def test_tailcorr_fluidum_exprep():
natom = 64
system = get_system_fluidum_grid(natom, ffatypes=['A', 'B', 'C'])
nlist = NeighborList(system)
scalings = Scalings(system)
# Initialize parameters
amps = np.array([2.0, 3.0, 4.0])
bs = np.array([4.5, 4.6, 4.7]) / angstrom
# Allocate some arrays for the pair potential
assert len(system.ffatypes) == 3
amp_cross = np.zeros((3, 3), float)
b_cross = np.zeros((3, 3), float)
amp_mix, amp_mix_coeff, b_mix, b_mix_coeff = 0, 0, 1, 0
for tr in [None, Switch3(3.0 * angstrom)]:
check_tailcorr_convergence(system,
PairPotExpRep,
'exp',
system.ffatype_ids,
amp_cross,
b_cross,
tr=tr,
amps=amps,
amp_mix=amp_mix,
amp_mix_coeff=amp_mix_coeff,
bs=bs,
b_mix=b_mix,
b_mix_coeff=b_mix_coeff)
def get_system(nmol, rho0=420.0 * kilogram / meter**3):
# Initial density
masses = np.ones((nmol, )) * (periodic[6].mass + 4 * periodic[1].mass)
# Initial volume
V0 = np.sum(masses) / rho0
# Estimate intermolecular distance based on the volume per molecule
l0 = (V0 / nmol)**(1.0 / 3.0)
# Setup the system
system = get_system_fluidum_grid(nmol, ffatypes=['CH4'], l0=l0)
system.masses = masses
return system
def test_tailcorr_fluidum_grimme():
natom = 64
system = get_system_fluidum_grid(natom)
nlist = NeighborList(system)
scalings = Scalings(system)
r0s = np.ones((natom,))*1.1*angstrom
r0s += np.random.normal(0.0,0.01*angstrom,r0s.shape[0])
c6s = np.ones((natom,))*0.2*1e-3*kjmol*nanometer**6
c6s += np.random.normal(0.0,0.01*angstrom,c6s.shape[0])
for tr in [None,Switch3(3.0*angstrom)]:
check_tailcorr_convergence(system, PairPotGrimme, 'r6', r0s, c6s, tr=tr)
def test_tailcorr_fluidum_lj():
natom = 64
system = get_system_fluidum_grid(natom)
nlist = NeighborList(system)
scalings = Scalings(system)
sigmas = np.ones((natom,))*2.1*angstrom
sigmas += np.random.normal(0.0,0.01*angstrom,sigmas.shape[0])
epsilons = np.ones((natom,))*0.15*kcalmol
epsilons += np.random.normal(0.0,0.001*kcalmol,epsilons.shape[0])
for tr in [None,Switch3(3.0*angstrom)]:
check_tailcorr_convergence(system, PairPotLJ, 'r6', sigmas, epsilons, tr=tr)
def test_tailcorr_fluidum_mm3():
natom = 64
system = get_system_fluidum_grid(natom)
nlist = NeighborList(system)
scalings = Scalings(system)
sigmas = np.ones((natom,))*1.1*angstrom
sigmas += np.random.normal(0.0,0.01*angstrom,sigmas.shape[0])
epsilons = np.ones((natom,))*0.15*kcalmol
epsilons += np.random.normal(0.0,0.001*kcalmol,epsilons.shape[0])
for onlypauli,decay in zip([0,1],['r6','exp']):
onlypaulis = np.ones((natom,),dtype=np.int32)*onlypauli
for tr in [None,Switch3(3.0*angstrom)]:
check_tailcorr_convergence(system, PairPotMM3, decay, sigmas, epsilons, onlypaulis, tr=tr)
def test_tailcorr_fluidum_grimme():
natom = 64
system = get_system_fluidum_grid(natom)
nlist = NeighborList(system)
scalings = Scalings(system)
r0s = np.ones((natom, )) * 1.1 * angstrom
r0s += np.random.normal(0.0, 0.01 * angstrom, r0s.shape[0])
c6s = np.ones((natom, )) * 0.2 * 1e-3 * kjmol * nanometer**6
c6s += np.random.normal(0.0, 0.01 * angstrom, c6s.shape[0])
for tr in [None, Switch3(3.0 * angstrom)]:
check_tailcorr_convergence(system,
PairPotGrimme,
'r6',
r0s,
c6s,
tr=tr)
def test_tailcorr_fluidum_lj():
