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_vlist_dihedral_cos_mil53():
system = get_system_mil53()
part = ForcePartValence(system)
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
fc = 2.1 + 0.01 * (0.3 * i1 + 0.7 * i2)
part.add_term(
PolyFour([0.0, -2.0 * fc, 0.0, 0.0],
DihedCos(i0, i1, i2, i3)))
energy = part.compute()
check_energy = 0.0
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
fc = 2.1 + 0.01 * (0.3 * i1 + 0.7 * i2)
delta0 = system.pos[i0] - system.pos[i1]
delta1 = system.pos[i2] - system.pos[i1]
delta2 = system.pos[i3] - system.pos[i2]
system.cell.mic(delta0)
system.cell.mic(delta1)
system.cell.mic(delta2)
cos = dihed_cos(
[delta0,
np.zeros(3, float), delta1, delta1 + delta2])[0]
check_energy += -2.0 * fc * cos**2
if not abs(energy - check_energy) < 1e-8:
raise AssertionError("Energy should be %10.9e, instead it is %10.9e" %
(check_energy, energy))
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_vlist_dihedral_cos_mil53():
system = get_system_mil53()
part = ForcePartValence(system)
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
fc = 2.1 + 0.01*(0.3*i1 + 0.7*i2)
part.add_term(PolyFour([0.0,-2.0*fc,0.0,0.0],DihedCos(i0,i1,i2,i3)))
energy = part.compute()
check_energy = 0.0
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
fc = 2.1 + 0.01*(0.3*i1 + 0.7*i2)
delta0 = system.pos[i0] - system.pos[i1]
delta1 = system.pos[i2] - system.pos[i1]
delta2 = system.pos[i3] - system.pos[i2]
system.cell.mic(delta0)
system.cell.mic(delta1)
system.cell.mic(delta2)
cos = dihed_cos([delta0, np.zeros(3, float), delta1, delta1+delta2])[0]
check_energy += -2.0*fc*cos**2
if not abs(energy - check_energy) < 1e-8:
raise AssertionError("Energy should be %10.9e, instead it is %10.9e" %(check_energy, energy))
def test_scaling_mil53():
system = get_system_mil53()
try:
scalings = Scalings(system)
success = False
except AssertionError:
success = True
assert success
def test_scaling_mil53():
system = get_system_mil53()
try:
scalings = Scalings(system)
success = False
except AssertionError:
success = True
assert success
def test_iclist_grad_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"],
]
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
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(DihedCos(i0,i1,i2,i3))
ic = iclist.ictab[0]
dlist.forward()
iclist.forward()
ic['grad'] = 1.0
iclist.back()
cos = ic['value']
grad_d0 = np.array([dlist.deltas[ic['i0']]['gx'], dlist.deltas[ic['i0']]['gy'], dlist.deltas[ic['i0']]['gz']])
grad_d1 = np.array([dlist.deltas[ic['i1']]['gx'], dlist.deltas[ic['i1']]['gy'], dlist.deltas[ic['i1']]['gz']])
grad_d2 = np.array([dlist.deltas[ic['i2']]['gx'], dlist.deltas[ic['i2']]['gy'], dlist.deltas[ic['i2']]['gz']])
delta0 = system.pos[i0] - system.pos[i1]
delta1 = system.pos[i2] - system.pos[i1]
delta2 = system.pos[i3] - system.pos[i2]
system.cell.mic(delta0)
system.cell.mic(delta1)
system.cell.mic(delta2)
check_cos, check_grad = dihed_cos([delta0, np.zeros(3, float), delta1, delta1+delta2],deriv=1)
check_grad_d0 = check_grad[0,:]
check_grad_d1 = -check_grad[0,:] - check_grad[1,:]
