def test_uig_eval_spline_0d_random():
cs = get_cosine_spline()
for i in xrange(15):
origin = np.random.uniform(-1, 1, 3)
grid_cell = get_random_cell(0.2, 3)
shape = np.random.randint(10, 20, 3)
pbc = np.array([0, 0, 0])
uig = UniformGrid(origin, grid_cell.rvecs, shape, pbc)
center = np.random.uniform(0, 2, 3)
output1 = np.zeros(uig.shape)
uig.eval_spline(cs, center, output1)
x, y, z = np.indices(shape)
x = x.ravel()
y = y.ravel()
z = z.ravel()
rvecs = grid_cell.rvecs
points = np.outer(x, rvecs[0]) + np.outer(y, rvecs[1]) + np.outer(z, rvecs[2])
points += origin
distances = np.sqrt(((points-center)**2).sum(axis=1))
output2 = cs(distances)
output2.shape = shape
assert abs(output1 - output2).max() < 1e-10
def test_cell():
for i in xrange(12):
chk = h5.File('horton.test.test_checkpoint.test_cell_%i' % i, driver='core', backing_store=False)
cell1 = get_random_cell(1.0, i%4)
coordinates = np.random.uniform(-1, 1, (5, 3))
numbers = np.random.randint(1, 11, 5)
sys1 = System(coordinates, numbers, cell=cell1, chk=chk)
del sys1
sys2 = System.from_file(chk)
assert (sys2.cell.rvecs == cell1.rvecs).all()
chk.close()
def setup_ranges_rcut(nvec):
a = 10**np.random.uniform(-1, 1)
cell = get_random_cell(a, nvec)
origin = np.random.uniform(-3 * a, 3 * a, 3)
center = np.random.uniform(-3 * a, 3 * a, 3)
rcut = np.random.uniform(0.2 * a, 5 * a)
ranges_begin, ranges_end = cell.get_ranges_rcut(origin - center, rcut)
ranges_low = ranges_begin - 2
ranges_high = ranges_end + 2
return cell, origin, center, rcut, ranges_begin, ranges_end, ranges_low, ranges_high
def test_load_dump_consistency():
sys0 = System.from_file(context.get_fn('test/water_element.xyz'))
sys0._cell = get_random_cell(5.0, 3)
with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
sys0.to_file('%s/POSCAR' % dn)
sys1 = System.from_file('%s/POSCAR' % dn)
assert (sys1.numbers == [8, 1, 1]).all()
assert abs(sys0.coordinates[1] - sys1.coordinates[0]).max() < 1e-10
assert abs(sys0.coordinates[0] - sys1.coordinates[1]).max() < 1e-10
assert abs(sys0.coordinates[2] - sys1.coordinates[2]).max() < 1e-10
assert abs(sys0.cell.rvecs - sys1.cell.rvecs).max() < 1e-10
def setup_ranges_rcut(nvec):
a = 10**np.random.uniform(-1, 1)
cell = get_random_cell(a, nvec)
origin = np.random.uniform(-3*a, 3*a, 3)
center = np.random.uniform(-3*a, 3*a, 3)
rcut = np.random.uniform(0.2*a, 5*a)
ranges_begin, ranges_end = cell.get_ranges_rcut(origin-center, rcut)
ranges_low = ranges_begin-2
ranges_high = ranges_end+2
return cell, origin, center, rcut, ranges_begin, ranges_end, ranges_low, ranges_high
def test_load_dump_consistency():
sys0 = System.from_file(context.get_fn('test/water_element.xyz'))
sys0._cell = get_random_cell(5.0, 3)
with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
sys0.to_file('%s/POSCAR' % dn)
sys1 = System.from_file('%s/POSCAR' % dn)
assert (sys1.numbers == [8, 1, 1]).all()
assert abs(sys0.coordinates[1] - sys1.coordinates[0]).max() < 1e-10
assert abs(sys0.coordinates[0] - sys1.coordinates[1]).max() < 1e-10
assert abs(sys0.coordinates[2] - sys1.coordinates[2]).max() < 1e-10
