def create_init_tasks(target_folder, param_file, output, fp_json, verbose = True) :
target_folder = os.path.abspath(target_folder)
output = os.path.abspath(output)
tool_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', 'template')
jdata = json.load(open(os.path.join(target_folder, param_file)))
fp_jdata = json.load(open(fp_json))
# fp settings
mass_map = jdata['mass_map']
type_map = jdata['type_map']
fp_style = fp_jdata['fp_style']
fp_pp_path = fp_jdata['fp_pp_path']
fp_pp_files = fp_jdata['fp_pp_files']
cwd_ = os.getcwd()
os.chdir(target_folder)
fp_pp_path = os.path.abspath(fp_pp_path)
os.chdir(cwd_)
# init data sys
init_data_prefix = jdata['init_data_prefix']
init_data_sys = jdata['init_data_sys']
for idx,ii in enumerate(init_data_sys):
sys = dpdata.LabeledSystem(os.path.join(init_data_prefix, ii), fmt = 'deepmd/npy', type_map = type_map)
nframes = sys.get_nframes()
sys_dir = os.path.join(output, 'init_system.%03d' % idx)
os.makedirs(sys_dir, exist_ok = True)
if verbose :
print('# working on ' + sys_dir)
with open(os.path.join(sys_dir,'record'), 'w') as fp:
fp.write(os.path.join(init_data_prefix, ii) + '\n')
for ff in range(nframes) :
task_dir = os.path.join(sys_dir, 'task.%06d' % ff)
os.makedirs(task_dir, exist_ok = True)
sys.to_vasp_poscar(os.path.join(task_dir, 'POSCAR'))
# make fp
cwd_ = os.getcwd()
os.chdir(task_dir)
for pp in fp_pp_files :
if os.path.lexists(pp) :
os.remove(pp)
os.symlink(os.path.relpath(os.path.join(output, pp)), pp)
if fp_style == 'vasp':
if os.path.lexists('INCAR') :
os.remove('INCAR')
os.symlink(os.path.relpath(os.path.join(output, 'INCAR')), 'INCAR')
elif fp_style == 'pwscf':
try:
fp_params = fp_jdata['user_fp_params']
user_input = True
except:
fp_params = fp_jdata['fp_params']
user_input = False
make_pwscf('.', fp_params, mass_map, fp_pp_files, fp_pp_files, user_input)
os.chdir(cwd_)
def test_post_fp_vasp_0(self):
with open(param_file, 'r') as fp:
jdata = json.load(fp)
jdata['use_ele_temp'] = 2
post_fp_vasp(0, jdata, rfailed=0.3)
sys = dpdata.LabeledSystem('iter.000000/02.fp/data.000/',
fmt='deepmd/raw')
self.assertEqual(sys.get_nframes(), 2)
if sys.data['coords'][0][1][0] < sys.data['coords'][1][1][0]:
idx = [1, 0]
else:
idx = [0, 1]
ref_coord = self.ref_coord[idx]
ref_cell = self.ref_cell[idx]
ref_e = self.ref_e[idx]
ref_f = self.ref_f[idx]
ref_v = self.ref_v[idx]
ref_at = self.ref_at
for ff in range(2):
self.assertAlmostEqual(ref_e[ff], sys.data['energies'][ff])
for ii in range(2):
self.assertEqual(ref_at[ff], sys.data['atom_types'][ff])
for ff in range(2):
for ii in range(2):
for dd in range(3):
self.assertAlmostEqual(ref_coord[ff][ii][dd],
sys.data['coords'][ff][ii][dd])
self.assertAlmostEqual(ref_f[ff][ii][dd],
sys.data['forces'][ff][ii][dd])
for ff in range(2):
for ii in range(3):
for jj in range(3):
self.assertAlmostEqual(ref_v[ff][ii][jj],
sys.data['virials'][ff][ii][jj],
places=5)
self.assertAlmostEqual(ref_cell[ff][ii][jj],
sys.data['cells'][ff][ii][jj])
self.assertTrue(
os.path.isfile('iter.000000/02.fp/data.000/set.000/aparam.npy'))
aparam = np.load('iter.000000/02.fp/data.000/set.000/aparam.npy')
natoms = sys.get_natoms()
self.assertEqual(natoms, 2)
self.assertEqual(list(list(aparam)[0]), [0, 0])
self.assertEqual(list(list(aparam)[1]), [1, 1])
def test_post_fp_vasp_1(self):
with open(param_file, 'r') as fp:
jdata = json.load(fp)
jdata['use_ele_temp'] = 1
post_fp_vasp(0, jdata, rfailed=0.3)
sys = dpdata.LabeledSystem('iter.000000/02.fp/data.001/',
fmt='deepmd/raw')
self.assertEqual(sys.get_nframes(), 1)
# if sys.data['coords'][0][1][0] < sys.data['coords'][1][1][0]:
# idx = [0]
# else :
idx = [1]
ref_coord = self.ref_coord[idx]
ref_cell = self.ref_cell[idx]
ref_e = self.ref_e[idx]
ref_f = self.ref_f[idx]
ref_v = self.ref_v[idx]
ref_at = self.ref_at
for ff in range(1):
self.assertAlmostEqual(ref_e[ff], sys.data['energies'][ff])
for ii in range(2):
self.assertEqual(ref_at[ff], sys.data['atom_types'][ff])
for ff in range(1):
for ii in range(2):
for dd in range(3):
self.assertAlmostEqual(ref_coord[ff][ii][dd],
sys.data['coords'][ff][ii][dd])
self.assertAlmostEqual(ref_f[ff][ii][dd],
sys.data['forces'][ff][ii][dd])
for ff in range(1):
for ii in range(3):
for jj in range(3):
self.assertAlmostEqual(ref_v[ff][ii][jj],
sys.data['virials'][ff][ii][jj],
places=5)
self.assertAlmostEqual(ref_cell[ff][ii][jj],
sys.data['cells'][ff][ii][jj])
fparam = np.load('iter.000000/02.fp/data.001/set.000/fparam.npy')
self.assertEqual(fparam.shape[0], 1)
self.assertEqual(list(fparam), [100000])
def test_coll(self):
with open(param_file, 'r') as fp:
jdata = json.load(fp)
jdata['out_dir'] = self.odir
coll_vasp_md(jdata)
sys = dpdata.LabeledSystem(self.odir + '/02.md/sys-004/deepmd//',
fmt='deepmd/raw')
self.assertEqual(sys.get_nframes(), 2)
if sys.data['coords'][0][1][0] < sys.data['coords'][1][1][0]:
idx = [1, 0]
else:
idx = [0, 1]
ref_coord = self.ref_coord[idx]
ref_cell = self.ref_cell[idx]
ref_e = self.ref_e[idx]
ref_f = self.ref_f[idx]
ref_v = self.ref_v[idx]
ref_at = self.ref_at
for ff in range(2):
self.assertAlmostEqual(ref_e[ff], sys.data['energies'][ff])
for ii in range(2):
self.assertEqual(ref_at[ff], sys.data['atom_types'][ff])
for ff in range(2):
for ii in range(2):
for dd in range(3):
self.assertAlmostEqual(ref_coord[ff][ii][dd],
sys.data['coords'][ff][ii][dd])
self.assertAlmostEqual(ref_f[ff][ii][dd],
sys.data['forces'][ff][ii][dd])
for ff in range(2):
for ii in range(3):
for jj in range(3):
self.assertAlmostEqual(ref_v[ff][ii][jj],
sys.data['virials'][ff][ii][jj],
places=5)
self.assertAlmostEqual(ref_cell[ff][ii][jj],
sys.data['cells'][ff][ii][jj])
