def test_from_index_amount(self):
# From voigt index
test = Strain.from_index_amount(2, 0.01)
should_be = np.zeros((3, 3))
should_be[2, 2] = 0.01
self.assertArrayAlmostEqual(test, should_be)
# from full-tensor index
test = Strain.from_index_amount((1, 2), 0.01)
should_be = np.zeros((3, 3))
should_be[1, 2] = should_be[2, 1] = 0.01
self.assertArrayAlmostEqual(test, should_be)
def test_from_index_amount(self):
# From voigt index
test = Strain.from_index_amount(2, 0.01)
should_be = np.zeros((3, 3))
should_be[2, 2] = 0.01
self.assertArrayAlmostEqual(test, should_be)
# from full-tensor index
test = Strain.from_index_amount((1, 2), 0.01)
should_be = np.zeros((3, 3))
should_be[1, 2] = should_be[2, 1] = 0.01
self.assertArrayAlmostEqual(test, should_be)
def make_vasp(jdata, conf_dir, norm_def=2e-3, shear_def=5e-3):
fp_params = jdata['vasp_params']
ecut = fp_params['ecut']
ediff = fp_params['ediff']
npar = fp_params['npar']
kpar = fp_params['kpar']
kspacing = fp_params['kspacing']
kgamma = fp_params['kgamma']
strain_start = jdata['strain_start']
strain_end = jdata['strain_end']
strain_step = jdata['strain_step']
strain_direct = jdata['strain_direct']
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, 'POSCAR')
# get equi poscar
equi_path = re.sub('confs', global_equi_name, conf_path)
equi_path = os.path.join(equi_path, 'vasp-k%.2f' % kspacing)
equi_contcar = os.path.join(equi_path, 'CONTCAR')
task_path = re.sub('confs', global_task_name, conf_path)
task_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
os.makedirs(task_path, exist_ok=True)
cwd = os.getcwd()
os.chdir(task_path)
if os.path.isfile('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(equi_contcar), 'POSCAR')
os.chdir(cwd)
task_poscar = os.path.join(task_path, 'POSCAR')
# stress
equi_outcar = os.path.join(equi_path, 'OUTCAR')
stress = vasp.get_stress(equi_outcar)
np.savetxt(os.path.join(task_path, 'equi.stress.out'), stress)
# gen strcture
ss = Structure.from_file(task_poscar)
# gen defomations
norm_strains = np.arange(strain_start, strain_end, strain_step)
print('gen with norm ' + str(norm_strains))
deformations = []
for ii in norm_strains:
strain = Strain.from_index_amount(strain_direct, ii)
deformations.append(strain.get_deformation_matrix())
deformed_structures = [
defo.apply_to_structure(ss) for defo in deformations
]
n_dfm = len(deformed_structures)
# gen incar
fc = vasp.make_vasp_relax_incar(ecut,
ediff,
True,
False,
False,
npar=npar,
kpar=kpar,
kspacing=None,
kgamma=None)
with open(os.path.join(task_path, 'INCAR'), 'w') as fp:
fp.write(fc)
# gen potcar
with open(task_poscar, 'r') as fp:
lines = fp.read().split('\n')
ele_list = lines[5].split()
potcar_map = jdata['potcar_map']
potcar_list = []
for ii in ele_list:
assert (os.path.exists(potcar_map[ii]))
potcar_list.append(potcar_map[ii])
with open(os.path.join(task_path, 'POTCAR'), 'w') as outfile:
for fname in potcar_list:
with open(fname) as infile:
outfile.write(infile.read())
# gen kpoints
fc = vasp.make_kspacing_kpoints(task_poscar, kspacing, kgamma)
with open(os.path.join(task_path, 'KPOINTS'), 'w') as fp:
fp.write(fc)
# gen tasks
cwd = os.getcwd()
for ii in range(n_dfm):
# make dir
dfm_path = os.path.join(task_path, 'dfm-%03d' % ii)
os.makedirs(dfm_path, exist_ok=True)
os.chdir(dfm_path)
for jj in ['POSCAR', 'POTCAR', 'INCAR', 'KPOINTS']:
if os.path.isfile(jj):
os.remove(jj)
# make conf
deformed_structures[ii].to('POSCAR', 'POSCAR')
# record strain
strain = Strain.from_deformation(deformations[ii])
