def run_hiphive(supercell, primitive, displacements, forces, options, symprec,
log_level):
"""Run hiphive
supercell : Supercell
Perfect supercell.
primitive : Primitive
Primitive cell.
displacements : ndarray
Displacements of atoms in supercell.
shape=(supercells, natom, 3)
forces : ndarray
Forces on atoms in supercell.
shape=(supercells, natom, 3)
options : str
Force constants calculation options.
log_level : int
Log control. 0: quiet, 1: normal, 2: verbose 3: debug
"""
ase_supercell = phonopy_atoms_to_ase(supercell)
ase_prim = phonopy_atoms_to_ase(primitive)
# setup training structures
structures = []
for d, f in zip(displacements, forces):
structure = ase_supercell.copy()
structure.new_array('displacements', d)
structure.new_array('forces', f)
structures.append(structure)
# parse options
if options is None:
options_dict = {}
else:
options_dict = _decode_options(options)
# select cutoff
max_cutoff = estimate_maximum_cutoff(ase_supercell) - 1e-5
if 'cutoff' in options_dict:
cutoff = options_dict['cutoff']
if cutoff > max_cutoff:
raise ValueError(
'Cutoff {:.4f} is larger than maximum allowed '
'cutoff, {:.4f}, for the given supercell.'
'\nDecrease cutoff or provide larger supercells.'.format(
cutoff, max_cutoff))
else:
cutoff = max_cutoff
# setup ClusterSpace
cutoffs = [cutoff]
cs = ClusterSpace(ase_prim, cutoffs, symprec=symprec)
cs.print_orbits()
sc = StructureContainer(cs)
for structure in structures:
sc.add_structure(structure)
n_rows, n_cols = sc.data_shape
if n_rows < n_cols:
raise ValueError('Fitting problem is under-determined.'
'\nProvide more structures or decrease cutoff.')
# Estimate error
opt = Optimizer(sc.get_fit_data(), train_size=0.75)
opt.train()
print(opt)
print('RMSE train : {:.4f}'.format(opt.rmse_train))
print('RMSE test : {:.4f}'.format(opt.rmse_test))
# Final train
opt = Optimizer(sc.get_fit_data(), train_size=1.0)
opt.train()
# get force constants
fcp = ForceConstantPotential(cs, opt.parameters)
fcs = fcp.get_force_constants(ase_supercell)
fc2 = fcs.get_fc_array(order=2)
return fc2
# train FCP
sc = StructureContainer(cs)
for i in range(3):
atoms = supercell.copy()
atoms.rattle(0.3, seed=100*i)
atoms = prepare_structure(atoms, supercell, calc=EMT())
sc.add_structure(atoms)
opt = Optimizer(sc.get_fit_data())
opt.train()
print(opt)
# get fcs
fcp = ForceConstantPotential(cs, opt.parameters)
fcs = fcp.get_force_constants(supercell)
# calculate reference forces
supercell_rattle = supercell.copy()
supercell_rattle.rattle(0.2)
calc = ForceConstantCalculator(fcs)
supercell_rattle.set_calculator(calc)
forces = supercell_rattle.get_forces()
np.savetxt('forces_hiphive.txt', forces)
# write gpumd files
write_atoms_gpumd('xyz.in', supercell_rattle)
write_r0('r0.in', supercell)
print('Structure container building ups are completed!')
############# Develop force constant potential model #################
# Fit models for 2nd and 3rd order
# fit_method: str to specify which fitting method to use
opt = Optimizer(sc.get_fit_data(),
fit_method='least-squares',
seed=seed_int_struct)
opt.train()
print(opt)
fcp = ForceConstantPotential(cs, opt.parameters)
########### Generate and save force constant of desired orders #############
fcs = fcp.get_force_constants(initial_structure)
# Set up hiPhive fcs folder
hiphive_filename = 'hiPhive_si_bulk/'
primitive_fname = 'hiPhive_si_bulk/atom_prim.xyz'
if not os.path.isdir(hiphive_filename):
os.mkdir(hiphive_filename)
write(primitive_fname, atoms_prim, format='xyz')
