def eos(self):
from aiida.orm import Code, Computer, CalculationFactory
import numpy as np
params = self.get_parameters()
x_material = params['x_material']
starting_alat = params['starting_alat']
alat_steps = params['alat_steps']
a_sweep = np.linspace(starting_alat * 0.85, starting_alat * 1.15, alat_steps).tolist()
aiidalogger.info("Storing a_sweep as " + str(a_sweep))
self.add_attribute('a_sweep', a_sweep)
for a in a_sweep:
self.append_to_report("Preparing structure {0} with alat {1}".format(x_material + "TiO3", a))
calc = self.get_pw_calculation(self.get_structure(alat=a, x_material=x_material),
self.get_pw_parameters(),
self.get_kpoints())
self.attach_calculation(calc)
self.next(self.optimize)
def eos(self):
from aiida.orm import Code, Computer, CalculationFactory
import numpy as np
params = self.get_parameters()
x_material = params['x_material']
starting_alat = params['starting_alat']
alat_steps = params['alat_steps']
a_sweep = np.linspace(starting_alat * 0.85, starting_alat * 1.15,
alat_steps).tolist()
aiidalogger.info("Storing a_sweep as " + str(a_sweep))
self.add_attribute('a_sweep', a_sweep)
for a in a_sweep:
self.append_to_report(
"Preparing structure {0} with alat {1}".format(
x_material + "TiO3", a))
calc = self.get_pw_calculation(
self.get_structure(alat=a, x_material=x_material),
self.get_pw_parameters(), self.get_kpoints())
self.attach_calculation(calc)
self.next(self.optimize)
def eos(self):
from aiida.orm import Code, Computer, CalculationFactory
import numpy as np
params = self.get_parameters()
# x_material = params['x_material']
# starting_alat = params['starting_alat']
structure_id = params['structure_id']
x_material = load_node(structure_id).get_formula()
alat_steps = params['alat_steps']
# a_sweep = np.linspace(starting_alat * 0.85, starting_alat * 1.15, alat_steps).tolist()
alat_scale = np.linspace(0.98, 1.02, alat_steps).tolist()
aiidalogger.info("Storing alat_scale as " + str(alat_scale))
self.add_attribute('alat_scale', alat_scale)
for a in alat_scale:
self.append_to_report(
"Preparing structure {0} with alat_scale {1}".format(
x_material, a))
calc = self.get_lapw_calculation(
self.get_structure(structure_id=structure_id, scale=a),
self.get_lapw_parameters(), self.get_kpoints())
self.attach_calculation(calc)
self.next(self.optimize)
def stress_tensor(self):
from aiida.orm import Code, Computer, CalculationFactory
import numpy as np
import spglib
params = self.get_parameters()
use_symmetry = True
use_symmetry = params['use_symmetry']
structure_id = params['structure_id']
x_material = load_node(structure_id).get_formula()
# alat_steps = params['alat_steps']
alat_steps = 5
eps = np.linspace(-0.008, 0.008, alat_steps).tolist()
aiidalogger.info("Storing eps as " + str(eps))
self.add_attribute('eps', eps)
if use_symmetry:
SGN = self.get_space_group_number(structure_id=structure_id)
else:
SGN = 1
self.append_to_report(x_material + " structure has space group number " + str(SGN))
LC = self.get_Laue_dict(space_group_number=SGN)
self.add_attribute('LC', LC)
# distorted_structure_index = range(len(eps * SCs))
# aiidalogger.info("Storing distorted_structure_index as " + str(distorted_structure_index))
# self.add_attribute('distorted_structure_index', distorted_structure_index)
def_list = self.get_distorted_index(structure_id=structure_id, LC=LC)
distorted_structure_index = []
eps_index = 0
for i in def_list:
for a in eps:
eps_index = eps_index + 1
distorted_structure_index.append(eps_index)
# M_eps = self.get_strain_matrix(eps=a, def_mtx_index=i)
M_Lagrange_eps = self.get_Lagrange_strain_matrix(eps=a, def_mtx_index=i)
self.append_to_report("Preparing structure {0} with alat_strain {1} for SC {2}".format(x_material, a, i))
calc = self.get_lapw_calculation(self.get_Lagrange_distorted_structure(structure_id=structure_id, M_Lagrange_eps=M_Lagrange_eps),
self.get_lapw_parameters(),
self.get_kpoints())
self.attach_calculation(calc)
self.add_attribute('distorted_structure_index', distorted_structure_index)
self.next(self.analyze)
def optimize(self):
from aiida.orm.data.parameter import ParameterData
alat_scale = self.get_attribute("alat_scale")
scale_index = self.get_attribute("scale_index")
params = self.get_parameters()
structure_id = params['structure_id']
x_material = load_node(structure_id).get_formula()
aiidalogger.info("Retrieving alat_scale as {0}".format(alat_scale))
# Get calculations/get_step_calculations
start_calcs = self.get_step_calculations(
self.eos) # .get_calculations()
# Calculate results
#-----------------------------------------