check_grad_d2 = check_grad[3,:]
if not abs(ic['value'] - check_cos) < 1e-8:
raise AssertionError("Dihed cos (%s[%i],%s[%i],%s[%i],%s[%i]) should have value %10.9e, instead it is %10.9e" %(
system.get_ffatype(i0),i0,
system.get_ffatype(i1),i1,
system.get_ffatype(i2),i2,
system.get_ffatype(i3),i3,
check_cos,
cos
))
if not np.sqrt(sum( (grad_d0 - check_grad_d0)**2 )) < 1e-8:
raise AssertionError("Dihed cos (%s[%i],%s[%i],%s[%i],%s[%i]) should have delta0_grad [%12.9f,%12.9f,%12.9f], \n"
"instead it is [%12.9f,%12.9f,%12.9f]" %(
system.get_ffatype(i0),i0,
system.get_ffatype(i1),i1,
system.get_ffatype(i2),i2,
system.get_ffatype(i3),i3,
check_grad_d0[0], check_grad_d0[1], check_grad_d0[2],
grad_d0[0], grad_d0[1], grad_d0[2],
))
if not np.sqrt(sum( (grad_d1 - check_grad_d1)**2 )) < 1e-8:
raise AssertionError("Dihed cos (%s[%i],%s[%i],%s[%i],%s[%i]) should have delta1_grad [%12.9f,%12.9f,%12.9f], \n"
"instead it is [%12.9f,%12.9f,%12.9f]" %(
system.get_ffatype(i0),i0,
system.get_ffatype(i1),i1,
system.get_ffatype(i2),i2,
system.get_ffatype(i3),i3,
check_grad_d1[0], check_grad_d1[1], check_grad_d1[2],
grad_d1[0], grad_d1[1], grad_d1[2],
))
if not np.sqrt(sum( (grad_d2 - check_grad_d2)**2 )) < 1e-8:
raise AssertionError("Dihed cos (%s[%i],%s[%i],%s[%i],%s[%i]) should have delta2_grad [%12.9f,%12.9f,%12.9f], \n"
"instead it is [%12.9f,%12.9f,%12.9f]" %(
system.get_ffatype(i0),i0,
system.get_ffatype(i1),i1,
system.get_ffatype(i2),i2,
system.get_ffatype(i3),i3,
check_grad_d2[0], check_grad_d2[1], check_grad_d2[2],
grad_d2[0], grad_d2[1], grad_d2[2],
))
def test_iclist_grad_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"],
]
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
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(DihedCos(i0, i1, i2, i3))
ic = iclist.ictab[0]
dlist.forward()
iclist.forward()
ic['grad'] = 1.0
iclist.back()
cos = ic['value']
grad_d0 = np.array([
dlist.deltas[ic['i0']]['gx'], dlist.deltas[ic['i0']]['gy'],
dlist.deltas[ic['i0']]['gz']
])
grad_d1 = np.array([
dlist.deltas[ic['i1']]['gx'], dlist.deltas[ic['i1']]['gy'],
dlist.deltas[ic['i1']]['gz']
])
grad_d2 = np.array([
dlist.deltas[ic['i2']]['gx'], dlist.deltas[ic['i2']]['gy'],
dlist.deltas[ic['i2']]['gz']
])
delta0 = system.pos[i0] - system.pos[i1]
delta1 = system.pos[i2] - system.pos[i1]
delta2 = system.pos[i3] - system.pos[i2]
system.cell.mic(delta0)
system.cell.mic(delta1)
system.cell.mic(delta2)
check_cos, check_grad = dihed_cos(
[delta0,
np.zeros(3, float), delta1, delta1 + delta2],
deriv=1)
check_grad_d0 = check_grad[0, :]
check_grad_d1 = -check_grad[0, :] - check_grad[1, :]
check_grad_d2 = check_grad[3, :]
if not abs(ic['value'] - check_cos) < 1e-8:
raise AssertionError(
"Dihed cos (%s[%i],%s[%i],%s[%i],%s[%i]) should have value %10.9e, instead it is %10.9e"
% (system.get_ffatype(i0), i0, system.get_ffatype(i1),
i1, system.get_ffatype(i2), i2,
system.get_ffatype(i3), i3, check_cos, cos))
if not np.sqrt(sum((grad_d0 - check_grad_d0)**2)) < 1e-8:
raise AssertionError(
"Dihed cos (%s[%i],%s[%i],%s[%i],%s[%i]) should have delta0_grad [%12.9f,%12.9f,%12.9f], \n"