# Explicitly set periodic boundary conditions (pbc) for replicated structures.
# This pbc infomration is now used when loading fcs to kaldo
# [True, True, True] means pbc is applied in all three directions.
replicated_structure.set_pbc(np.array([True, True, True]))
write('hiPhive_si_bulk/replicated_atoms.xyz',
replicated_structure,
format='xyz')
fcs.write(hiphive_filename + '/' + 'model2.fcs')
def calc_fcs(
phono3py,
calc,
unitcell_f='Unknown',
cp_files=None,
sym_fc=True,
fc_calc=None,
r_cut=None,
):
"""
fc_calc: None or 'alm'
r_cut: None or float. Use hiPhive if provided.
"""
# Check if structure is lower triangular cell
for c in ((0, 1), (0, 2), (1, 2)):
if phono3py.primitive.get_cell()[c[0], c[1]] != 0. and calc == 'lmp':
raise ValueError('Please provide lower triangular cell.')
#
phono3py.generate_displacements()
fc2_snd = phono3py.get_phonon_supercells_with_displacements()
fc3_snd = phono3py.get_supercells_with_displacements()
fc2_job_name = '{}-x{}{}{}_d0.010_sym{}-fc2'.format(
calc,
*np.diag(phono3py.get_phonon_supercell_matrix()),
phono3py._is_symmetry,
)
fc3_job_name = '{}-x{}{}{}_d0.030_sym{}-fc3'.format(
calc,
*np.diag(phono3py.get_supercell_matrix()),
phono3py._is_symmetry,
)
fc2_npy_name = '{}-forces.npy'.format(fc2_job_name)
fc3_npy_name = '{}-forces.npy'.format(fc3_job_name)
calc_dir = 'calcs'
fc2_path = '{}/{}'.format(calc_dir, fc2_job_name)
fc3_path = '{}/{}'.format(calc_dir, fc3_job_name)
#
from phonopy.interface.vasp import write_vasp
call('mkdir -p {}/poscars'.format(fc2_path), shell=True)
write_vasp('{}/poscars/SPOSCAR'.format(fc2_path),
phono3py.get_phonon_supercell())
for i in range(len(fc2_snd)):
write_vasp('{}/poscars/POSCAR-{:03d}'.format(fc2_path, i + 1),
fc2_snd[i])
#
call('mkdir -p {}/poscars'.format(fc3_path), shell=True)
write_vasp('{}/poscars/SPOSCAR'.format(fc3_path), phono3py.get_supercell())
for i in range(len(fc3_snd)):
write_vasp('{}/poscars/POSCAR-{:05d}'.format(fc3_path, i + 1),
fc3_snd[i])
try:
fc2_forces = np.load(fc2_npy_name)
except:
calc_fc2 = True
print('\n*** NOTE) Failed to load {} file. ***\n'.format(fc2_npy_name))
else:
calc_fc2 = False
print('\n=== NOTE) Loaded: {} ===\n'.format(fc2_npy_name))
if calc_fc2:
print('=== NOTE) Starting fc2 calculations! ===\n')
fc2_forces = []
for i in range(len(fc2_snd)):
folder = 'disp-{:03d}'.format(i + 1)
wdir = '{}/{}'.format(fc2_path, folder)
budir = '{}/bu-{}'.format(fc2_path, folder)
call('rm -rf {}'.format(budir), shell=True)
call('mv {} {}'.format(wdir, budir), shell=True)
call('mkdir -p {}'.format(wdir), shell=True)
write_vasp('{}/POSCAR'.format(wdir), fc2_snd[i])
fc2_forces.append(_calc_forces(wdir, calc, cp_files))
print(' == Progress: {}/{}'.format(i + 1, len(fc2_snd)))
np.save(fc2_npy_name, fc2_forces)
try:
fc3_forces = np.load(fc3_npy_name)
except:
calc_fc3 = True
print('\n*** NOTE) Failed to load {} file. ***\n'.format(fc3_npy_name))
else:
calc_fc3 = False
print('\n=== NOTE) Loaded: {} ===\n'.format(fc3_npy_name))
if calc_fc3:
print('=== NOTE) Starting fc3 calculations! ===\n')
fc3_forces = []
for i in range(len(fc3_snd)):
