def test_oop_dist_formaldehyde():
# All atoms in the y-z plane
system = get_system_formaldehyde()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(OopDist(2,3,1,0))
dlist.forward()
iclist.forward()
assert abs( iclist.ictab[0]['value'] - 0.0 ) < 1e-8
# Put the C atom out of the plane
system = get_system_formaldehyde()
system.pos[0,0] += 1.2*angstrom
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# Add a dummy ic to the iclist, so some delta vectors are stored with a
# minus sign. This enables to check that the (*ic).signs are implemented
# correctly.
iclist.add_ic(OopDist(1,3,2,0))
iclist.add_ic(OopDist(2,3,1,0))
dlist.forward()
iclist.forward()
assert abs( iclist.ictab[1]['value'] - 1.2*angstrom ) < 1e-8
# Check if the distance is invariant for permutations of the first three atoms
from itertools import permutations
for perm in permutations((1,2,3)):
iclist.add_ic(OopDist(perm[0],perm[1],perm[2],0))
dlist.forward()
iclist.forward()
for ic in iclist.ictab:
if ic['kind']==8:
assert abs( abs(ic['value']) - 1.2*angstrom ) < 1e-8
def test_oop_dist_formaldehyde():
# All atoms in the y-z plane
system = get_system_formaldehyde()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(OopDist(2,3,1,0))
dlist.forward()
iclist.forward()
assert abs( iclist.ictab[0]['value'] - 0.0 ) < 1e-8
# Put the C atom out of the plane
system = get_system_formaldehyde()
system.pos[0,0] += 1.2*angstrom
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(OopDist(2,3,1,0))
dlist.forward()
iclist.forward()
assert abs( iclist.ictab[0]['value'] - 1.2*angstrom ) < 1e-8
# Check if the distance is invariant for permutations of the first three atoms
from itertools import permutations
for perm in permutations((1,2,3)):
iclist.add_ic(OopDist(perm[0],perm[1],perm[2],0))
dlist.forward()
iclist.forward()
for ic in iclist.ictab:
if ic['kind']==8:
assert abs( abs(ic['value']) - 1.2*angstrom ) < 1e-8
def test_oop_dist_formaldehyde():
# All atoms in the y-z plane
system = get_system_formaldehyde()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(OopDist(2, 3, 1, 0))
dlist.forward()
iclist.forward()
assert abs(iclist.ictab[0]['value'] - 0.0) < 1e-8
# Put the C atom out of the plane
system = get_system_formaldehyde()
system.pos[0, 0] += 1.2 * angstrom
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# Add a dummy ic to the iclist, so some delta vectors are stored with a
# minus sign. This enables to check that the (*ic).signs are implemented
# correctly.
iclist.add_ic(OopDist(1, 3, 2, 0))
iclist.add_ic(OopDist(2, 3, 1, 0))
dlist.forward()
iclist.forward()
assert abs(iclist.ictab[1]['value'] - 1.2 * angstrom) < 1e-8
# Check if the distance is invariant for permutations of the first three atoms
from itertools import permutations
for perm in permutations((1, 2, 3)):
iclist.add_ic(OopDist(perm[0], perm[1], perm[2], 0))
dlist.forward()
iclist.forward()
for ic in iclist.ictab:
if ic['kind'] == 8:
assert abs(abs(ic['value']) - 1.2 * angstrom) < 1e-8
def get_ff_formaldehyde():
# This forcefield is based on UFF, but we only really care about
# out-of-plane angles
system = get_system_formaldehyde()
# Move the C atom to make the molecule non-planar
system.pos[0, 0] += 0.2 * angstrom
# Valence part
part_valence = ForcePartValence(system)
# Harmonic bonds
part_valence.add_term(
Harmonic(3.371456e3 * kjmol / angstrom**2, 1.219 * angstrom,
Bond(0, 1)))
part_valence.add_term(
Harmonic(1.484153e3 * kjmol / angstrom**2, 1.084 * angstrom,
Bond(0, 2)))
part_valence.add_term(
Harmonic(1.484153e3 * kjmol / angstrom**2, 1.084 * angstrom,
Bond(0, 3)))
# Harmonic bends
part_valence.add_term(
Harmonic(6.91928e2 * kjmol, np.cos(120.0 * deg), BendCos(1, 0, 2)))
part_valence.add_term(
Harmonic(6.91928e2 * kjmol, np.cos(120.0 * deg), BendCos(1, 0, 3)))
part_valence.add_term(
Harmonic(2.57789e2 * kjmol, np.cos(120.0 * deg), BendCos(2, 0, 3)))
# Out-of-plane angles
part_valence.add_term(Chebychev1(6.978 * kjmol, OopCos(2, 3, 1, 0)))
part_valence.add_term(Chebychev1(6.978 * kjmol, OopCos(1, 2, 3, 0)))
part_valence.add_term(Chebychev1(6.978 * kjmol, OopCos(1, 3, 2, 0)))
return ForceField(system, [part_valence], None)
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_inversion_formaldehyde():