e_calcs = [c.res.energy for c in start_calcs]
v_calcs = [c.res.volume for c in start_calcs]
# e_calcs = zip(*sorted(zip(alat_scale, e_calcs)))[1]
# v_calcs = zip(*sorted(zip(alat_scale, v_calcs)))[1]
e_calcs = zip(*sorted(zip(scale_index, e_calcs)))[1]
v_calcs = zip(*sorted(zip(scale_index, v_calcs)))[1]
# Add to report
#-----------------------------------------
for i in range(len(alat_scale)):
self.append_to_report(x_material + " simulated with alat_scale=" +
str(alat_scale[i]) + ", e=" +
str(e_calcs[i]))
# Find optimal alat
#-----------------------------------------
murnpars, ier = Murnaghan_fit(e_calcs, v_calcs)
# New optimal alat
optimal_alat = murnpars[3]**(1 / 3.0)
self.add_attribute('optimal_alat', optimal_alat)
vol0 = load_node(structure_id).get_cell_volume()
optimal_scale = (murnpars[3] / vol0)**(1 / 3.0)
self.add_attribute('optimal_scale', optimal_scale)
# Build last calculation
#-----------------------------------------
calc = self.get_lapw_calculation(
self.get_structure(structure_id=structure_id, scale=optimal_scale),
self.get_lapw_parameters(), self.get_kpoints())
self.attach_calculation(calc)
self.next(self.final_step)
def optimize(self):
from aiida.orm.data.parameter import ParameterData
alat_scale = self.get_attribute("alat_scale")
scale_index = self.get_attribute("scale_index")
params = self.get_parameters()
structure_id = params['structure_id']
x_material = load_node(structure_id).get_formula()
aiidalogger.info("Retrieving alat_scale as {0}".format(alat_scale))
# Get calculations/get_step_calculations
start_calcs = self.get_step_calculations(self.eos) # .get_calculations()
# Calculate results
#-----------------------------------------
e_calcs = [c.res.energy for c in start_calcs]
v_calcs = [c.res.volume for c in start_calcs]
# e_calcs = zip(*sorted(zip(alat_scale, e_calcs)))[1]
# v_calcs = zip(*sorted(zip(alat_scale, v_calcs)))[1]
e_calcs = zip(*sorted(zip(scale_index, e_calcs)))[1]
v_calcs = zip(*sorted(zip(scale_index, v_calcs)))[1]
# Add to report
#-----------------------------------------
for i in range(len(alat_scale)):
self.append_to_report(x_material + " simulated with alat_scale=" + str(alat_scale[i]) + ", e=" + str(e_calcs[i]))
# Find optimal alat
#-----------------------------------------
murnpars, ier = Murnaghan_fit(e_calcs, v_calcs)
# New optimal alat
optimal_alat = murnpars[3] ** (1 / 3.0)
self.add_attribute('optimal_alat', optimal_alat)
vol0 = load_node(structure_id).get_cell_volume()
optimal_scale = (murnpars[3] / vol0) ** (1 / 3.0)
self.add_attribute('optimal_scale', optimal_scale)
# Build last calculation
#-----------------------------------------
calc = self.get_lapw_calculation(self.get_structure(structure_id=structure_id, scale=optimal_scale),
self.get_lapw_parameters(),
self.get_kpoints())
self.attach_calculation(calc)
self.next(self.final_step)
def optimize(self):
from aiida.orm.data.parameter import ParameterData
x_material = self.get_parameter("x_material")
a_sweep = self.get_attribute("a_sweep")
aiidalogger.info("Retrieving a_sweep as {0}".format(a_sweep))
# Get calculations
start_calcs = self.get_step_calculations(
self.eos) # .get_calculations()
# Calculate results
#-----------------------------------------
e_calcs = [c.res.energy for c in start_calcs]
v_calcs = [c.res.volume for c in start_calcs]
e_calcs = zip(*sorted(zip(a_sweep, e_calcs)))[1]
v_calcs = zip(*sorted(zip(a_sweep, v_calcs)))[1]
# Add to report
#-----------------------------------------
for i in range(len(a_sweep)):
self.append_to_report(x_material + "Ti03 simulated with a=" +
str(a_sweep[i]) + ", e=" + str(e_calcs[i]))
# Find optimal alat
#-----------------------------------------
murnpars, ier = Murnaghan_fit(e_calcs, v_calcs)
# New optimal alat
optimal_alat = murnpars[3]**(1 / 3.0)
self.add_attribute('optimal_alat', optimal_alat)
# Build last calculation
#-----------------------------------------
calc = self.get_pw_calculation(
self.get_structure(alat=optimal_alat, x_material=x_material),
self.get_pw_parameters(), self.get_kpoints())
self.attach_calculation(calc)
self.next(self.final_step)
def optimize(self):
from aiida.orm.data.parameter import ParameterData
x_material = self.get_parameter("x_material")
a_sweep = self.get_attribute("a_sweep")
aiidalogger.info("Retrieving a_sweep as {0}".format(a_sweep))
# Get calculations
start_calcs = self.get_step_calculations(self.eos) # .get_calculations()
# Calculate results
#-----------------------------------------
e_calcs = [c.res.energy for c in start_calcs]
v_calcs = [c.res.volume for c in start_calcs]
e_calcs = zip(*sorted(zip(a_sweep, e_calcs)))[1]
