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_vlist_peroxide_dihed_cos_chebychev6():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
amp = np.random.normal(0, 1)
sign = np.random.randint(2)
if sign==0: sign = -1
vlist.add_term(Chebychev6(amp, DihedCos(0,1,2,3), sign=sign))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
psi = dihed_angle(system.pos)[0]
check_energy = 0.5*amp*(1.0+sign*np.cos(6*psi))
assert abs(energy - check_energy) < 1e-8
def test_vlist_peroxide_dihed_angle_cosine():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
mult = np.random.randint(1, 4)
amp = np.random.normal(0, 1)
phi0 = np.random.uniform(0, 2*np.pi)
vlist.add_term(Cosine(mult, amp, phi0, DihedAngle(0,1,2,3)))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
angle = dihed_angle(system.pos)[0]
check_energy = 0.5*amp*(1-np.cos(mult*(angle-phi0)))
assert abs(energy - check_energy) < 1e-8
def test_icgroup_cases():
sys = get_system_peroxide()
assert (BondGroup(sys).cases == sys.bonds).all()
assert BondGroup(sys, cases=[[1,2], [1,3]]).cases == [[1,2],[1,3]]
assert BondGroup(sys, rules=['8', '8']).cases == [[0,1]]
assert BondGroup(sys, rules=['1', '8']).cases == [[0,2],[1,3]]
assert BendGroup(sys).cases == [[2, 0, 1], [3, 1, 0]]
assert BendGroup(sys, cases=[[1,2,0], [0,1,3]]).cases == [[1,2,0],[0,1,3]]
def test_ic_list_dihedral_pernicious():
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(DihedAngle(0,1,2,3))
dlist.deltas[0] = (2.5645894177015855, -0.004063261303208772, 1.2798248429146284, 1, 2, 0.0, 0.0, 0.0)
dlist.deltas[1] = (2.0394633015500796, -0.0032335148484117426, -1.98698089493469, 2, 3, 0.0, 0.0, 0.0)
dlist.deltas[2] = (-1.8836397803889104, 0.0029844605526122576, -0.8613076025533011, 17, 3, 0.0, 0.0, 0.0)
iclist.ictab[0] = (4, 0, -1, 1, 1, 2, -1, 0, 0, 0.0, 0.0)
iclist.forward()
assert abs(abs(iclist.ictab[0]['value']) - np.pi) < 1e-8
def test_ic_list_dihedral_pernicious():
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
iclist.add_ic(DihedAngle(0, 1, 2, 3))
dlist.deltas[0] = (2.5645894177015855, -0.004063261303208772,
1.2798248429146284, 1, 2, 0.0, 0.0, 0.0)
dlist.deltas[1] = (2.0394633015500796, -0.0032335148484117426,
-1.98698089493469, 2, 3, 0.0, 0.0, 0.0)
dlist.deltas[2] = (-1.8836397803889104, 0.0029844605526122576,
-0.8613076025533011, 17, 3, 0.0, 0.0, 0.0)
iclist.ictab[0] = (4, 0, -1, 1, 1, 2, -1, 0, 0, 0.0, 0.0)
iclist.forward()
assert abs(abs(iclist.ictab[0]['value']) - np.pi) < 1e-8
def test_plumed_peroxide_bond():
system = get_system_peroxide()
# Linear restraint of the O-O bond
m, a0 = 2.3 * kjmol / angstrom, 0.9 * angstrom
# PLUMED input commands, remember that PLUMED starts counting atoms from 1
commands = "d: DISTANCE ATOMS=1,2\n"
commands += "RESTRAINT ARG=d AT=%.20f SLOPE=%.20f LABEL=restraint\n"%\
(a0/nanometer, m/kjmol*nanometer)
# Reference calculation:
def reference(system):
d = np.linalg.norm(system.pos[1] - system.pos[0])
return m * (d - a0)
check_plumed(system, commands, reference)
def test_merge():
system1 = get_system_quartz()
system2 = get_system_peroxide()
system = system1.merge(system2)
assert system1.natom + system2.natom == system.natom
assert np.all(system.numbers[:system1.natom] == system1.numbers)
assert np.all(system.numbers[system1.natom:] == system2.numbers)
assert np.all(system.pos[:system1.natom] == system1.pos)
assert np.all(system.pos[system1.natom:] == system2.pos)
assert system.charges is None
assert np.all(
[system1.get_ffatype(iatom) for iatom in range(system1.natom)
] == system.ffatypes[system.ffatype_ids[:system1.natom]])
assert np.all(
[system2.get_ffatype(iatom) for iatom in range(system2.natom)
] == system.ffatypes[system.ffatype_ids[system1.natom:]])
def test_iclist_peroxide_dihedral_angle():
number_of_tests=50
for i in xrange(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# The bonds are added randomly to get different situations in the delta list