assert abs(sys0.cell.rvecs - sys1.cell.rvecs).max() < 1e-10
def setup_select_inside(nvec):
a = 10**np.random.uniform(-1, 1)
grid_cell = get_random_cell(a, nvec)
nrep = 40
shape = np.array([nrep] * nvec)
pbc = np.random.randint(0, 2, nvec)
origin = np.random.uniform(-0.5 * nrep * a, 1.5 * nrep * a, 3)
center = np.random.uniform(0, nrep * a, 3)
rcut = np.random.uniform(0.1 * nrep * a)
ranges_begin, ranges_end = grid_cell.get_ranges_rcut(origin - center, rcut)
return grid_cell, origin, center, rcut, shape, pbc, ranges_begin, ranges_end
def test_symmetry_attrs():
generators = np.random.uniform(-1, 1, (5, 3, 4))
fracs = np.random.uniform(0, 1, (4, 3))
numbers = np.array([1, 6, 6, 1])
cell = get_random_cell(10.0, 3)
s = Symmetry('boo', generators, fracs, numbers, cell)
assert (s.labels == ['H0', 'C1', 'C2', 'H3']).all()
s = Symmetry('boo', generators, fracs, numbers, cell, ['q', 'w', 'e', 'r'])
assert s.name == 'boo'
assert (s.generators == generators).all()
assert s.natom == 4
assert s.fracs is s.fracs
assert s.numbers is numbers
assert s.cell is cell
def test_load_dump_consistency():
mol0 = IOData.from_file(context.get_fn('test/water_element.xyz'))
mol0.cell = get_random_cell(5.0, 3)
with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
mol0.to_file('%s/POSCAR' % dn)
mol1 = IOData.from_file('%s/POSCAR' % dn)
assert mol0.title == mol1.title
assert (mol1.numbers == [8, 1, 1]).all()
assert abs(mol0.coordinates[1] - mol1.coordinates[0]).max() < 1e-10
assert abs(mol0.coordinates[0] - mol1.coordinates[1]).max() < 1e-10
assert abs(mol0.coordinates[2] - mol1.coordinates[2]).max() < 1e-10
assert abs(mol0.cell.rvecs - mol1.cell.rvecs).max() < 1e-10
def test_symmetry_attrs():
generators = np.random.uniform(-1, 1, (5, 3, 4))
fracs = np.random.uniform(0, 1, (4, 3))
numbers = np.array([1, 6, 6, 1])
cell = get_random_cell(10.0, 3)
s = Symmetry('boo', generators, fracs, numbers, cell)
assert (s.labels == ['H0', 'C1', 'C2', 'H3']).all()
s = Symmetry('boo', generators, fracs, numbers, cell, ['q', 'w', 'e', 'r'])
assert s.name == 'boo'
assert (s.generators == generators).all()
assert s.natom == 4
assert s.fracs is s.fracs
assert s.numbers is numbers
assert s.cell is cell
def test_symmetry_attrs():
generators = np.random.uniform(-1, 1, (5, 3, 4))
fracs = np.random.uniform(0, 1, (4, 3))
numbers = np.array([1, 6, 6, 1])
cell = get_random_cell(10.0, 3)
s = Symmetry("boo", generators, fracs, numbers, cell)
assert (s.labels == ["H0", "C1", "C2", "H3"]).all()
s = Symmetry("boo", generators, fracs, numbers, cell, ["q", "w", "e", "r"])
assert s.name == "boo"
assert (s.generators == generators).all()
assert s.natom == 4
assert s.fracs is s.fracs
assert s.numbers is numbers
assert s.cell is cell
def test_pair_ewald3d_invariance_rcut():
np.random.seed(0)
alpha_scale = 4.5
gcut_scale = 1.5
delta = np.random.normal(0, 1, 3)
delta /= np.linalg.norm(delta)
cell = get_random_cell(1.0, 3)
results = []
for rcut in np.arange(10.0, 20.001, 1.0):
alpha = alpha_scale / rcut
gcut = gcut_scale * alpha
