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_gpos_vtens_mm3quartic_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(MM3Quartic(1.5, 2.0 + 0.01 * i, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)
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_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_gpos_vtens_oopdist_formaldehyde():
system = get_system_formaldehyde()
system.pos[0,0] += 0.0*angstrom
part = ForcePartValence(system)
part.add_term(Harmonic(0.0,0.0*angstrom,OopDist(2,3,1,0)))
check_gpos_part(system, part)
check_vtens_part(system, part)
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_gpos_vtens_polyfour_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(PolyFour([-0.5, 0.3, -0.16, 0.09], Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_ewald_vtens_neut_water32():
# fake water model, negative oxygens and neutral hydrogens
system = get_system_water32()
system.charges -= 0.1
for alpha in 0.05, 0.1, 0.2:
part_ewald_neut = ForcePartEwaldNeutralizing(system, alpha)
check_vtens_part(system, part_ewald_neut)
def test_ewald_gpos_vtens_reci_water32():
system = get_system_water32()
dielectric = 1.4
for alpha in 0.05, 0.1, 0.2:
part_ewald_reci = ForcePartEwaldReciprocal(system, alpha, gcut=alpha / 0.75, dielectric=dielectric)
check_gpos_part(system, part_ewald_reci)
check_vtens_part(system, part_ewald_reci)
def test_gpos_vtens_morse_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(Morse(0.3, 1.7, 2.0, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_bond_fues_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(Fues(0.3, 1.7, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_pointlinedist_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j, k in system.iter_angles():
part.add_term(Harmonic(0.3, 1.7, PointLineDistance(i, j, k)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_dihedral_cos_mil53():
system = get_system_mil53()
forbidden_dihedrals = [
["O_HY","AL","O_HY","AL"],
["O_HY","AL","O_HY","H_HY"],
["O_CA","AL","O_CA","C_CA"],
["O_CA","AL","O_HY","H_HY"],
["H_PH","C_PH","C_PC","C_PH"],
["H_PH","C_PH","C_PC","C_CA"],
["C_PH","C_PH","C_PC","C_PH"],
["C_PH","C_PH","C_PC","C_CA"],
["C_PC","C_PH","C_PH","H_PH"],
["C_PC","C_PH","C_PH","C_PC"],
["H_PH","C_PH","C_PH","H_PH"],
["C_PH","C_PC","C_CA","O_CA"],
]
idih = -1
for i1, i2 in system.bonds:
for i0 in system.neighs1[i1]:
if i0==i2: continue
for i3 in system.neighs1[i2]:
if i3==i1: continue
types = [system.get_ffatype(i0), system.get_ffatype(i1), system.get_ffatype(i2), system.get_ffatype(i3)]
if types in forbidden_dihedrals or types[::-1] in forbidden_dihedrals: continue
idih += 1
fc = 2.1 + 0.01*(0.3*i1 + 0.7*i2)
part = ForcePartValence(system)
part.add_term(PolyFour([-2.0*fc,0.0001,0.0,0.0],DihedCos(i0,i1,i2,i3)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_ewald_gpos_vtens_corr_water32():
system = get_system_water32()
scalings = Scalings(system, 0.0, 0.0, 0.5)
for alpha in 0.05, 0.1, 0.2:
part_ewald_corr = ForcePartEwaldCorrection(system, alpha, scalings, dielectric=0.8)
check_gpos_part(system, part_ewald_corr)
check_vtens_part(system, part_ewald_corr)
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_gpos_vtens_dihedral_cos_mil53():
system = get_system_mil53()
forbidden_dihedrals = [
["O_HY","AL","O_HY","AL"],
["O_HY","AL","O_HY","H_HY"],
["O_CA","AL","O_CA","C_CA"],
["O_CA","AL","O_HY","H_HY"],
["H_PH","C_PH","C_PC","C_PH"],
["H_PH","C_PH","C_PC","C_CA"],
["C_PH","C_PH","C_PC","C_PH"],
["C_PH","C_PH","C_PC","C_CA"],
["C_PC","C_PH","C_PH","H_PH"],
["C_PC","C_PH","C_PH","C_PC"],
["H_PH","C_PH","C_PH","H_PH"],
["C_PH","C_PC","C_CA","O_CA"],
]
idih = -1
for i1, i2 in system.bonds:
for i0 in system.neighs1[i1]:
if i0==i2: continue
for i3 in system.neighs1[i2]:
if i3==i1: continue
types = [system.get_ffatype(i0), system.get_ffatype(i1), system.get_ffatype(i2), system.get_ffatype(i3)]
if types in forbidden_dihedrals or types[::-1] in forbidden_dihedrals: continue
idih += 1
fc = 2.1 + 0.01*(0.3*i1 + 0.7*i2)
part = ForcePartValence(system)
part.add_term(PolyFour([-2.0*fc,0.0001,0.0,0.0],DihedCos(i0,i1,i2,i3)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_dihed_angle_cosine_peroxide():