np.savetxt('strain.out', strain)
# link incar, potcar, kpoints
os.symlink(os.path.relpath(os.path.join(task_path, 'INCAR')), 'INCAR')
os.symlink(os.path.relpath(os.path.join(task_path, 'POTCAR')),
'POTCAR')
os.symlink(os.path.relpath(os.path.join(task_path, 'KPOINTS')),
'KPOINTS')
cwd = os.getcwd()
def make_lammps(jdata, conf_dir, task_type):
fp_params = jdata['lammps_params']
model_dir = fp_params['model_dir']
type_map = fp_params['type_map']
model_dir = os.path.abspath(model_dir)
model_name = fp_params['model_name']
if not model_name:
models = glob.glob(os.path.join(model_dir, '*pb'))
model_name = [os.path.basename(ii) for ii in models]
else:
models = [os.path.join(model_dir, ii) for ii in model_name]
model_param = {
'model_name': fp_params['model_name'],
'param_type': fp_params['model_param_type']
}
ntypes = len(type_map)
strain_start = jdata['strain_start']
strain_end = jdata['strain_end']
strain_step = jdata['strain_step']
strain_direct = jdata['strain_direct']
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, 'POSCAR')
# get equi poscar
equi_path = re.sub('confs', global_equi_name, conf_path)
equi_path = os.path.join(equi_path, task_type)
equi_dump = os.path.join(equi_path, 'dump.relax')
task_path = re.sub('confs', global_task_name, conf_path)
task_path = os.path.join(task_path, task_type)
os.makedirs(task_path, exist_ok=True)
task_poscar = os.path.join(task_path, 'POSCAR')
lammps.poscar_from_last_dump(equi_dump, task_poscar, type_map)
# get equi stress
equi_log = os.path.join(equi_path, 'log.lammps')
stress = lammps.get_stress(equi_log)
np.savetxt(os.path.join(task_path, 'equi.stress.out'), stress)
# gen strcture
ss = Structure.from_file(task_poscar)
# gen defomations
norm_strains = np.arange(strain_start, strain_end, strain_step)
print('gen with norm ' + str(norm_strains))
deformations = []
for ii in norm_strains:
strain = Strain.from_index_amount(strain_direct, ii)
deformations.append(strain.get_deformation_matrix())
deformed_structures = [
defo.apply_to_structure(ss) for defo in deformations
]
n_dfm = len(deformed_structures)
# gen tasks
cwd = os.getcwd()
# make lammps.in
if task_type == 'deepmd':
fc = lammps.make_lammps_elastic('conf.lmp', ntypes,
lammps.inter_deepmd, model_name)
elif task_type == 'meam':
fc = lammps.make_lammps_elastic('conf.lmp', ntypes, lammps.inter_meam,
model_param)
f_lammps_in = os.path.join(task_path, 'lammps.in')
with open(f_lammps_in, 'w') as fp:
fp.write(fc)
cwd = os.getcwd()
if task_type == 'deepmd':
os.chdir(task_path)
for ii in model_name:
if os.path.exists(ii):
os.remove(ii)
for (ii, jj) in zip(models, model_name):
os.symlink(os.path.relpath(ii), jj)
share_models = glob.glob(os.path.join(task_path, '*pb'))
else:
share_models = models
for ii in range(n_dfm):
# make dir
dfm_path = os.path.join(task_path, 'dfm-%03d' % ii)
os.makedirs(dfm_path, exist_ok=True)
os.chdir(dfm_path)
for jj in ['conf.lmp', 'lammps.in'] + model_name:
if os.path.isfile(jj):
os.remove(jj)
# make conf
deformed_structures[ii].to('POSCAR', 'POSCAR')
lammps.cvt_lammps_conf('POSCAR', 'conf.lmp')
ptypes = vasp.get_poscar_types('POSCAR')
lammps.apply_type_map('conf.lmp', type_map, ptypes)
# record strain
strain = Strain.from_deformation(deformations[ii])
np.savetxt('strain.out', strain)
# link lammps.in
os.symlink(os.path.relpath(f_lammps_in), 'lammps.in')
# link models
for (ii, jj) in zip(share_models, model_name):
os.symlink(os.path.relpath(ii), jj)
cwd = os.getcwd()