diff --git a/dpdata/pwmat/movement.py b/dpdata/pwmat/movement.py index 2440641e..748744d6 100644 --- a/dpdata/pwmat/movement.py +++ b/dpdata/pwmat/movement.py @@ -18,7 +18,7 @@ def system_info(lines, type_idx_zero=False): nelm = 100 atomic_number = [] for idx, ii in enumerate(lines): - if "Position" in ii: + if ("Position" in ii) and ("nonperiodic_Position" not in ii): for kk in range(idx + 1, idx + 1 + natoms): min = kk for jj in range(kk + 1, idx + 1 + natoms): @@ -175,7 +175,7 @@ def analyze_block(lines, ntot, nelm): # cell.append([float(ss) # for ss in tmp_l.split()[0:3]]) # virial = np.zeros([3,3]) - elif "Position" in ii: + elif ("Position" in ii) and ("nonperiodic_Position" not in ii): for kk in range(idx + 1, idx + 1 + ntot): min = kk for jj in range(kk + 1, idx + 1 + ntot): diff --git a/tests/pwmat/MOVEMENT_1 b/tests/pwmat/MOVEMENT_1 new file mode 100644 index 00000000..94db8a20 --- /dev/null +++ b/tests/pwmat/MOVEMENT_1 @@ -0,0 +1,764 @@ + 72 atoms,Iteration (fs) = 0.1000000000E+01, Etot,Ep,Ek (eV) = -0.3576772281E+06 -0.3576828045E+06 0.5576424390E+01, SCF = 6 +P_sph(bar),Rcut_MD_sp(A) 0.000000E+00 0.000000E+00 + MD_INFO: METHOD(1-VV,2-NH,3-LV,4-LVPR,5-NHRP) TIME(fs) TEMP(K) DESIRED_TEMP(K) AVE_TEMP(K) TIME_INTERVAL(fs) TOT_TEMP(K) + 2 0.1000000000E+01 0.59918E+03 0.30000E+03 0.59918E+03 0.10000E+03 0.59918E+03 + TOTAL MOMENTUM + 0.78114E+00 -0.73795E+00 0.32709E+01 + MD_NH_INFO: Nose-Hoover Dynamics (NVT), IONS' THERMOSTAT VELOCITY(1/fs) + 0.1230339822E-01 + Lattice vector (Angstrom) + 0.1086378600E+02 0.0000000000E+00 0.0000000000E+00 stress (eV): 0.734547E+03 -0.240455E+00 -0.244180E+00 + 0.0000000000E+00 0.1086378600E+02 0.0000000000E+00 stress (eV): -0.240469E+00 0.734396E+03 -0.246855E+00 + 0.0000000000E+00 0.0000000000E+00 0.7242524000E+01 stress (eV): -0.244205E+00 -0.246843E+00 0.734414E+03 + Pressure Internal(Hartree/bohr^3) + -0.4679719258E-02 0.1531957367E-05 0.1555724326E-05 + 0.1531957367E-05 -0.4678760910E-02 0.1572648837E-05 + 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0.012513214518150 + 0.051724960335473 -0.037203011603299 -0.016421641447038 + 0.050653710103258 -0.034772794859077 0.005335094142859 +-0.011000331793801 0.017275684602558 0.012536074078033 + 0.018014529539251 0.052305789270276 0.046760600498551 \ No newline at end of file diff --git a/tests/test_pwmat_movement.py b/tests/test_pwmat_movement.py index e32c0f31..68a9e681 100644 --- a/tests/test_pwmat_movement.py +++ b/tests/test_pwmat_movement.py @@ -58,10 +58,73 @@ def test_energy(self): self.assertEqual(self.system.data["energies"][0], ref_energy) +class TestpwmatSinglePointEnergy1: + def test_atom_names(self): + self.assertEqual(self.system.data["atom_names"], ["Cu"]) + + def test_atom_numbs(self): + self.assertEqual(self.system.data["atom_numbs"], [72]) + + def test_atom_types(self): + ref_type = [0] * 72 + ref_type = np.array(ref_type) + for ii in range(ref_type.shape[0]): + self.assertEqual(self.system.data["atom_types"][ii], ref_type[ii]) + + def test_cell(self): + fp = open("pwmat/ref_cell_1") + cell = [] + for ii in fp: + cell.append([float(jj) for jj in ii.split()]) + cell = np.array(cell) + for ii in range(cell.shape[0]): + for jj in range(cell.shape[1]): + self.assertEqual(self.system.data["cells"][0][ii][jj], cell[ii][jj]) + fp.close() + + def test_coord(self): + fp = open("pwmat/ref_coord_1") + fp_cell = open("pwmat/ref_cell_1") + cell = [] + for ii in fp_cell: + cell.append([float(jj) for jj in ii.split()]) + cell = np.array(cell) + coord = [] + for ii in fp: + coord.append([float(jj) for jj in ii.split()]) + coord = np.array(coord) + coord = np.matmul(coord, cell) + for ii in range(coord.shape[0]): + for jj in range(coord.shape[1]): + self.assertEqual(self.system.data["coords"][0][ii][jj], coord[ii][jj]) + fp_cell.close() + fp.close() + + def test_force(self): + fp = open("pwmat/ref_force_1") + force = [] + for ii in fp: + force.append([float(jj) for jj in ii.split()]) + force = np.array(force) + for ii in range(force.shape[0]): + for jj in range(force.shape[1]): + self.assertEqual(self.system.data["forces"][0][ii][jj], -force[ii][jj]) + fp.close() + + def test_energy(self): + ref_energy = -0.3576828045e06 + self.assertEqual(self.system.data["energies"][0], ref_energy) + + class TestpwmatLabeledOutput(unittest.TestCase, TestpwmatSinglePointEnergy): def setUp(self): self.system = dpdata.LabeledSystem("pwmat/MOVEMENT", fmt="pwmat/MOVEMENT") +class TestpwmatLabeledOutput1(unittest.TestCase, TestpwmatSinglePointEnergy1): + def setUp(self): + self.system = dpdata.LabeledSystem("pwmat/MOVEMENT_1", fmt="pwmat/movement") + + if __name__ == "__main__": unittest.main()