def test_create_openmm_topology():
system, _ = get_system('cau13')
with pytest.raises(AssertionError):
create_openmm_topology(system)
rvecs = system.cell._get_rvecs().copy()
transform_lower_triangular(system.pos, rvecs, reorder=True)
reduce_box_vectors(rvecs)
system.cell.update_rvecs(rvecs)
topology = create_openmm_topology(system)
# verify box vectors are correct
a, b, c = topology.getPeriodicBoxVectors()
assert np.allclose(
a.value_in_unit(unit.angstrom),
rvecs[0, :] / molmod.units.angstrom,
)
assert np.allclose(
b.value_in_unit(unit.angstrom),
rvecs[1, :] / molmod.units.angstrom,
)
assert np.allclose(
c.value_in_unit(unit.angstrom),
rvecs[2, :] / molmod.units.angstrom,
)
def log_system(self):
"""Logs information about this system"""
log_header('system information', logger)
logger.info('')
logger.info('')
natom = self.system.natom
if self.box is not None:
system_type = 'periodic'
else:
system_type = 'non-periodic'
logger.info('number of atoms: {}'.format(natom))
logger.info('system type: ' + system_type)
logger.info('')
if self.box is not None:
lengths, angles = compute_lengths_angles(self.box, degree=True)
logger.info('initial box vectors (in angstrom):')
logger.info('\ta: {}'.format(self.box[0, :]))
logger.info('\tb: {}'.format(self.box[1, :]))
logger.info('\tc: {}'.format(self.box[2, :]))
logger.info('')
logger.info('initial box lengths (in angstrom):')
logger.info('\ta: {:.4f}'.format(lengths[0]))
logger.info('\tb: {:.4f}'.format(lengths[1]))
logger.info('\tc: {:.4f}'.format(lengths[2]))
logger.info('')
logger.info('initial box angles (in degrees):')
logger.info('\talpha: {:.4f}'.format(angles[0]))
logger.info('\tbeta : {:.4f}'.format(angles[1]))
logger.info('\tgamma: {:.4f}'.format(angles[2]))
logger.info('')
logger.info('')
rvecs = np.array(self.box) # create copy
transform_lower_triangular(np.zeros((1, 3)), rvecs, reorder=True)
reduce_box_vectors(rvecs)
lengths, angles = compute_lengths_angles(rvecs, degree=True)
logger.info('REDUCED box vectors (in angstrom):')
logger.info('\ta: {}'.format(rvecs[0, :]))
logger.info('\tb: {}'.format(rvecs[1, :]))
logger.info('\tc: {}'.format(rvecs[2, :]))
logger.info('')
logger.info('REDUCED box lengths (in angstrom):')
logger.info('\ta: {:.4f}'.format(lengths[0]))
logger.info('\tb: {:.4f}'.format(lengths[1]))
logger.info('\tc: {:.4f}'.format(lengths[2]))
logger.info('')
logger.info('REDUCED box angles (in degrees):')
logger.info('\talpha: {:.4f}'.format(angles[0]))
logger.info('\tbeta : {:.4f}'.format(angles[1]))
logger.info('\tgamma: {:.4f}'.format(angles[2]))
logger.info('')
logger.info('found {} prefixes:'.format(len(self.prefixes)))
for prefix in self.prefixes:
logger.info('\t' + prefix)
logger.info('')
logger.info('')
def test_wrap_coordinates():
for name in ['cau13', 'uio66', 'ppycof', 'mof5', 'mil53', 'cof5']:
ff = get_system(name, return_forcefield=True)
positions = ff.system.pos.copy()
rvecs = ff.system.cell._get_rvecs().copy()
rvecs_ = ff.system.cell._get_rvecs().copy()
ff.update_pos(positions)
ff.update_rvecs(rvecs)
e = ff.compute()
# make random periodic displacements
for i in range(100):
coefficients = np.random.randint(0, high=3, size=(3, 1))
atom = np.random.randint(0, high=ff.system.natom)
positions[atom, :] += np.sum(coefficients * rvecs, axis=0)
ff.update_pos(positions)
ff.update_rvecs(rvecs)
e0 = ff.compute()
assert np.allclose(e, e0)
wrap_coordinates(positions, rvecs, rectangular=False)
frac = np.dot(positions,
np.linalg.inv(rvecs)) # fractional coordinates