v_calcs = zip(*sorted(zip(a_sweep, v_calcs)))[1]
# Add to report
#-----------------------------------------
for i in range(len(a_sweep)):
self.append_to_report(x_material + "Ti03 simulated with a=" + str(a_sweep[i]) + ", e=" + str(e_calcs[i]))
# Find optimal alat
#-----------------------------------------
murnpars, ier = Murnaghan_fit(e_calcs, v_calcs)
# New optimal alat
optimal_alat = murnpars[3] ** (1 / 3.0)
self.add_attribute('optimal_alat', optimal_alat)
# Build last calculation
#-----------------------------------------
calc = self.get_pw_calculation(self.get_structure(alat=optimal_alat, x_material=x_material),
self.get_pw_parameters(),
self.get_kpoints())
self.attach_calculation(calc)
self.next(self.final_step)
def eos(self):
from aiida.orm import Code, Computer, CalculationFactory
import numpy as np
params = self.get_parameters()
# x_material = params['x_material']
# starting_alat = params['starting_alat']
structure_id = params['structure_id']
x_material = load_node(structure_id).get_formula()
alat_steps = params['alat_steps']
# a_sweep = np.linspace(starting_alat * 0.85, starting_alat * 1.15, alat_steps).tolist()
alat_scale = np.linspace(0.98, 1.02, alat_steps).tolist()
aiidalogger.info("Storing alat_scale as " + str(alat_scale))
self.add_attribute('alat_scale', alat_scale)
scale_index = []
scale_i = 0
for a in alat_scale:
scale_i = scale_i + 1
scale_index.append(scale_i)
self.append_to_report("Preparing structure {0} with alat_scale {1}".format(x_material, a))
calc = self.get_lapw_calculation(self.get_structure(structure_id=structure_id, scale=a),
self.get_lapw_parameters(),
self.get_kpoints())
self.attach_calculation(calc)
self.add_attribute('scale_index', scale_index)
self.next(self.optimize)
def analyze(self):
from aiida.orm.data.parameter import ParameterData
import numpy as np
import scipy.optimize as scimin
#%!%!%--- CONSTANTS ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!
_e = 1.602176565e-19 # elementary charge
# Bohr = 5.291772086e-11 # a.u. to meter
# Ha2eV = 27.211396132 # Ha to eV
# Tokbar= (_e*Ha2eV)/(1e8*Bohr**3) # Ha/[a.u.]^3 to kbar
# ToGPa = (_e*Ha2eV)/(1e9*Bohr**3) # Ha/[a.u.]^3 to GPa
angstrom = 1.0e-10 # angstrom to meter
ToGPa = _e / (1e9 * angstrom**3) # eV/[\AA]^3 to GPa
Tokbar = _e / (1e8 * angstrom**3) # eV/[\AA]^3 to kbar
#__________________________________________________________________________________________________
alat_steps = self.get_attribute("alat_steps")
eps = self.get_attribute("eps")
distorted_structure_index = self.get_attribute(
"distorted_structure_index")
#for i in range(len(eps)):
# self.append_to_report(" simulated with strain =" + ", e=" + str(eps[i]))
def_list = self.get_attribute("def_list")
params = self.get_parameters()
structure_id = params['structure_id']
x_material = load_node(structure_id).get_formula()
aiidalogger.info("Retrieving eps as {0}".format(eps))
# Get calculations/get_step_calculations
start_calcs = self.get_step_calculations(
self.stress_tensor) # .get_calculations()
# Calculate results
#-----------------------------------------
e_calcs = [c.res.energy for c in start_calcs]
e_calcs = zip(*sorted(zip(distorted_structure_index, e_calcs)))[1]
e_calcs_correct = e_calcs[::-1]
# Add to report
#-----------------------------------------
for i in range(len(distorted_structure_index)):
self.append_to_report(x_material + " simulated with strain =" +
str(distorted_structure_index[i]) + ", e=" +
str(e_calcs_correct[i]))
# Obtain stress tensor by polyfit
#-----------------------------------------
#alat_steps = 5
#SCs = int(len(distorted_structure_index) / alat_steps)
SCs = self.get_attribute("SCs")
A1 = []
energy = []
order = 3
#eps = np.linspace(-0.008, 0.008, alat_steps).tolist()
for i in range(SCs):
energy = e_calcs_correct[i * alat_steps:(i + 1) * alat_steps]
coeffs = np.polyfit(eps, energy, order)
A1.append(coeffs[order - 1] * ToGPa)
#lsq_coeffs, ier = lsq_fit(energy, eps)
#A1.append(lsq_coeffs[order-1]*ToGPa)
A1 = np.array(A1)
LC = self.get_attribute("LC")
S = self.get_stress_tensor_matrix(structure_id=structure_id,
LC=LC,
A1=A1)
self.append_to_report(x_material + " simulated with structure_id =" +
str(structure_id) +
" has stress tensor S11, S12, S13=" +
str(S[0, :]))
self.append_to_report(x_material + " simulated with structure_id =" +
str(structure_id) +
" has stress tensor S21, S22, S23=" +
str(S[1, :]))
self.append_to_report(x_material + " simulated with structure_id =" +
str(structure_id) +
" has stress tensor S31, S32, S33=" +
str(S[2, :]))
P = (S[0, 0] + S[1, 1] + S[2, 2]) / -3.
