def test_coord_trans(): natoms = 10 cell = np.array([[3, 0, 0], [1.1, 5, -0.04], [-0.33, 1.5, 7]]) cryst_const = crys.cell2cc(cell) coords_frac = rand(natoms, 3) coords = crys.coord_trans(coords=coords_frac, old=cell, new=np.identity(3)) st = crys.Structure(coords=coords, cell=cell) assert np.allclose(coords_frac, st.coords_frac) st = crys.Structure(coords_frac=coords_frac, cell=cell) assert np.allclose(coords, st.coords) st = crys.Structure(coords=coords, cell=cell) assert np.allclose(cryst_const, st.cryst_const)
def test_cell_tools(): # test known values: simple cubic cell_a = 5.0 cell = np.identity(3) * cell_a volume = cell_a**3.0 cryst_const = np.array([cell_a] * 3 + [90.0] * 3) np.testing.assert_array_almost_equal(crys.cell2cc(cell), cryst_const) np.testing.assert_array_almost_equal(crys.cc2cell(cryst_const), cell) np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const)) np.testing.assert_almost_equal(volume, crys.volume_cell(cell)) np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)), cell) np.testing.assert_array_almost_equal( crys.cell2cc(crys.cc2cell(cryst_const)), cryst_const) # random # # volume : volume_cc() always returns positive values, whereas det() and # volume_cell() may return the volume with negative sign but correct # magnitude. # cell : A random cell does also have a random orientation in space. It # does NOT conform the usual convention: a along x, b in x-y plane. # However, the cryst_const and volume must be invariant. cell = np.random.rand(3, 3) cryst_const = crys.cell2cc(cell) volume = abs(np.linalg.det(cell)) np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const)) np.testing.assert_almost_equal(volume, abs(crys.volume_cell(cell))) # this must always fail for random cells try: np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)), cell) except AssertionError: pass # Here, we convert cryst_const to a *different* cell which conforms to the # orientation convention, and back to cryst_const. np.testing.assert_array_almost_equal( crys.cell2cc(crys.cc2cell(cryst_const)), cryst_const) # 3d cell = rand(100, 3, 3) cc = crys.cell2cc3d(cell, axis=0) vol_cell = np.abs(crys.volume_cell3d(cell, axis=0)) vol_cc = crys.volume_cc3d(cc, axis=0) assert crys.cell2cc3d(cell, axis=0).shape == (100, 6) assert crys.cc2cell3d(cc, axis=0).shape == (100, 3, 3) assert vol_cc.shape == (100, ) assert vol_cell.shape == (100, ) aaae(vol_cell, vol_cc) aaae(crys.cell2cc3d(crys.cc2cell3d(cc)), cc)
def test_cell_tools(): # test known values: simple cubic cell_a = 5.0 cell = np.identity(3)*cell_a volume = cell_a**3.0 cryst_const = np.array([cell_a]*3 + [90.0]*3) np.testing.assert_array_almost_equal(crys.cell2cc(cell), cryst_const) np.testing.assert_array_almost_equal(crys.cc2cell(cryst_const), cell) np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const)) np.testing.assert_almost_equal(volume, crys.volume_cell(cell)) np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)), cell) np.testing.assert_array_almost_equal(crys.cell2cc(crys.cc2cell(cryst_const)), cryst_const) # random # # volume : volume_cc() always returns positive values, whereas det() and # volume_cell() may return the volume with negative sign but correct # magnitude. # cell : A random cell does also have a random orientation in space. It # does NOT conform the usual convention: a along x, b in x-y plane. # However, the cryst_const and volume must be invariant. cell = np.random.rand(3,3) cryst_const = crys.cell2cc(cell) volume = abs(np.linalg.det(cell)) np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const)) np.testing.assert_almost_equal(volume, abs(crys.volume_cell(cell))) # this must always fail for random cells try: