def test_bias_multiple_terms():
system = get_system_quartz()
part = ForcePartBias(system)
# Harmonic volume bias
cv0 = CVVolume(system)
K, q0 = 0.4, 0.9 * system.cell.volume
bias0 = HarmonicBias(K, q0, cv0)
part.add_term(bias0)
# Cosine of bending angle
cv1 = BendAngle(0, 1, 2)
m, a, phi0 = 1, 2.0, np.pi / 4.0
bias1 = Cosine(m, a, phi0, cv1)
part.add_term(bias1)
# Check energy
e = part.compute()
contributions = part.get_term_energies()
assert np.abs(e - np.sum(contributions)) < 1e-5
assert contributions[0] == bias0.compute()
# Check derivatives
check_gpos_part(system, part)
check_vtens_part(system, part)
# Check collective variable values
cv_values0 = part.get_term_cv_values(0)
assert cv_values0.shape[0] == 1
assert cv_values0[0] == cv0.compute()
cv_values1 = part.get_term_cv_values(1)
assert cv_values1.shape[0] == 1
delta0 = system.pos[1] - system.pos[0]
system.cell.mic(delta0)
delta2 = system.pos[1] - system.pos[2]
system.cell.mic(delta2)
phi = bend_angle([delta0, np.zeros(3, float), delta2])[0]
assert np.abs(cv_values1[0] - phi) < 1e-5
def test_nlist_quartz_20A():
system = get_system_quartz()
nlist = NeighborList(system)
rcut = 20*angstrom
nlist.request_rcut(rcut)
nlist.update()
nlist.check()
def test_bias_gaussianhills_quartz():
system = get_system_quartz()
# Volume
cv0 = CVVolume(system)
q0 = system.cell.volume
# Distance between 2 and 8
cv1 = CVInternalCoordinate(system, Bond(2, 8))
delta = system.pos[2] - system.pos[8]
system.cell.mic(delta)
q1 = np.linalg.norm(delta)
# Widths of the Gaussians
sigmas = np.array([10.0 * angstrom**3, 0.2 * angstrom])
bias = GaussianHills([cv0, cv1], sigmas)
# No hills added, energy should be zero
e = bias.compute()
assert e == 0.0
# Add one hill
K0 = 5 * kjmol
bias.add_hill(np.array([q0 + sigmas[0], q1 - 2 * sigmas[1]]), K0)
e = bias.compute()
assert np.abs(e - K0 * np.exp(-2.5)) < 1e-10
# Add another hill
K1 = 2 * kjmol
bias.add_hill(np.array([q0 - 3 * sigmas[0], q1 - 1 * sigmas[1]]), K1)
e = bias.compute()
assert np.abs(e - K0 * np.exp(-2.5) - K1 * np.exp(-5.0)) < 1e-10
# Test derivatives
bias.add_hill(np.array([q0 - 3 * sigmas[0], q1 - 1 * sigmas[1]]), K1)
part = ForcePartBias(system)
part.add_term(bias)
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_vlist_quartz_bonds():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
for i, j in system.bonds:
vlist.add_term(Harmonic(2.3, 3.04 + 0.1 * i, Bond(i, j)))
assert dlist.ndelta == len(system.bonds)
assert iclist.nic == len(system.bonds)
assert vlist.nv == len(system.bonds)
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
counter = 0
for i, j in system.bonds:
delta = system.pos[i] - system.pos[j]
system.cell.mic(delta)
d = np.linalg.norm(delta)
check_term = 0.5 * 2.3 * (d - 3.04 - 0.1 * i)**2
assert abs(check_term - vlist.vtab[counter]['energy']) < 1e-10
check_energy += check_term
counter += 1
assert abs(energy - check_energy) < 1e-8
def test_vlist_quartz_morse():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
for i, j in system.bonds:
vlist.add_term(Morse(2.3+i, 0.5, 2.0, Bond(i, j)))
assert dlist.ndelta == len(system.bonds)
assert iclist.nic == len(system.bonds)
assert vlist.nv == len(system.bonds)
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
counter = 0
for i, j in system.bonds:
delta = system.pos[i] - system.pos[j]
system.cell.mic(delta)
d = np.linalg.norm(delta)
check_term = (2.3+i)*(np.exp(-2*0.5*(d-2.0)) - 2.0*np.exp(-0.5*(d-2.0)))
