def generate_mb_envs_pos(positions0, species_1, cutoffs, cell, delt, d1, mask=None):
positions = [positions0]
noa = len(positions0)
positions_2 = deepcopy(positions0)
positions_2[0][d1 - 1] = delt
positions += [positions_2]
positions_3 = deepcopy(positions[0])
positions_3[0][d1 - 1] = -delt
positions += [positions_3]
test_struc = []
for i in range(3):
test_struc += [Structure(cell, species_1, positions[i])]
env_0 = []
env_p = []
env_m = []
for i in range(noa):
env_0 += [AtomicEnvironment(test_struc[0], i, cutoffs, cutoffs_mask=mask)]
env_p += [AtomicEnvironment(test_struc[1], i, cutoffs, cutoffs_mask=mask)]
env_m += [AtomicEnvironment(test_struc[2], i, cutoffs, cutoffs_mask=mask)]
return [env_0, env_p, env_m]
def GenGrid_serial(self, GP):
'''
generate grid data of mean prediction and L^{-1}k* for each triplet
implemented in a parallelized style
'''
# ------ get 3body kernel info ------
kernel, efk, cutoffs, hyps, hyps_mask = get_3bkernel(GP)
# ------ construct grids ------
nop = self.grid_num[0]
noa = self.grid_num[2]
bond_lengths = np.linspace(self.l_bounds[0], self.u_bounds[0], nop)
cos_angles = np.linspace(self.l_bounds[2], self.u_bounds[2], noa)
bond_means = np.zeros([nop, nop, noa])
bond_vars = np.zeros([nop, nop, noa, len(GP.alpha)])
env12 = AtomicEnvironment(self.bond_struc, 0, self.cutoffs)
if self.update:
if 'kv3' in os.listdir():
os.rmdir('kv3')
os.mkdir('kv3')
size = len(GP.training_data)
ds = [1, 2, 3]
k_v = np.zeros(3)
k12_v_all = np.zeros([len(bond_lengths), len(bond_lengths),
len(cos_angles), size*3])
for b1, r1 in enumerate(bond_lengths):
for b2, r2 in enumerate(bond_lengths):
for a12, cos_angle12 in enumerate(cos_angles):
x2 = r2 * cos_angle12
y2 = r2 * np.sqrt(1-cos_angle12**2)
r12 = np.linalg.norm(np.array([x2-r1, y2, 0]))
env12.bond_array_3 = np.array([[r1, 1, 0, 0],
[r2, 0, 0, 0]])
env12.cross_bond_dists = np.array([[0, r12], [r12, 0]])
for isample, sample in enumerate(GP.training_data):
for d in ds:
k_v[d-1] = kernel(env12, sample, 1, d,
hyps, cutoffs)
k12_v_all[b1, b2, a12, isample*3:isample*3+3] = k_v
for b1, r1 in enumerate(bond_lengths):
for b2, r2 in enumerate(bond_lengths):
for a12, cos_angle in enumerate(cos_angles):
k12_v = k12_v_all[b1, b2, a12, :]
bond_means[b1, b2, a12] = np.matmul(k12_v, GP.alpha)
if not self.mean_only:
bond_vars[b1, b2, a12, :] = solve_triangular(GP.l_mat, k12_v, lower=True)
# # ------ save mean and var to file -------
np.save('grid3_mean', bond_means)
np.save('grid3_var', bond_vars)
return bond_means, bond_vars
def test_env_methods(structure, mask, cutoff, result):
if mask is True:
mask = generate_mask(cutoff)
else:
mask = None
env_test = AtomicEnvironment(structure,
atom=0,
cutoffs=cutoff,
cutoffs_mask=mask)
assert str(env_test) == \
f'Atomic Env. of Type 1 surrounded by {result[0]} atoms' \
' of Types [1, 2, 3]'
the_dict = env_test.as_dict()
assert isinstance(the_dict, dict)
for key in ['positions', 'cell', 'atom', 'cutoffs', 'species']:
assert key in the_dict.keys()
remade_env = AtomicEnvironment.from_dict(the_dict)
assert isinstance(remade_env, AtomicEnvironment)
assert np.array_equal(remade_env.bond_array_2, env_test.bond_array_2)
if len(cutoff) > 1:
assert np.array_equal(remade_env.bond_array_3, env_test.bond_array_3)
if len(cutoff) > 2:
assert np.array_equal(remade_env.q_array, env_test.q_array)
def test_backwards_compatibility(structure, mask, cutoff, result):
"""
This test can be deleted if backwards compatibility is dropped for the
sake of code cleanup. (This test executes in about 5 milliseconds). Tests a
particular branch of code within the Environment's as_dict() method for
older pickled environments without a cutoffs mask.