results.append(pair_ewald(delta, cell, rcut, alpha, gcut))
results = np.array(results)
assert abs(results - results.mean()).max() < 1e-7
def test_load_dump_consistency():
mol0 = IOData.from_file(context.get_fn('test/water_element.xyz'))
mol0.cell = get_random_cell(5.0, 3)
with tmpdir('horton.io.test.test_vasp.test_load_dump_consistency') as dn:
mol0.to_file('%s/POSCAR' % dn)
mol1 = IOData.from_file('%s/POSCAR' % dn)
assert mol0.title == mol1.title
assert (mol1.numbers == [8, 1, 1]).all()
assert abs(mol0.coordinates[1] - mol1.coordinates[0]).max() < 1e-10
assert abs(mol0.coordinates[0] - mol1.coordinates[1]).max() < 1e-10
assert abs(mol0.coordinates[2] - mol1.coordinates[2]).max() < 1e-10
assert abs(mol0.cell.rvecs - mol1.cell.rvecs).max() < 1e-10
def test_pair_ewald3d_invariance_rcut():
np.random.seed(0)
alpha_scale = 4.5
gcut_scale = 1.5
delta = np.random.normal(0, 1, 3)
delta /= np.linalg.norm(delta)
cell = get_random_cell(1.0, 3)
results = []
for rcut in np.arange(10.0, 20.001, 1.0):
alpha = alpha_scale/rcut
gcut = gcut_scale*alpha
results.append(pair_ewald(delta, cell, rcut, alpha, gcut))
results = np.array(results)
assert abs(results - results.mean()).max() < 1e-7
def setup_select_inside(nvec):
a = 10**np.random.uniform(-1, 1)
grid_cell = get_random_cell(a, nvec)
nrep = 40
shape = np.array([nrep]*nvec)
pbc = np.random.randint(0, 2, nvec)
origin = np.random.uniform(-0.5*nrep*a, 1.5*nrep*a, 3)
center = np.random.uniform(0, nrep*a, 3)
rcut = np.random.uniform(0.1*nrep*a)
ranges_begin, ranges_end = grid_cell.get_ranges_rcut(origin-center, rcut)
return grid_cell, origin, center, rcut, shape, pbc, ranges_begin, ranges_end
def test_eval_spline_grid_3d_random():
npoint = 10
for i in xrange(10):
cell = get_random_cell(1.0, 3)
rvecs = cell.rvecs
points = np.dot(np.random.normal(-2, 3, (npoint, 3)), rvecs)
g = IntGrid(points, np.random.normal(0, 1.0, npoint))
cs = get_cosine_spline()
output1 = np.zeros(npoint)
center1 = np.random.uniform(-10, 10, 3)
g.eval_spline(cs, center1, output1, cell)
output2 = np.zeros(npoint)
center2 = center1 + np.dot(np.random.randint(-3, 3, 3), rvecs)
g.eval_spline(cs, center2, output2, cell)
assert abs(output1 - output2).max() < 1e-10
def test_eval_spline_grid_3d_random():
npoint = 10
for i in xrange(10):
cell = get_random_cell(1.0, 3)
rvecs = cell.rvecs
points = np.dot(np.random.normal(-2, 3, (npoint,3)), rvecs)
g = IntGrid(points, np.random.normal(0, 1.0, npoint))
cs = get_cosine_spline()
output1 = np.zeros(npoint)
center1 = np.random.uniform(-10, 10, 3)
g.eval_spline(cs, center1, output1, cell)
output2 = np.zeros(npoint)
center2 = center1 + np.dot(np.random.randint(-3, 3, 3), rvecs)
g.eval_spline(cs, center2, output2, cell)
assert abs(output1 - output2).max() < 1e-10
def test_uig_eval_spline_3d_random():
cs = get_cosine_spline()
for i in xrange(30):
origin = np.random.uniform(-1, 1, 3)
grid_cell = get_random_cell(0.3, 3)
shape = np.random.randint(10, 20, 3)
pbc = np.array([1, 1, 1])
uig = UniformGrid(origin, grid_cell.rvecs, shape, pbc)
rvecs = uig.get_cell().rvecs
output1 = np.zeros(uig.shape)
