def make_confs(self,
path_to_work,
path_to_equi,
refine=False):
path_to_work = os.path.abspath(path_to_work)
if os.path.exists(path_to_work):
dlog.warning('%s already exists' % path_to_work)
else:
os.makedirs(path_to_work)
path_to_equi = os.path.abspath(path_to_equi)
if 'start_confs_path' in self.parameter and os.path.exists(self.parameter['start_confs_path']):
init_path_list = glob.glob(os.path.join(self.parameter['start_confs_path'], '*'))
struct_init_name_list = []
for ii in init_path_list:
struct_init_name_list.append(ii.split('/')[-1])
struct_output_name = path_to_work.split('/')[-2]
assert struct_output_name in struct_init_name_list
path_to_equi = os.path.abspath(os.path.join(self.parameter['start_confs_path'],
struct_output_name, 'relaxation', 'relax_task'))
task_list = []
cwd = os.getcwd()
if self.reprod:
print('surface reproduce starts')
if 'init_data_path' not in self.parameter:
raise RuntimeError("please provide the initial data path to reproduce")
init_data_path = os.path.abspath(self.parameter['init_data_path'])
task_list = make_repro(init_data_path, self.init_from_suffix,
path_to_work, self.parameter.get('reprod_last_frame', True))
os.chdir(cwd)
else:
if refine:
print('surface refine starts')
task_list = make_refine(self.parameter['init_from_suffix'],
self.parameter['output_suffix'],
path_to_work)
os.chdir(cwd)
# record miller
init_from_path = re.sub(self.parameter['output_suffix'][::-1],
self.parameter['init_from_suffix'][::-1],
path_to_work[::-1], count=1)[::-1]
task_list_basename = list(map(os.path.basename, task_list))
for ii in task_list_basename:
init_from_task = os.path.join(init_from_path, ii)
output_task = os.path.join(path_to_work, ii)
os.chdir(output_task)
if os.path.isfile('miller.json'):
os.remove('miller.json')
if os.path.islink('miller.json'):
os.remove('miller.json')
os.symlink(os.path.relpath(os.path.join(init_from_task, 'miller.json')), 'miller.json')
os.chdir(cwd)
else:
equi_contcar = os.path.join(path_to_equi, 'CONTCAR')
if not os.path.exists(equi_contcar):
raise RuntimeError("please do relaxation first")
ptypes = vasp.get_poscar_types(equi_contcar)
# gen structure
ss = Structure.from_file(equi_contcar)
# gen slabs
all_slabs = generate_all_slabs(ss, self.miller, self.min_slab_size, self.min_vacuum_size)
os.chdir(path_to_work)
if os.path.isfile('POSCAR'):
os.remove('POSCAR')
if os.path.islink('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(equi_contcar), 'POSCAR')
# task_poscar = os.path.join(output, 'POSCAR')
for ii in range(len(all_slabs)):
output_task = os.path.join(path_to_work, 'task.%06d' % ii)
os.makedirs(output_task, exist_ok=True)
os.chdir(output_task)
for jj in ['INCAR', 'POTCAR', 'POSCAR', 'conf.lmp', 'in.lammps']:
if os.path.exists(jj):
os.remove(jj)
task_list.append(output_task)
print("# %03d generate " % ii, output_task, " \t %d atoms" % len(all_slabs[ii].sites))
# make confs
all_slabs[ii].to('POSCAR', 'POSCAR.tmp')
vasp.regulate_poscar('POSCAR.tmp', 'POSCAR')
vasp.sort_poscar('POSCAR', 'POSCAR', ptypes)
vasp.perturb_xz('POSCAR', 'POSCAR', self.pert_xz)
# record miller
dumpfn(all_slabs[ii].miller_index, 'miller.json')
os.chdir(cwd)
return task_list
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_confs(self, path_to_work, path_to_equi, refine=False):
path_to_work = os.path.abspath(path_to_work)
path_to_equi = os.path.abspath(path_to_equi)
task_list = []
cwd = os.getcwd()
equi_contcar = os.path.join(path_to_equi, 'CONTCAR')
ptypes = vasp.get_poscar_types(equi_contcar)
if not os.path.exists(equi_contcar):
raise RuntimeError("please do relaxation first")
# gen structure
ss = Structure.from_file(equi_contcar)
# gen slabs
all_slabs = generate_all_slabs(ss, self.max_miller, self.min_slab_size,
self.min_vacuum_size)
if refine:
task_list = make_refine(self.parameter['init_from_suffix'],
self.parameter['output_suffix'],
path_to_work, len(all_slabs))
# record miller
for ii in range(len(task_list)):
os.chdir(task_list[ii])
np.savetxt('miller.out', all_slabs[ii].miller_index, fmt='%d')
os.chdir(cwd)
if self.reprod:
if 'vasp_path' not in self.parameter:
raise RuntimeError(
"please provide the vasp_path for reproduction")
vasp_path = os.path.abspath(self.parameter['vasp_path'])
task_list = reproduce.make_repro(vasp_path, path_to_work)
os.chdir(cwd)
else:
os.chdir(path_to_work)
if os.path.isfile('POSCAR'):
os.remove('POSCAR')
os.symlink(os.path.relpath(equi_contcar), 'POSCAR')
# task_poscar = os.path.join(output, 'POSCAR')
for ii in range(len(all_slabs)):
output_task = os.path.join(path_to_work, 'task.%06d' % ii)
os.makedirs(output_task, exist_ok=True)
os.chdir(output_task)
for jj in [
'INCAR', 'POTCAR', 'POSCAR', 'conf.lmp', 'in.lammps'
]:
if os.path.exists(jj):
os.remove(jj)
task_list.append(output_task)
print("# %03d generate " % ii, output_task,
" \t %d atoms" % len(all_slabs[ii].sites))
# make confs
all_slabs[ii].to('POSCAR', 'POSCAR.tmp')
vasp.regulate_poscar('POSCAR.tmp', 'POSCAR')
vasp.sort_poscar('POSCAR', 'POSCAR', ptypes)
vasp.perturb_xz('POSCAR', 'POSCAR', self.pert_xz)
# record miller
np.savetxt('miller.out', all_slabs[ii].miller_index, fmt='%d')
os.chdir(cwd)
return task_list