folder = 'disp-{:05d}'.format(i + 1)
wdir = '{}/{}'.format(fc3_path, folder)
budir = '{}/bu-{}'.format(fc3_path, folder)
call('rm -rf {}'.format(budir), shell=True)
call('mv {} {}'.format(wdir, budir), shell=True)
call('mkdir -p {}'.format(wdir), shell=True)
write_vasp('{}/POSCAR'.format(wdir), fc3_snd[i])
fc3_forces.append(_calc_forces(wdir, calc, cp_files))
print(' == Progress: {}/{}'.format(i + 1, len(fc3_snd)))
np.save(fc3_npy_name, fc3_forces)
#
phono3py.phonon_forces = np.array(fc2_forces)
phono3py.forces = np.array(fc3_forces)
#
phono3py.produce_fc3(
symmetrize_fc3r=sym_fc,
fc_calculator=fc_calc,
)
phono3py.produce_fc2(
symmetrize_fc2=sym_fc,
fc_calculator=fc_calc,
)
if r_cut:
#
from ase.io import read
from ase.calculators.singlepoint import SinglePointDFTCalculator
fc2_disp_ds = phono3py.get_phonon_displacement_dataset()['first_atoms']
fc2_sposcar = read('{}/poscars/SPOSCAR'.format(fc2_path))
fc2_supers = []
for i in range(len(fc2_disp_ds)):
displacements = np.zeros(fc2_sposcar.get_positions().shape,
dtype=float)
displacements[fc2_disp_ds[i]
['number']] += fc2_disp_ds[i]['displacement']
fc2_supers.append(fc2_sposcar.copy())
fc2_supers[-1].new_array(
'displacements',
displacements,
)
fc2_supers[-1]._calc = SinglePointDFTCalculator(fc2_supers[-1])
fc2_supers[-1]._calc.results['forces'] = fc2_disp_ds[i]['forces']
# rotational sum rule
from hiphive import ForceConstants, ClusterSpace, StructureContainer
cs = ClusterSpace(fc2_sposcar, [r_cut])
sc = StructureContainer(cs)
for s in fc2_supers:
sc.add_structure(s)
from hiphive.fitting import Optimizer
opt = Optimizer(sc.get_fit_data(), train_size=1.0)
opt.train()
print(opt)
parameters = opt.parameters
from hiphive import ForceConstantPotential, enforce_rotational_sum_rules
parameters_rot = enforce_rotational_sum_rules(cs, parameters,
['Huang', 'Born-Huang'])
fcp_rot = ForceConstantPotential(cs, parameters_rot)
fcs = fcp_rot.get_force_constants(fc2_sposcar).get_fc_array(order=2)
phono3py.set_fc2(fcs)
# # Not implemented yet in hiPhive
# fc3_disp_ds = phono3py.get_displacement_dataset()['first_atoms']
# fc3_sposcar = read('{}/poscars/SPOSCAR'.format(fc3_path))
# fc3_supers = []
# for i in range(len(fc3_disp_ds)):
# displacements_1st = np.zeros(fc3_sposcar.get_positions().shape, dtype=float)
# displacements_1st[fc3_disp_ds[i]['number']] += fc3_disp_ds[i]['displacement']
# for j in range(len(fc3_disp_ds[i]['second_atoms'])):
# displacements_2nd = np.zeros(fc3_sposcar.get_positions().shape, dtype=float)
# displacements_2nd[fc3_disp_ds[i]['second_atoms'][j]['number']] += fc3_disp_ds[i]['second_atoms'][j]['displacement']
# displacements = displacements_1st + displacements_2nd
# fc3_supers.append(fc3_sposcar.copy())
# fc3_supers[-1].new_array(
# 'displacements',
# displacements,
# )
# fc3_supers[-1]._calc = SinglePointDFTCalculator(fc3_supers[-1])
# fc3_supers[-1]._calc.results['forces'] = fc3_disp_ds[i]['second_atoms'][j]['forces']
return phono3py
def run_hiphive(supercell, primitive, displacements, forces, options, symprec,
log_level):
"""Run hiphive.