assert abs(check_term - vlist.vtab[counter]['energy']) < 1e-10
check_energy += check_term
counter += 1
assert abs(energy - check_energy) < 1e-8
def test_nlist_quartz_20A():
system = get_system_quartz()
nlist = NeighborList(system)
rcut = 20 * angstrom
nlist.request_rcut(rcut)
nlist.update()
nlist.check()
def test_vlist_quartz_bend_angle():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
angles = []
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
vlist.add_term(Harmonic(1.5, 2.0+0.01*i2, BendAngle(i0, i1, i2)))
angles.append((i0, i1, i2))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
for row, (i0, i1, i2) in enumerate(angles):
delta0 = system.pos[i0] - system.pos[i1]
system.cell.mic(delta0)
delta2 = system.pos[i2] - system.pos[i1]
system.cell.mic(delta2)
angle = bend_angle([delta0, np.zeros(3, float), delta2])[0]
check_energy += 0.5*1.5*(angle-(2.0+0.01*i2))**2
assert abs(energy - check_energy) < 1e-8
def test_ewald_gpos_vtens_corr_quartz():
system = get_system_quartz().supercell(2, 2, 2)
scalings = Scalings(system, np.random.uniform(0.1, 0.9), np.random.uniform(0.1, 0.9), np.random.uniform(0.1, 0.9))
for alpha in 0.1, 0.2, 0.5:
part_ewald_corr = ForcePartEwaldCorrection(system, alpha, scalings)
check_gpos_part(system, part_ewald_corr)
check_vtens_part(system, part_ewald_corr)
def test_vlist_quartz_bonds():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
for i, j in system.bonds:
vlist.add_term(Harmonic(2.3, 3.04+0.1*i, Bond(i, j)))
assert dlist.ndelta == len(system.bonds)
assert iclist.nic == len(system.bonds)
assert vlist.nv == len(system.bonds)
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
counter = 0
for i, j in system.bonds:
delta = system.pos[i] - system.pos[j]
system.cell.mic(delta)
d = np.linalg.norm(delta)
check_term = 0.5*2.3*(d - 3.04-0.1*i)**2
assert abs(check_term - vlist.vtab[counter]['energy']) < 1e-10
check_energy += check_term
counter += 1
assert abs(energy - check_energy) < 1e-8
def test_ewald_gpos_vtens_corr_quartz():
system = get_system_quartz().supercell(2, 2, 2)
scalings = Scalings(system, np.random.uniform(0.1, 0.9), np.random.uniform(0.1, 0.9), np.random.uniform(0.1, 0.9))
for alpha in 0.1, 0.2, 0.5:
part_ewald_corr = ForcePartEwaldCorrection(system, alpha, scalings)
check_gpos_part(system, part_ewald_corr)
check_vtens_part(system, part_ewald_corr)
def test_detect_ffatypes():
system = get_system_quartz()
rules = [
('Si', '14'),
('O', '8'),
]
check_detect_ffatypes(system, rules)
def test_ewald_dd_quartz():
system = get_system_quartz().supercell(2, 2, 2)
system.radii = np.random.rand( system.natom)
system.radii2 = np.random.rand( system.natom)
dipoles = np.random.rand( system.natom, 3 )
system.dipoles = dipoles
check_alpha_dependence_dd(system)
def test_vlist_quartz_bend_angle():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
angles = []
for i1 in xrange(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
vlist.add_term(
Harmonic(1.5, 2.0 + 0.01 * i2, BendAngle(i0, i1, i2)))
angles.append((i0, i1, i2))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
for row, (i0, i1, i2) in enumerate(angles):
delta0 = system.pos[i0] - system.pos[i1]
system.cell.mic(delta0)
delta2 = system.pos[i2] - system.pos[i1]
system.cell.mic(delta2)
angle = bend_angle([delta0, np.zeros(3, float), delta2])[0]
check_energy += 0.5 * 1.5 * (angle - (2.0 + 0.01 * i2))**2
assert abs(energy - check_energy) < 1e-8
def test_cvvolume_quartz():
system = get_system_quartz()
cv = CVVolume(system)