np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)), cell) except AssertionError: pass # Here, we convert cryst_const to a *different* cell which conforms to the # orientation convention, and back to cryst_const. np.testing.assert_array_almost_equal(crys.cell2cc(crys.cc2cell(cryst_const)), cryst_const) # 3d cell = rand(100,3,3) cc = crys.cell2cc3d(cell, axis=0) vol_cell = np.abs(crys.volume_cell3d(cell, axis=0)) vol_cc = crys.volume_cc3d(cc, axis=0) assert crys.cell2cc3d(cell, axis=0).shape == (100,6) assert crys.cc2cell3d(cc, axis=0).shape == (100,3,3) assert vol_cc.shape == (100,) assert vol_cell.shape == (100,) aaae(vol_cell, vol_cc) aaae(crys.cell2cc3d(crys.cc2cell3d(cc)), cc)
def test_coord_trans(): natoms = 10 cell = np.array([[3,0,0], [1.1,5,-0.04], [-0.33,1.5,7]]) cryst_const = crys.cell2cc(cell) coords_frac = rand(natoms,3) coords = crys.coord_trans(coords=coords_frac, old=cell, new=np.identity(3)) st = crys.Structure(coords=coords, cell=cell) assert np.allclose(coords_frac, st.coords_frac) st = crys.Structure(coords_frac=coords_frac, cell=cell) assert np.allclose(coords, st.coords) st = crys.Structure(coords=coords, cell=cell) assert np.allclose(cryst_const, st.cryst_const)
def test_struct(): natoms = 10 cell = np.array([[3, 0, 0], [1.1, 5, -0.04], [-0.33, 1.5, 7]]) cryst_const = crys.cell2cc(cell) coords_frac = rand(natoms, 3) coords = crys.coord_trans(coords=coords_frac, old=cell, new=np.identity(3)) symbols = ['H'] * natoms stress = rand(3, 3) forces = rand(natoms, 3) # Use ``cell`` instead of ``cryst_const` as input such that # atoms.get_cell() test passes (see below for why -- cell orientation) st = Structure(coords_frac=coords_frac, symbols=symbols, cell=cell, stress=stress, forces=forces, etot=42) # Test if all getters work. for name in st.attr_lst: print(name) st.try_set_attr(name) assert getattr(st, name) is not None, "attr None: %s" % name assert eval('st.get_%s()' % name) is not None, "getter returns None: %s" % name aaae(coords_frac, st.coords_frac) aaae(cryst_const, st.cryst_const) aaae(coords, st.coords) assert st.natoms == natoms st = Structure(coords_frac=coords_frac, symbols=symbols, cell=cell) aaae(coords, st.get_coords()) # Cell calculated from cryst_const has defined orientation in space which may be # different from the original `cell`, but the volume and underlying cryst_const # must be the same. st = Structure(coords_frac=coords_frac, symbols=symbols, cryst_const=cryst_const) assert st.get_cell() is not None np.testing.assert_almost_equal(crys.volume_cell(cell), crys.volume_cell(st.get_cell())) aaae(cryst_const, crys.cell2cc(st.get_cell())) # units st = Structure(coords_frac=coords_frac, cell=cell, symbols=symbols, stress=stress, forces=forces, units={ 'length': 2, 'forces': 3, 'stress': 4 }) aaae(2 * coords, st.coords) aaae(3 * forces, st.forces) aaae(4 * stress, st.stress) traj = crys.struct2traj(st) assert traj.is_traj # copy(): Assert everything has another memory location = is a new copy of # the object. IntTypes are NOT copied by copy.deepcopy(), which we use in # Structure.copy(), apparently b/c they are always automatically copied # before in-place operations. Same for float type. # # >>> a=10; b=a; print id(a); print id(b) # 36669152 # 36669152 # >>> a*=100; print id(a); print id(b) # 72538264 # 36669152 # >>> a # 100 # >>> b # 10 # # >>> a=[1,2,3]; b=a; print id(a); print id(b) # 72624320 # 72624320 # >>> a[0] = 44; print id(a); print id(b) # 72624320 # 72624320 # >>> a # [44, 2, 3] # >>> b # [44, 2, 3] st2 = st.copy() for name in st.attr_lst: val = getattr(st, name) if val is not None and not (isinstance(val, int) or \ isinstance(val, float)): val2 = getattr(st2, name) assert id(val2) != id(val) assert_all_types_equal(val2, val)