supercell : Supercell
Perfect supercell.
primitive : Primitive
Primitive cell.
displacements : ndarray
Displacements of atoms in supercell.
shape=(supercells, natom, 3)
forces : ndarray
Forces on atoms in supercell.
shape=(supercells, natom, 3)
options : str
Force constants calculation options.
log_level : int
Log control. 0: quiet, 1: normal, 2: verbose 3: debug
"""
try:
from hiphive import ClusterSpace, ForceConstantPotential, StructureContainer
from hiphive.cutoffs import estimate_maximum_cutoff
from hiphive.fitting import Optimizer
from hiphive.input_output.logging_tools import set_config
except ImportError:
raise ImportError("hiPhive python module was not found.")
set_config(level=30)
ase_supercell = phonopy_atoms_to_ase(supercell)
ase_prim = phonopy_atoms_to_ase(primitive)
# setup training structures
structures = []
for d, f in zip(displacements, forces):
structure = ase_supercell.copy()
structure.new_array("displacements", d)
structure.new_array("forces", f)
structures.append(structure)
# parse options
if options is None:
options_dict = {}
else:
options_dict = _decode_options(options)
# select cutoff
max_cutoff = estimate_maximum_cutoff(ase_supercell) - 1e-5
if "cutoff" in options_dict:
cutoff = options_dict["cutoff"]
if cutoff > max_cutoff:
raise ValueError(
"Cutoff {:.4f} is larger than maximum allowed "
"cutoff, {:.4f}, for the given supercell."
"\nDecrease cutoff or provide larger supercells.".format(
cutoff, max_cutoff))
else:
cutoff = max_cutoff
# setup ClusterSpace
cutoffs = [cutoff]
cs = ClusterSpace(ase_prim, cutoffs, symprec=symprec)
cs.print_orbits()
sc = StructureContainer(cs)
for structure in structures:
sc.add_structure(structure)
n_rows, n_cols = sc.data_shape
if n_rows < n_cols:
raise ValueError("Fitting problem is under-determined."
"\nProvide more structures or decrease cutoff.")
# Estimate error
opt = Optimizer(sc.get_fit_data(), train_size=0.75)
opt.train()
print(opt)
print("RMSE train : {:.4f}".format(opt.rmse_train))
print("RMSE test : {:.4f}".format(opt.rmse_test))
# Final train
opt = Optimizer(sc.get_fit_data(), train_size=1.0)
opt.train()
# get force constants
fcp = ForceConstantPotential(cs, opt.parameters)
fcs = fcp.get_force_constants(ase_supercell)
fc2 = fcs.get_fc_array(order=2)
return fc2
def calculate_high_order_phi():
from ase.io import read
import numpy as np
from hiphive import ClusterSpace, StructureContainer
from hiphive.utilities import get_displacements
from hiphive import ForceConstantPotential
from hiphive.fitting import Optimizer
from hiphive.calculators import ForceConstantCalculator
import os
if os.path.exists('POSCAR-md'):
reference_structure = read('POSCAR-md')
else:
return None
if not os.path.exists('./vasprun_md.xml'):
return None
a = reference_structure.get_cell_lengths_and_angles()[0]
cs = ClusterSpace(reference_structure, [0.3 * a, 0.35 * a, 0.35 * a])
sc = None
#try:
# sc = StructureContainer.read("./structure_container")
# print("successfully loaded the structure container "+str(sc))
#except:
try:
fit_structures = []
atoms = read("./vasprun_md.xml", index=':')
for i, a in enumerate(atoms):
displacements = get_displacements(a, reference_structure)
atoms_tmp = reference_structure.copy()
atoms_tmp.new_array('displacements', displacements)
atoms_tmp.new_array('forces', a.get_forces())
atoms_tmp.positions = reference_structure.positions
fit_structures.append(atoms_tmp)
sc = StructureContainer(
cs) # need a cluster space to instantiate the object!
