def test_from_files(tmp_path):
system, pars = get_system('mil53')
configuration = Configuration(system, pars)
configuration.write(tmp_path / 'config.yml')
system.to_file(str(tmp_path / 'system.chk'))
with open(tmp_path / 'pars.txt', 'w+') as f:
f.write(pars)
path_system = tmp_path / 'system.chk'
path_pars = tmp_path / 'pars.txt'
path_config = tmp_path / 'config.yml'
configuration = Configuration.from_files(
chk=path_system,
txt=path_pars,
yml=path_config,
)
def test_update_properties(tmp_path):
system, pars = get_system('mil53')
configuration = Configuration(system, pars)
config = configuration.write()
config['yaff']['rcut'] = 15.0
config['yaff']['interaction_radius'] = 15.0
configuration.update_properties(config)
assert configuration.rcut == 15.0
def test_initialize_nonperiodic(tmp_path):
system, pars = get_system('alanine')
configuration = Configuration(system, pars)
configuration.log_system()
# write defaults
path_config = tmp_path / 'config.yml'
config = configuration.write(path_config)
with open(path_config, 'r') as f:
content = f.read()
assert content == """yaff: {}\n"""
def test_wrapper_openmm_mic():
system, pars = get_system('mil53')
configuration = Configuration(system, pars)
kind = 'all'
# YAFF and OpenMM use a different switching function. If it is disabled,
# the results between both are identical up to 6 decimals
configuration.switch_width = 0.0 # disable switching
configuration.rcut = 10.0 # request cutoff of 10 angstorm
configuration.cell_interaction_radius = 10.0
configuration.supercell = [2, 3, 5]
configuration.update_properties(configuration.write())
conversion = ExplicitConversion(pme_error_thres=1e-5)
seed_mm = conversion.apply(configuration, seed_kind=kind)
wrapper = OpenMMForceFieldWrapper.from_seed(seed_mm, 'Reference')
u = molmod.units.angstrom
seed_yaff = configuration.create_seed(kind=kind)
positions = seed_yaff.system.pos.copy() / u
rvecs = seed_yaff.system.cell._get_rvecs().copy() / u
e, _ = wrapper.evaluate(positions, rvecs, do_forces=True)
# make random periodic displacements
for i in range(5):
coefficients = np.random.randint(-3, high=3, size=(3, 1))
atom = np.random.randint(0, high=seed_yaff.system.natom, size=(10,))
positions[atom, :] += np.sum(coefficients * rvecs, axis=0)
e_ = wrapper.evaluate(positions, rvecs, do_forces=False)
assert np.allclose(e, e_)
# make random periodic displacements and rewrap coordinates
for i in range(5):
coefficients = np.random.randint(-3, high=3, size=(3, 1))
atom = np.random.randint(0, high=seed_yaff.system.natom, size=(10,))
positions[atom, :] += np.sum(coefficients * rvecs, axis=0)
wrap_coordinates(positions, rvecs, rectangular=True)
e_ = wrapper.evaluate(positions, rvecs, do_forces=False)
assert np.allclose(e, e_)
def test_periodic():
systems = ['uio66', 'cau13', 'mil53', 'ppycof', 'cof5', 'mof5']
platforms = ['Reference']
seed_kinds = ['covalent', 'dispersion', 'electrostatic']
# systematic constant offset in dispersion energy for COFs, unclear why
tolerance = {
('Reference', 'covalent'): 1e-6, # some MM3 terms have error 1e-7
('Reference', 'dispersion'): 1e-2, # some MM3 terms have error 1e-3
('Reference', 'electrostatic'): 1e-3,
#('CUDA', 'covalent'): 1e-3,
#('CUDA', 'dispersion'): 1e-3,
#('CUDA', 'electrostatic'): 1e-3,
}
nstates = 5
disp_ampl = 0.3
box_ampl = 0.3
for name in systems:
for platform in platforms:
for kind in seed_kinds:
system, pars = get_system(name)
configuration = Configuration(system, pars)
tol = tolerance[(platform, kind)]
# YAFF and OpenMM use a different switching function. If it is disabled,
# the results between both are identical up to 6 decimals
configuration.switch_width = 0.0 # disable switching
configuration.rcut = 13.0 # request cutoff of 13 angstorm
configuration.interaction_radius = 15.0
configuration.update_properties(configuration.write())
conversion = ExplicitConversion(pme_error_thres=5e-4)
seed_mm = conversion.apply(configuration, seed_kind=kind)
seed_yaff = configuration.create_seed(kind=kind)
wrapper_mm = OpenMMForceFieldWrapper.from_seed(
seed_mm, platform)
wrapper_yaff = YaffForceFieldWrapper.from_seed(seed_yaff)
assert wrapper_yaff.periodic # system should not be considered periodic
assert wrapper_mm.periodic # system should not be considered periodic
pos = seed_yaff.system.pos.copy()
rvecs = seed_yaff.system.cell._get_rvecs().copy()
for i in range(nstates):
dpos = np.random.uniform(-disp_ampl,
disp_ampl,
size=pos.shape)
drvecs = np.random.uniform(-box_ampl,
box_ampl,
size=rvecs.shape)
drvecs[0, 1] = 0
drvecs[0, 2] = 0
drvecs[1, 2] = 0
tmp = rvecs + drvecs
reduce_box_vectors(tmp)
energy_mm, forces_mm = wrapper_mm.evaluate(
(pos + dpos) / molmod.units.angstrom,
rvecs=tmp / molmod.units.angstrom,
)
energy, forces = wrapper_yaff.evaluate(
(pos + dpos) / molmod.units.angstrom,
rvecs=tmp / molmod.units.angstrom,
)
assert_tol(energy, energy_mm, tol)
assert_tol(forces, forces_mm, 10 * tol)