:return:
"""
if mask is True:
mask = generate_mask(cutoff)
else:
mask = None
env_test = deepcopy(
AtomicEnvironment(structure, atom=0, cutoffs=cutoff,
cutoffs_mask=mask))
pre_test_dict = env_test.as_dict()
delattr(env_test, "cutoffs_mask")
test_dict = env_test.as_dict()
assert pre_test_dict["cutoffs_mask"] == test_dict["cutoffs_mask"]
new_env = AtomicEnvironment.from_dict(test_dict)
assert isinstance(new_env, AtomicEnvironment)
assert str(new_env) == str(env_test)
def update_db(self, struc: Structure, forces: List,
custom_range: List[int] = (), energy: float = None):
"""Given a structure and forces, add local environments from the
structure to the training set of the GP. If energy is given, add the
entire structure to the training set.
Args:
struc (Structure): Input structure. Local environments of atoms
in this structure will be added to the training set of the GP.
forces (np.ndarray): Forces on atoms in the structure.
custom_range (List[int]): Indices of atoms whose local
environments will be added to the training set of the GP.
energy (float): Energy of the structure.
"""
# By default, use all atoms in the structure
noa = len(struc.positions)
update_indices = custom_range or list(range(noa))
# If forces are given, update the environment list.
if forces is not None:
for atom in update_indices:
env_curr = \
AtomicEnvironment(struc, atom, self.cutoffs,
cutoffs_mask=self.hyps_mask)
forces_curr = np.array(forces[atom])
self.training_data.append(env_curr)
self.training_labels.append(forces_curr)
# create numpy array of training labels
self.training_labels_np = np.hstack(self.training_labels)
# If an energy is given, update the structure list.
if energy is not None:
structure_list = [] # Populate with all environments of the struc
for atom in range(noa):
env_curr = \
AtomicEnvironment(struc, atom, self.cutoffs,
cutoffs_mask=self.hyps_mask)
structure_list.append(env_curr)
self.energy_labels.append(energy)
self.training_structures.append(structure_list)
self.energy_labels_np = np.array(self.energy_labels)
# update list of all labels
self.all_labels = np.concatenate((self.training_labels_np,
self.energy_labels_np))
self.sync_data()
def test_auto_sweep():
"""Test that the number of neighbors inside the local environment is
correctly computed."""
# Make an arbitrary non-cubic structure.
cell = np.array([[1.3, 0.5, 0.8], [-1.2, 1, 0.73], [-0.8, 0.1, 0.9]])
positions = np.array([[1.2, 0.7, 2.3], [3.1, 2.5, 8.9], [-1.8, -5.8, 3.0],
[0.2, 1.1, 2.1], [3.2, 1.1, 3.3]])
species = np.array([1, 2, 3, 4, 5])
arbitrary_structure = Structure(cell, species, positions)
# Construct an environment.
cutoffs = np.array([4., 3.])
arbitrary_environment = \
AtomicEnvironment(arbitrary_structure, 0, cutoffs)
# Count the neighbors.
n_neighbors_1 = len(arbitrary_environment.etypes)
# Reduce the sweep value, and check that neighbors are missing.
sweep_val = arbitrary_environment.sweep_val
arbitrary_environment.sweep_array = \
np.arange(-sweep_val + 1, sweep_val, 1)
arbitrary_environment.compute_env()
n_neighbors_2 = len(arbitrary_environment.etypes)
assert (n_neighbors_1 > n_neighbors_2)
# Increase the sweep value, and check that the count is the same.
arbitrary_environment.sweep_array = \
np.arange(-sweep_val - 1, sweep_val + 2, 1)
arbitrary_environment.compute_env()
n_neighbors_3 = len(arbitrary_environment.etypes)
assert (n_neighbors_1 == n_neighbors_3)
def adjust_cutoffs(self, new_cutoffs: Union[list, tuple, 'np.ndarray'],
reset_L_alpha=True,
train=True):
"""
Loop through atomic environment objects stored in the training data,
and re-compute cutoffs for each. Useful if you want to gauge the
impact of cutoffs given a certain training set! Unless you know
*exactly* what you are doing for some development or test purpose,
it is **highly** suggested that you call set_L_alpha and
re-optimize your hyperparameters afterwards as is default here.