# Test for an inversion term made by combining a Chebychev1 energy term with
# an out-of-plane cosine.
oop_fc = 1.0
system = get_system_formaldehyde()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
#Add a term for all out-of-plane angles with the carbon as center
vlist.add_term(Chebychev1(oop_fc, OopCos(2, 3, 1, 0)))
vlist.add_term(Chebychev1(oop_fc, OopCos(1, 2, 3, 0)))
vlist.add_term(Chebychev1(oop_fc, OopCos(1, 3, 2, 0)))
dlist.forward()
iclist.forward()
energy = vlist.forward()
#For a planar molecule the energy should be zero
check_energy = 0.0
assert abs(energy - check_energy) < 1e-8
#Now put the carbon out of the plane; the energy shoud rise
system.pos[0, 0] += 1.00000000 * angstrom
dlist.forward()
iclist.forward()
energy = vlist.forward()
#Calculate the energy manually
check_energy = 0.0
for term in iclist.ictab:
#Select the terms corresponding to oop cosines
if term[0] == 6:
check_energy += 0.5 * oop_fc * (1.0 - term['value'])
assert abs(energy - check_energy) < 1e-8
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_inversion_formaldehyde():
# Test for an inversion term made by combining a Chebychev1 energy term with
# an out-of-plane cosine.
oop_fc = 1.0
system = get_system_formaldehyde()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
#Add a term for all out-of-plane angles with the carbon as center
vlist.add_term(Chebychev1(oop_fc, OopCos(2,3,1,0)))
vlist.add_term(Chebychev1(oop_fc, OopCos(1,2,3,0)))
vlist.add_term(Chebychev1(oop_fc, OopCos(1,3,2,0)))
dlist.forward()
iclist.forward()
energy = vlist.forward()
#For a planar molecule the energy should be zero
check_energy = 0.0
assert abs(energy - check_energy) < 1e-8
#Now put the carbon out of the plane; the energy shoud rise
system.pos[0,0] += 1.00000000*angstrom
dlist.forward()
iclist.forward()
energy = vlist.forward()
#Calculate the energy manually
check_energy = 0.0
for term in iclist.ictab:
#Select the terms corresponding to oop cosines
if term[0]==6:
check_energy += 0.5*oop_fc*(1.0-term['value'])
assert abs(energy - check_energy) < 1e-8
def test_generator_formaldehyde_cross_consistency():
system = get_system_formaldehyde()
fn_pars1 = pkg_resources.resource_filename(__name__, '../../data/test/parameters_formaldehyde_cross.txt')
ff1 = ForceField.generate(system, fn_pars1)
fn_pars2 = pkg_resources.resource_filename(__name__, '../../data/test/parameters_formaldehyde_cross_alt.txt')
ff2 = ForceField.generate(system, fn_pars2)
energy1 = ff1.compute()
energy2 = ff2.compute()
np.testing.assert_allclose(energy1, energy2)
def test_oop_angle_formaldehyde():
system = get_system_formaldehyde()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(OopCos(2,3,1,0))
iclist.add_ic(OopAngle(2,3,1,0))
dlist.forward()
iclist.forward()
assert abs( iclist.ictab[0]['value'] - 1.0 ) < 1e-8
assert abs( iclist.ictab[1]['value'] - 0.0 ) < 1e-8
def test_oop_angle_formaldehyde():
system = get_system_formaldehyde()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(OopCos(2, 3, 1, 0))
iclist.add_ic(OopAngle(2, 3, 1, 0))
dlist.forward()
iclist.forward()
assert abs(iclist.ictab[0]['value'] - 1.0) < 1e-8
assert abs(iclist.ictab[1]['value'] - 0.0) < 1e-8
def test_generator_formaldehyde_oopangle():
system = get_system_formaldehyde()
fn_pars = pkg_resources.resource_filename(__name__, '../../data/test/parameters_formaldehyde_inversion.txt')
ff = ForceField.generate(system, fn_pars)
assert len(ff.parts) == 1
assert isinstance(ff.parts[0], ForcePartValence)
part_valence = ff.parts[0]
assert part_valence.dlist.ndelta == 3
assert (part_valence.iclist.ictab['kind'][0:3] == 6).all()
assert part_valence.iclist.nic == 3
assert (part_valence.vlist.vtab['kind'][0:3] == 5).all()
assert abs(part_valence.vlist.vtab['par0'] - 1.0*kjmol).all() < 1e-10
assert part_valence.vlist.nv == 3
def test_oop_meanangle_formaldehyde():
