def post_process(self, task_list):
cwd = os.getcwd()
poscar_start = os.path.abspath(
os.path.join(task_list[0], '..', 'POSCAR'))
os.chdir(os.path.join(task_list[0], '..'))
if os.path.isfile(os.path.join(task_list[0], 'INCAR')):
incar = incar_upper(
Incar.from_file(os.path.join(task_list[0], 'INCAR')))
kspacing = incar.get('KSPACING')
kgamma = incar.get('KGAMMA', False)
ret = vasp.make_kspacing_kpoints(poscar_start, kspacing, kgamma)
kp = Kpoints.from_string(ret)
if os.path.isfile('KPOINTS'):
os.remove('KPOINTS')
kp.write_file("KPOINTS")
os.chdir(cwd)
kpoints_universal = os.path.abspath(
os.path.join(task_list[0], '..', 'KPOINTS'))
for ii in task_list:
if os.path.isfile(os.path.join(ii, 'KPOINTS')):
os.remove(os.path.join(ii, 'KPOINTS'))
if os.path.islink(os.path.join(ii, 'KPOINTS')):
os.remove(os.path.join(ii, 'KPOINTS'))
os.chdir(ii)
os.symlink(os.path.relpath(kpoints_universal), 'KPOINTS')
os.chdir(cwd)
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, 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):
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) :
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, supercell, insert_ele):
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
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
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 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')
# 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_input_file(self, output_dir, task_type, task_param):
sepline(ch=output_dir)
dumpfn(task_param, os.path.join(output_dir, 'task.json'), indent=4)
assert (os.path.exists(self.incar)), 'no INCAR file for relaxation'
relax_incar_path = os.path.abspath(self.incar)
incar_relax = incar_upper(Incar.from_file(relax_incar_path))
# deal with relaxation
cal_type = task_param['cal_type']
cal_setting = task_param['cal_setting']
# user input INCAR for property calculation
if 'input_prop' in cal_setting and os.path.isfile(
cal_setting['input_prop']):
incar_prop = os.path.abspath(cal_setting['input_prop'])
incar = incar_upper(Incar.from_file(incar_prop))
# revise INCAR based on the INCAR provided in the "interaction"
else:
incar = incar_relax
if cal_type == 'relaxation':
relax_pos = cal_setting['relax_pos']
relax_shape = cal_setting['relax_shape']
relax_vol = cal_setting['relax_vol']
if [relax_pos, relax_shape, relax_vol] == [True, False, False]:
isif = 2
elif [relax_pos, relax_shape, relax_vol] == [True, True, True]:
isif = 3
elif [relax_pos, relax_shape,
relax_vol] == [True, True, False]:
isif = 4
elif [relax_pos, relax_shape,
relax_vol] == [False, True, False]:
isif = 5
elif [relax_pos, relax_shape,
relax_vol] == [False, True, True]:
isif = 6
elif [relax_pos, relax_shape,
relax_vol] == [False, False, True]:
isif = 7
elif [relax_pos, relax_shape,
relax_vol] == [False, False, False]:
nsw = 0
isif = 2
if not ('NSW' in incar and incar.get('NSW') == nsw):
dlog.info("%s setting NSW to %d" %
(self.make_input_file.__name__, nsw))
incar['NSW'] = nsw
else:
raise RuntimeError(
"not supported calculation setting for VASP")
if not ('ISIF' in incar and incar.get('ISIF') == isif):
dlog.info("%s setting ISIF to %d" %
(self.make_input_file.__name__, isif))
incar['ISIF'] = isif
elif cal_type == 'static':
nsw = 0
if not ('NSW' in incar and incar.get('NSW') == nsw):
dlog.info("%s setting NSW to %d" %
(self.make_input_file.__name__, nsw))
incar['NSW'] = nsw
else:
raise RuntimeError("not supported calculation type for VASP")
if 'ediff' in cal_setting:
dlog.info(
"%s setting EDIFF to %s" %
(self.make_input_file.__name__, cal_setting['ediff']))
incar['EDIFF'] = cal_setting['ediff']
