frac}})
s = trans.apply_transformation(struct)
oxitrans = OxidationStateDecorationTransformation({
'Li': 1,
'Fe': 2,
'P': 5,
'O': -2
})
s = oxitrans.apply_transformation(s)
alls = enum_trans.apply_transformation(s, 100)
self.assertEquals(len(alls), expected_ans[i])
self.assertIsInstance(trans.apply_transformation(s), Structure)
for s in alls:
self.assertIn("energy", s)
#make sure it works for non-oxidation state decorated structure
trans = SubstitutionTransformation({'Fe': {'Fe': 0.5}})
s = trans.apply_transformation(struct)
alls = enum_trans.apply_transformation(s, 100)
self.assertEquals(len(alls), 3)
self.assertIsInstance(trans.apply_transformation(s), Structure)
for s in alls:
self.assertNotIn("energy", s)
def test_get_energy_tersoff(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.Al12O18'),
check_for_POTCAR=False)
structure = p.structure
enrgy = get_energy_tersoff(structure)
self.assertIsInstance(enrgy, float)
print "tersoff energy", enrgy
def test_get_atoms(self):
if not aio.ase_loaded:
raise SkipTest("ASE not present. Skipping...")
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
structure = p.structure
atoms = aio.AseAtomsAdaptor.get_atoms(structure)
ase_composition = Composition.from_formula(atoms.get_name())
self.assertEqual(ase_composition, structure.composition)
def test_get_atoms(self):
if not aio.ase_loaded:
raise SkipTest("ASE not present. Skipping...")
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
structure = p.structure
atoms = aio.AseAtomsAdaptor.get_atoms(structure)
ase_composition = Composition(atoms.get_name())
self.assertEqual(ase_composition, structure.composition)
def test_CifWriter(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
writer = CifWriter(poscar.structure, find_spacegroup=True)
ans = """#generated using pymatgen
data_FePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 10.41176687
_cell_length_b 6.06717188
_cell_length_c 4.75948954
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 62
_chemical_formula_structural FePO4
_chemical_formula_sum 'Fe4 P4 O16'
_cell_volume 300.65685512
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Fe Fe1 1 0.218728 0.750000 0.474867 1
Fe Fe2 1 0.281272 0.250000 0.974867 1
Fe Fe3 1 0.718728 0.750000 0.025133 1
Fe Fe4 1 0.781272 0.250000 0.525133 1
P P5 1 0.094613 0.250000 0.418243 1
P P6 1 0.405387 0.750000 0.918243 1
P P7 1 0.594613 0.250000 0.081757 1
P P8 1 0.905387 0.750000 0.581757 1
O O9 1 0.043372 0.750000 0.707138 1
O O10 1 0.096642 0.250000 0.741320 1
O O11 1 0.165710 0.046072 0.285384 1
O O12 1 0.165710 0.453928 0.285384 1
O O13 1 0.334290 0.546072 0.785384 1
O O14 1 0.334290 0.953928 0.785384 1
O O15 1 0.403358 0.750000 0.241320 1
O O16 1 0.456628 0.250000 0.207138 1
O O17 1 0.543372 0.750000 0.792862 1
O O18 1 0.596642 0.250000 0.758680 1
O O19 1 0.665710 0.046072 0.214616 1
O O20 1 0.665710 0.453928 0.214616 1
O O21 1 0.834290 0.546072 0.714616 1
O O22 1 0.834290 0.953928 0.714616 1
O O23 1 0.903358 0.750000 0.258680 1
O O24 1 0.956628 0.250000 0.292862 1
"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
def test_CifWriter(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
writer = CifWriter(poscar.structure, find_spacegroup=True)
ans = """#generated using pymatgen
data_FePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 10.41176687
_cell_length_b 6.06717188
_cell_length_c 4.75948954
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 62
_chemical_formula_structural FePO4
_chemical_formula_sum 'Fe4 P4 O16'
_cell_volume 300.65685512
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Fe Fe1 1 0.218728 0.750000 0.474867 1
Fe Fe2 1 0.281272 0.250000 0.974867 1
Fe Fe3 1 0.718728 0.750000 0.025133 1
Fe Fe4 1 0.781272 0.250000 0.525133 1
P P5 1 0.094613 0.250000 0.418243 1
P P6 1 0.405387 0.750000 0.918243 1