:param new_cutoffs:
:return:
"""
old_structures = [env.structure for env in self.training_data]
old_atoms = [env.atom for env in self.training_data]
new_environments = [AtomicEnvironment(struc, atom, new_cutoffs) for
struc, atom in zip(old_structures, old_atoms)]
self.training_data = new_environments
# Ensure that training data and labels are still consistent
_global_training_data[self.name] = self.training_data
_global_training_labels[self.name] = self.training_labels_np
self.cutoffs = np.array(new_cutoffs)
if reset_L_alpha:
del self.l_mat
del self.ky_mat
self.set_L_alpha()
if train:
self.train()
def predict_on_atom_en(
param: Tuple[Structure, int, GaussianProcess]
) -> ('np.ndarray', 'np.ndarray', float):
"""
Return the forces/std. dev. uncertainty / energy associated with an
individual atom in a structure, without necessarily having cast it to a
chemical environment. In order to work with other functions,
all arguments are passed in as a tuple.
:param param: tuple of FLARE Structure, atom index, and Gaussian Process
object
:type param: Tuple(Structure, integer, GaussianProcess)
:return: 3-element force array, associated uncertainties, and local energy
:rtype: (np.ndarray, np.ndarray, float)
"""
# Unpack the input tuple, convert a chemical environment
structure, atom, gp = param
# Obtain the associated chemical environment
chemenv = AtomicEnvironment(structure, atom, gp.cutoffs)
comps = []
stds = []
# predict force components and standard deviations
for i in range(3):
force, var = gp.predict(chemenv, i + 1)
comps.append(float(force))
stds.append(np.sqrt(np.abs(var)))
# predict local energy
local_energy = gp.predict_local_energy(chemenv)
return np.array(comps), np.array(stds), local_energy
def update_db(self,
struc: Structure,
forces: list,
custom_range: List[int] = ()):
"""Given structure and forces, add to training set.
:param struc: structure to add to db
:type struc: Structure
:param forces: list of corresponding forces to add to db
:type forces: list<float>
:param custom_range: Indices to use in lieu of the whole structure
:type custom_range: List[int]
"""
# By default, use all atoms in the structure
noa = len(struc.positions)
update_indices = custom_range or list(range(noa))
for atom in update_indices:
env_curr = AtomicEnvironment(struc, atom, self.cutoffs)
forces_curr = np.array(forces[atom])
self.training_data.append(env_curr)
self.training_labels.append(forces_curr)
# create numpy array of training labels
self.training_labels_np = self.force_list_to_np(self.training_labels)
def methanol_gp():
the_gp = GaussianProcess(
kernel_name="2+3_mc",
hyps=np.array([
3.75996759e-06,
1.53990678e-02,
2.50624782e-05,
5.07884426e-01,
1.70172923e-03,
]),
cutoffs=np.array([5, 3]),
hyp_labels=["l2", "s2", "l3", "s3", "n0"],
maxiter=1,
opt_algorithm="L-BFGS-B",
)
with open(path.join(TEST_FILE_DIR, "methanol_envs.json"), "r") as f:
dicts = [loads(s) for s in f.readlines()]
for cur_dict in dicts:
force = cur_dict["forces"]
env = AtomicEnvironment.from_dict(cur_dict)
the_gp.add_one_env(env, force)
the_gp.set_L_alpha()
return the_gp
def update_db(self, struc: Structure, forces: List,
custom_range: List[int] = ()):
"""Given a structure and forces, add local environments from the
structure to the training set of the GP.
Args:
struc (Structure): Input structure. Local environments of atoms
in this structure will be added to the training set of the GP.
forces (np.ndarray): Forces on atoms in the structure.
custom_range (List[int]): Indices of atoms whose local
environments will be added to the training set of the GP.