natom = 64
system = get_system_fluidum_grid(natom)
nlist = NeighborList(system)
scalings = Scalings(system)
sigmas = np.ones((natom, )) * 2.1 * angstrom
sigmas += np.random.normal(0.0, 0.01 * angstrom, sigmas.shape[0])
epsilons = np.ones((natom, )) * 0.15 * kcalmol
epsilons += np.random.normal(0.0, 0.001 * kcalmol, epsilons.shape[0])
for tr in [None, Switch3(3.0 * angstrom)]:
check_tailcorr_convergence(system,
PairPotLJ,
'r6',
sigmas,
epsilons,
tr=tr)
def test_tailcorr_fluidum_ljcross():
system = get_system_fluidum_grid(64, ffatypes=['A','B','C','D'])
nlist = NeighborList(system)
scalings = Scalings(system)
assert system.nffatype == 4
eps_cross = np.array([[1.0,3.5,4.6,9.4],
[3.5,2.0,4.4,4.1],
[4.6,4.4,5.0,3.3],
[9.4,4.1,3.3,0.1]])*kcalmol
sig_cross = np.array([[0.2,0.5,1.6,1.4],
[0.5,1.0,2.4,1.1],
[1.6,2.4,1.0,2.3],
[1.4,1.1,2.3,0.9]])
assert np.all( np.abs( sig_cross - np.transpose(sig_cross) ) < 1e-15 )
assert np.all( np.abs( eps_cross - np.transpose(eps_cross) ) < 1e-15 )
for tr in [None,Switch3(3.0*angstrom)]:
check_tailcorr_convergence(system, PairPotLJCross, 'r6',
system.ffatype_ids, eps_cross, sig_cross, tr=tr)
def test_tailcorr_fluidum_exprep():
natom = 64
system = get_system_fluidum_grid(natom, ffatypes=['A','B','C'])
nlist = NeighborList(system)
scalings = Scalings(system)
# Initialize parameters
amps = np.array([2.0,3.0,4.0])
bs = np.array([4.5,4.6,4.7])/angstrom
# Allocate some arrays for the pair potential
assert len(system.ffatypes) == 3
amp_cross = np.zeros((3, 3), float)
b_cross = np.zeros((3, 3), float)
amp_mix, amp_mix_coeff, b_mix, b_mix_coeff = 0,0,1,0
for tr in [None,Switch3(3.0*angstrom)]:
check_tailcorr_convergence(system, PairPotExpRep, 'exp',
system.ffatype_ids, amp_cross, b_cross, tr=tr,
amps=amps, amp_mix=amp_mix, amp_mix_coeff=amp_mix_coeff,
bs=bs, b_mix=b_mix, b_mix_coeff=b_mix_coeff)
def test_tailcorr_fluidum_mm3():
natom = 64
system = get_system_fluidum_grid(natom)
nlist = NeighborList(system)
scalings = Scalings(system)
sigmas = np.ones((natom, )) * 1.1 * angstrom
sigmas += np.random.normal(0.0, 0.01 * angstrom, sigmas.shape[0])
epsilons = np.ones((natom, )) * 0.15 * kcalmol
epsilons += np.random.normal(0.0, 0.001 * kcalmol, epsilons.shape[0])
for onlypauli, decay in zip([0, 1], ['r6', 'exp']):
onlypaulis = np.ones((natom, ), dtype=np.int32) * onlypauli
for tr in [None, Switch3(3.0 * angstrom)]:
check_tailcorr_convergence(system,
PairPotMM3,
decay,
sigmas,
epsilons,
onlypaulis,
tr=tr)
def test_tailcorr_fluidum_ljcross():
system = get_system_fluidum_grid(64, ffatypes=['A', 'B', 'C', 'D'])
nlist = NeighborList(system)
scalings = Scalings(system)
assert system.nffatype == 4
eps_cross = np.array([[1.0, 3.5, 4.6, 9.4], [3.5, 2.0, 4.4, 4.1],
[4.6, 4.4, 5.0, 3.3], [9.4, 4.1, 3.3, 0.1]
]) * kcalmol
sig_cross = np.array([[0.2, 0.5, 1.6, 1.4], [0.5, 1.0, 2.4, 1.1],
[1.6, 2.4, 1.0, 2.3], [1.4, 1.1, 2.3, 0.9]])
assert np.all(np.abs(sig_cross - np.transpose(sig_cross)) < 1e-15)
assert np.all(np.abs(eps_cross - np.transpose(eps_cross)) < 1e-15)
for tr in [None, Switch3(3.0 * angstrom)]:
check_tailcorr_convergence(system,
PairPotLJCross,
'r6',
system.ffatype_ids,
eps_cross,
sig_cross,
tr=tr)