def test(self):
"""
Sets up a BMIM PF6 pair separated in y-direction with fixed cores.
Adds the Drude particles and related features (intramolecular exclusion
bonds, Thole screening) via helper functions.
Calculates the induced dipole moment and the diagonals of the
polarization tensor and compares against reference results, which where
reproduced with LAMMPS.
"""
box_l = 50
system = espressomd.System(box_l=[box_l, box_l, box_l])
np.random.seed(12)
# Reference Results, reproduced with LAMMPS
# Dipole Moments
ref_mu0_pf6 = [0.00177594, 0.16480996, -0.01605161]
ref_mu0_c1 = [0.00076652, 0.15238767, 0.00135291]
ref_mu0_c2 = [-0.00020222, 0.11084197, 0.00135842]
ref_mu0_c3 = [0.00059177, 0.23949626, -0.05238468]
ref_mu0_bmim = [0.00115606, 0.5027259, -0.04967335]
# Polarisation Tensor diagonals
ref_pol_pf6 = [
4.5535698335873445, 4.7558611769477697, 4.5546580162000554
]
ref_pol_bmim = [
13.126868394164262, 14.392582501485913, 16.824150151623762
]
# TIMESTEP
fs_to_md_time = 1.0e-2
time_step_fs = 0.5
dt = time_step_fs * fs_to_md_time
# COM TEMPERATURE
# Global thermostat temperature, for com and langevin.
# LangevinPerParticle temperature is set to 0 for drude and core to
# properly account for com forces. Like that, langevin thermostat can
# still be used for non-drude particles
SI_temperature = 300.0
gamma_com = 1.0
kb_kjmol = 0.0083145
temperature_com = SI_temperature * kb_kjmol
# COULOMB PREFACTOR (elementary charge)^2 / (4*pi*epsilon_0) in
# Angstrom * kJ/mol
coulomb_prefactor = 1.67101e5 * kb_kjmol
# POLARIZATION
# polarization = 1.0 (in (Angstrom^3)_CGS)
# alpha_SI = 4*Pi*eps_0 alpha_CGS;
# 4*Pi*epsilon_0*Angstrom^3/((elementary charge)^2*Angstrom^2*N_A/kJ)
conv_pol_CGS_SI = 7.197586e-4
# alpha = conv_pol_CGS_SI*args.polarization
# DRUDE/TOTAL MASS
# lamoureux03 used values 0.1-0.8 g/mol for drude mass
mass_drude = 0.8
mass_tot = 100.0
mass_core = mass_tot - mass_drude
mass_red_drude = mass_drude * mass_core / mass_tot
# SPRING CONSTANT DRUDE
# Used 1000kcal/mol/A^2 from lamoureux03a table 1 p 3031
k_drude = 4184.0
# in kJ/mol/A^2
T_spring = 2.0 * np.pi * np.sqrt(mass_drude / k_drude)
# T_spring_fs = T_spring/fs_to_md_time
# Period of free oscillation: T_spring = 2Pi/w; w = sqrt(k_d/m_d)
# TEMP DRUDE
# Used T* = 1K from lamoureux03a p 3031 (2) 'Cold drude oscillators
# regime'
SI_temperature_drude = 1.0
temperature_drude = SI_temperature_drude * kb_kjmol
# GAMMA DRUDE
# Thermostat relaxation time should be similar to T_spring
gamma_drude = mass_red_drude / T_spring
system.cell_system.skin = 0.4
system.time_step = dt
# Forcefield
types = {
"PF6": 0,
"BMIM_C1": 1,
"BMIM_C2": 2,
"BMIM_C3": 3,
"BMIM_COM": 4,
"PF6_D": 5,
"BMIM_C1_D": 6,
"BMIM_C2_D": 7,
"BMIM_C3_D": 8
}
charges = {
"PF6": -0.78,
"BMIM_C1": 0.4374,
"BMIM_C2": 0.1578,
"BMIM_C3": 0.1848,
"BMIM_COM": 0
}
polarizations = {
"PF6": 4.653,
"BMIM_C1": 5.693,
"BMIM_C2": 2.103,
"BMIM_C3": 7.409