"""
# By default, use all atoms in the structure
noa = len(struc.positions)
update_indices = custom_range or list(range(noa))
for atom in update_indices:
env_curr = AtomicEnvironment(struc, atom, self.cutoffs)
forces_curr = np.array(forces[atom])
self.training_data.append(env_curr)
self.training_labels.append(forces_curr)
# create numpy array of training labels
self.training_labels_np = np.hstack(self.training_labels)
_global_training_data[self.name] = self.training_data
_global_training_labels[self.name] = self.training_labels_np
def from_dict(dictionary):
"""Create GP object from dictionary representation."""
multihyps = dictionary.get('multihyps', False)
new_gp = GaussianProcess(kernel_name=dictionary['kernel_name'],
cutoffs=np.array(dictionary['cutoffs']),
hyps=np.array(dictionary['hyps']),
hyp_labels=dictionary['hyp_labels'],
parallel=dictionary.get('parallel', False) or
dictionary.get('par', False),
per_atom_par=dictionary.get('per_atom_par',
True),
n_cpus=dictionary.get(
'n_cpus') or dictionary.get('no_cpus'),
maxiter=dictionary['maxiter'],
opt_algorithm=dictionary.get(
'opt_algorithm', 'L-BFGS-B'),
multihyps=multihyps,
hyps_mask=dictionary.get('hyps_mask', None),
name=dictionary.get('name', 'default_gp')
)
# Save time by attempting to load in computed attributes
new_gp.training_data = [AtomicEnvironment.from_dict(env) for env in
dictionary['training_data']]
new_gp.training_labels = deepcopy(dictionary['training_labels'])
new_gp.training_labels_np = deepcopy(dictionary['training_labels_np'])
new_gp.likelihood = dictionary['likelihood']
new_gp.likelihood_gradient = dictionary['likelihood_gradient']
new_gp.training_labels_np = np.hstack(new_gp.training_labels)
_global_training_data[new_gp.name] = new_gp.training_data
_global_training_labels[new_gp.name] = new_gp.training_labels_np
# Save time by attempting to load in computed attributes
if len(new_gp.training_data) > 5000:
try:
new_gp.ky_mat = np.load(dictionary['ky_mat_file'])
new_gp.compute_matrices()
except:
new_gp.ky_mat = None
new_gp.l_mat = None
new_gp.alpha = None
new_gp.ky_mat_inv = None
filename = dictionary['ky_mat_file']
Warning("the covariance matrices are not loaded" \
f"because {filename} cannot be found")
else:
new_gp.ky_mat_inv = np.array(dictionary['ky_mat_inv']) \
if dictionary.get('ky_mat_inv') is not None else None
new_gp.ky_mat = np.array(dictionary['ky_mat']) \
if dictionary.get('ky_mat') is not None else None
new_gp.l_mat = np.array(dictionary['l_mat']) \
if dictionary.get('l_mat') is not None else None
new_gp.alpha = np.array(dictionary['alpha']) \
if dictionary.get('alpha') is not None else None
return new_gp
def predict_on_structure(structure: Structure,
gp: GaussianProcess,
n_cpus: int = None) -> ('np.ndarray', 'np.ndarray'):
"""
Return the forces/std. dev. uncertainty associated with each
individual atom in a structure. Forces are stored directly to the
structure and are also returned.
:param structure: FLARE structure to obtain forces for, with N atoms
:param gp: Gaussian Process model
:return: N x 3 numpy array of foces, Nx3 numpy array of uncertainties
:rtype: (np.ndarray, np.ndarray)
"""
# Loop through individual atoms, cast to atomic environments,
# make predictions
for n in range(structure.nat):
chemenv = AtomicEnvironment(structure, n, gp.cutoffs)
for i in range(3):
force, var = gp.predict(chemenv, i + 1)
structure.forces[n][i] = float(force)
structure.stds[n][i] = np.sqrt(np.abs(var))
forces = np.array(structure.forces)
stds = np.array(structure.stds)
return forces, stds
def predict_on_atom_en(
param: Tuple[Structure, int, GaussianProcess]
) -> ("np.ndarray", "np.ndarray", float):
"""
Return the forces/std. dev. uncertainty / energy associated with an
individual atom in a structure, without necessarily having cast it to a
chemical environment. In order to work with other functions,
all arguments are passed in as a tuple.