value = cv.compute()
assert np.abs(value - np.abs(np.linalg.det(system.cell.rvecs))) < 1e-10
check_gpos_cv_fd(cv)
check_vtens_cv_fd(cv)
def test_vlist_quartz_bonds_fues():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
for i, j in system.bonds:
vlist.add_term(Fues(2.3, 3.04+0.1*i, Bond(i, j)))
assert dlist.ndelta == len(system.bonds)
assert iclist.nic == len(system.bonds)
assert vlist.nv == len(system.bonds)
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
counter = 0
for i, j in system.bonds:
delta = system.pos[i] - system.pos[j]
system.cell.mic(delta)
d = np.linalg.norm(delta)
rv = 3.04+0.1*i
check_term = 0.5*2.3*rv**2*(1.0 + rv/d*(rv/d - 2.0))
if not abs(check_term - vlist.vtab[counter]['energy']) < 1e-10:
raise AssertionError("Error in energy of bond(%i,%i): energy = %.15f instead energy = %.15f" %(i,j,check_term,vlist.vtab[counter]['energy']))
check_energy += check_term
counter += 1
assert abs(energy - check_energy) < 1e-8
def test_vlist_quartz_bend_cos():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
angles = []
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
vlist.add_term(Harmonic(1.1+0.01*i0, -0.2, BendCos(i0, i1, i2)))
angles.append((i0, i1, i2))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
counter = 0
for row, (i0, i1, i2) in enumerate(angles):
delta0 = system.pos[i0] - system.pos[i1]
system.cell.mic(delta0)
delta2 = system.pos[i2] - system.pos[i1]
system.cell.mic(delta2)
c = bend_cos([delta0, np.zeros(3, float), delta2])[0]
check_term = 0.5*(1.1+0.01*i0)*(c+0.2)**2
assert abs(check_term - vlist.vtab[counter]['energy']) < 1e-10
check_energy += check_term
counter += 1
assert abs(energy - check_energy) < 1e-8
def test_gpos_vtens_quartz():
system = get_system_quartz()
rv_table = {
('Si', 'O'): 3.24970,
('O', 'Si', 'O'): 2.06457,
('Si', 'O', 'Si'): 1.80173,
}
fc_table = {
('Si', 'O'): 0.30978,
('O', 'Si', 'O'): 0.19282,
('Si', 'O', 'Si'): 0.00751,
}
part = ForcePartValence(system)
for i, j in system.bonds:
key = system.get_ffatype(i), system.get_ffatype(j)
part.add_term(Harmonic(fc_table[key], rv_table[key], Bond(i, j)))
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
key = system.get_ffatype(i0), system.get_ffatype(i1), system.get_ffatype(i2)
if i0 > i2:
part.add_term(Harmonic(fc_table[key], rv_table[key], BendAngle(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_vlist_quartz_morse():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
for i, j in system.bonds:
vlist.add_term(Morse(2.3 + i, 0.5, 2.0, Bond(i, j)))
assert dlist.ndelta == len(system.bonds)
assert iclist.nic == len(system.bonds)
assert vlist.nv == len(system.bonds)
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
counter = 0
for i, j in system.bonds:
delta = system.pos[i] - system.pos[j]
system.cell.mic(delta)
d = np.linalg.norm(delta)
check_term = (2.3 + i) * (np.exp(-2 * 0.5 *
(d - 2.0)) - 2.0 * np.exp(-0.5 *
(d - 2.0)))
assert abs(check_term - vlist.vtab[counter]['energy']) < 1e-10
check_energy += check_term
counter += 1
assert abs(energy - check_energy) < 1e-8
def test_ewald_dd_quartz():
system = get_system_quartz().supercell(2, 2, 2)
system.radii = np.random.rand(system.natom)
system.radii2 = np.random.rand(system.natom)
dipoles = np.random.rand(system.natom, 3)
system.dipoles = dipoles
check_alpha_dependence_dd(system)
def test_nlist_quartz_4A_shortest():
raise SkipTest('The mic routine fails to find the shortest distance in small skewed unit cells.')