P P7 1 0.594613 0.250000 0.081757 1
P P8 1 0.905387 0.750000 0.581757 1
O O9 1 0.043372 0.750000 0.707138 1
O O10 1 0.096642 0.250000 0.741320 1
O O11 1 0.165710 0.046072 0.285384 1
O O12 1 0.165710 0.453928 0.285384 1
O O13 1 0.334290 0.546072 0.785384 1
O O14 1 0.334290 0.953928 0.785384 1
O O15 1 0.403358 0.750000 0.241320 1
O O16 1 0.456628 0.250000 0.207138 1
O O17 1 0.543372 0.750000 0.792862 1
O O18 1 0.596642 0.250000 0.758680 1
O O19 1 0.665710 0.046072 0.214616 1
O O20 1 0.665710 0.453928 0.214616 1
O O21 1 0.834290 0.546072 0.714616 1
O O22 1 0.834290 0.953928 0.714616 1
O O23 1 0.903358 0.750000 0.258680 1
O O24 1 0.956628 0.250000 0.292862 1
"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
def test_get_lattice_from_lattice_type(self):
cif_structure = """#generated using pymatgen
data_FePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 10.41176687
_cell_length_b 6.06717188
_cell_length_c 4.75948954
_chemical_formula_structural FePO4
_chemical_formula_sum 'Fe4 P4 O16'
_cell_volume 300.65685512
_cell_formula_units_Z 4
_symmetry_cell_setting Orthorhombic
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Fe Fe1 1 0.218728 0.750000 0.474867 1
Fe Fe2 1 0.281272 0.250000 0.974867 1
Fe Fe3 1 0.718728 0.750000 0.025133 1
Fe Fe4 1 0.781272 0.250000 0.525133 1
P P5 1 0.094613 0.250000 0.418243 1
P P6 1 0.405387 0.750000 0.918243 1
P P7 1 0.594613 0.250000 0.081757 1
P P8 1 0.905387 0.750000 0.581757 1
O O9 1 0.043372 0.750000 0.707138 1
O O10 1 0.096642 0.250000 0.741320 1
O O11 1 0.165710 0.046072 0.285384 1
O O12 1 0.165710 0.453928 0.285384 1
O O13 1 0.334290 0.546072 0.785384 1
O O14 1 0.334290 0.953928 0.785384 1
O O15 1 0.403358 0.750000 0.241320 1
O O16 1 0.456628 0.250000 0.207138 1
O O17 1 0.543372 0.750000 0.792862 1
O O18 1 0.596642 0.250000 0.758680 1
O O19 1 0.665710 0.046072 0.214616 1
O O20 1 0.665710 0.453928 0.214616 1
O O21 1 0.834290 0.546072 0.714616 1
O O22 1 0.834290 0.953928 0.714616 1
O O23 1 0.903358 0.750000 0.258680 1
O O24 1 0.956628 0.250000 0.292862 1
"""
cp = CifParser.from_string(cif_structure)
s_test = cp.get_structures(False)[0]
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
s_ref = poscar.structure
sm = StructureMatcher(stol=0.05, ltol=0.01, angle_tol=0.1)
self.assertTrue(sm.fit(s_ref, s_test))
def test_apply_transformation(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
t = AutoOxiStateDecorationTransformation()
s = t.apply_transformation(p.structure)
expected_oxi = {"Li": 1, "P": 5, "O":-2, "Fe": 2}
for site in s:
self.assertEqual(site.specie.oxi_state,
expected_oxi[site.specie.symbol])
def check(self):
try:
oszicar = Oszicar(self.output_filename)
n = len(Poscar.from_file(self.input_filename).structure)
max_dE = max([s['dE'] for s in oszicar.ionic_steps[1:]]) / n
if max_dE > self.dE_threshold:
return True
except:
return False
def test_apply_transformations_complete_ranking(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
t1 = OxidationStateDecorationTransformation({"Li": 1, "Fe": 2, "P": 5,
"O":-2})
s = t1.apply_transformation(p.structure)
t = PartialRemoveSpecieTransformation("Li+", 0.5,
PartialRemoveSpecieTransformation.ALGO_COMPLETE)
self.assertEqual(len(t.apply_transformation(s, 10)), 6)
def test_apply_transformations_best_first(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
t1 = OxidationStateDecorationTransformation({"Li": 1, "Fe": 2, "P": 5,
"O":-2})
s = t1.apply_transformation(p.structure)
t = PartialRemoveSpecieTransformation("Li+", 0.5,
PartialRemoveSpecieTransformation.ALGO_BEST_FIRST)
self.assertEqual(len(t.apply_transformation(s)), 26)
def test_init(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
comp = poscar.structure.composition
self.assertEqual(comp, Composition("Fe4P4O16"))
#Vasp 4 type with symbols at the end.
