def test_mcmd_system():
system_file = pkg_resources.resource_filename(__name__,
'../data/lp_avg.chk')
ff_file = pkg_resources.resource_filename(__name__, '../data/pars.txt')
adsorbate_file = pkg_resources.resource_filename(__name__,
'../data/argon.chk')
T = 87 * kelvin
P = 1 * bar
MD_trial_fraction = 0.001
rcut = 15 * angstrom
from yaff.pes.eos import PREOS
eos = PREOS.from_name('argon')
fugacity = eos.calculate_fugacity(T, P)
mu = eos.calculate_mu(T, P)
print('Mu: ', mu / kjmol)
print('Fug: ', fugacity / bar)
mcmd = MCMD(system_file,
adsorbate_file,
ff_file,
T,
P,
fugacity,
MD_trial_fraction,
rcut,
fixed_N=25,
write_h5s=True)
mcmd.run_GCMC(5000, 100)
def test_mm3_tail():
system_file = pkg_resources.resource_filename(__name__, '../data/lp_avg.chk')
ff_file = pkg_resources.resource_filename(__name__, '../data/pars.txt')
adsorbate_file = pkg_resources.resource_filename(__name__, '../data/argon.chk')
T = 87 * kelvin
P = 1 * bar
MD_trial_fraction = 0.000
fugacity = P
mcmd = MCMD(system_file, adsorbate_file, ff_file, T, P, fugacity, MD_trial_fraction, 8*angstrom, fixed_N = 25)
# Try 10 configurations
for i in range(10):
N_frame = len(mcmd.pos)
new_pos = random_ads(mcmd.pos_ads, mcmd.rvecs)
pos = np.append(mcmd.pos, new_pos, axis=0)
Z_ads = 1
plen = len(pos)
e_vdw_insert_base = MM3_insert(pos, len(pos)-mcmd.nads, mcmd.N_frame, mcmd.rvecs_flat, mcmd.data.sigmas[:plen], mcmd.data.epsilons[:plen], 30*angstrom)
print('base: ', e_vdw_insert_base/kjmol)
for rcut in 25, 20, 15, 12, 10:
e_vdw_insert = MM3_insert(pos, len(pos)-mcmd.nads, mcmd.N_frame, mcmd.rvecs_flat, mcmd.data.sigmas[:plen], mcmd.data.epsilons[:plen], rcut*angstrom)
print(rcut, e_vdw_insert/kjmol)
assert np.abs(e_vdw_insert_base - e_vdw_insert)/kjmol < 0.2
def test_lj_insert():
system_file = pkg_resources.resource_filename(__name__, '../data/lp_avg.chk')
ff_file = pkg_resources.resource_filename(__name__, '../data/pars.txt')
adsorbate_file = pkg_resources.resource_filename(__name__, '../data/argon.chk')
T = 87 * kelvin
P = 1 * bar
MD_trial_fraction = 0.000
rcut = 15 * angstrom
fugacity = P
# Try 10 configurations
for i in range(10):
mcmd = MCMD(system_file, adsorbate_file, ff_file, T, P, fugacity, MD_trial_fraction, rcut, fixed_N = 25)
N_frame = len(mcmd.pos)
new_pos = random_ads(mcmd.pos_ads, mcmd.rvecs)
pos = np.append(mcmd.pos, new_pos, axis=0)
new_pos2 = random_ads(mcmd.pos_ads, mcmd.rvecs)
pos2 = np.append(pos, new_pos2, axis=0)
Z_ads = 2
plen = len(pos)
plen2 = len(pos2)
e_vdw = LJ(pos2, N_frame, Z_ads, mcmd.rvecs_flat, mcmd.data.sigmas[:plen2], mcmd.data.epsilons[:plen2], rcut)
e_vdw_insert = LJ_insert(pos, len(pos)-mcmd.nads, mcmd.N_frame, mcmd.rvecs_flat, mcmd.data.sigmas[:plen], mcmd.data.epsilons[:plen], mcmd.rcut)
e_vdw_insert += LJ_insert(pos2, len(pos2)-mcmd.nads, mcmd.N_frame, mcmd.rvecs_flat, mcmd.data.sigmas[:plen2], mcmd.data.epsilons[:plen2], mcmd.rcut)
print(e_vdw/kjmol, e_vdw_insert/kjmol)