system = get_system_quartz()
nlist = NeighborList(system)
nlist.request_rcut(4*angstrom)
nlist.update()
check_nlist_shortest(system, nlist)
def test_cell_quartz():
cell = get_system_quartz().cell
assert cell.rvecs.shape == (3, 3)
assert cell.gvecs.shape == (3, 3)
assert abs(cell.volume - abs(np.linalg.det(cell.rvecs))) < 1e-10
assert abs(np.dot(cell.gvecs, cell.rvecs.transpose()) -
np.identity(3)).max() < 1e-5
def test_vlist_quartz_bonds_fues():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
for i, j in system.bonds:
vlist.add_term(Fues(2.3, 3.04 + 0.1 * i, Bond(i, j)))
assert dlist.ndelta == len(system.bonds)
assert iclist.nic == len(system.bonds)
assert vlist.nv == len(system.bonds)
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
counter = 0
for i, j in system.bonds:
delta = system.pos[i] - system.pos[j]
system.cell.mic(delta)
d = np.linalg.norm(delta)
rv = 3.04 + 0.1 * i
check_term = 0.5 * 2.3 * rv**2 * (1.0 + rv / d * (rv / d - 2.0))
if not abs(check_term - vlist.vtab[counter]['energy']) < 1e-10:
raise AssertionError(
"Error in energy of bond(%i,%i): energy = %.15f instead energy = %.15f"
% (i, j, check_term, vlist.vtab[counter]['energy']))
check_energy += check_term
counter += 1
assert abs(energy - check_energy) < 1e-8
def test_gpos_vtens_quartz():
system = get_system_quartz()
rv_table = {
('Si', 'O'): 3.24970,
('O', 'Si', 'O'): 2.06457,
('Si', 'O', 'Si'): 1.80173,
}
fc_table = {
('Si', 'O'): 0.30978,
('O', 'Si', 'O'): 0.19282,
('Si', 'O', 'Si'): 0.00751,
}
part = ForcePartValence(system)
for i, j in system.bonds:
key = system.get_ffatype(i), system.get_ffatype(j)
part.add_term(Harmonic(fc_table[key], rv_table[key], Bond(i, j)))
for i1 in xrange(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
key = system.get_ffatype(i0), system.get_ffatype(
i1), system.get_ffatype(i2)
if i0 > i2:
part.add_term(
Harmonic(fc_table[key], rv_table[key],
BendAngle(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_vlist_quartz_bend_cos():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
angles = []
for i1 in xrange(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
vlist.add_term(
Harmonic(1.1 + 0.01 * i0, -0.2, BendCos(i0, i1, i2)))
angles.append((i0, i1, i2))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# compute energy manually
check_energy = 0.0
counter = 0
for row, (i0, i1, i2) in enumerate(angles):
delta0 = system.pos[i0] - system.pos[i1]
system.cell.mic(delta0)
delta2 = system.pos[i2] - system.pos[i1]
system.cell.mic(delta2)
c = bend_cos([delta0, np.zeros(3, float), delta2])[0]
check_term = 0.5 * (1.1 + 0.01 * i0) * (c + 0.2)**2
assert abs(check_term - vlist.vtab[counter]['energy']) < 1e-10
check_energy += check_term
counter += 1
assert abs(energy - check_energy) < 1e-8
def test_bks_vtens_gpos_parts():
system = get_system_quartz()
fn_pars = context.get_fn('test/parameters_bks.txt')
ff = ForceField.generate(system, fn_pars, smooth_ei=True, reci_ei='ignore')
for part in ff.parts:
check_vtens_part(system, part, ff.nlist)
check_gpos_part(system, part, ff.nlist)
def test_ewald_gpos_vtens_reci_quartz():