poscar_string = """Test1
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
direct
0.000000 0.000000 0.000000 Si
0.750000 0.500000 0.750000 F
"""
poscar = Poscar.from_string(poscar_string)
self.assertEqual(poscar.structure.composition, Composition("SiF"))
poscar_string = ""
self.assertRaises(ValueError, Poscar.from_string, poscar_string)
#Vasp 4 tyle file with default names, i.e. no element symbol found.
poscar_string = """Test2
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
direct
0.000000 0.000000 0.000000
0.750000 0.500000 0.750000
"""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
poscar = Poscar.from_string(poscar_string)
self.assertEqual(poscar.structure.composition, Composition("HHe"))
#Vasp 4 tyle file with default names, i.e. no element symbol found.
poscar_string = """Test3
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
Selective dynamics
direct
0.000000 0.000000 0.000000 T T T Si
0.750000 0.500000 0.750000 F F F O
"""
poscar = Poscar.from_string(poscar_string)
self.assertEqual(poscar.selective_dynamics,
[[True, True, True], [False, False, False]])
self.selective_poscar = poscar
def test_init(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
comp = poscar.structure.composition
self.assertEqual(comp, Composition("Fe4P4O16"))
#Vasp 4 type with symbols at the end.
poscar_string = """Test1
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
direct
0.000000 0.000000 0.000000 Si
0.750000 0.500000 0.750000 F
"""
poscar = Poscar.from_string(poscar_string)
self.assertEqual(poscar.structure.composition, Composition("SiF"))
poscar_string = ""
self.assertRaises(ValueError, Poscar.from_string, poscar_string)
#Vasp 4 tyle file with default names, i.e. no element symbol found.
poscar_string = """Test2
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
direct
0.000000 0.000000 0.000000
0.750000 0.500000 0.750000
"""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
poscar = Poscar.from_string(poscar_string)
self.assertEqual(poscar.structure.composition, Composition("HHe"))
#Vasp 4 tyle file with default names, i.e. no element symbol found.
poscar_string = """Test3
1.0
3.840198 0.000000 0.000000
1.920099 3.325710 0.000000
0.000000 -2.217138 3.135509
1 1
Selective dynamics
direct
0.000000 0.000000 0.000000 T T T Si
0.750000 0.500000 0.750000 F F F O
"""
poscar = Poscar.from_string(poscar_string)
self.assertEqual(poscar.selective_dynamics, [[True, True, True],
[False, False, False]])
self.selective_poscar = poscar
def buildPOSCAR(iat, fposcar="POSCAR"):
"""
Build POSCAR file according to atom for wich CL calculation is required. The
corresponding atom is placed in first position in the POSCAR.
