class DeformedStructureSetTest(PymatgenTest):
def setUp(self):
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.structure = Structure(lattice, ["Si", "Si"],
[[0, 0, 0], [0.75, 0.5, 0.75]])
self.default_dss = DeformedStructureSet(self.structure)
def test_init(self):
with self.assertRaises(ValueError):
DeformedStructureSet(self.structure, num_norm=5)
DeformedStructureSet(self.structure, num_shear=5)
self.assertEqual(self.structure, self.default_dss.undeformed_structure)
def test_as_strain_dict(self):
strain_dict = self.default_dss.as_strain_dict()
for i, def_struct in enumerate(self.default_dss):
test_strain = IndependentStrain(self.default_dss.deformations[i])
strain_keys = [
strain for strain in list(strain_dict.keys())
if (strain == test_strain).all()
]
self.assertEqual(len(strain_keys), 1)
self.assertEqual(self.default_dss.def_structs[i],
strain_dict[strain_keys[0]])
class DeformedStructureSetTest(PymatgenTest):
def setUp(self):
self.structure = self.get_structure("Sn")
self.default_dss = DeformedStructureSet(self.structure)
def test_init(self):
with self.assertRaises(ValueError):
DeformedStructureSet(self.structure, num_norm=5)
with self.assertRaises(ValueError):
DeformedStructureSet(self.structure, num_shear=5)
self.assertEqual(self.structure, self.default_dss.undeformed_structure)
# Test symmetry
dss_symm = DeformedStructureSet(self.structure, symmetry=True)
# Should be 4 strains for normal, 2 for shear (since +/- shear
# are symmetrically equivalent)
self.assertEqual(len(dss_symm), 6)
def test_as_strain_dict(self):
strain_dict = self.default_dss.as_strain_dict()
for i, def_struct in enumerate(self.default_dss):
test_strain = IndependentStrain(self.default_dss.deformations[i])
strain_keys = [
strain for strain in list(strain_dict.keys())
if (strain == test_strain).all()
]
self.assertEqual(len(strain_keys), 1)
self.assertEqual(self.default_dss.def_structs[i],
strain_dict[strain_keys[0]])
class DeformedStructureSetTest(PymatgenTest):
def setUp(self):
self.structure = self.get_structure("Sn")
self.default_dss = DeformedStructureSet(self.structure)
def test_init(self):
with self.assertRaises(ValueError):
DeformedStructureSet(self.structure, num_norm=5)
with self.assertRaises(ValueError):
DeformedStructureSet(self.structure, num_shear=5)
self.assertEqual(self.structure, self.default_dss.undeformed_structure)
# Test symmetry
dss_symm = DeformedStructureSet(self.structure, symmetry=True)
# Should be 4 strains for normal, 2 for shear (since +/- shear
# are symmetrically equivalent)
self.assertEqual(len(dss_symm), 6)
def test_as_strain_dict(self):
strain_dict = self.default_dss.as_strain_dict()
for i, def_struct in enumerate(self.default_dss):
test_strain = IndependentStrain(self.default_dss.deformations[i])
strain_keys = [strain for strain in list(strain_dict.keys())
if (strain == test_strain).all()]
self.assertEqual(len(strain_keys), 1)
self.assertEqual(self.default_dss.def_structs[i],
strain_dict[strain_keys[0]])
class DeformedStructureSetTest(PymatgenTest):
def setUp(self):
lattice = Lattice(
[[3.8401979337, 0.00, 0.00], [1.9200989668, 3.3257101909, 0.00], [0.00, -2.2171384943, 3.1355090603]]
)
self.structure = Structure(lattice, ["Si", "Si"], [[0, 0, 0], [0.75, 0.5, 0.75]])
self.default_dss = DeformedStructureSet(self.structure)
def test_init(self):
with self.assertRaises(ValueError):
DeformedStructureSet(self.structure, num_norm=5)
with self.assertRaises(ValueError):
DeformedStructureSet(self.structure, num_shear=5)
self.assertEqual(self.structure, self.default_dss.undeformed_structure)
def test_as_strain_dict(self):
strain_dict = self.default_dss.as_strain_dict()
for i, def_struct in enumerate(self.default_dss):
test_strain = IndependentStrain(self.default_dss.deformations[i])
strain_keys = [strain for strain in list(strain_dict.keys()) if (strain == test_strain).all()]
self.assertEqual(len(strain_keys), 1)
self.assertEqual(self.default_dss.def_structs[i], strain_dict[strain_keys[0]])
import pymatgen as mg
from pymatgen.analysis.elasticity.strain import DeformedStructureSet
import os
from shutil import copyfile
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.analysis.elasticity.stress import Stress
from pymatgen.analysis.elasticity.elastic import ElasticTensor
structure = mg.Structure.from_file("POSCAR")
def_set = DeformedStructureSet(structure)
strains = def_set.as_strain_dict()
calculations = []
for x in range(1, 25):
calculations.append('poscar%s' % x)
match_dict = {}
for calc in calculations:
struct = mg.Structure.from_file(calc + "/POSCAR")
vrun = Vasprun(calc + '/vasprun.xml', parse_dos=False, parse_eigen=False)
stress = Stress(vrun.ionic_steps[-1]['stress'])
for strain in strains:
if strains[strain].lattice == struct.lattice:
match_dict[strain] = stress
elastics = ElasticTensor.from_stress_dict(match_dict)
with open("elasts.txt", 'w') as f:
f.write(str(elastics.voigt) + '\n')
f.write(str(elastics.k_voigt) + '\n')