system = get_system_quartz()
for alpha in 0.1, 0.2, 0.5:
part_ewald_reci = ForcePartEwaldReciprocal(system,
alpha,
gcut=alpha / 0.5)
check_gpos_part(system, part_ewald_reci)
check_vtens_part(system, part_ewald_reci)
def test_scaling_quartz():
system = get_system_quartz().supercell(2, 2, 2)
stab = Scalings(system).stab
assert (stab['a'] > stab['b']).all()
assert len(stab) == sum(len(system.neighs1[i]) + len(system.neighs2[i]) for i in xrange(system.natom))/2
for i0, i1, scale, nbond in stab:
assert scale == 0.0
assert i0 in system.neighs1[i1] or i0 in system.neighs2[i1]
assert nbond == 1 or nbond == 2
def test_remove_duplicate1():
system1 = get_system_quartz()
system2 = system1.remove_duplicate()
assert system1.natom == system2.natom
assert system1.nbond == system2.nbond
assert (system1.numbers == system2.numbers).all()
assert (system1.pos == system2.pos).all()
assert (system1.ffatype_ids == system2.ffatype_ids).all()
assert system1.neighs1 == system2.neighs1
def test_nlist_quartz_4A_shortest():
raise SkipTest(
'The mic routine fails to find the shortest distance in small skewed unit cells.'
)
system = get_system_quartz()
nlist = NeighborList(system)
nlist.request_rcut(4 * angstrom)
nlist.update()
check_nlist_shortest(system, nlist)
def test_ewald_quartz():
# These are the energy contributions that one should get:
# alpha REAL RECI CORR
# 0.05 -3.5696637e-02 6.8222205e-29 -2.5814534e-01
# 0.10 1.3948043e-01 2.2254505e-08 -4.3332242e-01
# 0.20 1.7482393e-01 2.9254105e-03 -4.7159132e-01
# 0.50 5.6286111e-04 7.7869316e-01 -1.0730980e+00
# 1.00 2.6807119e-12 4.6913539e+00 -4.9851959e+00
system = get_system_quartz().supercell(2, 2, 2)
check_alpha_depedence(system)
def test_ewald_quartz():
# These are the energy contributions that one should get:
# alpha REAL RECI CORR
# 0.05 -3.5696637e-02 6.8222205e-29 -2.5814534e-01
# 0.10 1.3948043e-01 2.2254505e-08 -4.3332242e-01
# 0.20 1.7482393e-01 2.9254105e-03 -4.7159132e-01
# 0.50 5.6286111e-04 7.7869316e-01 -1.0730980e+00
# 1.00 2.6807119e-12 4.6913539e+00 -4.9851959e+00
system = get_system_quartz().supercell(2, 2, 2)
check_alpha_depedence(system)
def test_scaling_quartz():
system = get_system_quartz().supercell(2, 2, 2)
stab = Scalings(system).stab
assert (stab['a'] > stab['b']).all()
assert len(stab) == sum(
len(system.neighs1[i]) + len(system.neighs2[i])
for i in xrange(system.natom)) / 2
for i0, i1, scale, nbond in stab:
assert scale == 0.0
assert i0 in system.neighs1[i1] or i0 in system.neighs2[i1]
assert nbond == 1 or nbond == 2
def test_quartz():
system = get_system_quartz()
groups = [
(np.array([0, 2, 8, 1]), np.array([0.3, 0.2, 0.4, 0.3])),
]
comlist = COMList(system, groups)
comlist.forward()
com_a = comlist.pos[0].copy()
system.pos[2] += system.cell.rvecs[0]
comlist.forward()
np.testing.assert_almost_equal(com_a, comlist.pos[0])
def test_remove_duplicate2():
system1 = get_system_quartz()
system2 = system1.supercell(1, 2, 1)
system2.cell = system1.cell
system3 = system2.remove_duplicate()
assert system1.natom == system3.natom
assert system1.nbond == system3.nbond