"""
from pymatgen.io.vaspio.vasp_input import Poscar
poscar = Poscar.from_file(fposcar)
site = poscar.structure.pop(iat)
poscar.structure.insert(0, site.specie, site.frac_coords)
poscar.write_file("POSCAR_CL.vasp")
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
self.struct = poscar.structure
self.mitparamset = MITVaspInputSet()
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MaterialsProjectVaspInputSet()
self.userparamset = MaterialsProjectVaspInputSet(
{'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}}
)
self.mitggaparam = MITGGAVaspInputSet()
def run_task(self, fw_spec):
user_incar_settings= {"NPAR": 2}
if self.line:
MPNonSCFVaspInputSet.from_previous_vasp_run(os.getcwd(), mode="Line", copy_chgcar=False,
user_incar_settings=user_incar_settings,)
kpath = HighSymmKpath(Poscar.from_file("POSCAR").structure)
return FWAction(stored_data={"kpath": kpath.kpath,
"kpath_name": kpath.name})
else:
MPNonSCFVaspInputSet.from_previous_vasp_run(os.getcwd(), mode="Uniform", copy_chgcar=False,
user_incar_settings=user_incar_settings)
return FWAction()
def test_init(self):
filepath = os.path.join(test_dir, 'POSCAR')
p = Poscar.from_file(filepath)
original_s = p.structure
modifier = StructureEditor(original_s)
modifier.add_oxidation_state_by_element({"Li": 1, "Fe": 2,
"P": 5, "O":-2})
s = modifier.modified_structure
ham = EwaldSummation(s)
self.assertAlmostEqual(ham.real_space_energy, -354.91294268, 4,
"Real space energy incorrect!")
self.assertAlmostEqual(ham.reciprocal_space_energy, 25.475754801, 4)
self.assertAlmostEqual(ham.point_energy, -790.463835033, 4,
"Point space energy incorrect!")
self.assertAlmostEqual(ham.total_energy, -1119.90102291, 2,
"Total space energy incorrect!")
self.assertAlmostEqual(ham.forces[0,0], -1.98818620e-01, 4,
"Forces incorrect")
self.assertAlmostEqual(sum(sum(abs(ham.forces))), 915.925354346, 4,
"Forces incorrect")
self.assertAlmostEqual(sum(sum(ham.real_space_energy_matrix)),
- 354.91294268, 4,
"Real space energy matrix incorrect!")
self.assertAlmostEqual(sum(sum(ham.reciprocal_space_energy_matrix)),
25.475754801, 4,
"Reciprocal space energy matrix incorrect!")
self.assertAlmostEqual(sum(ham.point_energy_matrix), -790.463835033,
4, "Point space energy matrix incorrect!")
self.assertAlmostEqual(sum(sum(ham.total_energy_matrix)),
- 1119.90102291, 2,
"Total space energy matrix incorrect!")
#note that forces are not individually tested, but should work fine.
self.assertRaises(ValueError, EwaldSummation, original_s)
#try sites with charge.
charges = []
for site in original_s:
if site.specie.symbol == "Li":
charges.append(1)
elif site.specie.symbol == "Fe":
charges.append(2)
elif site.specie.symbol == "P":
charges.append(5)
else:
charges.append(-2)
editor = StructureEditor(original_s)
editor.add_site_property('charge', charges)
ham2 = EwaldSummation(editor.modified_structure)
self.assertAlmostEqual(ham2.real_space_energy, -354.91294268, 4,
"Real space energy incorrect!")
