def make_vasp(jdata, conf_dir):
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']
conf_path = os.path.abspath(conf_dir)
equi_path = re.sub('confs', global_task_name, conf_path)
os.makedirs(equi_path, exist_ok=True)
cwd = os.getcwd()
from_poscar = os.path.join(conf_path, 'POSCAR')
to_poscar = os.path.join(equi_path, 'POSCAR')
if os.path.exists(to_poscar):
assert (filecmp.cmp(from_poscar, to_poscar))
else:
os.chdir(equi_path)
os.symlink(os.path.relpath(from_poscar), 'POSCAR')
os.chdir(cwd)
is_alloy = \
os.path.exists(
os.path.join(
os.path.join(conf_path, '..'),
'alloy'
)
)
vasp_path = os.path.join(equi_path, 'vasp-k%.2f' % kspacing)
os.makedirs(vasp_path, exist_ok=True)
os.chdir(vasp_path)
print(vasp_path)
# gen incar
if is_alloy:
fc = vasp.make_vasp_relax_incar(ecut, ediff, True, True, True, npar,
kpar, kspacing, kgamma)
else:
fc = vasp.make_vasp_relax_incar(ecut, ediff, False, True, True, npar,
kpar, kspacing, kgamma)
with open('INCAR', 'w') as fp:
fp.write(fc)
# gen poscar
if os.path.exists('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(to_poscar), 'POSCAR')
# gen potcar
with open('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('POTCAR', 'w') as outfile:
for fname in potcar_list:
with open(fname) as infile:
outfile.write(infile.read())
os.chdir(cwd)
def make_vasp(jdata, conf_dir) :
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']
vol_start = jdata['vol_start']
vol_end = jdata['vol_end']
vol_step = jdata['vol_step']
conf_path = os.path.abspath(conf_dir)
task_path = re.sub('confs', global_task_name, conf_path)
os.makedirs(task_path, exist_ok = True)
cwd = os.getcwd()
from_poscar = os.path.join(conf_path, 'POSCAR')
to_poscar = os.path.join(task_path, 'POSCAR')
if os.path.exists(to_poscar) :
assert(filecmp.cmp(from_poscar, to_poscar))
else :
os.chdir(task_path)
os.symlink(os.path.relpath(from_poscar), 'POSCAR')
os.chdir(cwd)
vol_to_poscar = vasp.poscar_vol(to_poscar) / vasp.poscar_natoms(to_poscar)
# print(to_poscar, vol_to_poscar)
is_alloy = \
os.path.exists(
os.path.join(
os.path.join(conf_path, '..'),
'alloy'
)
)
vasp_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
os.makedirs(vasp_path, exist_ok = True)
os.chdir(vasp_path)
# gen incar
if is_alloy :
fc = vasp.make_vasp_relax_incar(ecut, ediff, True, True, False, npar, kpar, kspacing, kgamma)
else :
fc = vasp.make_vasp_relax_incar(ecut, ediff, False, True, False, npar, kpar, kspacing, kgamma)
with open('INCAR', 'w') as fp :
fp.write(fc)
# gen potcar
with open(to_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('POTCAR', 'w') as outfile:
for fname in potcar_list:
with open(fname) as infile:
outfile.write(infile.read())
# loop over volumes
for vol in np.arange(vol_start, vol_end, vol_step) :
vol_path = os.path.join(vasp_path, 'vol-%.2f' % vol)
os.makedirs(vol_path, exist_ok = True)
os.chdir(vol_path)
print(vol_path)
for ii in ['INCAR', 'POTCAR', 'POSCAR.orig', 'POSCAR'] :
if os.path.exists(ii) :
os.remove(ii)
# link incar, potcar
os.symlink(os.path.relpath(os.path.join(vasp_path, 'INCAR')), 'INCAR')
os.symlink(os.path.relpath(os.path.join(vasp_path, 'POTCAR')), 'POTCAR')
# gen poscar
os.symlink(os.path.relpath(to_poscar), 'POSCAR.orig')
scale = (vol / vol_to_poscar) ** (1./3.)