assert system1.numbers.sum() == system3.numbers.sum()
assert abs(system1.pos.mean(axis=0) -
system3.pos.mean(axis=0)).max() < 1e-10
assert system1.ffatype_ids.sum() == system3.ffatype_ids.sum()
def test_subsystem():
system1 = get_system_quartz()
system1.dipoles = np.random.rand(system1.natom, 3)
system2 = system1.subsystem((system1.numbers == 8).nonzero()[0])
assert system2.natom == 6
assert (system2.numbers == 8).all()
assert len(system2.bonds) == 0
assert system2.scopes is None
assert system2.get_ffatype(0) == 'O'
assert (system2.charges == -0.9).all()
assert (system1.cell.rvecs == system2.cell.rvecs).all()
assert np.shape(system2.dipoles)[1] == 3
def get_ff_bks(**kwargs):
system = get_system_quartz()
if kwargs.pop('align_ax', False):
system.align_cell(np.array([[1, 0, 0], [0, 1, 1]]), True)
rvecs = system.cell.rvecs.copy()
rvecs[1, 0] = 0.0
rvecs[2, 0] = 0.0
rvecs[0, 1] = 0.0
rvecs[0, 2] = 0.0
system.cell.update_rvecs(rvecs)
fn_pars = pkg_resources.resource_filename(__name__, '../../data/test/parameters_bks.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def get_ff_bks(**kwargs):
system = get_system_quartz()
if kwargs.pop('align_ax', False):
system.align_cell(np.array([[1, 0, 0], [0, 1, 1]]), True)
rvecs = system.cell.rvecs.copy()
rvecs[1, 0] = 0.0
rvecs[2, 0] = 0.0
rvecs[0, 1] = 0.0
rvecs[0, 2] = 0.0
system.cell.update_rvecs(rvecs)
fn_pars = context.get_fn('test/parameters_bks.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def test_nlist_quartz_110A():
system = get_system_quartz()
nlist = NeighborList(system)
rcut = 110 * angstrom
nlist.request_rcut(rcut)
nlist.update()
assert (nlist.neighs['r0'][:nlist.nneigh] <= nlist.rmax[0]).all()
assert (nlist.neighs['r0'][:nlist.nneigh] >= -nlist.rmax[0]).all()
assert (nlist.neighs['r1'][:nlist.nneigh] <= nlist.rmax[1]).all()
assert (nlist.neighs['r1'][:nlist.nneigh] >= -nlist.rmax[1]).all()
assert (nlist.neighs['r2'][:nlist.nneigh] <= nlist.rmax[2]).all()
assert (nlist.neighs['r2'][:nlist.nneigh] >= 0).all()
def get_ff_bks(**kwargs):
system = get_system_quartz()
if kwargs.pop('align_ax', False):
system.align_cell(np.array([[1, 0, 0], [0, 1, 1]]), True)
rvecs = system.cell.rvecs.copy()
rvecs[1, 0] = 0.0
rvecs[2, 0] = 0.0
rvecs[0, 1] = 0.0
rvecs[0, 2] = 0.0
system.cell.update_rvecs(rvecs)
fn_pars = context.get_fn('test/parameters_bks.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def test_cvinternalcoordinate_quartz():
system = get_system_quartz()
ic = Bond(1, 3)
cv = CVInternalCoordinate(system, ic)
value = cv.compute()
assert value == cv.get_last_computed_value()
delta = system.pos[3] - system.pos[1]
system.cell.mic(delta)
reference = bond_length([np.zeros(3, float), delta])[0]
assert np.abs(value - reference) < 1e-8
check_gpos_cv_fd(cv)
check_vtens_cv_fd(cv)
def test_iclist_quartz_bonds():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
for i, j in system.bonds:
iclist.add_ic(Bond(i, j))
dlist.forward()
iclist.forward()
for row, (i, j) in enumerate(system.bonds):
delta = system.pos[j] - system.pos[i]
system.cell.mic(delta)
assert abs(iclist.ictab[row]['value'] - bond_length([np.zeros(3, float), delta])[0]) < 1e-5