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
p = Poscar.from_file(filepath)
self.structure = p.structure
bv = BVAnalyzer()
valences = bv.get_valences(self.structure)
el = [site.species_string for site in self.structure.sites]
valence_dict = dict(zip(el, valences))
self.rad_dict = {}
for k, v in valence_dict.items():
self.rad_dict[k] = Specie(k, v).ionic_radius
assert len(self.rad_dict) == len(self.structure.composition)
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
p = Poscar.from_file(filepath)
self.structure = p.structure
bv = BVAnalyzer()
valences = bv.get_valences(self.structure)
el = [site.species_string for site in self.structure.sites]
valence_dict = dict(zip(el, valences))
self.rad_dict = {}
for k, v in valence_dict.items():
self.rad_dict[k] = Specie(k,v).ionic_radius
assert len(self.rad_dict) == len(self.structure.composition)
def setUp(self):
filepath = os.path.join(test_dir, "POSCAR")
poscar = Poscar.from_file(filepath)
self.struct = poscar.structure
self.mitparamset = MITVaspInputSet()
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MPVaspInputSet()
self.userparamset = MPVaspInputSet({"MAGMOM": {"Fe": 10, "S": -5, "Mn3+": 100}})
self.mitggaparam = MITGGAVaspInputSet()
self.mpstaticparamset = MPStaticVaspInputSet()
self.mpnscfparamsetu = MPNonSCFVaspInputSet({"NBANDS": 50}, mode="Uniform")
self.mpnscfparamsetl = MPNonSCFVaspInputSet({"NBANDS": 60}, mode="Line")
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 3, 4]])
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg = SpacegroupAnalyzer(self.structure, 0.001)
self.disordered_structure = self.get_structure('Li10GeP2S12')
self.disordered_sg = SpacegroupAnalyzer(self.disordered_structure, 0.001)
s = p.structure.copy()
site = s[0]
del s[0]
s.append(site.species_and_occu, site.frac_coords)
self.sg3 = SpacegroupAnalyzer(s, 0.001)
graphite = self.get_structure('Graphite')
graphite.add_site_property("magmom", [0.1] * len(graphite))
self.sg4 = SpacegroupAnalyzer(graphite, 0.001)
def test_static_constructors(self):
kpoints = Kpoints.gamma_automatic([3, 3, 3], [0, 0, 0])
self.assertEqual(kpoints.style, "Gamma")
self.assertEqual(kpoints.kpts, [[3, 3, 3]])
kpoints = Kpoints.monkhorst_automatic([2, 2, 2], [0, 0, 0])
self.assertEqual(kpoints.style, "Monkhorst")
self.assertEqual(kpoints.kpts, [[2, 2, 2]])
kpoints = Kpoints.automatic(100)
self.assertEqual(kpoints.style, "Automatic")
self.assertEqual(kpoints.kpts, [[100]])
filepath = os.path.join(test_dir, "POSCAR")
poscar = Poscar.from_file(filepath)
kpoints = Kpoints.automatic_density(poscar.structure, 500)
self.assertEqual(kpoints.kpts, [[2, 3, 4]])
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg = SpacegroupAnalyzer(self.structure, 0.001)
self.disordered_structure = self.get_structure('Li10GeP2S12')
self.disordered_sg = SpacegroupAnalyzer(self.disordered_structure,
0.001)
s = p.structure.copy()
site = s[0]
del s[0]
s.append(site.species_and_occu, site.frac_coords)
self.sg3 = SpacegroupAnalyzer(s, 0.001)
graphite = self.get_structure('Graphite')
graphite.add_site_property("magmom", [0.1] * len(graphite))
self.sg4 = SpacegroupAnalyzer(graphite, 0.001)
def setUp(self):
filepath = os.path.join(test_dir, "INCAR")
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, "POSCAR")
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..", "test_files")
)
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, "POTCAR")
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, "KPOINTS.auto")
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def setUp(self):
filepath = os.path.join(test_dir, 'INCAR')
incar = Incar.from_file(filepath)
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
if "VASP_PSP_DIR" not in os.environ:
test_potcar_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
"test_files"))
os.environ["VASP_PSP_DIR"] = test_potcar_dir
filepath = os.path.join(test_dir, 'POTCAR')
potcar = Potcar.from_file(filepath)
filepath = os.path.join(test_dir, 'KPOINTS.auto')
kpoints = Kpoints.from_file(filepath)
self.vinput = VaspInput(incar, kpoints, poscar, potcar)
def test_init(self):
filepath = os.path.join(test_dir, 'POSCAR')
p = Poscar.from_file(filepath)
original_s = p.structure
s = original_s.copy()
s.add_oxidation_state_by_element({"Li": 1, "Fe": 2, "P": 5, "O": -2})
ham = EwaldSummation(s)
self.assertAlmostEqual(ham.real_space_energy, -354.91294268, 4,
"Real space energy incorrect!")
self.assertAlmostEqual(ham.reciprocal_space_energy, 25.475754801, 4)
self.assertAlmostEqual(ham.point_energy, -790.463835033, 4,
"Point space energy incorrect!")
