def setUp(self):
_jdata = {
"structures": ["confs/mp-141"],
"interaction": {
"type": "vasp",
"incar": "vasp_input/INCAR.rlx",
"potcar_prefix": ".",
"potcars": {
"Yb": "vasp_input/POTCAR"
}
},
"properties": [{
"type": "surface",
"min_slab_size": 10,
"min_vacuum_size": 11,
"pert_xz": 0.01,
"max_miller": 1,
"cal_type": "relaxation"
}]
}
self.equi_path = 'confs/mp-141/relaxation/relax_task'
self.source_path = 'equi/vasp'
self.target_path = 'confs/mp-141/surface_00'
if not os.path.exists(self.equi_path):
os.makedirs(self.equi_path)
self.confs = _jdata["structures"]
self.inter_param = _jdata["interaction"]
self.prop_param = _jdata['properties']
self.surface = Surface(_jdata['properties'][0])
def make_property_instance(paramters):
"""
Make an instance of Property
"""
prop_type = paramters['type']
if prop_type == 'eos':
return EOS(paramters)
elif prop_type == 'elastic':
return Elastic(paramters)
elif prop_type == 'vacancy':
return Vacancy(paramters)
elif prop_type == 'interstitial':
return Interstitial(paramters)
elif prop_type == 'surface':
return Surface(paramters)
else:
raise RuntimeError(f'unknown property type {prop_type}')
class TestSurface(unittest.TestCase):
def setUp(self):
_jdata = {
"structures": ["confs/mp-141"],
"interaction": {
"type": "vasp",
"incar": "vasp_input/INCAR.rlx",
"potcar_prefix": ".",
"potcars": {
"Yb": "vasp_input/POTCAR"
}
},
"properties": [{
"type": "surface",
"min_slab_size": 10,
"min_vacuum_size": 11,
"pert_xz": 0.01,
"max_miller": 1,
"cal_type": "relaxation"
}]
}
self.equi_path = 'confs/mp-141/relaxation/relax_task'
self.source_path = 'equi/vasp'
self.target_path = 'confs/mp-141/surface_00'
if not os.path.exists(self.equi_path):
os.makedirs(self.equi_path)
self.confs = _jdata["structures"]
self.inter_param = _jdata["interaction"]
self.prop_param = _jdata['properties']
self.surface = Surface(_jdata['properties'][0])
def tearDown(self):
if os.path.exists(os.path.abspath(os.path.join(self.equi_path, '..'))):
shutil.rmtree(os.path.abspath(os.path.join(self.equi_path, '..')))
if os.path.exists(self.equi_path):
shutil.rmtree(self.equi_path)
if os.path.exists(self.target_path):
shutil.rmtree(self.target_path)
def test_task_type(self):
self.assertEqual('surface', self.surface.task_type())
def test_task_param(self):
self.assertEqual(self.prop_param[0], self.surface.task_param())
def test_make_confs_0(self):
if not os.path.exists(os.path.join(self.equi_path, 'CONTCAR')):
with self.assertRaises(RuntimeError):
self.surface.make_confs(self.target_path, self.equi_path)
shutil.copy(os.path.join(self.source_path, 'mp-141.vasp'),
os.path.join(self.equi_path, 'CONTCAR'))
task_list = self.surface.make_confs(self.target_path, self.equi_path)
self.assertEqual(len(task_list), 7)
dfm_dirs = glob.glob(os.path.join(self.target_path, 'task.*'))
incar0 = Incar.from_file(os.path.join('vasp_input', 'INCAR.rlx'))
incar0['ISIF'] = 4
self.assertEqual(
os.path.realpath(os.path.join(self.equi_path, 'CONTCAR')),
os.path.realpath(os.path.join(self.target_path, 'POSCAR')))
ref_st = Structure.from_file(os.path.join(self.target_path, 'POSCAR'))
dfm_dirs.sort()
for ii in dfm_dirs:
st_file = os.path.join(ii, 'POSCAR')
self.assertTrue(os.path.isfile(st_file))
st0 = Structure.from_file(st_file)
st1_file = os.path.join(ii, 'POSCAR.tmp')
self.assertTrue(os.path.isfile(st1_file))
st1 = Structure.from_file(st1_file)
miller_json_file = os.path.join(ii, 'miller.json')
self.assertTrue(os.path.isfile(miller_json_file))
miller_json = loadfn(miller_json_file)
sl = SlabGenerator(ref_st, miller_json,
self.prop_param[0]["min_slab_size"],
self.prop_param[0]["min_vacuum_size"])
slb = sl.get_slab()
st2 = Structure(slb.lattice, slb.species, slb.frac_coords)
self.assertEqual(len(st1), len(st2))