"instead it is [%12.9f,%12.9f,%12.9f]" % (
system.get_ffatype(i0),
i0,
system.get_ffatype(i1),
i1,
system.get_ffatype(i2),
i2,
system.get_ffatype(i3),
i3,
check_grad_d0[0],
check_grad_d0[1],
check_grad_d0[2],
grad_d0[0],
grad_d0[1],
grad_d0[2],
))
if not np.sqrt(sum((grad_d1 - check_grad_d1)**2)) < 1e-8:
raise AssertionError(
"Dihed cos (%s[%i],%s[%i],%s[%i],%s[%i]) should have delta1_grad [%12.9f,%12.9f,%12.9f], \n"
"instead it is [%12.9f,%12.9f,%12.9f]" % (
system.get_ffatype(i0),
i0,
system.get_ffatype(i1),
i1,
system.get_ffatype(i2),
i2,
system.get_ffatype(i3),
i3,
check_grad_d1[0],
check_grad_d1[1],
check_grad_d1[2],
grad_d1[0],
grad_d1[1],
grad_d1[2],
))
if not np.sqrt(sum((grad_d2 - check_grad_d2)**2)) < 1e-8:
raise AssertionError(
"Dihed cos (%s[%i],%s[%i],%s[%i],%s[%i]) should have delta2_grad [%12.9f,%12.9f,%12.9f], \n"
"instead it is [%12.9f,%12.9f,%12.9f]" % (
system.get_ffatype(i0),
i0,
system.get_ffatype(i1),
i1,
system.get_ffatype(i2),
i2,
system.get_ffatype(i3),
i3,
check_grad_d2[0],
check_grad_d2[1],
check_grad_d2[2],
grad_d2[0],
grad_d2[1],
grad_d2[2],
))
def test_iclist_mil53_dihedral_angles():
system = get_system_mil53()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
ic_values = []
gpos = np.zeros(system.pos.shape)
forbidden_dihedrals = [
["O_HY", "AL", "O_HY", "AL"],
["O_HY", "AL", "O_HY", "H_HY"],
["O_CA", "AL", "O_CA", "C_CA"],
]
for i1, i2 in system.bonds:
# Add bonds here to avoid that all ic signs are +1
iclist.add_ic(Bond(i2, i1))
for i0 in system.neighs1[i1]:
if i0 == i2: continue
for i3 in system.neighs1[i2]:
if i3 == i1: continue
# Compute using molmod
delta0 = system.pos[i0] - system.pos[i1]
delta1 = system.pos[i2] - system.pos[i1]
delta2 = system.pos[i3] - system.pos[i2]
system.cell.mic(delta0)
system.cell.mic(delta1)
system.cell.mic(delta2)
pos = np.zeros((4, 3))
pos[0] = system.pos[i1] + delta0
pos[1] = system.pos[i1]
pos[2] = system.pos[i1] + delta1
pos[3] = pos[2] + delta2
phi0, dphi0 = dihed_angle(pos, deriv=1)
# Compute value using yaff
iic = iclist.add_ic(DihedAngle(i0, i1, i2, i3))
ic = iclist.ictab[iic]
dlist.forward()
iclist.forward()
phi1 = ic['value']
if np.abs(phi1 - phi0) > 1e-8:
raise AssertionError(
"DihedralAngle(%d,%d,%d,%d): molmod "
"value = %12.8f yaff value = %12.8f diff = %12.2e" %
(i0, i1, i2, i3, phi0, phi1, phi0 - phi1))
# Compute derivative using yaff
gpos[:] = 0.0
ic['grad'] = 1.0
iclist.back()
dlist.back(gpos, None)
# Derivative of DihedCos fails in these cases, and DihedAngle
# derivatives are base on this
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
ddiff = gpos[[i0, i1, i2, i3]] - dphi0
if np.any(np.abs(ddiff) > 1e-6):
raise AssertionError(
"DihedralAngle(%d,%d,%d,%d): largest "
"absolute derivative deviation = %12.2e" %
(i0, i1, i2, i3, np.amax(np.abs(ddiff))))
def test_scaling_mil53():
system = get_system_mil53()
with assert_raises(AssertionError):
scalings = Scalings(system)
def test_scaling_mil53():
system = get_system_mil53()
with assert_raises(AssertionError):
scalings = Scalings(system)