# print(scale)
vasp.poscar_scale('POSCAR.orig', 'POSCAR', scale)
# print(vol_path, vasp.poscar_vol('POSCAR') / vasp.poscar_natoms('POSCAR'))
os.chdir(cwd)
def _make_vasp(jdata, conf_dir, supercell, insert_ele):
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']
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')
assert os.path.exists(
equi_contcar), "Please compute the equilibrium state using vasp first"
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')
# gen strcture
print("task poscar: ", task_poscar)
ss = Structure.from_file(task_poscar)
# gen defects
vds = InterstitialGenerator(ss, insert_ele)
dss = []
for jj in vds:
dss.append(jj.generate_defect_structure(supercell))
# gen incar
fc = vasp.make_vasp_relax_incar(ecut,
ediff,
True,
True,
True,
npar=npar,
kpar=kpar,
kspacing=kspacing,
kgamma=kgamma)
with open(os.path.join(task_path, 'INCAR'), 'w') as fp:
fp.write(fc)
# gen tasks
copy_str = "%sx%sx%s" % (supercell[0], supercell[1], supercell[2])
cwd = os.getcwd()
for ii in range(len(dss)):
struct_path = os.path.join(
task_path, 'struct-%s-%s-%03d' % (insert_ele, copy_str, ii))
print('# generate %s' % (struct_path))
os.makedirs(struct_path, exist_ok=True)
os.chdir(struct_path)
for jj in ['POSCAR', 'POTCAR', 'INCAR']:
if os.path.isfile(jj):
os.remove(jj)
# make conf
dss[ii].to('POSCAR', 'POSCAR')
# gen potcar
with open('POSCAR', 'r') as fp:
lines = fp.read().split('\n')
ele_list = lines[5].split()
os.chdir(cwd)
potcar_map = jdata['potcar_map']
potcar_list = []
for ii in ele_list:
assert os.path.exists(os.path.abspath(
potcar_map[ii])), "No POTCAR in the potcar_map of %s" % (ii)
potcar_list.append(os.path.abspath(potcar_map[ii]))
os.chdir(struct_path)
with open('POTCAR', 'w') as outfile:
for fname in potcar_list:
with open(fname) as infile:
outfile.write(infile.read())
# link incar
os.symlink(os.path.relpath(os.path.join(task_path, 'INCAR')), 'INCAR')
# save supercell
np.savetxt('supercell.out', supercell, fmt='%d')
os.chdir(cwd)
def make_vasp(jdata, conf_dir, norm_def = 2e-3, shear_def = 5e-3) :
norm_def = jdata['norm_deform']
shear_def = jdata['shear_deform']
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, 'POSCAR')
# get equi poscar
if 'relax_incar' in jdata.keys():
vasp_str='vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str='vasp-k%.2f' % kspacing
equi_path = re.sub('confs', global_equi_name, conf_path)
equi_path = os.path.join(equi_path, vasp_str)
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_str)
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 = [-norm_def, -0.5*norm_def, 0.5*norm_def, norm_def]
shear_strains = [-shear_def, -0.5*shear_def, 0.5*shear_def, shear_def]
dfm_ss = DeformedStructureSet(ss,
symmetry = False,
norm_strains = norm_strains,
shear_strains = shear_strains)
n_dfm = len(dfm_ss)
# gen incar
if 'relax_incar' in jdata.keys():
relax_incar_path = jdata['relax_incar']
assert(os.path.exists(relax_incar_path))
relax_incar_path = os.path.abspath(relax_incar_path)
fc = open(relax_incar_path).read()
kspacing =float(re.findall((r"KSPACING(.+?)\n"),fc)[0].replace('=',''))
kgamma =('T' in re.findall((r"KGAMMA(.+?)\n"),fc)[0])
else :
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']
fc = vasp.make_vasp_relax_incar(ecut, ediff, True, False, False, npar=npar,kpar=kpar, kspacing = kspacing, kgamma = kgamma)
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(os.path.abspath(potcar_map[ii])),"No POTCAR in the potcar_map of %s"%(ii)
potcar_list.append(os.path.abspath(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
dfm_ss.deformed_structures[ii].to('POSCAR', 'POSCAR')
# record strain
strain = Strain.from_deformation(dfm_ss.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_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_vasp(jdata, conf_dir, max_miller=2, relax_box=False, static=False):
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']
min_slab_size = jdata['min_slab_size']
min_vacuum_size = jdata['min_vacuum_size']