:param param: tuple of FLARE Structure, atom index, and Gaussian Process
object
:type param: Tuple(Structure, integer, GaussianProcess)
:return: 3-element force array, associated uncertainties, and local energy
:rtype: (np.ndarray, np.ndarray, float)
"""
# Unpack the input tuple, convert a chemical environment
structure, atom, gp = param
# Obtain the associated chemical environment
chemenv = AtomicEnvironment(structure, atom, gp.cutoffs, cutoffs_mask=gp.hyps_mask)
# Predict forces / std. dev / energy
force, var = gp.predict_force_xyz(chemenv)
std = np.sqrt(np.abs(var))
local_energy = gp.predict_local_energy(chemenv)
return force, std, local_energy
def calculate_mgp_serial(self, atoms):
nat = len(atoms)
struc_curr = Structure(np.array(atoms.cell),
atoms.get_atomic_numbers(), atoms.positions)
forces = np.zeros((nat, 3))
stress = np.zeros((nat, 6))
stds = np.zeros((nat, 3))
for n in range(nat):
chemenv = AtomicEnvironment(struc_curr, n, self.mgp_model.cutoffs)
f, v, vir = self.mgp_model.predict(chemenv, mean_only=False)
forces[n] = f
stress[n] = vir
stds[n] = np.sqrt(np.absolute(v))
self.results['forces'] = forces
self.results['stds'] = stds
self.results['stresses'] = stress
self.results['stress'] = np.sum(stress, axis=0)
# TODO: implement energy mapping
self.results['local_energies'] = np.zeros(forces.shape)
self.results['energy'] = 0
atoms.get_uncertainties = self.get_uncertainties
return forces
def predict_on_structure_en(
structure: Structure,
gp: GaussianProcess,
n_cpus: int = None) -> ('np.ndarray', 'np.ndarray', 'np.ndarray'):
"""
Return the forces/std. dev. uncertainty / local energy associated with each
individual atom in a structure. Forces are stored directly to the
structure and are also returned.
:param structure: FLARE structure to obtain forces for, with N atoms
:param gp: Gaussian Process model
:param n_cpus: Dummy parameter passed as an argument to allow for
flexibility when the callable may or may not be parallelized
:return: N x 3 array of forces, N x 3 array of uncertainties,
N-length array of energies
:rtype: (np.ndarray, np.ndarray, np.ndarray)
"""
# Set up local energy array
local_energies = np.array([0 for _ in range(structure.nat)])
# Loop through atoms in structure and predict forces, uncertainties,
# and energies
for n in range(structure.nat):
chemenv = AtomicEnvironment(structure, n, gp.cutoffs)
for i in range(3):
force, var = gp.predict(chemenv, i + 1)
structure.forces[n][i] = float(force)
structure.stds[n][i] = np.sqrt(np.abs(var))
local_energies[n] = gp.predict_local_energy(chemenv)
forces = np.array(structure.forces)
stds = np.array(structure.stds)
return forces, stds, local_energies
def predict_on_atom_efs(param):
"""Predict the local energy, forces, and partial stresses and predictive
variances of a chemical environment."""
structure, atom, gp = param
chemenv = AtomicEnvironment(structure, atom, gp.cutoffs)
return gp.predict_efs(chemenv)
def predict_on_structure_en(self):
for n in range(self.structure.nat):
chemenv = AtomicEnvironment(self.structure, n, self.gp.cutoffs)
for i in range(3):
force, var = self.gp.predict(chemenv, i + 1)
self.structure.forces[n][i] = float(force)
self.structure.stds[n][i] = np.sqrt(np.absolute(var))
self.local_energies[n] = self.gp.predict_local_energy(chemenv)
def predict_on_structure_en(
structure: Structure,
gp: GaussianProcess,
n_cpus: int = None,
write_to_structure: bool = True,
selective_atoms: List[int] = None,
skipped_atom_value=0) -> ('np.ndarray', 'np.ndarray', 'np.ndarray'):
"""
Return the forces/std. dev. uncertainty / local energy associated with each
individual atom in a structure. Forces are stored directly to the
structure and are also returned.