system = get_system_formaldehyde()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(OopMeanAngle(2,3,1,0))
iclist.add_ic(OopAngle(1,2,3,0))
iclist.add_ic(OopAngle(2,3,1,0))
iclist.add_ic(OopAngle(3,1,2,0))
dlist.forward()
iclist.forward()
mean = 0.0
for i in xrange(4):
assert abs( iclist.ictab[i]['value'] - 0.0) < 1e-8
if i > 0: mean += iclist.ictab[i]['value']
mean /= 3
assert abs(iclist.ictab[0]['value'] - mean) < 1e-8
def test_oop_meanangle_formaldehyde():
system = get_system_formaldehyde()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(OopMeanAngle(2, 3, 1, 0))
iclist.add_ic(OopAngle(1, 2, 3, 0))
iclist.add_ic(OopAngle(2, 3, 1, 0))
iclist.add_ic(OopAngle(3, 1, 2, 0))
dlist.forward()
iclist.forward()
mean = 0.0
for i in range(4):
assert abs(iclist.ictab[i]['value'] - 0.0) < 1e-8
if i > 0: mean += iclist.ictab[i]['value']
mean /= 3
assert abs(iclist.ictab[0]['value'] - mean) < 1e-8
def get_ff_formaldehyde():
# This forcefield is based on UFF, but we only really care about
# out-of-plane angles
system = get_system_formaldehyde()
# Move the C atom to make the molecule non-planar
system.pos[0,0] += 0.2*angstrom
# Valence part
part_valence = ForcePartValence(system)
# Harmonic bonds
part_valence.add_term(Harmonic(3.371456e3*kjmol/angstrom**2, 1.219*angstrom, Bond(0, 1)))
part_valence.add_term(Harmonic(1.484153e3*kjmol/angstrom**2, 1.084*angstrom, Bond(0, 2)))
part_valence.add_term(Harmonic(1.484153e3*kjmol/angstrom**2, 1.084*angstrom, Bond(0, 3)))
# Harmonic bends
part_valence.add_term(Harmonic(6.91928e2*kjmol, np.cos(120.0*deg), BendCos(1,0,2)))
part_valence.add_term(Harmonic(6.91928e2*kjmol, np.cos(120.0*deg), BendCos(1,0,3)))
part_valence.add_term(Harmonic(2.57789e2*kjmol, np.cos(120.0*deg), BendCos(2,0,3)))
# Out-of-plane angles
part_valence.add_term(Chebychev1(6.978*kjmol, OopCos(2,3,1,0)))
part_valence.add_term(Chebychev1(6.978*kjmol, OopCos(1,2,3,0)))
part_valence.add_term(Chebychev1(6.978*kjmol, OopCos(1,3,2,0)))
return ForceField(system, [part_valence], None)
def test_generator_formaldehyde_cross():
system = get_system_formaldehyde()
fn_pars = pkg_resources.resource_filename(__name__, '../../data/test/parameters_formaldehyde_cross.txt')
ff = ForceField.generate(system, fn_pars)
assert len(ff.parts) == 1
assert isinstance(ff.parts[0], ForcePartValence)
part_valence = ff.parts[0]
assert part_valence.dlist.ndelta == 3
for i, j in system.bonds:
row0 = part_valence.dlist.lookup.get((i, j))
row1 = part_valence.dlist.lookup.get((j, i))
assert row0 is not None or row1 is not None
assert part_valence.iclist.nic == 5
vlist = part_valence.vlist
iclist = vlist.iclist
assert part_valence.vlist.nv == 6
for irow in range(vlist.nv):
row = vlist.vtab[irow]
assert row['kind'] == 3
atoms = vlist.lookup_atoms(irow)
if atoms in ( [[[2, 0]], [[0, 1]]], [[[3, 0]], [[0, 1]]] ):
# Bond-Bond H-C-O
np.testing.assert_allclose(row['par0'], 20.0*(kjmol/angstrom**2), rtol=0.0, atol=1e-10)
np.testing.assert_allclose(row['par1'], 0.947*angstrom, rtol=0.0, atol=1e-10)
np.testing.assert_allclose(row['par2'], 1.23*angstrom, rtol=0.0, atol=1e-10)
elif atoms in ( [[[2, 0]], [[0, 2], [0, 1]]], [[[3, 0]], [[0, 3], [0, 1]]] ):
# Bond-Angle H-C-O
np.testing.assert_allclose(row['par0'], 10.0*(kjmol/angstrom/rad), rtol=0.0, atol=1e-10)
np.testing.assert_allclose(row['par1'], 0.947*angstrom, rtol=0.0, atol=1e-10)
np.testing.assert_allclose(row['par2'], 121.0*deg, rtol=0.0, atol=1e-10)
elif atoms in ( [[[0, 1]], [[0, 2], [0, 1]]], [[[0, 1]], [[0, 3], [0, 1]]] ):
# Bond-Angle O-C-H
np.testing.assert_allclose(row['par0'], 15.0*(kjmol/angstrom/rad), rtol=0.0, atol=1e-10)
np.testing.assert_allclose(row['par1'], 1.23*angstrom, rtol=0.0, atol=1e-10)
np.testing.assert_allclose(row['par2'], 121.0*deg, rtol=0.0, atol=1e-10)
else:
raise AssertionError('Some internal coordinates were missing.')
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_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)