pert_xz = jdata['pert_xz']
# get conf poscar
# conf_path = os.path.abspath(conf_dir)
# conf_poscar = os.path.join(conf_path, 'POSCAR')
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, 'vasp-k%.2f' % kspacing)
equi_path = os.path.abspath(equi_path)
equi_contcar = os.path.join(equi_path, 'CONTCAR')
assert os.path.exists(
equi_contcar), "Please compute the equilibrium state using vasp first"
task_path = re.sub('confs', global_task_name, conf_dir)
task_path = os.path.abspath(task_path)
if static:
task_path = os.path.join(task_path, 'vasp-static-k%.2f' % kspacing)
else:
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')
ptypes = vasp.get_poscar_types(task_poscar)
# gen strcture
ss = Structure.from_file(task_poscar)
# gen slabs
all_slabs = generate_all_slabs(ss, max_miller, min_slab_size,
min_vacuum_size)
# gen incar
if static:
fc = vasp.make_vasp_static_incar(ecut,
ediff,
npar=npar,
kpar=kpar,
kspacing=kspacing,
kgamma=kgamma)
else:
fc = vasp.make_vasp_relax_incar(ecut,
ediff,
True,
relax_box,
False,
npar=npar,
kpar=kpar,
kspacing=kspacing,
kgamma=kgamma)
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(os.path.abspath(
potcar_map[ii])), "No POTCAR in the potcar_map of %s" % (ii)
potcar_list.append(os.path.abspath(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 tasks
cwd = os.getcwd()
for ii in range(len(all_slabs)):
slab = all_slabs[ii]
miller_str = "m%d.%d.%dm" % (
slab.miller_index[0], slab.miller_index[1], slab.miller_index[2])
# make dir
struct_path = os.path.join(task_path,
'struct-%03d-%s' % (ii, miller_str))
os.makedirs(struct_path, exist_ok=True)
os.chdir(struct_path)
for jj in ['POSCAR', 'POTCAR', 'INCAR']:
if os.path.isfile(jj):
os.remove(jj)
print("# %03d generate " % ii, struct_path,
" \t %d atoms" % len(slab.sites))
# make conf
slab.to('POSCAR', 'POSCAR.tmp')
vasp.regulate_poscar('POSCAR.tmp', 'POSCAR')
vasp.sort_poscar('POSCAR', 'POSCAR', ptypes)
vasp.perturb_xz('POSCAR', 'POSCAR', pert_xz)
# record miller
np.savetxt('miller.out', slab.miller_index, fmt='%d')
# 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')
cwd = os.getcwd()
def _make_vasp(jdata, conf_dir, supercell, insert_ele):
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']
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')
# gen strcture
print("task poscar: ", task_poscar)
ss = Structure.from_file(task_poscar)
# gen defects
vds = InterstitialGenerator(ss, insert_ele)
dss = []
for jj in vds:
dss.append(jj.generate_defect_structure(supercell))
# gen incar
fc = vasp.make_vasp_relax_incar(ecut,
ediff,
True,
True,
True,
1,
1,
kspacing=kspacing,
kgamma=kgamma)
with open(os.path.join(task_path, 'INCAR'), 'w') as fp:
fp.write(fc)
# gen tasks
copy_str = "%sx%sx%s" % (supercell[0], supercell[1], supercell[2])
cwd = os.getcwd()
for ii in range(len(dss)):
struct_path = os.path.join(
task_path, 'struct-%s-%s-%03d' % (insert_ele, copy_str, ii))
print('# generate %s' % (struct_path))
os.makedirs(struct_path, exist_ok=True)
os.chdir(struct_path)
for jj in ['POSCAR', 'POTCAR', 'INCAR']:
if os.path.isfile(jj):
os.remove(jj)
# make conf
dss[ii].to('POSCAR', 'POSCAR')
# gen potcar
_gen_potcar(jdata, 'POSCAR', 'POTCAR')
# link incar
os.symlink(os.path.relpath(os.path.join(task_path, 'INCAR')), 'INCAR')
# save supercell
np.savetxt('supercell.out', supercell, fmt='%d')
os.chdir(cwd)
def make_vasp(jdata, conf_dir, supercell = [1,1,1]) :
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']
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')
# gen structure from equi poscar
edge = Structure.from_file(task_poscar)
edge.make_supercell([supercell[0],supercell[1],1])
center=int(supercell[0]*int(supercell[1]/2)+supercell[0]/2)
s=[center+supercell[0]*ii for ii in range(int(supercell[1]/2+1))]
# gen edge dislocation
edge.remove_sites(s)
edge.make_supercell([1,1,supercell[2]])
# gen screw dislocation
screw = Structure.from_file(task_poscar)