self.assertAlmostEqual(ham.total_energy, -1119.90102291, 2,
"Total space energy incorrect!")
self.assertAlmostEqual(ham.forces[0, 0], -1.98818620e-01, 4,
"Forces incorrect")
self.assertAlmostEqual(sum(sum(abs(ham.forces))), 915.925354346, 4,
"Forces incorrect")
self.assertAlmostEqual(sum(sum(ham.real_space_energy_matrix)),
-354.91294268, 4,
"Real space energy matrix incorrect!")
self.assertAlmostEqual(sum(sum(ham.reciprocal_space_energy_matrix)),
25.475754801, 4,
"Reciprocal space energy matrix incorrect!")
self.assertAlmostEqual(sum(ham.point_energy_matrix), -790.463835033, 4,
"Point space energy matrix incorrect!")
self.assertAlmostEqual(sum(sum(ham.total_energy_matrix)),
-1119.90102291, 2,
"Total space energy matrix incorrect!")
#note that forces are not individually tested, but should work fine.
self.assertRaises(ValueError, EwaldSummation, original_s)
#try sites with charge.
charges = []
for site in original_s:
if site.specie.symbol == "Li":
charges.append(1)
elif site.specie.symbol == "Fe":
charges.append(2)
elif site.specie.symbol == "P":
charges.append(5)
else:
charges.append(-2)
original_s.add_site_property('charge', charges)
ham2 = EwaldSummation(original_s)
self.assertAlmostEqual(ham2.real_space_energy, -354.91294268, 4,
"Real space energy incorrect!")
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg = SymmetryFinder(self.structure, 0.001)
parser = CifParser(os.path.join(test_dir, 'Li10GeP2S12.cif'))
self.disordered_structure = parser.get_structures()[0]
self.disordered_sg = SymmetryFinder(self.disordered_structure, 0.001)
s = p.structure.copy()
site = s[0]
del s[0]
s.append(site.species_and_occu, site.frac_coords)
self.sg3 = SymmetryFinder(s, 0.001)
parser = CifParser(os.path.join(test_dir, 'Graphite.cif'))
graphite = parser.get_structures()[0]
graphite.add_site_property("magmom", [0.1] * len(graphite))
self.sg4 = SymmetryFinder(graphite, 0.001)
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
p = Poscar.from_file(filepath)
self.structure = p.structure
bv = BVAnalyzer()
self.structure = bv.get_oxi_state_decorated_structure(self.structure)
valences = bv.get_valences(self.structure)
radii = []
for i in range(len(valences)):
el = self.structure.sites[i].specie.symbol
radius = Specie(el, valences[i]).ionic_radius
radii.append(radius)
el = [site.species_string for site in self.structure.sites]
self.rad_dict = dict(zip(el, radii))
for el in self.rad_dict.keys():
print((el, self.rad_dict[el].real))
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
p = Poscar.from_file(filepath)
self.structure = p.structure
bv = BVAnalyzer()
self.structure = bv.get_oxi_state_decorated_structure(self.structure)
valences = bv.get_valences(self.structure)
radii = []
for i in range(len(valences)):
el = self.structure.sites[i].specie.symbol
radius = Specie(el, valences[i]).ionic_radius
radii.append(radius)
el = [site.species_string for site in self.structure.sites]
self.rad_dict = dict(zip(el, radii))
for el in self.rad_dict.keys():
print((el, self.rad_dict[el].real))
def test_symmetrized(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
writer = CifWriter(poscar.structure, find_spacegroup=True,
symprec=0.1)
ans = """#generated using pymatgen
data_FePO4
_symmetry_space_group_name_H-M Pnma
_cell_length_a 10.41176687
_cell_length_b 6.06717188
_cell_length_c 4.75948954
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 62
_chemical_formula_structural FePO4
_chemical_formula_sum 'Fe4 P4 O16'