}
masses = {
"PF6": 144.96,
"BMIM_C1": 67.07,
"BMIM_C2": 15.04,
"BMIM_C3": 57.12,
"BMIM_COM": 0
}
masses["BMIM_COM"] = masses["BMIM_C1"] + \
masses["BMIM_C2"] + masses["BMIM_C3"]
box_center = 0.5 * np.array(3 * [box_l])
system.min_global_cut = 3.5
# Place Particles
dmol = 5.0
# Test Anion
pos_pf6 = box_center + np.array([0, dmol, 0])
system.part.add(id=0,
type=types["PF6"],
pos=pos_pf6,
q=charges["PF6"],
mass=masses["PF6"],
fix=[1, 1, 1])
pos_com = box_center - np.array([0, dmol, 0])
system.part.add(id=2,
type=types["BMIM_C1"],
pos=pos_com + [0, -0.527, 1.365],
q=charges["BMIM_C1"],
mass=masses["BMIM_C1"],
fix=[1, 1, 1])
system.part.add(id=4,
type=types["BMIM_C2"],
pos=pos_com + [0, 1.641, 2.987],
q=charges["BMIM_C2"],
mass=masses["BMIM_C2"],
fix=[1, 1, 1])
system.part.add(id=6,
type=types["BMIM_C3"],
pos=pos_com + [0, 0.187, -2.389],
q=charges["BMIM_C3"],
mass=masses["BMIM_C3"],
fix=[1, 1, 1])
system.thermostat.set_langevin(kT=temperature_com,
gamma=gamma_com,
seed=42)
p3m = espressomd.electrostatics.P3M(prefactor=coulomb_prefactor,
accuracy=1e-4,
mesh=3 * [18],
cao=5)
system.actors.add(p3m)
# Drude related Bonds
thermalized_dist_bond = espressomd.interactions.ThermalizedBond(
temp_com=temperature_com,
gamma_com=gamma_com,
r_cut=1.0,
temp_distance=temperature_drude,
gamma_distance=gamma_drude,
seed=123)
harmonic_bond = espressomd.interactions.HarmonicBond(k=k_drude,
r_0=0.0,
r_cut=1.0)
system.bonded_inter.add(thermalized_dist_bond)
system.bonded_inter.add(harmonic_bond)
drude_helpers.add_drude_particle_to_core(
system, harmonic_bond, thermalized_dist_bond, system.part[0], 1,
types["PF6_D"], polarizations["PF6"], mass_drude,
coulomb_prefactor, 2.0)
drude_helpers.add_drude_particle_to_core(
system, harmonic_bond, thermalized_dist_bond, system.part[2], 3,
types["BMIM_C1_D"], polarizations["BMIM_C1"], mass_drude,
coulomb_prefactor, 2.0)
drude_helpers.add_drude_particle_to_core(
system, harmonic_bond, thermalized_dist_bond, system.part[4], 5,
types["BMIM_C2_D"], polarizations["BMIM_C2"], mass_drude,
coulomb_prefactor, 2.0)
drude_helpers.add_drude_particle_to_core(
system, harmonic_bond, thermalized_dist_bond, system.part[6], 7,
types["BMIM_C3_D"], polarizations["BMIM_C3"], mass_drude,
coulomb_prefactor, 2.0)
# Setup and add Drude-Core SR exclusion bonds
drude_helpers.setup_and_add_drude_exclusion_bonds(system)
# Setup intramol SR exclusion bonds once
drude_helpers.setup_intramol_exclusion_bonds(
system, [6, 7, 8], [1, 2, 3],
[charges["BMIM_C1"], charges["BMIM_C2"], charges["BMIM_C3"]])
# Add bonds per molecule
drude_helpers.add_intramol_exclusion_bonds(system, [3, 5, 7],
[2, 4, 6])
# Thole
drude_helpers.add_all_thole(system)
def dipole_moment(id_core, id_drude):
pc = system.part[id_core]
pd = system.part[id_drude]
v = pd.pos - pc.pos
return pd.q * v
def measure_dipole_moments():
dm_pf6 = []
dm_C1 = []
dm_C2 = []
dm_C3 = []
system.integrator.run(115)
