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_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_iclist_quartz_bend_cos():
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(BendCos(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_cos([delta0, np.zeros(3, float), delta2])[0]) < 1e-5
def test_iclist_quartz_bend_cos():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
angles = []
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
iclist.add_ic(BendCos(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_cos([delta0, np.zeros(3, float), delta2])[0]) < 1e-5