def evaluate(self, symbols_and_values_in, symbol_out):
tensor = ElasticTensor.from_voigt(symbols_and_values_in.get('E_ij'))
if symbol_out == 'E':
return tensor.y_mod
return None
def _evaluate(self, symbol_values):
structure = symbol_values['structure']
cij = symbol_values['C_ij']
elastic_tensor = ElasticTensor.from_voigt(cij)
debye_temp = elastic_tensor.debye_temperature(structure)
return {'d': debye_temp}
def elastic_constant(self,
structure,
potential,
supercell=(1, 1, 1),
nd=0.01,
ns=0.05,
num_norm=4,
num_shear=4,
etol=1e-6,
ftol=1e-6,
nsearch=2000,
neval=10000):
norm_strains = np.linspace(-nd, nd, num_norm).tolist()
shear_strains = np.linspace(-ns, ns, num_shear).tolist()
conventional_structure = self.conventional_structure(structure)
deformation_set = DeformedStructureSet(conventional_structure *
supercell,
norm_strains=norm_strains,
shear_strains=shear_strains)
strains = []
stresses = []
if self.calculator_type == 'lammps':
relax_lammps_script = load_lammps_set('relax')
relax_lammps_script['fix'] = []
relax_lammps_script['minimize'] = '%f %f %d %d' % (etol, ftol,
nsearch, neval)
kwargs = {'lammps_set': relax_lammps_script}
elif self.calculator_type == 'lammps_cython':
kwargs = {
'lammps_additional_commands': [
'min_style cg',
'minimize %f %f %d %d' % (etol, ftol, nsearch, neval)
]
}
async def calculate():
futures = []
for deformation, deformed_structure in zip(
deformation_set.deformations, deformation_set):
strains.append(Strain.from_deformation(deformation))
futures.append(await
self.calculator.submit(deformed_structure,
potential,
properties={'stress'},
**kwargs))
for result in await asyncio.gather(*futures):
stress = Stress(np.array(result['results']['stress']) *
1e-4) # Convert to GPa
stresses.append(stress)
self._run_async_func(calculate())
return ElasticTensor.from_independent_strains(strains, stresses,
Stress(np.zeros((3, 3))))
def get_debye_temp(mpid):
"""
Calculates the debye temperature from eleastic tensors on the Materials Project
Credits: Joseph Montoya
"""
pd.np.seterr(over="ignore") # ignore overflow in double scalars
data = mpr.get_data(mpid)[0]
struct = Structure.from_str(data['cif'], fmt='cif')
c_ij = ElasticTensor.from_voigt(data['elasticity']['elastic_tensor'])
td = c_ij.debye_temperature(struct)
return td
def evaluate(self,
symbols_and_values_in,
symbol_out):
if symbol_out == 'Cij':
tensor = ComplianceTensor.from_voigt(symbols_and_values_in.get('Sij'))
return tensor.elastic_tensor.voigt
elif symbol_out == 'Sij':
tensor = ElasticTensor.from_voigt(symbols_and_values_in.get('Cij'))
return tensor.compliance_tensor.voigt
return None
def elastic_constant(self, structure, potential, supercell=(1, 1, 1),
nd=0.01, ns=0.05, num_norm=4, num_shear=4,
etol=1e-6, ftol=1e-6, nsearch=2000, neval=10000):
norm_strains = np.linspace(-nd, nd, num_norm).tolist()
shear_strains = np.linspace(-ns, ns, num_shear).tolist()
conventional_structure = self.conventional_structure(structure)
deformation_set = DeformedStructureSet(conventional_structure * supercell,
norm_strains=norm_strains,
shear_strains=shear_strains)
strains = []
stresses = []
if self.calculator_type == 'lammps':
relax_lammps_script = load_lammps_set('relax')
relax_lammps_script['fix'] = []
relax_lammps_script['minimize'] = '%f %f %d %d' % (etol, ftol, nsearch, neval)
kwargs = {'lammps_set': relax_lammps_script}
elif self.calculator_type == 'lammps_cython':
kwargs = {'lammps_additional_commands': [
'min_style cg',
'minimize %f %f %d %d' % (etol, ftol, nsearch, neval)
]}
async def calculate():
futures = []
for deformation, deformed_structure in zip(deformation_set.deformations, deformation_set):
strains.append(Strain.from_deformation(deformation))
futures.append(await self.calculator.submit(
deformed_structure, potential,
properties={'stress'},
**kwargs))
for result in await asyncio.gather(*futures):
stress = Stress(np.array(result['results']['stress']) * 1e-4) # Convert to GPa
stresses.append(stress)
self._run_async_func(calculate())
return ElasticTensor.from_independent_strains(strains, stresses, Stress(np.zeros((3, 3))))
subprocess.call(['lammps', '-i', 'lammps.in'],
cwd=deformation_directory,
stdout=subprocess.PIPE)
lammps_log = LammpsLog(os.path.join(deformation_directory, 'lammps.log'))
stress = Stress(lammps_log.get_stress(-1))
strained_structures.append({
'strain': strain,
'structrure': strained_structure,
'stress': stress / -10000.0 # bar to GPa
})
strains = [defo['strain'] for defo in strained_structures]
stresses = [defo['stress'] for defo in strained_structures]
elastic = ElasticTensor.from_pseudoinverse(strains, stresses)
print('Stiffness Tensor')
for row in elastic.voigt:
print(
'{:+8.1f} {:+8.1f} {:+8.1f} {:+8.1f} {:+8.1f} {:+8.1f}\n'.format(*row))
print('Shear Modulus G_V', elastic.g_voigt)
print('Shear Modulus G_R', elastic.g_reuss)
print('Shear Modulus G_vrh', elastic.g_vrh)
print('Bulk Modulus K_V', elastic.k_voigt)
print('Bulk Modulus K_R', elastic.k_reuss)
print('Bulk Modulus K_vrh', elastic.k_vrh)
print('Elastic Anisotropy', elastic.universal_anisotropy)