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Cosine(3, 1.5, 2 * np.pi / 3, DihedAngle(0, 1, 2, 3)))
print(dihed_angle(system.pos)[0] / np.pi)
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_mm3quartic_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(MM3Quartic(1.5, 2.0+0.01*i, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_bond_fues_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(Fues(0.3, 1.7, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_morse_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(Morse(0.3, 1.7, 2.0, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_oopdist_formaldehyde():
system = get_system_formaldehyde()
system.pos[0, 0] += 0.0 * angstrom
part = ForcePartValence(system)
part.add_term(Harmonic(0.0, 0.0 * angstrom, OopDist(2, 3, 1, 0)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_poly4_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(Poly4(0.001, 0.002, 0.271, -0.32793, 0.23151, 1.78, Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_ewald_vtens_neut_water32():
# fake water model, negative oxygens and neutral hydrogens
system = get_system_water32()
system.charges -= 0.1
for alpha in 0.05, 0.1, 0.2:
part_ewald_neut = ForcePartEwaldNeutralizing(system, alpha)
check_vtens_part(system, part_ewald_neut)
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_gpos_vtens_polyfour_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j in system.bonds:
part.add_term(PolyFour([-0.5, 0.3, -0.16, 0.09], Bond(i, j)))
check_gpos_part(system, part)
check_vtens_part(system, part)
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_gpos_vtens_2T():
system = get_system_2T()
rv_table = {
('H', 'Si', 'H'): 1.80861,
('Si', 'O'): 3.24970,
('H', 'O'): 1.96022,
('O', 'Si', 'O'): 2.06457,
('O', 'Si'): 3.24970,
('O', 'Si', 'H'): 1.85401,
('Si', 'O', 'Si'): 1.80173,
('Si', 'O', 'H'): 1.55702,
('H', 'O', 'Si'): 1.55702,
('Si', 'H'): 2.87853,
('H', 'Si'): 2.87853,
('H', 'Si', 'O'): 1.85401,
('O', 'H'): 1.96022,
}
fc_table = {
('H', 'Si', 'H'): 0.09376,
('Si', 'O'): 0.30978,
('H', 'O'): 0.60322,
('O', 'Si', 'O'): 0.19282,
('O', 'Si'): 0.30978,
('O', 'Si', 'H'): 0.11852,
('Si', 'O', 'Si'): 0.00751,
('Si', 'O', 'H'): 0.04271,
('H', 'O', 'Si'): 0.04271,
('Si', 'H'): 0.18044,
('H', 'Si'): 0.18044,
('H', 'Si', 'O'): 0.11852,
('O', 'H'): 0.60322,
}
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)
# same test but with Fues bonds instead of Harmonic bonds
part = ForcePartValence(system)
for i, j in system.bonds:
key = system.get_ffatype(i), system.get_ffatype(j)
part.add_term(Fues(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_gpos_vtens_2T():
system = get_system_2T()
rv_table = {
('H', 'Si', 'H'): 1.80861,
('Si', 'O'): 3.24970,
('H', 'O'): 1.96022,
('O', 'Si', 'O'): 2.06457,
('O', 'Si'): 3.24970,
('O', 'Si', 'H'): 1.85401,
('Si', 'O', 'Si'): 1.80173,
('Si', 'O', 'H'): 1.55702,
('H', 'O', 'Si'): 1.55702,
('Si', 'H'): 2.87853,
('H', 'Si'): 2.87853,
('H', 'Si', 'O'): 1.85401,
('O', 'H'): 1.96022,
}
fc_table = {
('H', 'Si', 'H'): 0.09376,
('Si', 'O'): 0.30978,
('H', 'O'): 0.60322,
('O', 'Si', 'O'): 0.19282,
('O', 'Si'): 0.30978,
('O', 'Si', 'H'): 0.11852,
('Si', 'O', 'Si'): 0.00751,
('Si', 'O', 'H'): 0.04271,
('H', 'O', 'Si'): 0.04271,
('Si', 'H'): 0.18044,
('H', 'Si'): 0.18044,
('H', 'Si', 'O'): 0.11852,
('O', 'H'): 0.60322,
}
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)
# same test but with Fues bonds instead of Harmonic bonds
part = ForcePartValence(system)
for i, j in system.bonds:
key = system.get_ffatype(i), system.get_ffatype(j)
part.add_term(Fues(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_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_gpos_vtens_sqpointlinedist_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i, j, k in system.iter_angles():
# Add this term so no all signs of deltas are 1
part.add_term(Harmonic(0.4, 1.0, Bond(j, i)))
part.add_term(Harmonic(0.3, 1.7, SqPointLineDistance(i, j, k)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_ub_water():
system = get_system_water32()
part = ForcePartValence(system)