assert np.all(frac >= 0)
assert np.all(frac <= 1)
assert np.allclose(rvecs, rvecs_) # rvecs should not change
ff.update_pos(positions)
ff.update_rvecs(rvecs)
e1 = ff.compute()
assert np.allclose(e0, e1)
with pytest.raises(AssertionError):
wrap_coordinates(positions, rvecs, rectangular=True)
# transform rvecs
transform_lower_triangular(positions, rvecs, reorder=False)
reduce_box_vectors(rvecs)
wrap_coordinates(positions, rvecs, rectangular=True)
for i in range(positions.shape[0]):
assert np.all(np.abs(positions[i, :]) < np.diag(rvecs))
ff.update_pos(positions)
ff.update_rvecs(rvecs)
e2 = ff.compute()
assert np.allclose(e0, e2)
# reorder rvecs
transform_lower_triangular(positions, rvecs, reorder=True)
reduce_box_vectors(rvecs)
wrap_coordinates(positions, rvecs, rectangular=True)
for i in range(positions.shape[0]):
assert np.all(np.abs(positions[i, :]) < np.diag(rvecs))
ff.update_pos(positions)
ff.update_rvecs(rvecs)
e3 = ff.compute()
assert np.allclose(e0, e3)
def test_lattice_reduction():
system, pars = get_system('cau13')
pos = system.pos.copy()
rvecs = system.cell._get_rvecs().copy()
# use reduction algorithm from Bekker, and transform to diagonal
reduced = do_gram_schmidt_reduction(rvecs)
reduced_LT = np.linalg.cholesky(reduced @ reduced.T)
assert np.allclose(reduced_LT, np.diag(np.diag(reduced_LT))) # diagonal
# transform to lower triangular
transform_lower_triangular(pos, rvecs, reorder=True)
reduce_box_vectors(rvecs)
# assert equality of diagonal elements from both methods
np.testing.assert_almost_equal(np.diag(rvecs), np.diag(reduced_LT))
def test_transform_symmetric():
system, pars = get_system('mil53')
pos = system.pos.copy()
rvecs = system.cell._get_rvecs().copy()
# transform to symmetric form
transform_symmetric(pos, rvecs)
assert np.allclose(rvecs, rvecs.T)
# transform to triangular, and back to symmetric
rvecs_ = rvecs.copy()
pos_ = pos.copy()
transform_lower_triangular(pos_, rvecs_, reorder=False)
transform_symmetric(pos_, rvecs_)
# assert equality
np.testing.assert_almost_equal(rvecs_, rvecs)
np.testing.assert_almost_equal(pos_, pos)
def test_transform_lower_triangular():
for i in range(100):
trial = np.random.uniform(-20, 20, size=(3, 3))
trial *= np.sign(np.linalg.det(trial))
assert np.linalg.det(trial) > 0
pos = np.random.uniform(-100, 100, size=(10, 3))
transform_lower_triangular(pos, trial) # in-place
# comparison with cholesky made inside transform_lower_triangular
for name in ['cau13', 'uio66']: # FAILS ON COBDP; ewald_reci changes
ff = get_system(name, return_forcefield=True) # nonrectangular system
gpos0 = np.zeros((ff.system.natom, 3))
energy0 = ff.compute(gpos0, None)
rvecs = ff.system.cell._get_rvecs().copy()
transform_lower_triangular(ff.system.pos, rvecs, reorder=True)
assert is_lower_triangular(rvecs)
ff.update_pos(ff.system.pos)
ff.update_rvecs(rvecs)
gpos1 = np.zeros((ff.system.natom, 3))
energy1 = ff.compute(gpos1, None)
np.testing.assert_almost_equal( # energy should remain the same
energy0,
energy1,
)
def test_estimate_virial_stress():
def energy_func(positions, rvecs):
ff.update_pos(positions)
ff.update_rvecs(rvecs)
return ff.compute()
# verify numerical pressure computation for number of benchmark systems
# include anisotropic systems and LJ
dh = 1e-5
for name in ['cau13', 'uio66', 'ppycof', 'lennardjones']:
ff = get_system(name, return_forcefield=True)
positions = ff.system.pos.copy()
rvecs = ff.system.cell._get_rvecs().copy()
vtens = np.zeros((3, 3))
ff.compute(None, vtens)