sc.delete_all_structures()
for ii, s in enumerate(fit_structures):
try:
sc.add_structure(s)
except Exception as e:
print(ii, e)
pass
except:
pass
if sc is not None:
try:
opt = Optimizer(sc.get_fit_data(),
fit_method="ardr",
train_size=0.9)
opt.train()
fcp = ForceConstantPotential(cs, opt.parameters)
fcs = fcp.get_force_constants(reference_structure)
except Exception as e:
print(e)
return None
from core.external.vasp.anharmonic_score import AnharmonicScore
sigmas_2 = None
sigmas_3 = None
sigmas_4 = None
try:
scorer = AnharmonicScore(md_frames='./vasprun_md.xml',
ref_frame='./POSCAR-md',
force_constants=fcs.get_fc_array(2),
include_third_order=False,
include_fourth_order=False)
sigmas_2, _ = scorer.structural_sigma(return_trajectory=False)
except:
pass
try:
scorer = AnharmonicScore(md_frames='./vasprun_md.xml',
ref_frame='./POSCAR-md',
force_constants=fcs.get_fc_array(2),
include_third_order=True,
third_order_fc=fcs.get_fc_array(3),
include_fourth_order=False)
sigmas_3, _ = scorer.structural_sigma(return_trajectory=False)
except:
pass
try:
scorer = AnharmonicScore(md_frames='./vasprun_md.xml',
ref_frame='./POSCAR-md',
force_constants=fcs.get_fc_array(2),
include_third_order=True,
third_order_fc=fcs.get_fc_array(3),
include_fourth_order=True,
fourth_order_fc=fcs.get_fc_array(4))
sigmas_4, _ = scorer.structural_sigma(return_trajectory=False)
except:
pass
f = open('sigmas.dat', 'w')
f.write('sigma_2' + '\t' + str(sigmas_2) + '\n')
f.write('sigma_3' + '\t' + str(sigmas_3) + '\n')
f.write('sigma_4' + '\t' + str(sigmas_4) + '\n')
f.close()
def calc_phonon(
calculator,
phonon,
acoustic_sum_rule=True,
rot_sum_rule=False,
r_cut=None,
F_0_correction=False,
verbose=False,
ase_calc=None,
cp_files=None,
subscript=None,
fc_calc=None,
):
"""
calc -- Specify calculator. One of these. [vasp, lmp, amp, amp_tf, amp_tf_bunch]
phonon -- Phonopy phonon object.
"""