if 'ediffg' in cal_setting:
dlog.info(
"%s setting EDIFFG to %s" %
(self.make_input_file.__name__, cal_setting['ediffg']))
incar['EDIFFG'] = cal_setting['ediffg']
if 'encut' in cal_setting:
dlog.info(
"%s setting ENCUT to %s" %
(self.make_input_file.__name__, cal_setting['encut']))
incar['ENCUT'] = cal_setting['encut']
if 'kspacing' in cal_setting:
dlog.info(
"%s setting KSAPCING to %s" %
(self.make_input_file.__name__, cal_setting['kspacing']))
incar['KSAPCING'] = cal_setting['kspacing']
if 'kgamma' in cal_setting:
dlog.info(
"%s setting KGAMMA to %s" %
(self.make_input_file.__name__, cal_setting['kgamma']))
incar['KGAMMA'] = cal_setting['kgamma']
try:
kspacing = incar.get('KSPACING')
except KeyError:
raise RuntimeError("KSPACING must be given in INCAR")
if 'KGAMMA' in incar:
kgamma = incar.get('KGAMMA')
else:
kgamma = False
incar.write_file(os.path.join(output_dir, '../INCAR'))
cwd = os.getcwd()
os.chdir(output_dir)
if not os.path.islink('INCAR'):
os.symlink('../INCAR', 'INCAR')
elif not '../INCAR' == os.readlink('INCAR'):
os.remove('INCAR')
os.symlink('../INCAR', 'INCAR')
os.chdir(cwd)
ret = vasp.make_kspacing_kpoints(self.path_to_poscar, kspacing, kgamma)
kp = Kpoints.from_string(ret)
kp.write_file(os.path.join(output_dir, "KPOINTS"))
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']
supercell_matrix = jdata['supercell_matrix']
band_path = jdata['band']
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, '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)
print(task_path)
if os.path.isfile('POSCAR-unitcell'):
os.remove('POSCAR-unitcell')
if os.path.isfile('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(equi_contcar), 'POSCAR-unitcell')
os.chdir(cwd)
task_poscar = os.path.join(task_path, 'POSCAR-unitcell')
# gen incar
fc = vasp.make_vasp_phonon_incar(ecut,
ediff,
npar,
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 band.conf
os.chdir(task_path)
with open('band.conf', 'w') as fp:
fp.write('ATOM_NAME = ')
for ii in ele_list:
fp.write(ii)
fp.write(' ')
fp.write('\n')
fp.write(
'DIM = %d %d %d\n' %
(supercell_matrix[0], supercell_matrix[1], supercell_matrix[2]))
fp.write('BAND = %s\n' % band_path)
fp.write('FORCE_CONSTANTS=READ')
# gen POSCAR
os.system('phonopy -d --dim="%d %d %d" -c POSCAR-unitcell' %
(supercell_matrix[0], supercell_matrix[1], supercell_matrix[2]))
os.symlink('SPOSCAR', 'POSCAR')
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']
supercell_matrix = jdata['supercell_matrix']
band_path = jdata['band']
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, '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)
print(task_path)
if os.path.isfile('POSCAR-unitcell'):
os.remove('POSCAR-unitcell')
if os.path.isfile('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(equi_contcar), 'POSCAR-unitcell')
os.chdir(cwd)
task_poscar = os.path.join(task_path, 'POSCAR-unitcell')
# gen incar
fc = vasp.make_vasp_phonon_incar(ecut,
ediff,
1,
1,
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 band.conf
os.chdir(task_path)
with open('band.conf', 'w') as fp:
fp.write('ATOM_NAME = ')
for ii in ele_list:
fp.write(ii)
fp.write(' ')
fp.write('\n')
fp.write(
'DIM = %d %d %d\n' %
(supercell_matrix[0], supercell_matrix[1], supercell_matrix[2]))
fp.write('BAND = %s\n' % band_path)
fp.write('FORCE_CONSTANTS=READ')
# gen POSCAR
'''
phonon = phonopy.load(supercell_matrix=supercell_matrix,
primitive_matrix='auto',
unitcell_filename='POSCAR-unitcell')
phonon.save(filename='phonopy_disp.yaml')
with open('phonopy_disp.yaml', 'r') as f:
temp = yaml.load(f.read())
with open('POSCAR', 'w') as fp:
for ii in ele_list:
fp.write(ii)
fp.write(' ')
fp.write('\n')