def test_traj(): natoms = 10 nstep = 100 cell = rand(nstep,3,3) stress = rand(nstep,3,3) forces = rand(nstep,natoms,3) etot = rand(nstep) cryst_const = crys.cell2cc3d(cell, axis=0) coords_frac = rand(nstep,natoms,3) coords = crys.coord_trans3d(coords=coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep,axis=0), axis=1, timeaxis=0) assert cryst_const.shape == (nstep, 6) assert coords.shape == (nstep,natoms,3) symbols = ['H']*natoms # automatically calculated: # coords # cell # pressure # velocity (from coords) # temperature (from ekin) # ekin (from velocity) traj = Trajectory(coords_frac=coords_frac, cell=cell, symbols=symbols, forces=forces, stress=stress, etot=etot, timestep=1, ) # Test if all getters work. for name in traj.attr_lst: print "test if getters work:", name traj.try_set_attr(name) assert getattr(traj, name) is not None, "attr None: %s" %name assert eval('traj.get_%s()'%name) is not None, "getter returns None: %s" %name print "test if getters work:", name, "... ok" aaae(coords_frac, traj.coords_frac) aaae(coords, traj.coords) aaae(cryst_const, traj.cryst_const) aaae(np.trace(stress, axis1=1, axis2=2)/3.0, traj.pressure) assert traj.coords.shape == (nstep,natoms,3) assert traj.cell.shape == (nstep,3,3) assert traj.velocity.shape == (nstep, natoms, 3) assert traj.temperature.shape == (nstep,) assert traj.ekin.shape == (nstep,) assert traj.nstep == nstep assert traj.natoms == natoms traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cell=cell) aaae(coords, traj.coords) # Cell calculated from cryst_const has defined orientation in space which may be # different from the original `cell`, but the volume and underlying cryst_const # must be the same. traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cryst_const=cryst_const) np.testing.assert_almost_equal(crys.volume_cell3d(cell), crys.volume_cell3d(traj.cell)) aaae(cryst_const, crys.cell2cc3d(traj.cell)) # extend arrays cell2d = rand(3,3) cc2d = crys.cell2cc(cell2d) traj = Trajectory(coords_frac=coords_frac, cell=cell2d, symbols=symbols) assert traj.cell.shape == (nstep,3,3) assert traj.cryst_const.shape == (nstep,6) for ii in range(traj.nstep): assert (traj.cell[ii,...] == cell2d).all() assert (traj.cryst_const[ii,:] == cc2d).all() traj = Trajectory(coords_frac=coords_frac, cryst_const=cc2d, symbols=symbols) assert traj.cell.shape == (nstep,3,3) assert traj.cryst_const.shape == (nstep,6) for ii in range(traj.nstep): assert (traj.cryst_const[ii,:] == cc2d).all() # units traj = Trajectory(coords_frac=coords_frac, cell=cell, symbols=symbols, stress=stress, forces=forces, units={'length': 2, 'forces': 3, 'stress': 4}) aaae(2*coords, traj.coords) aaae(3*forces, traj.forces) aaae(4*stress, traj.stress) # iterate, check if Structures are complete traj = Trajectory(coords=coords, symbols=symbols, cell=cell, forces=forces, stress=stress, etot=etot, timestep=1.0) for struct in traj: assert struct.is_struct, "st is not Structure" assert not struct.is_traj, "st is Trajectory" assert_attrs_not_none(struct) struct = traj[0] for attr_name in traj.attr_lst: if attr_name in struct.attrs_only_traj: msg = "tr[0] %s is not None" %attr_name assert getattr(struct,attr_name) is None, msg else: msg = "tr[0] %s is None" %attr_name assert getattr(struct,attr_name) is not None, msg # slices, return traj keys = traj.attr_lst[:] tsl = traj[10:80:2] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) tsl = traj[slice(10,80,2)] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) tsl = traj[np.s_[10:80:2]] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) assert tsl.is_traj # iteration over sliced traj tsl = traj[10:80:2] for x in tsl: pass for x in tsl.copy(): pass # repeat iter for i in range(2): cnt = 0 for st in traj: cnt += 1 assert cnt == nstep, "%i, %i" %(cnt, nstep) # copy traj2 = traj.copy() for name in traj.attr_lst: val = getattr(traj,name) if val is not None and not (isinstance(val, types.IntType) or \ isinstance(val, types.FloatType)): val2 = getattr(traj2,name) print "test copy:", name, type(val), type(val2) assert id(val2) != id(val) assert_all_types_equal(val2, val) assert_dict_with_all_types_equal(traj.