def _check_confs(testCase, idx, jdata):
md_dir = os.path.join('iter.%06d' % idx, '01.model_devi')
tasks = glob.glob(os.path.join(md_dir, 'task.*'))
tasks.sort()
cur_job = jdata['model_devi_jobs'][idx]
sys_idx = cur_job['sys_idx']
sys_configs = jdata['sys_configs']
poscars = []
for ii in sys_idx:
sys_poscars = []
for ss in sys_configs[ii]:
tmp_poscars = glob.glob(ss)
sys_poscars += tmp_poscars
sys_poscars.sort()
poscars.append(sys_poscars)
for ii in tasks:
conf_file = os.path.join(ii, 'conf.lmp')
l_conf_file = os.path.basename(os.readlink(conf_file))
poscar_file = poscars[int(l_conf_file.split('.')[0])][int(
l_conf_file.split('.')[1])]
sys_0 = dpdata.System(conf_file, type_map=jdata['type_map'])
sys_1 = dpdata.System(poscar_file)
test_atom_names(testCase, sys_0, sys_1)
test_atom_types(testCase, sys_0, sys_1)
test_cell(testCase, sys_0, sys_1)
test_coord(testCase, sys_0, sys_1)
def _check_poscars(testCase, idx, fp_task_max, type_map):
fp_path = os.path.join('iter.%06d' % idx, '02.fp')
candi_files = glob.glob(os.path.join(fp_path, 'candidate.shuffled.*.out'))
candi_files.sort()
sys_idx = [str(os.path.basename(ii).split('.')[2]) for ii in candi_files]
for sidx, ii in zip(sys_idx, candi_files):
md_task = []
f_idx = []
with open(ii) as fp:
for ii in fp:
md_task.append(ii.split()[0])
f_idx.append(ii.split()[1])
md_task = md_task[:fp_task_max]
f_idx = f_idx[:fp_task_max]
cc = 0
for tt, ff in zip(md_task, f_idx):
traj_file = os.path.join(tt, 'traj', '%d.lammpstrj' % int(ff))
poscar_file = os.path.join(fp_path,
'task.%03d.%06d' % (int(sidx), cc),
'POSCAR')
cc += 1
sys0 = dpdata.System(traj_file,
fmt='lammps/dump',
type_map=type_map)
sys1 = dpdata.System(poscar_file, fmt='vasp/poscar')
test_atom_names(testCase, sys0, sys1)