screw.make_supercell([supercell[0], supercell[1], supercell[2]],to_unit_cell=False)
c=[]
for jj in range(math.ceil(supercell[0]/2)):
for ii in range(supercell[2]):
c.append(ii+jj*supercell[2])
v0 = np.asarray(screw._sites[0].coords, float) - np.asarray(screw._sites[1].coords, float)
for kk in range(math.ceil(supercell[1]/2)):
dc=[ii+kk*supercell[0]*supercell[2] for ii in c]
v=(math.ceil(supercell[1]/2)-kk)/math.ceil(supercell[1]/2)*v0
screw.translate_sites(dc, vector=v, frac_coords=False, to_unit_cell=False)
dss = []
dss.append(edge)
dss.append(screw)
# gen incar
fc = vasp.make_vasp_relax_incar(ecut, ediff, True, True, True, npar, kpar, kspacing = kspacing, kgamma = kgamma)
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 tasks
copy_str = "%sx%sx%s" % (supercell[0], supercell[1], supercell[2])
cwd = os.getcwd()
for ii in range(len(dss)) :
struct_path = os.path.join(task_path, 'struct-%s-%s' % (copy_str,task_dict[ii]))
print('# generate %s' % (struct_path))
os.makedirs(struct_path, exist_ok=True)
os.chdir(struct_path)
for jj in ['POSCAR', 'POTCAR', 'INCAR'] :
if os.path.isfile(jj):
os.remove(jj)
# make conf
dss[ii].to('POSCAR', 'POSCAR')
# 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')
# save supercell
np.savetxt('supercell.out', supercell, fmt='%d')
os.chdir(cwd)
def make_vasp(jdata, conf_dir) :
vol_start = jdata['vol_start']
vol_end = jdata['vol_end']
vol_step = jdata['vol_step']
eos_relax_cell_shape = jdata.get('eos_relax_cell_shape', True)
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, 'POSCAR')
if 'relax_incar' in jdata.keys():
vasp_str='vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str='vasp-k%.2f' % kspacing
# get equi poscar
equi_path = re.sub('confs', global_equi_name, conf_path)
equi_path = os.path.join(equi_path, vasp_str)
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_str)
os.makedirs(task_path, exist_ok = True)
# link poscar
cwd = os.getcwd()
from_poscar = os.path.join(equi_contcar)
to_poscar = os.path.join(task_path, 'POSCAR')
if os.path.exists(to_poscar) :
assert(filecmp.cmp(from_poscar, to_poscar))
else :
os.chdir(task_path)
os.symlink(os.path.relpath(from_poscar), 'POSCAR')
os.chdir(cwd)
vol_to_poscar = vasp.poscar_vol(to_poscar) / vasp.poscar_natoms(to_poscar)
# print(to_poscar, vol_to_poscar)
is_alloy = \
os.path.exists(
os.path.join(
os.path.join(conf_path, '..'),
'alloy'
)
)
# read potcar
with open(to_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(os.path.abspath(potcar_map[ii])),"No POTCAR in the potcar_map of %s"%(ii)
potcar_list.append(os.path.abspath(potcar_map[ii]))
# gen incar
if 'relax_incar' in jdata.keys():
relax_incar_path = jdata['relax_incar']
assert(os.path.exists(relax_incar_path))
relax_incar_path = os.path.abspath(relax_incar_path)
incar = incar_upper(Incar.from_file(relax_incar_path))
if eos_relax_cell_shape:
isif = 4
else:
isif = 2
if incar.get('ISIF') != isif:
dlog.info("%s:%s setting ISIF to %d" % (__file__, make_vasp.__name__, isif))
incar['ISIF'] = isif
fc = incar.get_string()
kspacing = incar['KSPACING']
kgamma = incar['KGAMMA']
else :
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']
fc = vasp.make_vasp_relax_incar(ecut, ediff, is_alloy, True, False, npar, kpar, kspacing, kgamma)
os.chdir(task_path)
with open('INCAR', 'w') as fp :
fp.write(fc)
# gen potcar
with open('POTCAR', 'w') as outfile:
for fname in potcar_list:
with open(fname) as infile:
outfile.write(infile.read())
# loop over volumes
for vol in np.arange(vol_start, vol_end, vol_step) :
vol_path = os.path.join(task_path, 'vol-%.2f' % vol)
os.makedirs(vol_path, exist_ok = True)
os.chdir(vol_path)
for ii in ['INCAR', 'POTCAR', 'POSCAR.orig', 'POSCAR'] :
if os.path.exists(ii) :
os.remove(ii)
# link incar, potcar
os.symlink(os.path.relpath(os.path.join(task_path, 'INCAR')), 'INCAR')
os.symlink(os.path.relpath(os.path.join(task_path, 'POTCAR')), 'POTCAR')
# gen poscar
os.symlink(os.path.relpath(to_poscar), 'POSCAR.orig')
scale = (vol / vol_to_poscar) ** (1./3.)