:param structure: FLARE structure to obtain forces for, with N atoms
:param gp: Gaussian Process model
:param n_cpus: Dummy parameter passed as an argument to allow for
flexibility when the callable may or may not be parallelized
:return: N x 3 array of forces, N x 3 array of uncertainties,
N-length array of energies
:rtype: (np.ndarray, np.ndarray, np.ndarray)
"""
# Set up local energy array
forces = np.zeros((structure.nat, 3))
stds = np.zeros((structure.nat, 3))
local_energies = np.zeros(structure.nat)
forces = np.zeros(shape=(structure.nat, 3))
stds = np.zeros(shape=(structure.nat, 3))
if selective_atoms:
forces.fill(skipped_atom_value)
stds.fill(skipped_atom_value)
local_energies.fill(skipped_atom_value)
else:
selective_atoms = []
# Loop through atoms in structure and predict forces, uncertainties,
# and energies
for n in range(structure.nat):
if selective_atoms and n not in selective_atoms:
continue
chemenv = AtomicEnvironment(structure,
n,
gp.cutoffs,
cutoffs_mask=gp.hyps_mask)
for i in range(3):
force, var = gp.predict(chemenv, i + 1)
forces[n][i] = float(force)
stds[n][i] = np.sqrt(np.abs(var))
if write_to_structure and structure.forces is not None:
structure.forces[n][i] = float(force)
structure.stds[n][i] = np.sqrt(np.abs(var))
local_energies[n] = gp.predict_local_energy(chemenv)
return forces, stds, local_energies
def another_env(cutoffs, delt):
cell = 10.0 * np.eye(3)
# atomic structure 1
pos_1 = np.vstack([[0, 0, 0], 0.1*random([3, 3])])
pos_1[1, 1] += 1
pos_1[2, 0] += 1
pos_1[3, :2] += 1
pos_2 = deepcopy(pos_1)
pos_2[0][0] = delt
pos_3 = deepcopy(pos_1)
pos_3[0][0] = -delt
species_1 = [1, 1, 1, 1]
test_structure_1 = Structure(cell, species_1, pos_1)
test_structure_2 = Structure(cell, species_1, pos_2)
test_structure_3 = Structure(cell, species_1, pos_3)
# atom 0, original position
env1_1_0 = AtomicEnvironment(test_structure_1, 0, cutoffs)
# atom 0, 0 perturbe along x
env1_2_0 = AtomicEnvironment(test_structure_2, 0, cutoffs)
# atom 1, 0 perturbe along x
env1_2_1 = AtomicEnvironment(test_structure_2, 1, cutoffs)
# atom 2, 0 perturbe along x
env1_2_2 = AtomicEnvironment(test_structure_2, 2, cutoffs)
# atom 0, 0 perturbe along -x
env1_3_0 = AtomicEnvironment(test_structure_3, 0, cutoffs)
# atom 1, 0 perturbe along -x
env1_3_1 = AtomicEnvironment(test_structure_3, 1, cutoffs)
# atom 2, 0 perturbe along -x
env1_3_2 = AtomicEnvironment(test_structure_3, 2, cutoffs)
# create env 2
pos_1 = np.vstack([[0, 0, 0], 0.1*random([3, 3])])
pos_1[1, 1] += 1
pos_1[2, 0] += 1
pos_1[3, :2] += 1
pos_2 = deepcopy(pos_1)
pos_2[0][0] = delt
pos_3 = deepcopy(pos_1)
pos_3[0][0] = -delt
species_2 = [1, 2, 2, 1]
test_structure_1 = Structure(cell, species_2, pos_1)
env2_1_0 = AtomicEnvironment(test_structure_1, 0, cutoffs)
return env1_1_0, env1_2_0, env1_3_0, \
env1_2_1, env1_3_1, env1_2_2, env1_3_2, env2_1_0
def test_pred_on_elements():
the_gp = GaussianProcess(kernel_name="2+3_mc",
hyps=np.array([
3.75996759e-06, 1.53990678e-02,
2.50624782e-05, 5.07884426e-01, 1.70172923e-03
]),
cutoffs=np.array([7, 3]),
hyp_labels=['l2', 's2', 'l3', 's3', 'n0'],
maxiter=1,
opt_algorithm='L-BFGS-B')
with open('./test_files/methanol_frames.json', 'r') as f:
frames = [Structure.from_dict(loads(s)) for s in f.readlines()]
with open('./test_files/methanol_envs.json', 'r') as f:
data_dicts = [loads(s) for s in f.readlines()[:6]]
envs = [AtomicEnvironment.from_dict(d) for d in data_dicts]
forces = [np.array(d['forces']) for d in data_dicts]
seeds = list(zip(envs, forces))
all_frames = deepcopy(frames)
tt = TrajectoryTrainer(frames,
gp=the_gp,
shuffle_frames=False,
rel_std_tolerance=0,
abs_std_tolerance=0,
abs_force_tolerance=.001,
skip=5,
min_atoms_per_train=100,
pre_train_seed_envs=seeds,
pre_train_seed_frames=[frames[-1]],
