def test_general_array_atom_quotient():
sym = sym_quotient_translational_00_xyz()
callbacks = symmetry.GeneralArrayCallbacks(['atom'])
disp_atoms, disp_carts, disp_values = zip(*[
DispData(0, [ 0.1, 0, 0], data=np.array([ 1., 2., 3.])),
DispData(0, [-0.1, 0, 0], data=np.array([-1., -2., -3.])),
])
derivs = symmetry.expand_derivs_by_symmetry(
callbacks=callbacks, disp_atoms=disp_atoms, disp_carts=disp_carts, disp_values=disp_values,
oper_cart_rots=sym.oper_cart_rots, oper_perms=sym.oper_perms, quotient_perms=sym.quotient_perms,
)
derivs = np.array(derivs.tolist())
assert np.allclose(derivs, np.array([[
[10, 20, 30], # derivative w.r.t. atom 0 x
[10, 20, 30], # derivative w.r.t. atom 0 y
[10, 20, 30], # derivative w.r.t. atom 0 z
], [
[30, 10, 20], # derivative w.r.t. atom 1 x
[30, 10, 20], # derivative w.r.t. atom 1 y
[30, 10, 20], # derivative w.r.t. atom 1 z
], [
[20, 30, 10], # derivative w.r.t. atom 2 x
[20, 30, 10], # derivative w.r.t. atom 2 y
[20, 30, 10], # derivative w.r.t. atom 2 z
]]))
def test_pure_translation():
for (description, sym) in [
('SEPARATE TRANSLATIONS', sym_quotient_translational_010101()),
('EMBEDDED TRANSLATIONS', sym_embedded_translational_010101()),
]:
print(f'TRYING {description}')
callbacks = symmetry.GeneralArrayCallbacks([])
disp_atoms, disp_carts, disp_values = zip(*[
DispData(0, [ 0.1, 0, 0], data=np.array( 1.)),
DispData(0, [-0.1, 0, 0], data=np.array(-1.)),
DispData(0, [ 0, 0.1, 0], data=np.array( 2.)),
DispData(0, [ 0, -0.1, 0], data=np.array(-2.)),
DispData(0, [ 0, 0, 0.1], data=np.array( 3.)),
DispData(0, [ 0, 0, -0.1], data=np.array(-3.)),
DispData(1, [ 0.1, 0, 0], data=np.array( 4.)),
DispData(1, [-0.1, 0, 0], data=np.array(-4.)),
DispData(1, [ 0, 0.1, 0], data=np.array( 5.)),
DispData(1, [ 0, -0.1, 0], data=np.array(-5.)),
DispData(1, [ 0, 0, 0.1], data=np.array( 6.)),
DispData(1, [ 0, 0, -0.1], data=np.array(-6.)),
])
derivs = symmetry.expand_derivs_by_symmetry(
callbacks=callbacks, disp_atoms=disp_atoms, disp_carts=disp_carts, disp_values=disp_values,
oper_cart_rots=sym.oper_cart_rots, oper_perms=sym.oper_perms, quotient_perms=sym.quotient_perms,
)
derivs = np.array(derivs.tolist())
assert np.allclose(derivs, np.array([
[10, 20, 30], # gradient w.r.t. atom 0
[40, 50, 60], # gradient w.r.t. atom 1
[10, 20, 30], # gradient w.r.t. atom 2
[40, 50, 60], # gradient w.r.t. atom 3
[10, 20, 30], # gradient w.r.t. atom 4
[40, 50, 60], # gradient w.r.t. atom 5
]))
def test_general_array_atom():
sym = sym_xyz_3_atom()
callbacks = symmetry.GeneralArrayCallbacks(['atom'])
disp_atoms, disp_carts, disp_values = zip(*[
# because the operator is no longer in the site symmetry, we need more disps
DispData(0, [ 0.1, 0, 0], data=np.array([ 2., 3., 4.])),
DispData(0, [-0.1, 0, 0], data=np.array([-2., -3., -4.])),
DispData(0, [ 0, 0.1, 0], data=np.array([ 5., 6., 7.])),
DispData(0, [ 0, -0.1, 0], data=np.array([-5., -6., -7.])),
DispData(0, [ 0, 0, 0.1], data=np.array([ 8., 9., 10.])),
DispData(0, [ 0, 0, -0.1], data=np.array([-8., -9., -10.])),
])
print(sym.oper_perms)