self.append_to_report(x_material + " simulated with structure_id =" +
str(structure_id) + " has pressure =" + str(P) +
" GPa")
self.next(self.exit)
def stress_tensor(self):
from aiida.orm import Code, Computer, CalculationFactory
import numpy as np
import spglib
params = self.get_parameters()
use_symmetry = True
use_symmetry = params['use_symmetry']
structure_id = params['structure_id']
x_material = load_node(structure_id).get_formula()
# alat_steps = params['alat_steps']
alat_steps = 5
eps = np.linspace(-0.008, 0.008, alat_steps).tolist()
aiidalogger.info("Storing eps as " + str(eps))
self.add_attribute('eps', eps)
self.add_attribute('alat_steps', alat_steps)
if use_symmetry:
SGN = self.get_space_group_number(structure_id=structure_id)
else:
SGN = 1
self.append_to_report(x_material +
" structure has space group number " + str(SGN))
LC = self.get_Laue_dict(space_group_number=SGN)
self.add_attribute('LC', LC)
# distorted_structure_index = range(len(eps * SCs))
# aiidalogger.info("Storing distorted_structure_index as " + str(distorted_structure_index))
# self.add_attribute('distorted_structure_index', distorted_structure_index)
def_list = self.get_Lagrange_distorted_index(structure_id=structure_id,
LC=LC)
self.add_attribute('def_list', def_list)
SCs = len(def_list)
self.add_attribute('SCs', SCs)
distorted_structure_index = []
eps_index = 0
for i in def_list:
for a in eps:
eps_index = eps_index + 1
distorted_structure_index.append(eps_index)
self.add_attribute('distorted_structure_index',
distorted_structure_index)
for ii in distorted_structure_index:
a = eps[ii % alat_steps - 1]
i = def_list[int((ii - 1) / alat_steps)]
M_Lagrange_eps = self.get_Lagrange_strain_matrix(eps=a,
def_mtx_index=i)
distorted_structure = self.get_Lagrange_distorted_structure(
structure_id=structure_id, M_Lagrange_eps=M_Lagrange_eps)
calc = self.get_pw_calculation(distorted_structure,
self.get_pw_parameters(),
self.get_kpoints())
self.attach_calculation(calc)
self.append_to_report(
"Preparing structure {0} with alat_strain {1} for SC {2}".
format(x_material, a, i))
self.append_to_report(
"Distorted structure with index {0} has ID {1}".format(
ii, distorted_structure.id))
self.append_to_report("Calculation with pk {0}".format(calc.id))
self.next(self.analyze)
def analyze(self):
from aiida.orm.data.parameter import ParameterData
import numpy as np
import scipy.optimize as scimin
#%!%!%--- CONSTANTS ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!
_e = 1.602176565e-19 # elementary charge
# Bohr = 5.291772086e-11 # a.u. to meter
# Ha2eV = 27.211396132 # Ha to eV
# Tokbar= (_e*Ha2eV)/(1e8*Bohr**3) # Ha/[a.u.]^3 to kbar
# ToGPa = (_e*Ha2eV)/(1e9*Bohr**3) # Ha/[a.u.]^3 to GPa
angstrom = 1.0e-10 # angstrom to meter
ToGPa = _e/(1e9*angstrom**3) # eV/[\AA]^3 to GPa
Tokbar = _e/(1e8*angstrom**3) # eV/[\AA]^3 to kbar
#__________________________________________________________________________________________________
alat_steps = self.get_attribute("alat_steps")
eps = self.get_attribute("eps")
distorted_structure_index = self.get_attribute("distorted_structure_index")
#for i in range(len(eps)):
# self.append_to_report(" simulated with strain =" + ", e=" + str(eps[i]))
def_list = self.get_attribute("def_list")
params = self.get_parameters()
structure_id = params['structure_id']
x_material = load_node(structure_id).get_formula()
aiidalogger.info("Retrieving eps as {0}".format(eps))
# Get calculations/get_step_calculations
start_calcs = self.get_step_calculations(self.stress_tensor) # .get_calculations()
# Calculate results
#-----------------------------------------
e_calcs = [c.res.energy for c in start_calcs]
e_calcs = zip(*sorted(zip(distorted_structure_index, e_calcs)))[1]
e_calcs_correct = e_calcs[::-1]
# Add to report
#-----------------------------------------
for i in range(len(distorted_structure_index)):
self.append_to_report(x_material + " simulated with strain =" + str(distorted_structure_index[i]) + ", e=" + str(e_calcs_correct[i]))
# Obtain stress tensor by polyfit
#-----------------------------------------
#alat_steps = 5
#SCs = int(len(distorted_structure_index) / alat_steps)
SCs = self.get_attribute("SCs")
A1 = []
energy = []
order = 3
#eps = np.linspace(-0.008, 0.008, alat_steps).tolist()
for i in range(SCs):
energy = e_calcs_correct[i*alat_steps:(i+1)*alat_steps]
coeffs = np.polyfit(eps, energy, order)
A1.append(coeffs[order-1]*ToGPa)
#lsq_coeffs, ier = lsq_fit(energy, eps)
#A1.append(lsq_coeffs[order-1]*ToGPa)
A1 = np.array(A1)
LC = self.get_attribute("LC")
S = self.get_stress_tensor_matrix(structure_id=structure_id, LC=LC, A1=A1)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has stress tensor S11, S12, S13=" + str(S[0,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has stress tensor S21, S22, S23=" + str(S[1,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has stress tensor S31, S32, S33=" + str(S[2,:]))
P = (S[0,0]+S[1,1]+S[2,2])/-3.