_cell_volume 300.65685512
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
2 '-x, -y, -z'
3 '-x+1/2, -y, z+1/2'
4 'x+1/2, y, -z+1/2'
5 'x+1/2, -y+1/2, -z+1/2'
6 '-x+1/2, y+1/2, z+1/2'
7 '-x, y+1/2, -z'
8 'x, -y+1/2, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Fe Fe1 4 0.218728 0.750000 0.474867 1
P P2 4 0.094613 0.250000 0.418243 1
O O3 4 0.043372 0.750000 0.707138 1
O O4 4 0.096642 0.250000 0.741320 1
O O5 8 0.165710 0.046072 0.285384 1"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
self.struct = poscar.structure
self.mitparamset = MITVaspInputSet()
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MPVaspInputSet()
self.userparamset = MPVaspInputSet(
{'MAGMOM': {
"Fe": 10,
"S": -5,
"Mn3+": 100
}})
self.mitggaparam = MITGGAVaspInputSet()
self.mpstaticparamset = MPStaticVaspInputSet()
self.mpnscfparamsetu = MPNonSCFVaspInputSet({"NBANDS": 50},
mode="Uniform")
self.mpnscfparamsetl = MPNonSCFVaspInputSet({"NBANDS": 60},
mode="Line")
def run_task(self, fw_spec):
user_incar_settings = {"NPAR": 2}
if self.line:
MPNonSCFVaspInputSet.from_previous_vasp_run(
os.getcwd(),
mode="Line",
copy_chgcar=False,
user_incar_settings=user_incar_settings,
)
kpath = HighSymmKpath(Poscar.from_file("POSCAR").structure)
return FWAction(stored_data={
"kpath": kpath.kpath,
"kpath_name": kpath.name
})
else:
MPNonSCFVaspInputSet.from_previous_vasp_run(
os.getcwd(),
mode="Uniform",
copy_chgcar=False,
user_incar_settings=user_incar_settings)
return FWAction()
def buildPOSCAR(iat, fposcar="POSCAR"):
"""
Build POSCAR file according to atom for wich CL calculation is required. The
corresponding atom is placed in first position in the POSCAR.
"""
poscar = Poscar.from_file(fposcar, read_velocities=False)
# move up the selected atom and ad "_" to differentiate it
site = poscar.structure.pop(iat)
poscar.structure.insert(0, mg.DummySpecie("_" + site.specie.symbol),
site.frac_coords)
poscar.write_file("POSCAR_CL.vasp")
# remove the _ symbol on 6th line
with open("POSCAR_CL.vasp", "r") as f:
lines = f.readlines()
lines[5] = "".join(["%4s" % el.strip("_")
for el in lines[5].split()]) + "\n"
lines = "".join(lines)
with open("POSCAR_CL.vasp", "w") as f:
f.write(lines)
def test_apply_transformation(self):
trans = MagOrderingTransformation({"Fe": 5})
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
check_for_POTCAR=False)
s = p.structure
alls = trans.apply_transformation(s, 10)
self.assertEqual(len(alls), 3)
f = SpacegroupAnalyzer(alls[0]["structure"], 0.1)
self.assertEqual(f.get_spacegroup_number(), 31)
model = IsingModel(5, 5)
trans = MagOrderingTransformation({"Fe": 5}, energy_model=model)
alls2 = trans.apply_transformation(s, 10)
#Ising model with +J penalizes similar neighbor magmom.
self.assertNotEqual(alls[0]["structure"], alls2[0]["structure"])
self.assertEqual(alls[0]["structure"], alls2[2]["structure"])
s = self.get_structure('Li2O')
#Li2O doesn't have magnetism of course, but this is to test the
# enumeration.
trans = MagOrderingTransformation({"Li+": 1}, max_cell_size=3)
alls = trans.apply_transformation(s, 100)
self.assertEqual(len(alls), 10)
def test_setattr(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
self.assertRaises(ValueError, setattr, poscar, 'velocities',
[[0, 0, 0]])
poscar.selective_dynamics = np.array([[True, False, False]] * 24)
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
self.structure = p.structure
self.sg1 = SymmetryFinder(self.structure, 0.001).get_spacegroup()