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
part.add_term(Harmonic(2.1,2.0*angstrom,UreyBradley(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_ewald_gpos_vtens_reci_water32():
system = get_system_water32()
dielectric = 1.4
for alpha in 0.05, 0.1, 0.2:
part_ewald_reci = ForcePartEwaldReciprocal(system,
alpha,
gcut=alpha / 0.75,
dielectric=dielectric)
check_gpos_part(system, part_ewald_reci)
check_vtens_part(system, part_ewald_reci)
def test_gpos_vtens_bend_cos_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
part.add_term(Harmonic(1.1+0.01*i0, -0.2, BendCos(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_ub_water():
system = get_system_water32()
part = ForcePartValence(system)
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
part.add_term(Harmonic(2.1,2.0*angstrom,UreyBradley(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_mm3benda_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
part.add_term(MM3Bend(1.5, 2.0+0.01*i2, BendAngle(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_bend_cos_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
part.add_term(Harmonic(1.1+0.01*i0, -0.2, BendCos(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_mm3benda_water32():
system = get_system_water32()
part = ForcePartValence(system)
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
part.add_term(MM3Bend(1.5, 2.0+0.01*i2, BendAngle(i0, i1, i2)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_ewald_gpos_vtens_corr_water32():
system = get_system_water32()
scalings = Scalings(system, 0.0, 0.0, 0.5)
for alpha in 0.05, 0.1, 0.2:
part_ewald_corr = ForcePartEwaldCorrection(system,
alpha,
scalings,
dielectric=0.8)
check_gpos_part(system, part_ewald_corr)
check_vtens_part(system, part_ewald_corr)
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_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_gpos_vtens_dihed_cos_chebychev6_peroxide():
#Test for positive sign in polynomial
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Chebychev6(1.5, DihedCos(0, 1, 2, 3), sign=1))
check_gpos_part(system, part)
check_vtens_part(system, part)
#Test for negative sign in polynomial
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Chebychev6(1.5, DihedCos(0, 1, 2, 3), sign=-1))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_dihed_cos_chebychev6_peroxide():
#Test for positive sign in polynomial
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Chebychev6(1.5, DihedCos(0,1,2,3), sign=1))
check_gpos_part(system, part)
check_vtens_part(system, part)
#Test for negative sign in polynomial
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Chebychev6(1.5, DihedCos(0,1,2,3), sign=-1))
check_gpos_part(system, part)
check_vtens_part(system, part)
def check_plumed(system, commands, reference):
with tmpdir(__name__, 'check_plumed') as dirname:
# Write PLUMED commands to file
fn = os.path.join(dirname, 'plumed.dat')
with open(fn, 'w') as f:
f.write(commands)
# Setup Plumed
plumed = ForcePartPlumed(system, fn=fn)
# Compare with direct calculation
e = plumed.compute()
eref = reference(system)
check_gpos_part(system, plumed)
check_vtens_part(system, plumed)
assert np.abs(e - eref) < 1e-3 * kjmol
def test_gpos_vtens_cross_water32():
system = get_system_water32()
part = ForcePartValence(system)
for j in xrange(system.natom):
if len(system.neighs1[j]) == 2:
i, k = system.neighs1[j]
part.add_term(Cross(
1.2,
1.7,
1.9,
Bond(i, j),
Bond(j, k),
))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_cross_water32():
system = get_system_water32()
part = ForcePartValence(system)
for j in range(system.natom):
if len(system.neighs1[j])==2:
i, k = system.neighs1[j]
part.add_term(Cross(
1.2,
1.7,
1.9,
Bond(i, j),
Bond(j, k),
))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_pair_pot_eidip_water():
#Setup system and force part
system, nlist, scalings, part_pair, pair_pot, pair_fn = get_part_water_eidip()
#Check energy from Yaff with manually computed energy
check_pair_pot_water(system, nlist, scalings, part_pair, pair_pot, pair_fn, 1.0e-12)
check_gpos_part(system, part_pair, nlist)
check_vtens_part(system, part_pair, nlist, symm_vtens=False)