assert np.abs(e_vdw - e_vdw_insert) < 1e-8
def test_ei_rcut():
system_file = pkg_resources.resource_filename(__name__, '../data/lp_avg.chk')
ff_file = pkg_resources.resource_filename(__name__, '../data/pars.txt')
adsorbate_file = pkg_resources.resource_filename(__name__, '../data/CO2.chk')
T = 87 * kelvin
P = 1 * bar
MD_trial_fraction = 0.000
fugacity = P
def get_total_ei(rcut, new_pos, new_pos2):
mcmd = MCMD(system_file, adsorbate_file, ff_file, T, P, fugacity, MD_trial_fraction, rcut, fixed_N = 25)
sfac = Sfac(mcmd.pos, mcmd.N_frame, mcmd.rvecs_flat, mcmd.charges, mcmd.alpha, mcmd.gcut)
pos = np.append(mcmd.pos, new_pos, axis=0)
pos2 = np.append(pos, new_pos2, axis=0)
Z_ads = 2
plen = len(pos)
plen2 = len(pos2)
ei_insert_1 = electrostatics_realspace_insert(mcmd.N_frame, len(pos)-mcmd.nads, pos, mcmd.rvecs_flat, mcmd.data.charges[:plen], mcmd.data.radii[:plen], rcut, mcmd.alpha, mcmd.gcut)
sfac = np.array(ewald_insertion(sfac, new_pos, mcmd.rvecs_flat, mcmd.data.charges_ads, mcmd.alpha, mcmd.gcut))
ew_insert_1 = ewald_from_sfac(sfac, mcmd.rvecs_flat, mcmd.alpha, mcmd.gcut)
ei_insert_2 = ei_insert_1 + electrostatics_realspace_insert(mcmd.N_frame, len(pos2)-mcmd.nads, pos2, mcmd.rvecs_flat, mcmd.data.charges[:plen2], mcmd.data.radii[:plen2], rcut, mcmd.alpha, mcmd.gcut)
sfac = np.array(ewald_insertion(sfac, new_pos2, mcmd.rvecs_flat, mcmd.data.charges_ads, mcmd.alpha, mcmd.gcut))
ew_insert_2 = ewald_from_sfac(sfac, mcmd.rvecs_flat, mcmd.alpha, mcmd.gcut)
ei_full_2 = electrostatics(pos2, mcmd.N_frame, 2, mcmd.rvecs_flat, mcmd.data.charges[:plen2], mcmd.data.radii[:plen2], rcut, mcmd.alpha, mcmd.gcut)
return ew_insert_2 + ei_insert_2, ei_full_2
# Try 10 configurations
for i in range(10):
mcmd = MCMD(system_file, adsorbate_file, ff_file, T, P, fugacity, MD_trial_fraction, 30*angstrom, fixed_N = 25)
sfac = Sfac(mcmd.pos, mcmd.N_frame, mcmd.rvecs_flat, mcmd.charges, mcmd.alpha, mcmd.gcut)
new_pos = random_ads(mcmd.pos_ads, mcmd.rvecs)
new_pos2 = random_ads(mcmd.pos_ads, mcmd.rvecs)
ei_base, ei_base_check = get_total_ei(30*angstrom, new_pos, new_pos2)
print('base: ', ei_base/kjmol)
assert(np.abs(ei_base - ei_base_check) < 1e-8)
for rcut in 25, 20, 15, 12, 10:
ei, ei_check = get_total_ei(rcut*angstrom, new_pos, new_pos2)
print(rcut, ei/kjmol)
assert np.abs(ei_base - ei)/kjmol < 0.2
assert(np.abs(ei - ei_check) < 1e-8)
def test_ei_insert():
system_file = pkg_resources.resource_filename(__name__, '../data/lp_avg.chk')
ff_file = pkg_resources.resource_filename(__name__, '../data/pars.txt')
adsorbate_file = pkg_resources.resource_filename(__name__, '../data/CO2.chk')
T = 87 * kelvin
P = 1 * bar
MD_trial_fraction = 0.000
rcut = 15 * angstrom
fugacity = P
# Try 10 configurations
for i in range(10):
mcmd = MCMD(system_file, adsorbate_file, ff_file, T, P, fugacity, MD_trial_fraction, rcut, fixed_N = 25)
sfac = Sfac(mcmd.pos, mcmd.N_frame, mcmd.rvecs_flat, mcmd.charges, mcmd.alpha, mcmd.gcut)