# Check if structure is lower triangular cell
# for c in ((0,1), (0,2), (1,2)):
# if phonon._primitive.get_cell()[c[0],c[1]] != 0. and calculator == 'lmp':
# raise ValueError('Please provide lower triangular cell.')
import sys
if verbose:
np.set_printoptions(threshold=sys.maxsize)
if fc_calc == 'alm':
disp = phonon.get_displacements()
delta = np.linalg.norm(disp[0][0])
disp = np.concatenate([[np.zeros(disp.shape[1:])], disp], axis=0)
else:
delta = np.linalg.norm(phonon.get_displacements()[0][1:4])
disp = [[0, 0, 0, 0]] + phonon.get_displacements()
job_name = '{}-x{}{}{}_d{:5.3f}_sym{}'.format(
calculator,
*np.diag(phonon.get_supercell_matrix()),
delta,
phonon._is_symmetry,
)
if subscript is not None:
job_name += '_s' + str(subscript)
# Define names
npy_name = '{}-fc2-forces.npy'.format(job_name)
if phonon._nac_params is not None:
nac = True
else:
nac = False
pckl_name = '{}-RSR{}-rcut{}-NAC{}-fc2.bin'.format(job_name, rot_sum_rule,
r_cut, nac)
calc_dir = './calcs/{}'.format(job_name)
# Environment preset
call(['rm -rf ' + calc_dir + '/poscars'], shell=True)
call(['mkdir -p ' + calc_dir + '/poscars'], shell=True)
call(['cp SPOSCAR POSCAR-000'], shell=True)
call(['mv POSCAR-* SPOSCAR ' + calc_dir + '/poscars/'], shell=True)
# Load saved pickle file
print('')
try:
forces = np.load(npy_name)
if forces is None:
raise ValueError(' Error:: npy file is not containing forces info')
except:
print(
'<< CAUTION >> Fail to load npy file. << CAUTION >>'
.center(120))
print(('<< CAUTION >>' + ':: Expected file name ::'.center(43) +
'<< CAUTION >>').center(120))
print(('<< CAUTION >>' + npy_name.center(43) +
'<< CAUTION >>').center(120))
do_calc = True
else:
print('>>>>>>> Pickle file "{}" has been loaded. <<<<<<<<'.format(
npy_name).center(120))
do_calc = False
print('')
if do_calc:
if calculator == 'vasp':
calc = calc_vasp
elif calculator == 'lmp':
calc = calc_lmp
elif calculator == 'ase_calc':
calc = calc_ase_calc
elif calculator == 'amp_tf':
calc = calc_amp_tf
elif calculator == 'amp_tf_bunch':
calc = calc_amp_tf_bunch
else:
raise ValueError(
'Unknown calculator ({}) has been provided.'.format(
calculator))
print(">>>>>>> {} calculation will be carried out. <<<<<<<<".format(
calculator).center(120))
forces = calc(phonon, disp, calc_dir, F_0_correction, ase_calc,
cp_files)
np.save(npy_name, forces)
if verbose:
print('\n\n' + 'forces' + '\n' + str(forces))
phonon.set_forces(forces)
# Produce fc
phonon.produce_force_constants(fc_calculator=fc_calc)
if acoustic_sum_rule:
phonon.symmetrize_force_constants()
if r_cut:
if rot_sum_rule:
#
from ase.io import read
from ase.calculators.singlepoint import SinglePointDFTCalculator
sposcar = read(calc_dir + '/poscars/SPOSCAR')
supers = []
for i in range(len(forces)):
supers.append(sposcar.copy())
displacements = np.zeros(sposcar.get_positions().shape,
dtype=float)
displacements[disp[i + 1][0]] += disp[i + 1][1:]
supers[-1].new_array(
'displacements',
displacements,
)
supers[-1]._calc = SinglePointDFTCalculator(supers[-1])
supers[-1]._calc.results['forces'] = forces[i]
# rotational sum rule
from hiphive import ForceConstants, ClusterSpace, StructureContainer
cs = ClusterSpace(sposcar, [r_cut])
sc = StructureContainer(cs)
for s in supers:
sc.add_structure(s)
from hiphive.fitting import Optimizer
opt = Optimizer(sc.get_fit_data(), train_size=1.0)
opt.train()
print(opt)
parameters = opt.parameters
from hiphive import ForceConstantPotential, enforce_rotational_sum_rules
parameters_rot = enforce_rotational_sum_rules(
cs, parameters, ['Huang', 'Born-Huang'])
fcp_rot = ForceConstantPotential(cs, parameters_rot)
fcs = fcp_rot.get_force_constants(sposcar).get_fc_array(order=2)
phonon.set_force_constants(fcs)
else:
phonon.set_force_constants_zero_with_radius(r_cut)
if verbose:
print('\n\ndisplacement_dataset =>\n\n')
print(phonon.get_displacement_dataset())
print('\n\nforce_constants =>\n\n')
print(phonon.get_force_constants())
import pickle as pckl
pckl.dump(phonon, open(pckl_name, 'wb'), protocol=2)
return phonon