#Again, but with a truncation scheme (truncation scheme settings are ridiculous,
#but this is needed to see an effect for water)
#Setup system and force part
system, nlist, scalings, part_pair, pair_pot, pair_fn = get_part_water_eidip(rcut=2.0*angstrom,switch_width=1.5*angstrom)
#Check energy from Yaff with manually computed energy
check_pair_pot_water(system, nlist, scalings, part_pair, pair_pot, pair_fn, 1.0e-12)
check_gpos_part(system, part_pair, nlist)
check_vtens_part(system, part_pair, nlist, symm_vtens=False)
def test_bias_gaussianhills_alanine():
ff = get_alaninedipeptide_amber99ff()
cv = CVInternalCoordinate(ff.system, DihedAngle(4, 6, 8, 14))
sigma = 0.35 * rad
bias = GaussianHills(cv, sigma)
e = bias.compute()
assert e == 0.0
K, phi0 = 3 * kjmol, -2.5 * rad
bias.add_hill(phi0, K)
e = bias.compute()
phi = cv.compute()
eref = K * np.exp(-(phi - phi0)**2 / 2 / sigma**2)
assert np.abs(e - eref) < 1e-10 * kjmol
part = ForcePartBias(ff.system)
part.add_term(bias)
check_gpos_part(ff.system, part)
check_vtens_part(ff.system, part)
def test_bias_lowerwallvolume_quartz():
system = get_system_quartz()
cv = CVVolume(system)
K, q0 = 0.4, system.cell.volume
bias = LowerWallBias(K, q0, cv)
rvecs_orig = system.cell.rvecs.copy()
part = ForcePartBias(system)
part.add_term(bias)
for scale in [0.5, 2.0]:
rvecs = rvecs_orig * scale
system.cell.update_rvecs(rvecs)
e = bias.compute()
if system.cell.volume < q0:
eref = 0.5 * K * (system.cell.volume - q0)**2
else:
eref = 0.0
assert np.abs(e - eref) < 1e-8
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_bias_gaussianhills_alanine_periodic():
ff = get_alaninedipeptide_amber99ff()
cv = CVInternalCoordinate(ff.system, DihedAngle(4, 6, 8, 14))
sigma = 0.35 * rad
bias = GaussianHills(cv, sigma, periodicities=2.0 * np.pi)
e = bias.compute()
assert e == 0.0
K, phi0 = 3 * kjmol, -2.5 * rad
bias.add_hill(phi0, K)
e = bias.compute()
phi = cv.compute()
eref = K * np.exp(-(phi - phi0)**2 / 2 / sigma**2)
assert np.abs(e - eref) < 1e-10 * kjmol
# Another hill, two periods away, so should give the same energy
# once more
bias.add_hill(phi0 - 4.0 * np.pi, K)
e = bias.compute()
assert np.abs(e - 2 * eref) < 1e-10 * kjmol
part = ForcePartBias(ff.system)
part.add_term(bias)
check_gpos_part(ff.system, part)
check_vtens_part(ff.system, part)
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_gpos_vtens_dihed_angle_peroxide():
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Harmonic(1.5, 1.0, DihedAngle(0,1,2,3)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_oopcos_formaldehyde():
system = get_system_formaldehyde()
part = ForcePartValence(system)
part.add_term(Harmonic(2.1,0.0*angstrom,OopCos(2,3,1,0)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_gpos_vtens_pair_pot_caffeine_exprep_5A_case2():
system, nlist, scalings, part_pair, pair_fn = get_part_caffeine_exprep_5A(1, 2.385e-2, 1, 7.897e-3)
check_gpos_part(system, part_pair, nlist)
check_vtens_part(system, part_pair, nlist)
def test_gpos_vtens_pair_pot_caffeine_dampdisp_9A():
system, nlist, scalings, part_pair, pair_fn = get_part_caffeine_dampdisp_9A()
check_gpos_part(system, part_pair, nlist)
check_vtens_part(system, part_pair, nlist)
def test_gpos_vtens_pair_pot_caffeine_ei2_10A():
system, nlist, scalings, part_pair, pair_fn = get_part_caffeine_ei3_10A()
check_gpos_part(system, part_pair, nlist)
check_vtens_part(system, part_pair, nlist)
def test_gpos_vtens_dihed_cos6_peroxide():
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Harmonic(1.1, -0.2, DihedCos6(0,1,2,3)))
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_vtens_pext_1():
system = get_system_polyethylene4()
part = ForcePartPressure(system, 1.0)
check_vtens_part(system, part)
def test_vtens_pext_2():
system = get_system_graphene8()
part = ForcePartPressure(system, 1.0)
check_vtens_part(system, part)
def test_vtens_pext_3():
system = get_system_water32()
part = ForcePartPressure(system, 1.0)
check_vtens_part(system, part)
def test_gpos_vtens_dihed_angle_cosine_peroxide():
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Cosine(3, 1.5, 2*np.pi/3, DihedAngle(0,1,2,3)))
check_gpos_part(system, part)
check_vtens_part(system, part)