__dict__, traj2.__dict__, keys=traj.attr_lst)
def test_traj(): natoms = 10 nstep = 100 cell = rand(nstep, 3, 3) stress = rand(nstep, 3, 3) forces = rand(nstep, natoms, 3) etot = rand(nstep) cryst_const = crys.cell2cc3d(cell, axis=0) coords_frac = rand(nstep, natoms, 3) coords = crys.coord_trans3d(coords=coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep, axis=0), axis=1, timeaxis=0) assert cryst_const.shape == (nstep, 6) assert coords.shape == (nstep, natoms, 3) symbols = ['H'] * natoms # automatically calculated: # coords # cell # pressure # velocity (from coords) # temperature (from ekin) # ekin (from velocity) traj = Trajectory( coords_frac=coords_frac, cell=cell, symbols=symbols, forces=forces, stress=stress, etot=etot, timestep=1, ) # Test if all getters work. for name in traj.attr_lst: print("test if getters work:", name) traj.try_set_attr(name) assert getattr(traj, name) is not None, "attr None: %s" % name assert eval('traj.get_%s()' % name) is not None, "getter returns None: %s" % name print("test if getters work:", name, "... ok") aaae(coords_frac, traj.coords_frac) aaae(coords, traj.coords) aaae(cryst_const, traj.cryst_const) aaae(np.trace(stress, axis1=1, axis2=2) / 3.0, traj.pressure) assert traj.coords.shape == (nstep, natoms, 3) assert traj.cell.shape == (nstep, 3, 3) assert traj.velocity.shape == (nstep, natoms, 3) assert traj.temperature.shape == (nstep, ) assert traj.ekin.shape == (nstep, ) assert traj.nstep == nstep assert traj.natoms == natoms traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cell=cell) aaae(coords, traj.coords) # Cell calculated from cryst_const has defined orientation in space which may be # different from the original `cell`, but the volume and underlying cryst_const # must be the same. traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cryst_const=cryst_const) np.testing.assert_almost_equal(crys.volume_cell3d(cell), crys.volume_cell3d(traj.cell)) aaae(cryst_const, crys.cell2cc3d(traj.cell)) # extend arrays cell2d = rand(3, 3) cc2d = crys.cell2cc(cell2d) traj = Trajectory(coords_frac=coords_frac, cell=cell2d, symbols=symbols) assert traj.cell.shape == (nstep, 3, 3) assert traj.cryst_const.shape == (nstep, 6) for ii in range(traj.nstep): assert (traj.cell[ii, ...] == cell2d).all() assert (traj.cryst_const[ii, :] == cc2d).all() traj = Trajectory(coords_frac=coords_frac, cryst_const=cc2d, symbols=symbols) assert traj.cell.shape == (nstep, 3, 3) assert traj.cryst_const.shape == (nstep, 6) for ii in range(traj.nstep): assert (traj.cryst_const[ii, :] == cc2d).all() # units traj = Trajectory(coords_frac=coords_frac, cell=cell, symbols=symbols, stress=stress, forces=forces, units={ 'length': 2, 'forces': 3, 'stress': 4 }) aaae(2 * coords, traj.coords) aaae(3 * forces, traj.forces) aaae(4 * stress, traj.stress) # iterate, check if Structures are complete traj = Trajectory(coords=coords, symbols=symbols, cell=cell, forces=forces, stress=stress, etot=etot, timestep=1.0) for struct in traj: assert struct.is_struct, "st is not Structure" assert not struct.is_traj, "st is Trajectory" assert_attrs_not_none(struct) struct = traj[0] for