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has pressure =" + str(P) + " GPa")
self.next(self.exit)
def analyze(self):
from aiida.orm.data.parameter import ParameterData
import numpy as np
x_material = self.get_parameter("x_material")
a_sweep = self.get_attribute("a_sweep")
aiidalogger.info("Retrieving a_sweep as {0}".format(a_sweep))
# Get calculations
start_calcs = self.get_step_calculations(
self.stress_tensor) # .get_calculations()
# Calculate results
#-----------------------------------------
alat_steps = params['alat_steps']
s_calcs = np.linspace(-0.002, 0.002, alat_steps).tolist()
e_calcs = [c.res.energy for c in start_calcs]
v_calcs = [c.res.volume for c in start_calcs]
e_calcs = zip(*sorted(zip(a_sweep, e_calcs)))[1]
v_calcs = zip(*sorted(zip(a_sweep, v_calcs)))[1]
s_calcs = zip(*sorted(zip(a_sweep, s_calcs)))[1]
# Add to report
#-----------------------------------------
for i in range(len(a_sweep)):
self.append_to_report(x_material + "Ti03 simulated with a=" +
str(a_sweep[i]) + ", s=" + str(s_calcs[i]) +
", e=" + str(e_calcs[i]))
s_pymatgen = s.get_pymatgen()
import pymatgen as mg
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
finder = SpacegroupAnalyzer(s_pymatgen)
SGN = finder.get_space_group_number()
#%!%!%--- Classify the Space-Group Number ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!
if (1 <= SGN and SGN <= 2): # Triclinic
LC = 'N'
SCs = 6
elif (3 <= SGN and SGN <= 15): # Monoclinic
LC = 'M'
SCs = 4
elif (16 <= SGN and SGN <= 74): # Orthorhombic
LC = 'O'
SCs = 3
elif (75 <= SGN and SGN <= 88): # Tetragonal II
LC = 'TII'
SCs = 2
elif (89 <= SGN and SGN <= 142): # Tetragonal I
LC = 'TI'
SCs = 2
elif (143 <= SGN and SGN <= 148): # Rhombohedral II
LC = 'RII'
SCs = 2
elif (149 <= SGN and SGN <= 167): # Rhombohedral I
LC = 'RI'
SCs = 2
elif (168 <= SGN and SGN <= 176): # Hexagonal II
LC = 'HII'
SCs = 2
elif (177 <= SGN and SGN <= 194): # Hexagonal I
LC = 'HI'
SCs = 2
elif (195 <= SGN and SGN <= 206): # Cubic II
LC = 'CII'
SCs = 1
elif (207 <= SGN and SGN <= 230): # Cubic I
LC = 'CI'
SCs = 1
else:
sys.exit('\n ... Oops ERROR: WRONG Space-Group Number !?!?!?\n')
#%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%#
#%!%!% ------------ Calculating the first derivative and Cross-Validation Error ------------ %!%!%#
#%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%#
A1 = []
mdri = 0.002
ordri = 1
strain = []
energy = []
strain = copy.copy(s_calcs)
energy = copy.copy(e_calcs)
coeffs = np.polyfit(strain, energy, ordri)
A1.append(coeffs[ordri - 1])
A1 = np.array(A1)
if (len(A1) != SCs):
sys.exit('\n ... Oops ERROR: The number of data is NOT equal to ' + \
str(SCs)+'\n')
S = zeros((3, 3))
#%!%!%--- Cubic structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%
if (LC == 'CI' or \
LC == 'CII'):
S[0, 0] = A1[0] / 3.
S[1, 1] = S[0, 0]
S[2, 2] = S[0, 0]
#--------------------------------------------------------------------------------------------------
#%!%!%--- Hexagonal, Rhombohedral, and Tetragonal structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%
if (LC == 'HI' or \
LC == 'HII'or \
LC == 'RI' or \
LC == 'RII'or \
LC == 'TI' or \
LC == 'TII'):
S[0, 0] = (A1[0] - 1. * A1[1]) / 3.
S[1, 1] = S[0, 0]
S[2, 2] = (A1[0] + 2. * A1[1]) / 3.
#--------------------------------------------------------------------------------------------------
#%!%!%--- Orthorhombic structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!
if (LC == 'O'):
S[0, 0] = (A1[0] - 2. * A1[1] - 2. * A1[2]) / 3.
S[1, 1] = (A1[0] + 2. * A1[1]) / 3.
S[2, 2] = (A1[0] + 2. * A1[2]) / 3.