# print(scale)
vasp.poscar_scale('POSCAR.orig', 'POSCAR', scale)
# print(vol_path, vasp.poscar_vol('POSCAR') / vasp.poscar_natoms('POSCAR'))
# gen kpoints
fc = vasp.make_kspacing_kpoints('POSCAR', kspacing, kgamma)
with open('KPOINTS', 'w') as fp: fp.write(fc)
#copy cvasp
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
shutil.copyfile(cvasp_file, os.path.join(vol_path,'cvasp.py'))
os.chdir(cwd)
def make_vasp(jdata, conf_dir):
conf_path = os.path.abspath(conf_dir)
equi_path = re.sub('confs', global_task_name, conf_path)
os.makedirs(equi_path, exist_ok=True)
cwd = os.getcwd()
from_poscar = os.path.join(conf_path, 'POSCAR')
to_poscar = os.path.join(equi_path, 'POSCAR')
if os.path.exists(to_poscar):
assert (filecmp.cmp(from_poscar, to_poscar))
else:
os.chdir(equi_path)
os.symlink(os.path.relpath(from_poscar), 'POSCAR')
os.chdir(cwd)
is_alloy = \
os.path.exists(
os.path.join(
os.path.join(conf_path, '..'),
'alloy'
)
)
# read potcar
with open(to_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(os.path.abspath(
potcar_map[ii])), "No POTCAR in the potcar_map of %s" % (ii)
potcar_list.append(os.path.abspath(potcar_map[ii]))
# gen incar
if 'relax_incar' in jdata.keys():
relax_incar_path = jdata['relax_incar']
assert (os.path.exists(relax_incar_path))
relax_incar_path = os.path.abspath(relax_incar_path)
incar = incar_upper(Incar.from_file(relax_incar_path))
isif = 3
if incar.get('ISIF') != isif:
dlog.info("%s:%s setting ISIF to %d" %
(__file__, make_vasp.__name__, isif))
incar['ISIF'] = isif
fc = incar.get_string()
kspacing = incar['KSPACING']
kgamma = incar['KGAMMA']
vasp_path = os.path.join(equi_path, 'vasp-relax_incar')
else:
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']
fc = vasp.make_vasp_relax_incar(ecut, ediff, is_alloy, True, True,
npar, kpar, kspacing, kgamma)
vasp_path = os.path.join(equi_path, 'vasp-k%.2f' % kspacing)
os.makedirs(vasp_path, exist_ok=True)
os.chdir(vasp_path)
# write incar
with open('INCAR', 'w') as fp:
fp.write(fc)
# gen poscar
if os.path.exists('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(to_poscar), 'POSCAR')
# gen kpoints
fc = vasp.make_kspacing_kpoints('POSCAR', kspacing, kgamma)
with open('KPOINTS', 'w') as fp:
fp.write(fc)
#copy cvasp
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
shutil.copyfile(cvasp_file, 'cvasp.py')
# gen potcar
with open('POTCAR', 'w') as outfile:
for fname in potcar_list:
with open(fname) as infile:
outfile.write(infile.read())
os.chdir(cwd)
def make_vasp(jdata, conf_dir, supercell=[1, 1, 1]):
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, 'POSCAR')
# get equi poscar
if 'relax_incar' in jdata.keys():
vasp_str = 'vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str = 'vasp-k%.2f' % kspacing
equi_path = re.sub('confs', global_equi_name, conf_path)
equi_path = os.path.join(equi_path, vasp_str)
equi_contcar = os.path.join(equi_path, 'CONTCAR')
assert os.path.exists(
equi_contcar), "Please compute the equilibrium state using vasp first"
task_path = re.sub('confs', global_task_name, conf_path)
task_path = os.path.join(task_path, vasp_str)
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')
# gen strcture
ss = Structure.from_file(task_poscar)
# gen defects
vds = VacancyGenerator(ss)
dss = []
for jj in vds:
dss.append(jj.generate_defect_structure(supercell))
# gen incar
if 'relax_incar' in jdata.keys():
relax_incar_path = jdata['relax_incar']
assert (os.path.exists(relax_incar_path))