N_frame = len(mcmd.pos)
new_pos = random_ads(mcmd.pos_ads, mcmd.rvecs)
pos = np.append(mcmd.pos, new_pos, axis=0)
new_pos2 = random_ads(mcmd.pos_ads, mcmd.rvecs)
pos2 = np.append(pos, new_pos2, axis=0)
Z_ads = 2
plen = len(pos)
plen2 = len(pos2)
ei_insert_1 = electrostatics_realspace_insert(mcmd.N_frame, len(pos)-mcmd.nads, pos, mcmd.rvecs_flat, mcmd.data.charges[:plen], mcmd.data.radii[:plen], mcmd.rcut, mcmd.alpha, mcmd.gcut)
sfac = np.array(ewald_insertion(sfac, new_pos, mcmd.rvecs_flat, mcmd.data.charges_ads, mcmd.alpha, mcmd.gcut))
ew_insert_1 = ewald_from_sfac(sfac, mcmd.rvecs_flat, mcmd.alpha, mcmd.gcut)
ei_full_1 = electrostatics(pos, mcmd.N_frame, 1, mcmd.rvecs_flat, mcmd.data.charges[:plen], mcmd.data.radii[:plen], mcmd.rcut, mcmd.alpha, mcmd.gcut)
print(ei_insert_1/kjmol, ew_insert_1/kjmol, ei_full_1/kjmol)
assert (np.abs(ei_full_1 - ei_insert_1 - ew_insert_1) < 1e-8).all()
ei_insert_2 = ei_insert_1 + electrostatics_realspace_insert(mcmd.N_frame, len(pos2)-mcmd.nads, pos2, mcmd.rvecs_flat, mcmd.data.charges[:plen2], mcmd.data.radii[:plen2], mcmd.rcut, mcmd.alpha, mcmd.gcut)
sfac = np.array(ewald_insertion(sfac, new_pos2, mcmd.rvecs_flat, mcmd.data.charges_ads, mcmd.alpha, mcmd.gcut))
ew_insert_2 = ewald_from_sfac(sfac, mcmd.rvecs_flat, mcmd.alpha, mcmd.gcut)
ei_full_2 = electrostatics(pos2, mcmd.N_frame, 2, mcmd.rvecs_flat, mcmd.data.charges[:plen2], mcmd.data.radii[:plen2], mcmd.rcut, mcmd.alpha, mcmd.gcut)
print(ei_insert_2/kjmol, ew_insert_2/kjmol, ei_full_2/kjmol)
assert (np.abs(ei_full_2 - ei_insert_2 - ew_insert_2) < 1e-8).all()
def get_total_ei(rcut, new_pos, new_pos2):
mcmd = MCMD(system_file, adsorbate_file, ff_file, T, P, fugacity, MD_trial_fraction, rcut, fixed_N = 25)
sfac = Sfac(mcmd.pos, mcmd.N_frame, mcmd.rvecs_flat, mcmd.charges, mcmd.alpha, mcmd.gcut)
pos = np.append(mcmd.pos, new_pos, axis=0)
pos2 = np.append(pos, new_pos2, axis=0)
Z_ads = 2
plen = len(pos)
plen2 = len(pos2)
ei_insert_1 = electrostatics_realspace_insert(mcmd.N_frame, len(pos)-mcmd.nads, pos, mcmd.rvecs_flat, mcmd.data.charges[:plen], mcmd.data.radii[:plen], rcut, mcmd.alpha, mcmd.gcut)
sfac = np.array(ewald_insertion(sfac, new_pos, mcmd.rvecs_flat, mcmd.data.charges_ads, mcmd.alpha, mcmd.gcut))
ew_insert_1 = ewald_from_sfac(sfac, mcmd.rvecs_flat, mcmd.alpha, mcmd.gcut)
ei_insert_2 = ei_insert_1 + electrostatics_realspace_insert(mcmd.N_frame, len(pos2)-mcmd.nads, pos2, mcmd.rvecs_flat, mcmd.data.charges[:plen2], mcmd.data.radii[:plen2], rcut, mcmd.alpha, mcmd.gcut)
sfac = np.array(ewald_insertion(sfac, new_pos2, mcmd.rvecs_flat, mcmd.data.charges_ads, mcmd.alpha, mcmd.gcut))
ew_insert_2 = ewald_from_sfac(sfac, mcmd.rvecs_flat, mcmd.alpha, mcmd.gcut)
ei_full_2 = electrostatics(pos2, mcmd.N_frame, 2, mcmd.rvecs_flat, mcmd.data.charges[:plen2], mcmd.data.radii[:plen2], rcut, mcmd.alpha, mcmd.gcut)
return ew_insert_2 + ei_insert_2, ei_full_2