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
iclist.add_ic(DihedAngle(0,1,2,3))
dlist.forward()
iclist.forward()
assert iclist.ictab[3]['kind']==4 #assert the third ic is DihedralAngle
assert abs(iclist.ictab[3]['value'] - dihed_angle(system.pos)[0]) < 1e-5
def test_iclist_peroxide_dihedral_cos6():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
system.pos += np.random.normal(0.0, 0.1, system.pos.shape)*angstrom
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# The bonds are added randomly to get different situations in the delta list
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
iclist.add_ic(DihedCos6(0,1,2,3))
dlist.forward()
iclist.forward()
angle = dihed_angle(system.pos)[0]
print('psi=%.3f deg: target=%.6f value=%.6f' %(angle/deg, np.cos(6*angle), iclist.ictab[3]['value']))
assert abs(iclist.ictab[3]['value'] - np.cos(6*angle)) < 1e-5
def test_iclist_peroxide_dihedral_cos():
number_of_tests = 50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# The bonds are added randomly to get different situations in the delta list
bonds = []
while len(bonds) < 3:
i0, i1 = [
int(x) for x in np.random.uniform(low=0, high=4, size=2)
] #pick 2 random atoms
if i0 == i1 or (i0, i1) in bonds or (i1, i0) in bonds: continue
if (i0, i1) in system.bonds or (i1, i0) in system.bonds:
iclist.add_ic(Bond(i0, i1))
bonds.append((i0, i1))
iclist.add_ic(DihedCos(0, 1, 2, 3))
dlist.forward()
iclist.forward()
assert iclist.ictab[3]['kind'] == 3 #assert the third ic is DihedralCos
assert abs(iclist.ictab[3]['value'] - dihed_cos(system.pos)[0]) < 1e-5
def test_vlist_peroxide_dihed_angle():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
vlist.add_term(Harmonic(1.5, 0.1 , DihedAngle(0,1,2,3)))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
angle = dihed_angle(system.pos)[0]
check_energy = 0.5*1.5*(angle-0.1)**2
assert abs(energy - check_energy) < 1e-8
def test_vlist_peroxide_dihed_angle():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
vlist.add_term(Harmonic(1.5, 0.1 , DihedAngle(0,1,2,3)))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
angle = dihed_angle(system.pos)[0]
check_energy = 0.5*1.5*(angle-0.1)**2
assert abs(energy - check_energy) < 1e-8
def test_iclist_peroxide_dihedral_cos6():
number_of_tests = 50
for i in range(number_of_tests):
system = get_system_peroxide()
system.pos += np.random.normal(0.0, 0.1, system.pos.shape) * angstrom
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# The bonds are added randomly to get different situations in the delta list
bonds = []
while len(bonds) < 3:
i0, i1 = [
int(x) for x in np.random.uniform(low=0, high=4, size=2)
] #pick 2 random atoms
if i0 == i1 or (i0, i1) in bonds or (i1, i0) in bonds: continue
if (i0, i1) in system.bonds or (i1, i0) in system.bonds:
iclist.add_ic(Bond(i0, i1))
bonds.append((i0, i1))
iclist.add_ic(DihedCos6(0, 1, 2, 3))
dlist.forward()
iclist.forward()
angle = dihed_angle(system.pos)[0]
print('psi=%.3f deg: target=%.6f value=%.6f' %
(angle / deg, np.cos(6 * angle), iclist.ictab[3]['value']))
assert abs(iclist.ictab[3]['value'] - np.cos(6 * angle)) < 1e-5
def test_iter_matches_peroxide_graphene8():
system0 = get_system_graphene8()
system1 = get_system_peroxide()
assert len(list(system0.iter_matches(system1))) == 0
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)
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_dihed_cos_peroxide():
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Harmonic(1.1, -0.2, DihedCos(0, 1, 2, 3)))
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)))
check_gpos_part(system, part)
check_vtens_part(system, part)
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_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_cut_bonds():
system = get_system_peroxide()
system.cut_bonds([0, 2])
assert (system.bonds == [[0, 2], [1, 3]]).all()