def electrostatics_test(b, r=3, r0=None):
if r0 is None:
r0 = np.sum(b.get_positions(), axis=0) / len(a)
k1 = [(1, 1)[i] for i in b.get_pbc()]
k3 = [(1, 3)[i] for i in b.get_pbc()]
# Check multipole moments
mp = MultipoleExpansion(L_MAX, r, k3, r0)
mp.update(b, b.get_initial_charges())
# Store moments and field for later
moments = mp.get_moments()
M0_l_mp, M_L_mp = moments[1]
phi_mp, E_mp = mp.get_potential_and_field(b)
# Check if the field is the derivative of the potential
b.set_calculator(mp)
ffd, f0, err = check_forces(b)
if debug:
print("Finite differences forces:")
print(ffd)
print("Analytical forces:")
print(f0)
print("Error:")
print(err)
assert err < TOL_FOR
# ffd, f0, err = check_field(b, mp)
# if debug:
# print "Finite differences field:"
# print ffd
# print "Analytical field:"
# print f0
# print "Error:"
# print err
#
# assert err < TOL_FIELD
# Next neighbor shell by direct summation
mp = MultipoleExpansion(L_MAX, r * r * r, k1, r0)
mp.update(b, b.get_initial_charges())
phi_dir, E_dir = mp.get_potential_and_field(b)
# Multipole moments from large cell,
# transform symmetrically around the origin
#rep = [ (r-1)/2 if i else 0 for i in b.get_pbc() ]
#rep = [ (-(r-1)/2, (r-1)/2) if i else (0, 0) for i in b.get_pbc() ]
rep = [(0, (r - 1) / 2)[i] for i in b.get_pbc()]
rep = [((0, 0), (-(r - 1) / 2, (r - 1) / 2))[i] for i in b.get_pbc()]
c = b.extended_copy(tuple(rep))
M0_l, M_L = get_moments(c.get_positions(), c.get_initial_charges(), L_MAX,
r0)
#print M_L
#print M_L_mp
err_mom0 = np.max(np.abs(M0_l - M0_l_mp))
err_mom = np.max(np.abs(M_L - M_L_mp))
if debug:
print("error(mom) = ", err_mom0, err_mom)
assert err_mom0 < TOL_MOM[r]
assert err_mom < TOL_MOM[r]
# Compare fields and potentials obtained by the multipole expansion
# and from direct summation
err_phi = np.max(np.abs(phi_mp - phi_dir))
err_E = np.max(np.abs(E_mp - E_dir))
if debug:
print("error(phi) = ", err_phi)
print("error(E) = ", err_E)
assert err_phi < TOL_PHI[r]
assert err_E < TOL_E[r]
for calc in [calc2, calc3]:
atoms.set_calculator(calc)
# Relax (twist) the structure
q = optimize.FIRE(atoms, trajectory='polyethene.trj', logfile=None)
q.run(fmax=0.5)
# Displace atoms from their equilibrium positions and check forces
atoms.rattle(0.1)
# Check electrostatics only
# atoms.set_initial_charges([1.0,1.0,1.0,1.0,-1.0,-1.0,-1.0,-1.0])
# atoms.set_calculator(calc.st.es)
# Check forces from finite differences
ffd, f0, err = check_forces(atoms, dx=1e-6)
if debug:
print "Finite differences forces:"
print ffd
print "Analytical forces:"
print f0
print "Difference:"
print abs(ffd - f0)
print "Error:"
print err
assert err < 1e-5
# Check energy conservation from a molecular dynamics run
assert check_energy_conservation(atoms,
dt=0.25 * units.fs,
for calc in [ calc2, calc3 ]:
atoms.set_calculator(calc)
# Relax (twist) the structure
q = optimize.FIRE(atoms,trajectory='polyethene.trj',logfile=None)
q.run(fmax=0.5)
# Displace atoms from their equilibrium positions and check forces
atoms.rattle(0.1)
# Check electrostatics only
# atoms.set_initial_charges([1.0,1.0,1.0,1.0,-1.0,-1.0,-1.0,-1.0])
# atoms.set_calculator(calc.st.es)
# Check forces from finite differences
ffd, f0, err = check_forces(atoms, dx=1e-6)
if debug:
print "Finite differences forces:"
print ffd
print "Analytical forces:"
print f0
print "Difference:"
print abs(ffd-f0)
print "Error:"
print err
assert err < 1e-5
# Check energy conservation from a molecular dynamics run
assert check_energy_conservation(atoms,dt=0.25*units.fs,steps=100,
tol=0.01,plot=debug)
def electrostatics_test(b, r=3, r0=None):
if r0 is None:
r0 = np.sum(b.get_positions(), axis=0)/len(a)
k1 = [ (1,1)[i] for i in b.get_pbc() ]
k3 = [ (1,3)[i] for i in b.get_pbc() ]
# Check multipole moments
mp = MultipoleExpansion(L_MAX, r, k3, r0)
mp.update(b, b.get_initial_charges())
# Store moments and field for later
moments = mp.get_moments()
M0_l_mp, M_L_mp = moments[1]
phi_mp, E_mp = mp.get_potential_and_field(b)
# Check if the field is the derivative of the potential
b.set_calculator(mp)
ffd, f0, err = check_forces(b)
if debug:
print "Finite differences forces:"
print ffd
print "Analytical forces:"
print f0
print "Error:"
print err
assert err < TOL_FOR
# ffd, f0, err = check_field(b, mp)
# if debug:
# print "Finite differences field:"
# print ffd
# print "Analytical field:"
# print f0
# print "Error:"
# print err
#
# assert err < TOL_FIELD
# Next neighbor shell by direct summation
mp = MultipoleExpansion(L_MAX, r*r*r, k1, r0)
mp.update(b, b.get_initial_charges())
phi_dir, E_dir = mp.get_potential_and_field(b)
# Multipole moments from large cell,
# transform symmetrically around the origin
#rep = [ (r-1)/2 if i else 0 for i in b.get_pbc() ]
#rep = [ (-(r-1)/2, (r-1)/2) if i else (0, 0) for i in b.get_pbc() ]
rep = [ (0,(r-1)/2)[i] for i in b.get_pbc() ]
rep = [ ((0,0),(-(r-1)/2, (r-1)/2))[i] for i in b.get_pbc() ]
c = b.extended_copy(tuple(rep))
M0_l, M_L = get_moments(c.get_positions(), c.get_initial_charges(), L_MAX, r0)
#print M_L
#print M_L_mp
err_mom0 = np.max(np.abs(M0_l-M0_l_mp))
err_mom = np.max(np.abs(M_L-M_L_mp))
if debug:
print "error(mom) = ", err_mom0, err_mom
assert err_mom0 < TOL_MOM[r]
assert err_mom < TOL_MOM[r]
# Compare fields and potentials obtained by the multipole expansion
# and from direct summation
err_phi = np.max(np.abs(phi_mp-phi_dir))
err_E = np.max(np.abs(E_mp-E_dir))
if debug:
print "error(phi) = ", err_phi
print "error(E) = ", err_E
assert err_phi < TOL_PHI[r]
assert err_E < TOL_E[r]