center1 = np.random.uniform(-3, 3, 3)
uig.eval_spline(cs, center1, output1)
output2 = np.zeros(uig.shape)
center2 = center1 + np.dot(np.random.randint(-3, 3, 3), rvecs)
uig.eval_spline(cs, center2, output2)
assert abs(output1 - output2).max() < 1e-10
def test_eval_spline_grid_add_random():
npoint = 10
cs = get_cosine_spline()
for i in xrange(10):
cell = get_random_cell(1.0, np.random.randint(4))
points = np.random.normal(-2, 3, (npoint,3))
g = IntGrid(points, np.random.normal(0, 1.0, npoint))
output1 = np.zeros(npoint)
center1 = np.random.uniform(-2, 2, 3)
g.eval_spline(cs, center1, output1, cell)
output2 = np.zeros(npoint)
center2 = np.random.uniform(-2, 2, 3)
g.eval_spline(cs, center2, output2, cell)
output3 = np.zeros(npoint)
g.eval_spline(cs, center1, output3, cell)
g.eval_spline(cs, center2, output3, cell)
assert abs(output1 + output2 - output3).max() < 1e-10
def test_uig_eval_spline_1d_random():
cs = get_cosine_spline()
for i in xrange(15):
origin = np.random.uniform(-1, 1, 3)
grid_cell = get_random_cell(0.2, 3)
shape = np.random.randint(10, 20, 3)
pbc = np.array([0, 0, 0])
pbc[np.random.randint(3)] = 1
uig = UniformGrid(origin, grid_cell.rvecs, shape, pbc)
tmp = uig.shape*pbc
rvecs = grid_cell.rvecs*tmp.reshape(-1,1)
output1 = np.zeros(uig.shape)
center1 = np.random.uniform(0, 1, 3)
uig.eval_spline(cs, center1, output1)
output2 = np.zeros(uig.shape)
center2 = center1 + np.dot(np.random.randint(-3, 3, 3), rvecs)
uig.eval_spline(cs, center2, output2)
assert abs(output1 - output2).max() < 1e-10
def test_eval_spline_grid_add_random():
npoint = 10
cs = get_cosine_spline()
for i in xrange(10):
cell = get_random_cell(1.0, np.random.randint(4))
points = np.random.normal(-2, 3, (npoint, 3))
g = IntGrid(points, np.random.normal(0, 1.0, npoint))
output1 = np.zeros(npoint)
center1 = np.random.uniform(-2, 2, 3)
g.eval_spline(cs, center1, output1, cell)
output2 = np.zeros(npoint)
center2 = np.random.uniform(-2, 2, 3)
g.eval_spline(cs, center2, output2, cell)
output3 = np.zeros(npoint)
g.eval_spline(cs, center1, output3, cell)
g.eval_spline(cs, center2, output3, cell)
assert abs(output1 + output2 - output3).max() < 1e-10
def test_uig_eval_spline_add_random():
cs = get_cosine_spline()
for i in xrange(20):
origin = np.random.uniform(-1, 1, 3)
grid_cell = get_random_cell(0.2, 3)
shape = np.random.randint(10, 20, 3)
pbc = np.random.randint(0, 2, 3).astype(int)
uig = UniformGrid(origin, grid_cell.rvecs, shape, pbc)
output1 = np.zeros(uig.shape)
center1 = np.random.uniform(0, 1, 3)
uig.eval_spline(cs, center1, output1)
output2 = np.zeros(uig.shape)
center2 = np.random.uniform(0, 1, 3)
uig.eval_spline(cs, center2, output2)
output3 = np.zeros(uig.shape)
uig.eval_spline(cs, center1, output3)
uig.eval_spline(cs, center2, output3)
assert abs(output1 + output2 - output3).max() < 1e-10
def test_from_parameters3():
for i in xrange(10):
cell0 = get_random_cell(1.0, 3)
check_from_parameters(cell0)
def test_from_parameters3():
for i in xrange(10):
cell0 = get_random_cell(1.0, 3)
check_from_parameters(cell0)