unit = molmod.units.pascal * 1e6
pressure = np.trace(vtens) / np.linalg.det(rvecs) / unit
dUdh = estimate_cell_derivative(positions,
rvecs,
energy_func,
dh=dh,
use_triangular_perturbation=False)
vtens_numerical = rvecs.T @ dUdh
pressure_ = np.trace(vtens_numerical) / np.linalg.det(rvecs) / unit
assert abs(pressure -
pressure_) < 1e-3 # require at least kPa accuracy
assert np.allclose(vtens_numerical, vtens, atol=1e-5)
transform_lower_triangular(positions, rvecs, reorder=True)
ff.update_pos(positions)
ff.update_rvecs(rvecs)
vtens = np.zeros((3, 3))
ff.compute(None, vtens)
pressure_LT = np.trace(vtens) / np.linalg.det(rvecs) / unit
dUdh = estimate_cell_derivative(positions,
rvecs,
energy_func,
dh=dh,
use_triangular_perturbation=True)
vtens_numerical = rvecs.T @ dUdh
pressure_LT_ = np.trace(vtens_numerical) / np.linalg.det(rvecs) / unit
assert abs(pressure_LT - pressure) < 1e-8 # should be identical
assert abs(pressure_LT_ - pressure_) < 1e-3 # require kPa accuracy
#assert np.allclose(vtens_numerical, vtens, atol=1e-5)
# VTENS != VTENS_NUMERICAL HERE!
transform_symmetric(positions, rvecs)
ff.update_pos(positions)
ff.update_rvecs(rvecs)
vtens = np.zeros((3, 3))
ff.compute(None, vtens)
pressure_S = np.trace(vtens) / np.linalg.det(rvecs) / unit
dUdh = estimate_cell_derivative(positions, rvecs, energy_func, dh=dh)
vtens_numerical = rvecs.T @ dUdh
assert np.allclose(vtens_numerical, vtens_numerical.T, atol=1e5)
pressure_S_ = np.trace(vtens_numerical) / np.linalg.det(rvecs) / unit
assert abs(pressure_S - pressure) < 1e-8 # should be identical
assert abs(pressure_S_ - pressure_) < 1e-3 # require kPa accuracy
assert np.allclose(vtens_numerical, vtens, atol=1e-5)
# check evaluate_using_reduced=True gives same results
dUdh_r = estimate_cell_derivative(positions,
rvecs,
energy_func,
dh=dh,
evaluate_using_reduced=True)
vtens_numerical_r = rvecs.T @ dUdh_r
assert np.allclose(vtens_numerical_r, vtens_numerical_r.T, atol=1e-5)
assert np.allclose(vtens_numerical_r, vtens_numerical, atol=1e-5)
def create_topology(self):
"""Creates the topology for the current configuration"""
if self.topology is not None:
positions = self.system.pos / molmod.units.angstrom
if self.box is not None:
assert tuple(self.determine_supercell()) == (1, 1, 1)
box = self.box.copy()
transform_lower_triangular(positions, box, reorder=True)
reduce_box_vectors(box)
#wrap_coordinates(positions, box)
# copy topology
topology = deepcopy(self.topology)
topology.setPeriodicBoxVectors(box * unit.angstrom)
return self.topology, positions
topology = mm.app.Topology()
chain = topology.addChain()
natoms = self.system.natom
count = 0
if self.box is not None:
supercell = self.determine_supercell()
# compute box vectors and allocate positions array
box = np.array(supercell)[:, np.newaxis] * self.box
positions = np.zeros((np.prod(supercell) * natoms, 3))
# construct map of atom indices to residues
atom_index_mapping = {}
for template, residues in self.residues.items():
for i, residue in enumerate(residues):
for j, atom in enumerate(residue):
atom_index_mapping[atom] = (template, i, j)
included_atoms = list(atom_index_mapping.keys())
assert tuple(sorted(included_atoms)) == tuple(range(natoms))
def name_residue(image, template, residue_index):
"""Defines the name of a specific residue"""
return str(image) + '_' + str(template) + '_' + str(i)
atoms_list = [] # necessary for adding bonds to topology
for image, index in enumerate(np.ndindex(tuple(supercell))):