#--------------------------------------------------------------------------------------------------
#%!%!%--- Monoclinic structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!
if (LC == 'M'):
S[0, 0] = (A1[0] - 2. * A1[1] - 2. * A1[2]) / 3.
S[1, 1] = (A1[0] + 2. * A1[1]) / 3.
S[2, 2] = (A1[0] + 2. * A1[2]) / 3.
if (unique_axis == 'a'): S[1, 2] = A1[3] / 2.
if (unique_axis == 'b'): S[0, 2] = A1[3] / 2.
if (unique_axis == 'c'): S[0, 1] = A1[3] / 2.
#--------------------------------------------------------------------------------------------------
#%!%!%--- Triclinic structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%
if (LC == 'N'):
S[0, 0] = (A1[0] + 2. * A1[2]) / 3.,
S[1, 1] = (A1[0] + 2. * A1[1]) / 3.,
S[2, 2] = (A1[0] - 2. * (A1[1] + A1[2])) / 3.,
S[1, 2] = A1[3] / 2.,
S[0, 2] = A1[4] / 2.,
S[0, 1] = A1[5] / 2.
#--------------------------------------------------------------------------------------------------
#%!%!%--- Calculating the Pressure ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%
for i in range(2):
for j in range(i + 1, 3):
S[j, i] = S[i, j]
eV_over_ang3_toGPa = 160.21766208
v0i = int((alat_steps + 1) / 2)
V0 = v_calcs[v0i]
S = S / V0 * eV_over_ang3_toGPa
P = (S[0, 0] + S[1, 1] + S[2, 2]) / -3. * eV_over_ang3_toGPa
#--------------------------------------------------------------------------------------------------
self.append_to_report(x_material + "Ti03 simulated with a=" +
str(a_sweep[v0i]) + ", e=" + str(e_calcs[v0i]))
self.append_to_report("stress tensor matrix = " + str(S[0, 0]) +
str(S[0, 1]) + str(S[0, 2]))
self.append_to_report("stress tensor matrix = " + str(S[1, 0]) +
str(S[1, 1]) + str(S[1, 2]))
self.append_to_report("stress tensor matrix = " + str(S[2, 0]) +
str(S[2, 1]) + str(S[2, 2]))
self.append_to_report("external pressure in GPa = " + str(P))
self.next(self.exit)
def analyze(self):
from aiida.orm.data.parameter import ParameterData
import numpy as np
import scipy.optimize as scimin
#%!%!%--- CONSTANTS ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!
_e = 1.602176565e-19 # elementary charge
# Bohr = 5.291772086e-11 # a.u. to meter
# Ha2eV = 27.211396132 # Ha to eV
# Tokbar= (_e*Ha2eV)/(1e8*Bohr**3) # Ha/[a.u.]^3 to kbar
# ToGPa = (_e*Ha2eV)/(1e9*Bohr**3) # Ha/[a.u.]^3 to GPa
angstrom = 1.0e-10 # angstrom to meter
ToGPa = _e/(1e9*angstrom**3) # eV/[\AA]^3 to GPa
Tokbar = _e/(1e8*angstrom**3) # eV/[\AA]^3 to kbar
#__________________________________________________________________________________________________
alat_steps = self.get_attribute("alat_steps")
eps = self.get_attribute("eps")
distorted_structure_index = self.get_attribute("distorted_structure_index")
#for i in range(len(eps)):
# self.append_to_report(" simulated with strain =" + ", e=" + str(eps[i]))
def_list = self.get_attribute("def_list")
params = self.get_parameters()
structure_id = params['structure_id']
x_material = load_node(structure_id).get_formula()
aiidalogger.info("Retrieving eps as {0}".format(eps))
# Get calculations/get_step_calculations
start_calcs = self.get_step_calculations(self.stress_tensor) # .get_calculations()
# Calculate results
#-----------------------------------------
e_calcs = [c.res.energy for c in start_calcs]
e_calcs = zip(*sorted(zip(distorted_structure_index, e_calcs)))[1]
e_calcs_correct = e_calcs[::-1]
# Add to report
#-----------------------------------------
for i in range(len(distorted_structure_index)):
self.append_to_report(x_material + " simulated with strain =" + str(distorted_structure_index[i]) + ", e=" + str(e_calcs_correct[i]))
# Obtain stress tensor by polyfit
#-----------------------------------------
#alat_steps = 5
#SCs = int(len(distorted_structure_index) / alat_steps)
SCs = self.get_attribute("SCs")
A2 = []
energy = []
fit_order = 3
#eps = np.linspace(-0.008, 0.008, alat_steps).tolist()
for i in range(ECs):
energy = e_calcs_correct[i*alat_steps:(i+1)*alat_steps]
coeffs = np.polyfit(eps, energy, fit_order)
A1.append(coeffs[fit_order-1]*ToGPa)
#lsq_coeffs, ier = lsq_fit(energy, eps)
#A1.append(lsq_coeffs[order-1]*ToGPa)
A2 = np.array(A2)
LC = self.get_attribute("LC")
C = self.get_elastic_constant_matrix(structure_id=structure_id, LC=LC, A2=A2)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has stress tensor in GPa C11 ... C16=" + str(C[0,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has stress tensor in GPa C21 ... C26=" + str(C[1,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has stress tensor in GPa C31 ... C36=" + str(C[2,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has stress tensor in GPa C41 ... C46=" + str(C[3,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has stress tensor in GPa C51 ... C56=" + str(C[4,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has stress tensor in GPa C61 ... C66=" + str(C[5,:]))