relax_incar_path = os.path.abspath(relax_incar_path)
incar = incar_upper(Incar.from_file(relax_incar_path))
fc = incar.get_string()
kspacing = incar['KSPACING']
kgamma = incar['KGAMMA']
else:
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']
fc = vasp.make_vasp_relax_incar(ecut,
ediff,
True,
True,
True,
npar=npar,
kpar=kpar,
kspacing=kspacing,
kgamma=kgamma)
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(os.path.abspath(
potcar_map[ii])), "No POTCAR in the potcar_map of %s" % (ii)
potcar_list.append(os.path.abspath(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 tasks
copy_str = "%sx%sx%s" % (supercell[0], supercell[1], supercell[2])
cwd = os.getcwd()
for ii in range(len(dss)):
struct_path = os.path.join(task_path,
'struct-%s-%03d' % (copy_str, ii))
print('# generate %s' % (struct_path))
os.makedirs(struct_path, exist_ok=True)
os.chdir(struct_path)
for jj in ['POSCAR', 'POTCAR', 'INCAR']:
if os.path.isfile(jj):
os.remove(jj)
# make conf
dss[ii].to('POSCAR', 'POSCAR')
# 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')
# save supercell
np.savetxt('supercell.out', supercell, fmt='%d')
# write kp
fc = vasp.make_kspacing_kpoints('POSCAR', kspacing, kgamma)
with open('KPOINTS', 'w') as fp:
fp.write(fc)
#copy cvasp
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
shutil.copyfile(cvasp_file, os.path.join(struct_path, 'cvasp.py'))
os.chdir(cwd)
def make_vasp(jdata, conf_dir):
default_norm_def = 2e-3
default_shear_def = 5e-3
norm_def = jdata.get('norm_deform', default_norm_def)
shear_def = jdata.get('shear_deform', default_shear_def)
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, 'POSCAR')
if 'relax_incar' in jdata.keys():
vasp_str = 'vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str = 'vasp-k%.2f' % kspacing
# get equi poscar
equi_path = re.sub('confs', global_equi_name, conf_path)
equi_path = os.path.join(equi_path, vasp_str)
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_str)
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 = [-norm_def, -0.5 * norm_def, 0.5 * norm_def, norm_def]
shear_strains = [-shear_def, -0.5 * shear_def, 0.5 * shear_def, shear_def]
dfm_ss = DeformedStructureSet(ss,
symmetry=False,
norm_strains=norm_strains,
shear_strains=shear_strains)
n_dfm = len(dfm_ss)
# gen incar
if 'relax_incar' in jdata.keys():
relax_incar_path = jdata['relax_incar']
assert (os.path.exists(relax_incar_path))
relax_incar_path = os.path.abspath(relax_incar_path)
incar = incar_upper(Incar.from_file(relax_incar_path))
if incar.get('ISIF') != 2:
dlog.info("%s:%s setting ISIF to 2" %
(__file__, make_vasp.__name__))
incar['ISIF'] = 2
fc = incar.get_string()
kspacing = incar['KSPACING']
kgamma = incar['KGAMMA']
else:
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']
fc = vasp.make_vasp_relax_incar(ecut,
ediff,
True,
False,
False,
npar=npar,
kpar=kpar,
kspacing=kspacing,
kgamma=kgamma)
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(os.path.abspath(
potcar_map[ii])), "No POTCAR in the potcar_map of %s" % (ii)
potcar_list.append(os.path.abspath(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
dfm_ss.deformed_structures[ii].to('POSCAR', 'POSCAR')
# record strain
strain = Strain.from_deformation(dfm_ss.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')
#copy cvasp
if ('cvasp' in jdata) and (jdata['cvasp'] == True):
shutil.copyfile(cvasp_file, os.path.join(dfm_path, 'cvasp.py'))
os.chdir(cwd)