attr_name in traj.attr_lst: if attr_name in struct.attrs_only_traj: msg = "tr[0] %s is not None" % attr_name assert getattr(struct, attr_name) is None, msg else: msg = "tr[0] %s is None" % attr_name assert getattr(struct, attr_name) is not None, msg # slices, return traj keys = traj.attr_lst[:] tsl = traj[10:80:2] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) tsl = traj[slice(10, 80, 2)] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) tsl = traj[np.s_[10:80:2]] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) assert tsl.is_traj # iteration over sliced traj tsl = traj[10:80:2] for x in tsl: pass for x in tsl.copy(): pass # repeat iter for i in range(2): cnt = 0 for st in traj: cnt += 1 assert cnt == nstep, "%i, %i" % (cnt, nstep) # copy traj2 = traj.copy() for name in traj.attr_lst: val = getattr(traj, name) if val is not None and not (isinstance(val, int) or \ isinstance(val, float)): val2 = getattr(traj2, name) print("test copy:", name, type(val), type(val2)) assert id(val2) != id(val) assert_all_types_equal(val2, val) assert_dict_with_all_types_equal(traj.__dict__, traj2.__dict__, keys=traj.attr_lst)
def test_struct(): natoms = 10 cell = np.array([[3,0,0], [1.1,5,-0.04], [-0.33,1.5,7]]) cryst_const = crys.cell2cc(cell) coords_frac = rand(natoms,3) coords = crys.coord_trans(coords=coords_frac, old=cell, new=np.identity(3)) symbols = ['H']*natoms stress = rand(3,3) forces = rand(natoms,3) # Use ``cell`` instead of ``cryst_const` as input such that # atoms.get_cell() test passes (see below for why -- cell orientation) st = Structure(coords_frac=coords_frac, symbols=symbols, cell=cell, stress=stress, forces=forces, etot=42) # Test if all getters work. for name in st.attr_lst: print name st.try_set_attr(name) assert getattr(st, name) is not None, "attr None: %s" %name assert eval('st.get_%s()'%name) is not None, "getter returns None: %s" %name aaae(coords_frac, st.coords_frac) aaae(cryst_const, st.cryst_const) aaae(coords, st.coords) assert st.natoms == natoms st = Structure(coords_frac=coords_frac, symbols=symbols, cell=cell) aaae(coords, st.get_coords()) # Cell calculated from cryst_const has defined orientation in space which may be # different from the original `cell`, but the volume and underlying cryst_const # must be the same. st = Structure(coords_frac=coords_frac, symbols=symbols, cryst_const=cryst_const) assert st.get_cell() is not None np.testing.assert_almost_equal(crys.volume_cell(cell), crys.volume_cell(st.get_cell())) aaae(cryst_const, crys.cell2cc(st.get_cell())) # units st = Structure(coords_frac=coords_frac, cell=cell, symbols=symbols, stress=stress, forces=forces, units={'length': 2, 'forces': 3, 'stress': 4}) aaae(2*coords, st.coords) aaae(3*forces, st.forces) aaae(4*stress, st.stress) traj = crys.struct2traj(st) assert traj.is_traj # copy(): Assert everything has another memory location = is a new copy of # the object. IntTypes are NOT copied by copy.deepcopy(), which we use in # Structure.copy(), apparently b/c they are always automatically copied # before in-place operations. Same for float type. # # >>> a=10; b=a; print id(a); print id(b) # 36669152 # 36669152 # >>> a*=100; print id(a); print id(b) # 72538264 # 36669152 # >>> a # 100 # >>> b # 10 # # >>> a=[1,2,3]; b=a; print id(a); print id(b) # 72624320 # 72624320 # >>> a[0] = 44; print id(a); print id(b) # 72624320 # 72624320 # >>> a # [44, 2, 3] # >>> b # [44, 2, 3] st2 = st.copy() for name in st.attr_lst: val = getattr(st,name) if val is not None and not (isinstance(val, types.IntType) or \ isinstance(val, types.FloatType)): val2 = getattr(st2,name) assert id(val2) != id(val) assert_all_types_equal(val2, val)