def test_bias_harmonicvolume_quartz():
system = get_system_quartz()
cv = CVVolume(system)
K, q0 = 0.4, 0.9 * system.cell.volume
bias = HarmonicBias(K, q0, cv)
part = ForcePartBias(system)
part.add_term(bias)
e = part.compute()
echeck = 0.5 * K * (system.cell.volume - q0)**2
assert np.abs(e - echeck) < 1e-8
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_nlist_quartz_110A():
system = get_system_quartz()
nlist = NeighborList(system)
rcut = 110*angstrom
nlist.request_rcut(rcut)
nlist.update()
assert (nlist.neighs['r0'][:nlist.nneigh] <= nlist.rmax[0]).all()
assert (nlist.neighs['r0'][:nlist.nneigh] >= -nlist.rmax[0]).all()
assert (nlist.neighs['r1'][:nlist.nneigh] <= nlist.rmax[1]).all()
assert (nlist.neighs['r1'][:nlist.nneigh] >= -nlist.rmax[1]).all()
assert (nlist.neighs['r2'][:nlist.nneigh] <= nlist.rmax[2]).all()
assert (nlist.neighs['r2'][:nlist.nneigh] >= 0).all()
def get_ff_bks(**kwargs):
system = get_system_quartz()
if kwargs.pop('align_ax', False):
system.align_cell(np.array([[1, 0, 0], [0, 1, 1]]), True)
rvecs = system.cell.rvecs.copy()
rvecs[1, 0] = 0.0
rvecs[2, 0] = 0.0
rvecs[0, 1] = 0.0
rvecs[0, 2] = 0.0
system.cell.update_rvecs(rvecs)
fn_pars = pkg_resources.resource_filename(
__name__, '../../data/test/parameters_bks.txt')
return ForceField.generate(system, fn_pars, **kwargs)
def test_quartz_vtens():
system = get_system_quartz()
groups = [
(np.array([0, 2, 8, 1]),
np.array([0.3, 0.2, 0.4, 0.3])),
(np.array([1, 3, 4, 5]),
np.array([0.3, 0.4, 0.1, 0.2])),
]
comlist = COMList(system, groups)
part = ForcePartValence(system, comlist)
part.add_term(Harmonic(2.1, 0.5, Bond(0, 1)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_iclist_quartz_bonds():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
for i, j in system.bonds:
iclist.add_ic(Bond(i, j))
dlist.forward()
iclist.forward()
for row, (i, j) in enumerate(system.bonds):
delta = system.pos[j] - system.pos[i]
system.cell.mic(delta)
assert abs(iclist.ictab[row]['value'] -
bond_length([np.zeros(3, float), delta])[0]) < 1e-5
def test_bks_isfinite():
system = get_system_quartz()
fn_pars = context.get_fn('test/parameters_bks.txt')
ff = ForceField.generate(system, fn_pars)
assert np.isfinite(ff.part_pair_dampdisp.pair_pot.c6_cross).all()
assert np.isfinite(ff.part_pair_dampdisp.pair_pot.b_cross).all()
ff.compute()
assert np.isfinite(ff.part_pair_exprep.energy)
assert np.isfinite(ff.part_pair_ei.energy)
assert np.isfinite(ff.part_ewald_reci.energy)
assert np.isfinite(ff.part_ewald_cor.energy)
assert np.isfinite(ff.part_ewald_neut.energy)
assert np.isfinite(ff.part_pair_dampdisp.energy)
assert np.isfinite(ff.energy)
def test_plumed_quartz_volume():
system = get_system_quartz()
# Harmonic restraint of the volume
kappa, V0 = 1.6 * kjmol / angstrom**6, 110 * angstrom**3
# PLUMED input commands
commands = "vol: VOLUME\n"
commands += "RESTRAINT ARG=vol AT=%.20f KAPPA=%.20f LABEL=restraint\n"%\
(V0/nanometer**3,kappa/kjmol*nanometer**6)
# Reference calculation
def reference(system):
return 0.5 * kappa * (system.cell.volume - V0)**2