S = np.linalg.inv(C)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Elastic compliance matrix in 1/GPa S11 ... S16=" + str(S[0,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Elastic compliance matrix in 1/GPa S21 ... S26=" + str(S[1,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Elastic compliance matrix in 1/GPa S31 ... S36=" + str(S[2,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Elastic compliance matrix in 1/GPa S41 ... S46=" + str(S[3,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Elastic compliance matrix in 1/GPa S51 ... S56=" + str(S[4,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Elastic compliance matrix in 1/GPa S61 ... S66=" + str(S[5,:]))
eigval=np.linalg.eig(C)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Eigenvalues of elastic constant (stiffness) matrix:=" + str(eigval[0,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Eigenvalues of elastic constant (stiffness) matrix:=" + str(eigval[1,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Eigenvalues of elastic constant (stiffness) matrix:=" + str(eigval[2,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Eigenvalues of elastic constant (stiffness) matrix:=" + str(eigval[3,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Eigenvalues of elastic constant (stiffness) matrix:=" + str(eigval[4,:]))
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Eigenvalues of elastic constant (stiffness) matrix:=" + str(eigval[5,:]))
#%!%!%--- Calculating the elastic moduli ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%
BV = (C[0,0]+C[1,1]+C[2,2]+2*(C[0,1]+C[0,2]+C[1,2]))/9
GV = ((C[0,0]+C[1,1]+C[2,2])-(C[0,1]+C[0,2]+C[1,2])+3*(C[3,3]+C[4,4]+C[5,5]))/15
EV = (9*BV*GV)/(3*BV+GV)
nuV= (1.5*BV-GV)/(3*BV+GV)
BR = 1/(S[0,0]+S[1,1]+S[2,2]+2*(S[0,1]+S[0,2]+S[1,2]))
GR =15/(4*(S[0,0]+S[1,1]+S[2,2])-4*(S[0,1]+S[0,2]+S[1,2])+3*(S[3,3]+S[4,4]+S[5,5]))
ER = (9*BR*GR)/(3*BR+GR)
nuR= (1.5*BR-GR)/(3*BR+GR)
BH = 0.50*(BV+BR)
GH = 0.50*(GV+GR)
EH = (9.*BH*GH)/(3.*BH+GH)
nuH= (1.5*BH-GH)/(3.*BH+GH)
AVR= 100.*(GV-GR)/(GV+GR)
#--------------------------------------------------------------------------------------------------
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Voigt bulk modulus, B_V (Gpa)" + BV)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Voigt shear modulus, G_V (Gpa)" + GV)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Reuss bulk modulus, B_R (Gpa)" + BR)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Reuss shear modulus, G_R (Gpa)" + GR)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Hill bulk modulus, B_H (Gpa)" + BH)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Hill shear modulus, G_H (Gpa)" + GH)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Voigt Young modulus, E_V (Gpa)" + EV)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Voigt Poisson ratio, nu_V" + nuV)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Reuss Young modulus, E_R (Gpa)" + ER)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Reuss Poisson ratio, nu_R " + nuR)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Hill Young modulus, E_H (Gpa)" + EH)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Hill Poisson modulus, nu_H (Gpa)" + nuH)
self.append_to_report(x_material + " simulated with structure_id =" + str(structure_id) + " has Elastic Anisotropy in polycrystalline, AVR =" + nuH)
self.next(self.exit)
def analyze(self):
from aiida.orm.data.parameter import ParameterData
import numpy as np
x_material = self.get_parameter("x_material")
a_sweep = self.get_attribute("a_sweep")
aiidalogger.info("Retrieving a_sweep as {0}".format(a_sweep))
# Get calculations
start_calcs = self.get_step_calculations(self.stress_tensor) # .get_calculations()
# Calculate results
#-----------------------------------------
alat_steps = params['alat_steps']
s_calcs = np.linspace(-0.002, 0.002, alat_steps).tolist()
e_calcs = [c.res.energy for c in start_calcs]
v_calcs = [c.res.volume for c in start_calcs]
e_calcs = zip(*sorted(zip(a_sweep, e_calcs)))[1]
v_calcs = zip(*sorted(zip(a_sweep, v_calcs)))[1]
s_calcs = zip(*sorted(zip(a_sweep, s_calcs)))[1]
# Add to report
#-----------------------------------------
for i in range(len(a_sweep)):
self.append_to_report(x_material + "Ti03 simulated with a=" + str(a_sweep[i]) + ", s=" + str(s_calcs[i]) + ", e=" + str(e_calcs[i]))
s_pymatgen = s.get_pymatgen()
import pymatgen as mg
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
finder = SpacegroupAnalyzer(s_pymatgen)
SGN = finder.get_space_group_number()
#%!%!%--- Classify the Space-Group Number ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!
