def test_dlp3(): cells = [] cells.append( np.array([[23.9999973028, 0.0, 0.0], [0.0, 23.9999973028, 0.0], [0.0, 0.0, 23.9999973028]])) cells.append( np.array([[23.9999947494, 0.0, 0.0], [0.0, 23.9999947494, 0.0], [0.0, 0.0, 23.9999947494]])) cells.append( np.array([[23.9999911871, 0.0, 0.0], [0.0, 23.9999911871, 0.0], [0.0, 0.0, 23.9999911871]])) traj = aseIO.read(fd3, format='dlp-history', index=slice(0, None)) assert len(traj) == 3 traj = aseIO.iread(fd3, format='dlp-history', index=slice(0, None)) for i, frame in enumerate(traj): assert len(frame) == 4 assert all(frame.symbols == 'OHHX') assert np.isclose(frame.get_cell(), cells[i]).all() symbols = frame.get_chemical_symbols() traj = iread_dlp_history(fd3, symbols) for i, frame in enumerate(traj): assert len(frame) == 4 assert all(frame.symbols == 'OHHX') assert np.isclose(frame.get_cell(), cells[i]).all() assert frame.has('initial_charges')
def test_dlp(): cells = [] cells.append( np.array([[23.01, -0.3943E-01, 0.4612E-01], [-0.9486E-01, 22.98, 0.4551], [0.6568, 0.7694, 19.21]])) cells.append( np.array([[22.90, -0.3925E-01, 0.4591E-01], [-0.9443E-01, 22.88, 0.4531], [0.6538, 0.7660, 19.12]])) cells.append( np.array([[22.73, -0.3896E-01, 0.4557E-01], [-0.9374E-01, 22.71, 0.4497], [0.6490, 0.7603, 18.98]])) traj = aseIO.read(fd, format='dlp-history', index=slice(0, None)) assert len(traj) == 3 traj = aseIO.iread(fd, format='dlp-history', index=slice(0, None)) for i, frame in enumerate(traj): assert len(frame) == 2 assert all(frame.symbols == 'ONi') assert np.isclose(frame.get_cell(), cells[i]).all() symbols = frame.get_chemical_symbols() traj = iread_dlp_history(fd, symbols) for i, frame in enumerate(traj): assert len(frame) == 2 assert all(frame.symbols == 'ONi') assert np.isclose(frame.get_cell(), cells[i]).all()
7.7056E+00 -3.4445E+00 2.0241E+00 2.4898E+00 -4.4453E+00 3.0289E+01 2.8009E+04 -4.5827E+04 3.0655E+05 """) cells = [] cells.append(np.array([[23.01, -0.3943E-01, 0.4612E-01], [-0.9486E-01, 22.98, 0.4551], [0.6568, 0.7694, 19.21]])) cells.append(np.array([[22.90, -0.3925E-01, 0.4591E-01], [-0.9443E-01, 22.88, 0.4531], [0.6538, 0.7660, 19.12]])) cells.append(np.array([[22.73, -0.3896E-01, 0.4557E-01], [-0.9374E-01, 22.71, 0.4497], [0.6490, 0.7603, 18.98]])) traj = aseIO.read(fd, format='dlp-history', index=slice(0,None)) assert len(traj) == 3 traj = aseIO.iread(fd, format='dlp-history', index=slice(0,None)) for i, frame in enumerate(traj): assert len(frame) == 2 assert frame[0].symbol == 'O' assert frame[1].symbol == 'Ni' assert np.isclose(frame.get_cell(),cells[i]).all() symbols = frame.get_chemical_symbols() traj = iread_dlp_history(fd, symbols) for i, frame in enumerate(traj): assert len(frame) == 2 assert frame[0].symbol == 'O' assert frame[1].symbol == 'Ni' assert np.isclose(frame.get_cell(),cells[i]).all()