for _ in range(100):
system.integrator.run(1)
dm_pf6.append(dipole_moment(0, 1))
dm_C1.append(dipole_moment(2, 3))
dm_C2.append(dipole_moment(4, 5))
dm_C3.append(dipole_moment(6, 7))
dm_pf6_m = np.mean(dm_pf6, axis=0)
dm_C1_m = np.mean(dm_C1, axis=0)
dm_C2_m = np.mean(dm_C2, axis=0)
dm_C3_m = np.mean(dm_C3, axis=0)
dm_sum_bmim = dm_C1_m + dm_C2_m + dm_C3_m
res = dm_pf6_m, dm_C1_m, dm_C2_m, dm_C3_m, dm_sum_bmim
return res
def setElectricField(E):
E = np.array(E)
for p in system.part:
p.ext_force = p.q * E
def calc_pol(mu0, muE, E):
pol = (muE - mu0) / E / conv_pol_CGS_SI
return pol
def measure_pol(Es, dim):
E = [0.0, 0.0, 0.0]
E[dim] = Es
setElectricField(E)
mux_pf6, _, _, _, mux_bmim = measure_dipole_moments()
return calc_pol(mu0_pf6[dim], mux_pf6[dim],
Es), calc_pol(mu0_bmim[dim], mux_bmim[dim], Es)
mu0_pf6, mu0_c1, mu0_c2, mu0_c3, mu0_bmim = measure_dipole_moments()
eA_to_Debye = 4.8032047
atol = 1e-2
rtol = 1e-2
np.testing.assert_allclose(ref_mu0_pf6,
eA_to_Debye * mu0_pf6,
atol=atol,
rtol=rtol)
np.testing.assert_allclose(ref_mu0_c1,
eA_to_Debye * mu0_c1,
atol=atol,
rtol=rtol)
np.testing.assert_allclose(ref_mu0_c2,
eA_to_Debye * mu0_c2,
atol=atol,
rtol=rtol)
np.testing.assert_allclose(ref_mu0_c3,
eA_to_Debye * mu0_c3,
atol=atol,
rtol=rtol)
np.testing.assert_allclose(ref_mu0_bmim,
eA_to_Debye * mu0_bmim,
atol=atol,
rtol=rtol)
pol_pf6 = []
pol_bmim = []
# E = 1 V/A in kJ / (Avogadro Number) / Angstrom / elementary charge
Efield = 96.48536
res = measure_pol(Efield, 0)
pol_pf6.append(res[0])
pol_bmim.append(res[1])
res = measure_pol(Efield, 1)
pol_pf6.append(res[0])
pol_bmim.append(res[1])
res = measure_pol(Efield, 2)
pol_pf6.append(res[0])
pol_bmim.append(res[1])
np.testing.assert_allclose(ref_pol_pf6, pol_pf6, atol=atol, rtol=rtol)
np.testing.assert_allclose(ref_pol_bmim,
pol_bmim,
atol=atol,
rtol=rtol)
for i in cation_c2_ids:
drude_helpers.add_drude_particle_to_core(
system, harmonic_bond, thermalized_dist_bond, system.part[i],
i + 1, types["BMIM_C2_D"], polarizations["BMIM_C2"],
args.mass_drude, coulomb_prefactor)
for i in cation_c3_ids:
drude_helpers.add_drude_particle_to_core(
system, harmonic_bond, thermalized_dist_bond, system.part[i],
i + 1, types["BMIM_C3_D"], polarizations["BMIM_C3"],
args.mass_drude, coulomb_prefactor)
drude_helpers.setup_and_add_drude_exclusion_bonds(system)
if args.thole:
print("-->Adding Thole interactions")
drude_helpers.add_all_thole(system)
if args.intra_ex:
# SETUP BONDS ONCE
print("-->Adding intramolecular exclusions")
drude_helpers.setup_intramol_exclusion_bonds(
system,
[types["BMIM_C1_D"], types["BMIM_C2_D"], types["BMIM_C3_D"]],
[types["BMIM_C1"], types["BMIM_C2"], types["BMIM_C3"]],
[charges["BMIM_C1"], charges["BMIM_C2"], charges["BMIM_C3"]])
# ADD SR EX BONDS PER MOLECULE
for i in cation_c1_ids:
drude_helpers.add_intramol_exclusion_bonds(system,
[i + 1, i + 3, i + 5],
[i, i + 2, i + 4])