derivs = symmetry.expand_derivs_by_symmetry(
callbacks=callbacks, disp_atoms=disp_atoms, disp_carts=disp_carts, disp_values=disp_values,
oper_cart_rots=sym.oper_cart_rots, oper_perms=sym.oper_perms, quotient_perms=sym.quotient_perms,
)
derivs = np.array(derivs.tolist())
assert np.allclose(derivs, np.array([[
[20, 30, 40], # deriv w.r.t. atom 0 x
[50, 60, 70], # deriv w.r.t. atom 0 y
[80, 90, 100], # deriv w.r.t. atom 0 z
], [
[100, 80, 90], # deriv w.r.t. atom 1 x
[ 40, 20, 30], # deriv w.r.t. atom 1 y
[ 70, 50, 60], # deriv w.r.t. atom 1 z
], [
[60, 70, 50], # deriv w.r.t. atom 2 x
[90, 100, 80], # deriv w.r.t. atom 2 y
[30, 40, 20], # deriv w.r.t. atom 2 z
]]))
def test_gpaw_grid_C4_z():
N_c = (5, 5, 3) # grid dimensions
nspins = 1
cart_rot_generator = np.array([[0, -1, 0], [1, 0, 0], [0, 0, 1]])
perm_generator = np.array([3, 0, 1, 2])
op_scc_generator = np.array([[0, 1, 0], [-1, 0, 0], [0, 0, 1]]) # gpaw's op_scc is transposed (operates on row vectors)
oper_cart_rots = test_utils.cyclic_group(cart_rot_generator, compose_rot, make_rot_hashable)
oper_perms = test_utils.cyclic_group(perm_generator, compose_perm, make_perm_hashable)
op_scc = test_utils.cyclic_group(op_scc_generator, compose_rot_T, make_rot_hashable)
ft_sc = np.zeros((4, 3))
quotient_perms = None
supercell = (1, 1, 1)
callbacks = symmetry.GpawLcaoVTCallbacks__from_parts(nspins=nspins, N_c=N_c, op_scc=op_scc, ft_sc=ft_sc, supercell=supercell, pbc_c=True)
def data_pointed(index_tuple, value):
""" Creates Vt data with a single nonzero value. """
array = np.zeros((nspins,) + N_c)
array[(0,) + index_tuple] = value
return array
data_zero = np.zeros((nspins,) + N_c)
disp_atoms, disp_carts, disp_values = zip(*[
DispData(0, [ 0.1, 0, 0], data=data_pointed((2, 0, 2), 1.0)),
DispData(0, [-0.1, 0, 0], data=data_pointed((2, 0, 2), -1.0)),
DispData(0, [ 0, 0.1, 0], data=data_zero),
DispData(0, [ 0, -0.1, 0], data=data_zero),
DispData(0, [ 0, 0, 0.1], data=data_zero),
DispData(0, [ 0, 0, -0.1], data=data_zero),
])
derivs = symmetry.expand_derivs_by_symmetry(
callbacks=callbacks, disp_atoms=disp_atoms, disp_carts=disp_carts, disp_values=disp_values,
oper_cart_rots=oper_cart_rots, oper_perms=oper_perms, quotient_perms=quotient_perms,
)
derivs = np.array(derivs.tolist())
expected = np.array([[
data_pointed((2, 0, 2), 10.0), # derivative w.r.t. atom 0 x
data_zero, # derivative w.r.t. atom 0 y
data_zero, # derivative w.r.t. atom 0 z
], [
data_zero, # derivative w.r.t. atom 1 x
data_pointed((0, 2, 2), 10.0), # derivative w.r.t. atom 1 y
data_zero, # derivative w.r.t. atom 1 z
], [
data_pointed(((-2)%5, 0, 2), -10.0), # derivative w.r.t. atom 2 x
data_zero, # derivative w.r.t. atom 2 y
data_zero, # derivative w.r.t. atom 2 z
], [
data_zero, # derivative w.r.t. atom 3 x
data_pointed((0, (-2)%5, 2), -10.0), # derivative w.r.t. atom 3 y
data_zero, # derivative w.r.t. atom 3 z
]])
print('actual', list(zip(*np.where(derivs))))
print('expected', list(zip(*np.where(expected))))
np.testing.assert_allclose(derivs, expected)
def test_general_array_vec():
sym = sym_xyz_1_atom()