# initialize residues and track them in a dict
current_residues = {}
for template, residues in self.residues.items():
for i, residue in enumerate(residues):
name = name_residue(image, template, i)
residue = topology.addResidue(
name=name,
chain=chain,
id=name,
)
current_residues[(template, i)] = residue
# add atoms to corresponding residue in topology (in their
# original order). Atoms are named with their element symbol
# as well as an index that starts counting at one
count = np.ones(118, dtype=np.int32) # counts elements
for j in range(natoms):
key = atom_index_mapping[j]
template = key[0]
residue_index = key[1]
atom_index = key[2]
number = self.system.numbers[j]
e = mm.app.Element.getByAtomicNumber(number)
atom_name = e.symbol + str(count[number])
atom = topology.addAtom(
name=atom_name,
element=e,
residue=current_residues[(template, residue_index)])
atoms_list.append(atom)
count[number] += 1
# generate positions for this image
image_pos = self.system.pos / molmod.units.angstrom
translate = np.dot(np.array(index), self.box).reshape(1, 3)
image_pos += translate
start = (image) * natoms
stop = (image + 1) * natoms
positions[start:stop, :] = image_pos.copy()
# apply cell reduction and wrap coordinates (similar to create_seed)
transform_lower_triangular(positions, box, reorder=True)
reduce_box_vectors(box)
#wrap_coordinates(positions, box)
topology.setPeriodicBoxVectors(box * unit.angstrom)
# add bonds from supercell system object
system = self.system.supercell(*supercell)
for bond in system.bonds:
topology.addBond(
atoms_list[bond[0]],
atoms_list[bond[1]],
)
else: # similar workflow, but without the supercell generation
positions = self.system.pos / molmod.units.angstrom
# construct map of atom indices to residues
atom_index_mapping = {}
for template, residues in self.residues.items():
for i, residue in enumerate(residues):
for j, atom in enumerate(residue):
atom_index_mapping[atom] = (template, i, j)
included_atoms = list(atom_index_mapping.keys())
assert tuple(sorted(included_atoms)) == tuple(range(natoms))
def name_residue(template, residue_index):
"""Defines the name of a specific residue"""
return str(template) + '_' + str(residue_index)
atoms_list = [] # necessary for adding bonds to topology
# initialize residues and track them in a dict
current_residues = {}
for template, residues in self.residues.items():
for i, residue in enumerate(residues):
name = name_residue(template, i)
residue = topology.addResidue(
name='r' + str(i),
chain=chain,
#id='r' + str(i),
)
current_residues[(template, i)] = residue
# add atoms to corresponding residue in topology (in their
# original order)
for j in range(natoms):
key = atom_index_mapping[j]
template = key[0]
residue_index = key[1]
atom_index = key[2]
e = mm.app.Element.getByAtomicNumber(self.system.numbers[j])
atom_name = 'a' + str(j)
atom = topology.addAtom(
name=atom_name,
element=e,
residue=current_residues[(template, residue_index)])
atoms_list.append(atom)
# add bonds from system object
for bond in self.system.bonds:
topology.addBond(
atoms_list[bond[0]],
atoms_list[bond[1]],
)
return topology, positions
def create_seed(self, kind='all'):
"""Creates a seed for constructing a yaff.ForceField object
The returned seed contains all objects that are required in order to
generate the force field object unambiguously. Specifically, this
involves a yaff.System object, a yaff.FFArgs object with the correct
parameter settings, and a yaff.Parameters object that contains the
actual force field parameters.