check_plumed(system, commands, reference)
def test_iclist_quartz_bend_angle():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
angles = []
for i1 in xrange(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
iclist.add_ic(BendAngle(i0, i1, i2))
angles.append((i0, i1, i2))
dlist.forward()
iclist.forward()
for row, (i0, i1, i2) in enumerate(angles):
delta0 = system.pos[i1] - system.pos[i0]
system.cell.mic(delta0)
delta2 = system.pos[i1] - system.pos[i2]
system.cell.mic(delta2)
assert abs(iclist.ictab[row]['value'] - bend_angle([delta0, np.zeros(3, float), delta2])[0]) < 1e-5
def test_ewald_reci_volchange_quartz():
system = get_system_quartz()
dielectric = 1.2
for alpha in 0.1, 0.2, 0.5:
part_ewald_reci = ForcePartEwaldReciprocal(system, alpha, gcut=alpha / 0.5, dielectric=dielectric)
# compute the energy
energy1 = part_ewald_reci.compute()
# distort the cell and restore to the original volume
volume = system.cell.volume
reduced = np.dot(system.pos, system.cell.gvecs.transpose())
new_rvecs = system.cell.rvecs * np.random.uniform(0.9, 1.0)
new_volume = np.linalg.det(new_rvecs)
new_rvecs *= (volume / new_volume) ** (1.0 / 3.0)
system.pos[:] = np.dot(reduced, new_rvecs)
system.cell.update_rvecs(new_rvecs)
# recompute the energy
energy2 = part_ewald_reci.compute()
# energies must be the same
assert abs(energy1 - energy2) < 1e-5 * abs(energy1)
def test_ewald_corr_quartz():
from scipy.special import erf
system = get_system_quartz().supercell(2, 2, 2)
for alpha in 0.05, 0.1, 0.2:
scalings = Scalings(
system, np.random.uniform(0.1, 0.9), np.random.uniform(0.1, 0.9), np.random.uniform(0.1, 0.9)
)
part_ewald_corr = ForcePartEwaldCorrection(system, alpha, scalings)
energy1 = part_ewald_corr.compute()
# self-interaction corrections
energy2 = -alpha / np.sqrt(np.pi) * (system.charges ** 2).sum()
# corrections from scaled interactions
for i0, i1, scale, nbond in scalings.stab:
delta = system.pos[i0] - system.pos[i1]
system.cell.mic(delta)
d = np.linalg.norm(delta)
term = erf(alpha * d) / d * (1 - scale) * system.charges[i0] * system.charges[i1]
energy2 -= term
assert abs(energy1 - energy2) < 1e-10
def test_dlist_quartz_bonds():
system = get_system_quartz()
dlist = get_dlist_bonds(system)
check_dlist(system, dlist)
def test_dlist_quartz_random():
system = get_system_quartz()
dlist = get_dlist_random(system)
check_dlist(system, dlist)
def test_ewald_gpos_vtens_reci_quartz():
system = get_system_quartz()
for alpha in 0.1, 0.2, 0.5:
part_ewald_reci = ForcePartEwaldReciprocal(system, alpha, gcut=alpha / 0.5)
check_gpos_part(system, part_ewald_reci)
check_vtens_part(system, part_ewald_reci)
def test_topology_quartz():
system = get_system_quartz()
check_topology_slow(system)
def test_nlist_quartz_6A_skin3A():
system = get_system_quartz()
check_nlist_skin(system, 6*angstrom, 3*angstrom)
def test_cell_quartz():
cell = get_system_quartz().cell
assert cell.rvecs.shape == (3, 3)
assert cell.gvecs.shape == (3, 3)
assert abs(cell.volume - abs(np.linalg.det(cell.rvecs))) < 1e-10
assert abs(np.dot(cell.gvecs, cell.rvecs.transpose()) - np.identity(3)).max() < 1e-5