data=open('POSCAR-unitcell', 'r')
next(data)
fp.write(data.readline())
for ii in temp['supercell']['lattice']:
fp.write(str(ii).replace(',', '').replace('[', '').replace(']','\n'))
for ii in ele_list:
fp.write(str(str(temp['supercell']['points']).count(ii)))
fp.write(' ')
fp.write('\n')
fp.write('Direct\n')
for ii in temp['supercell']['points']:
fp.write(str(ii['coordinates']).replace(',', '').replace('[', '').replace(']', '\n'))
'''
os.system('phonopy -d --dim="%d %d %d" -c POSCAR-unitcell' %
(supercell_matrix[0], supercell_matrix[1], supercell_matrix[2]))
os.system('cp SPOSCAR POSCAR')
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)
def make_vasp(jdata, conf_dir) :
supercell_matrix=jdata['supercell_matrix']
band_path=jdata['band']
if 'relax_incar' in jdata.keys():
vasp_str='vasp-relax_incar'
else:
vasp_str='vasp-k%.2f' % kspacing
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, '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)
if 'user_incar' in jdata.keys():
vasp_user_str='vasp-user_incar'
else:
vasp_user_str='vasp-k%.2f' % kspacing
task_path = os.path.join(task_path, vasp_user_str)
os.makedirs(task_path, exist_ok=True)
cwd = os.getcwd()
os.chdir(task_path)
print(task_path)
if os.path.isfile('POSCAR-unitcell') :
os.remove('POSCAR-unitcell')
if os.path.isfile('POSCAR') :
os.remove('POSCAR')
os.symlink(os.path.relpath(equi_contcar), 'POSCAR-unitcell')
os.chdir(cwd)
task_poscar = os.path.join(task_path, 'POSCAR-unitcell')
# gen incar
if 'user_incar' in jdata.keys():
user_incar_path = jdata['user_incar']
assert(os.path.exists(user_incar_path))
user_incar_path = os.path.abspath(user_incar_path)
incar = incar_upper(Incar.from_file(user_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_phonon_incar(ecut, ediff, npar, 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)
# 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(task_path,'cvasp.py'))
# gen band.conf
os.chdir(task_path)
with open('band.conf','w') as fp:
fp.write('ATOM_NAME = ')
for ii in ele_list:
fp.write(ii)
fp.write(' ')
fp.write('\n')
fp.write('DIM = %d %d %d\n'%(supercell_matrix[0],supercell_matrix[1],supercell_matrix[2]))
fp.write('BAND = %s\n'%band_path)
fp.write('FORCE_CONSTANTS=READ')
# gen POSCAR
os.system('phonopy -d --dim="%d %d %d" -c POSCAR-unitcell'%(supercell_matrix[0],supercell_matrix[1],supercell_matrix[2]))
os.symlink('SPOSCAR', 'POSCAR')
def make_vasp(jdata, conf_dir, max_miller=2, relax_box=False, static=False):
min_slab_size = jdata['min_slab_size']
min_vacuum_size = jdata['min_vacuum_size']
pert_xz = jdata['pert_xz']
if 'relax_incar' in jdata.keys():
vasp_str = 'vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str = 'vasp-k%.2f' % (kspacing)
# 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_str)
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:
if 'scf_incar' in jdata.keys():
vasp_static_str = 'vasp-static-scf_incar'
else:
vasp_static_str = 'vasp-static-k%.2f' % (kspacing)
task_path = os.path.join(task_path, vasp_static_str)
else:
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')
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:
if 'scf_incar' in jdata.keys():
scf_incar_path = jdata['scf_incar']
assert (os.path.exists(scf_incar_path))
scf_incar_path = os.path.abspath(scf_incar_path)
incar = incar_upper(Incar.from_file(scf_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_static_incar(ecut,
ediff,
npar=npar,
kpar=kpar,
kspacing=kspacing,
kgamma=kgamma)
else:
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,
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')
# 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'))
cwd = os.getcwd()