callbacks = symmetry.GeneralArrayCallbacks(['cart'])
disp_atoms, disp_carts, disp_values = zip(*[
DispData(0, [ 0.1, 0, 0], data=np.array([ 1., 0, 0])),
DispData(0, [-0.1, 0, 0], data=np.array([-1., 0, 0])),
])
derivs = symmetry.expand_derivs_by_symmetry(
callbacks=callbacks, disp_atoms=disp_atoms, disp_carts=disp_carts, disp_values=disp_values,
oper_cart_rots=sym.oper_cart_rots, oper_perms=sym.oper_perms, quotient_perms=sym.quotient_perms,
)
derivs = np.array(derivs.tolist())
assert np.allclose(derivs, np.array([[
[10, 0, 0],
[0, 10, 0],
[0, 0, 10],
]]))
def do_elph_symmetry(
data_subdir: str,
params_fd: dict,
supercell,
all_displacements: tp.Iterable[AseDisplacement],
symmetry_type: tp.Optional[str],
):
atoms = Cluster(ase.build.bulk('C'))
# a supercell exactly like ElectronPhononCoupling makes
supercell_atoms = atoms * supercell
quotient_perms = list(
interop.ase_repeat_translational_symmetry_perms(len(atoms), supercell))
# Make sure the grid matches our calculations (we repeated the grid of the groundstate)
params_fd = copy.deepcopy(params_fd)
params_fd['gpts'] = GPAW('gs.gpw').wfs.gd.N_c * list(supercell)
if 'h' in params_fd:
del params_fd['h']
wfs_with_sym = get_wfs_with_sym(params_fd=params_fd,
supercell_atoms=supercell_atoms,
symmetry_type=symmetry_type)
calc_fd = GPAW(**params_fd)
# GPAW displaces the center cell for some reason instead of the first cell
elph = ElectronPhononCoupling(atoms,
calc=calc_fd,
supercell=supercell,
calculate_forces=True)
displaced_cell_index = elph.offset
del elph # just showing that we don't use these anymore
del calc_fd
get_displaced_index = lambda prim_atom: displaced_cell_index * len(
atoms) + prim_atom
all_displacements = list(all_displacements)
disp_atoms = [get_displaced_index(disp.atom) for disp in all_displacements]
disp_carts = [
disp.cart_displacement(DISPLACEMENT_DIST) for disp in all_displacements
]
disp_values = [
read_elph_input(data_subdir, disp) for disp in all_displacements
]
full_Vt = np.empty((len(supercell_atoms), 3) + disp_values[0][0].shape)
full_dH = np.empty((len(supercell_atoms), 3), dtype=object)
full_forces = np.empty((len(supercell_atoms), 3) + disp_values[0][2].shape)
lattice = supercell_atoms.get_cell()[...]
oper_cart_rots = interop.gpaw_op_scc_to_cart_rots(
wfs_with_sym.kd.symmetry.op_scc, lattice)
if world.rank == 0:
full_values = symmetry.expand_derivs_by_symmetry(
disp_atoms, # disp -> atom
disp_carts, # disp -> 3-vec
disp_values, # disp -> T (displaced value, optionally minus equilibrium value)
elph_callbacks(wfs_with_sym, supercell), # how to work with T
oper_cart_rots, # oper -> 3x3
oper_perms=wfs_with_sym.kd.symmetry.a_sa, # oper -> atom' -> atom
quotient_perms=quotient_perms,
)
for a in range(len(full_values)):
for c in range(3):
full_Vt[a][c] = full_values[a][c][0]
full_dH[a][c] = full_values[a][c][1]
full_forces[a][c] = full_values[a][c][2]
else:
# FIXME
# the symmetry part is meant to be done in serial but we should return back to
# our original parallel state after it...
pass
return full_Vt, full_dH, full_forces