Because tests are typically performed on isolated parts of a force
field, it is possible to generate different seeds corresponding
to different parts -- this is done using the kind parameter. Allowed
values are:
- all:
generates the entire force field
- covalent
generates only the covalent part of the force field.
- nonbonded
generates only the nonbonded part of the force field,
including both dispersion and electrostatics.
- dispersion
generates only the dispersion part of the force field,
which is basically the nonbonded part minus the
electrostatics.
- electrostatic
generates only the electrostatic part
Parameters
----------
kind : str, optional
specifies the kind of seed to be created. Allowed values are
'all', 'covalent', 'nonbonded', 'dispersion', 'electrostatic'
"""
assert kind in [
'all', 'covalent', 'nonbonded', 'dispersion', 'electrostatic'
]
parameters = self.parameters.copy()
if kind == 'all':
pass # do nothing, all prefixes should be retained
elif kind == 'covalent':
# pop all dispersion and electrostatic prefixes:
for key in (DISPERSION_PREFIXES + ELECTROSTATIC_PREFIXES):
parameters.sections.pop(key,
None) # returns None if not present
elif kind == 'nonbonded':
# retain only dispersion and electrostatic
sections = {}
for key in (DISPERSION_PREFIXES + ELECTROSTATIC_PREFIXES):
section = parameters.sections.get(key, None)
if section is not None: # only add if present
sections[key] = section
parameters = yaff.Parameters(sections)
elif kind == 'dispersion':
# retain only dispersion
sections = {}
for key in DISPERSION_PREFIXES:
section = parameters.sections.get(key, None)
if section is not None: # only add if present
sections[key] = section
parameters = yaff.Parameters(sections)
elif kind == 'electrostatic':
# retain only electrostatic
sections = {}
for key in ELECTROSTATIC_PREFIXES:
section = parameters.sections.get(key, None)
if section is not None: # only add if present
sections[key] = section
parameters = yaff.Parameters(sections)
else:
raise NotImplementedError(kind + ' not known.')
# construct FFArgs instance and set properties
ff_args = yaff.FFArgs()
if self.box is not None:
supercell = self.determine_supercell()
system = self.system.supercell(*supercell)
# apply reduction
rvecs = system.cell._get_rvecs().copy()
transform_lower_triangular(system.pos, rvecs, reorder=True)
reduce_box_vectors(rvecs)
#wrap_coordinates(system.pos, rvecs)
system.cell.update_rvecs(rvecs)
else:
system = self.system
if self.rcut is not None:
ff_args.rcut = self.rcut * molmod.units.angstrom
else:
ff_args.rcut = 1e10 # humongous value; for nonperiodic systems
if self.switch_width is not None and (self.switch_width != 0.0):
ff_args.tr = yaff.Switch3(self.switch_width *
molmod.units.angstrom)
else:
ff_args.tr = None
if self.tailcorrections is not None:
ff_args.tailcorrections = self.tailcorrections
if self.ewald_alphascale is not None:
ff_args.alpha_scale = self.ewald_alphascale
if self.ewald_gcutscale is not None:
ff_args.gcut_scale = self.ewald_gcutscale
return YaffSeed(system, parameters, ff_args)