if (1 <= SGN and SGN <= 2): # Triclinic
LC = 'N'
SCs= 6
elif(3 <= SGN and SGN <= 15): # Monoclinic
LC = 'M'
SCs= 4
elif(16 <= SGN and SGN <= 74): # Orthorhombic
LC = 'O'
SCs= 3
elif(75 <= SGN and SGN <= 88): # Tetragonal II
LC = 'TII'
SCs= 2
elif(89 <= SGN and SGN <= 142): # Tetragonal I
LC = 'TI'
SCs= 2
elif(143 <= SGN and SGN <= 148): # Rhombohedral II
LC = 'RII'
SCs= 2
elif(149 <= SGN and SGN <= 167): # Rhombohedral I
LC = 'RI'
SCs= 2
elif(168 <= SGN and SGN <= 176): # Hexagonal II
LC = 'HII'
SCs= 2
elif(177 <= SGN and SGN <= 194): # Hexagonal I
LC = 'HI'
SCs= 2
elif(195 <= SGN and SGN <= 206): # Cubic II
LC = 'CII'
SCs= 1
elif(207 <= SGN and SGN <= 230): # Cubic I
LC = 'CI'
SCs= 1
else: sys.exit('\n ... Oops ERROR: WRONG Space-Group Number !?!?!?\n')
#%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%#
#%!%!% ------------ Calculating the first derivative and Cross-Validation Error ------------ %!%!%#
#%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%#
A1 = []
mdri = 0.002
ordri = 1
strain = []
energy = []
strain = copy.copy(s_calcs)
energy = copy.copy(e_calcs)
coeffs = np.polyfit(strain, energy, ordri)
A1.append(coeffs[ordri-1])
A1 = np.array(A1)
if (len(A1) != SCs):
sys.exit('\n ... Oops ERROR: The number of data is NOT equal to ' + \
str(SCs)+'\n')
S = zeros((3,3))
#%!%!%--- Cubic structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%
if (LC == 'CI' or \
LC == 'CII'):
S[0,0] = A1[0]/3.
S[1,1] = S[0,0]
S[2,2] = S[0,0]
#--------------------------------------------------------------------------------------------------
#%!%!%--- Hexagonal, Rhombohedral, and Tetragonal structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%
if (LC == 'HI' or \
LC == 'HII'or \
LC == 'RI' or \
LC == 'RII'or \
LC == 'TI' or \
LC == 'TII'):
S[0,0] = (A1[0] - 1.*A1[1])/3.
S[1,1] = S[0,0]
S[2,2] = (A1[0] + 2.*A1[1])/3.
#--------------------------------------------------------------------------------------------------
#%!%!%--- Orthorhombic structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!
if (LC == 'O'):
S[0,0] = (A1[0] - 2.*A1[1] - 2.*A1[2])/3.
S[1,1] = (A1[0] + 2.*A1[1])/3.
S[2,2] = (A1[0] + 2.*A1[2])/3.
#--------------------------------------------------------------------------------------------------
#%!%!%--- Monoclinic structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!
if (LC == 'M'):
S[0,0] = (A1[0] - 2.*A1[1] - 2.*A1[2])/3.
S[1,1] = (A1[0] + 2.*A1[1])/3.
S[2,2] = (A1[0] + 2.*A1[2])/3.
if (unique_axis == 'a'): S[1,2] = A1[3]/2.
if (unique_axis == 'b'): S[0,2] = A1[3]/2.
if (unique_axis == 'c'): S[0,1] = A1[3]/2.
#--------------------------------------------------------------------------------------------------
#%!%!%--- Triclinic structures ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%
if (LC == 'N'):
S[0,0] = (A1[0] + 2.* A1[2])/3.,
S[1,1] = (A1[0] + 2.* A1[1])/3.,
S[2,2] = (A1[0] - 2.*(A1[1] + A1[2]))/3.,
S[1,2] = A1[3]/2.,
S[0,2] = A1[4]/2.,
S[0,1] = A1[5]/2.
#--------------------------------------------------------------------------------------------------
#%!%!%--- Calculating the Pressure ---%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%!%
for i in range(2):
for j in range(i+1, 3):
S[j,i] = S[i,j]
eV_over_ang3_toGPa = 160.21766208
v0i = int((alat_steps + 1) / 2)
V0 = v_calcs [v0i]
S = S / V0 * eV_over_ang3_toGPa
P = (S[0,0]+S[1,1]+S[2,2])/-3.*eV_over_ang3_toGPa
#--------------------------------------------------------------------------------------------------
self.append_to_report(x_material + "Ti03 simulated with a=" + str(a_sweep[v0i]) + ", e=" + str(e_calcs[v0i]))
self.append_to_report("stress tensor matrix = " + str(S[0,0]) + str(S[0,1]) + str(S[0,2]))
self.append_to_report("stress tensor matrix = " + str(S[1,0]) + str(S[1,1]) + str(S[1,2]))
self.append_to_report("stress tensor matrix = " + str(S[2,0]) + str(S[2,1]) + str(S[2,2]))
self.append_to_report("external pressure in GPa = " + str(P) )
self.next(self.exit)