max_atoms_from_frame=4,
output_name='meth_test',
model_format='json',
atom_checkpoint_interval=50,
pre_train_atoms_per_element={'H': 1},
predict_atoms_per_element={
'H': 0,
'C': 1,
'O': 0
})
# Set to predict only on Carbon after training on H to ensure errors are
# high and that they get added to the gp
tt.run()
# Ensure forces weren't written directly to structure
for i in range(len(all_frames)):
assert np.array_equal(all_frames[i].forces, frames[i].forces)
# Assert that Carbon atoms were correctly added
assert the_gp.training_statistics['envs_by_species']['C'] > 2
for f in glob(f"meth_test*"):
remove(f)
for f in glob(f"gp_from_aimd*"):
remove(f)
def predict_on_structure(structure: Structure, gp: GaussianProcess):
for n in range(structure.nat):
chemenv = AtomicEnvironment(structure, n, gp.cutoffs)
for i in range(3):
force, var = gp.predict(chemenv, i + 1)
structure.forces[n][i] = float(force)
structure.stds[n][i] = np.sqrt(np.abs(var))
forces = np.array(structure.forces)
stds = np.array(structure.stds)
return forces, stds
def predict_on_structure(
structure: Structure,
gp: GaussianProcess,
n_cpus: int = None,
write_to_structure: bool = True,
selective_atoms: List[int] = None,
skipped_atom_value=0,
) -> ("np.ndarray", "np.ndarray"):
"""
Return the forces/std. dev. uncertainty associated with each
individual atom in a structure. Forces are stored directly to the
structure and are also returned.
:param structure: FLARE structure to obtain forces for, with N atoms
:param gp: Gaussian Process model
:param write_to_structure: Write results to structure's forces,
std attributes
:param selective_atoms: Only predict on these atoms; e.g. [0,1,2] will
only predict and return for those atoms
:param skipped_atom_value: What value to use for atoms that are skipped.
Defaults to 0 but other options could be e.g. NaN. Will NOT
write this to the structure if write_to_structure is True.
:return: N x 3 numpy array of foces, Nx3 numpy array of uncertainties
:rtype: (np.ndarray, np.ndarray)
"""
forces = np.zeros((structure.nat, 3))
stds = np.zeros((structure.nat, 3))
if selective_atoms:
forces.fill(skipped_atom_value)
stds.fill(skipped_atom_value)
else:
selective_atoms = []
for n in range(structure.nat):
# Skip the atoms which we aren't predicting on if
# selective atoms is on.
if n not in selective_atoms and selective_atoms:
continue
chemenv = AtomicEnvironment(structure, n, gp.cutoffs, cutoffs_mask=gp.hyps_mask)
force, var = gp.predict_force_xyz(chemenv)
std = np.sqrt(np.abs(var))
forces[n] = force
stds[n] = std
if write_to_structure:
structure.forces[n] = force
structure.stds[n] = std
return forces, stds
def test_seed_and_run():
the_gp = GaussianProcess(
kernel_name="2+3_mc",
hyps=np.array([
3.75996759e-06,
1.53990678e-02,
2.50624782e-05,
5.07884426e-01,
1.70172923e-03,
]),
cutoffs=np.array([5, 3]),
hyp_labels=["l2", "s2", "l3", "s3", "n0"],
maxiter=1,
opt_algorithm="L-BFGS-B",
)
with open(path.join(TEST_FILE_DIR, "methanol_frames.json"), "r") as f:
frames = [Structure.from_dict(loads(s)) for s in f.readlines()]
with open(path.join(TEST_FILE_DIR, "methanol_envs.json"), "r") as f:
data_dicts = [loads(s) for s in f.readlines()[:6]]
envs = [AtomicEnvironment.from_dict(d) for d in data_dicts]
forces = [np.array(d["forces"]) for d in data_dicts]
seeds = list(zip(envs, forces))
tt = TrajectoryTrainer(
frames,
gp=the_gp,
shuffle_frames=True,
rel_std_tolerance=0,
abs_std_tolerance=0,
skip=10,
pre_train_seed_envs=seeds,
pre_train_seed_frames=[frames[-1]],
max_atoms_from_frame=4,
output_name="meth_test",
model_format="pickle",
train_checkpoint_interval=1,
pre_train_atoms_per_element={"H": 1},
)
tt.run()
with open("meth_test_model.pickle", "rb") as f:
new_gp = pickle.load(f)
test_env = envs[0]
for d in [1, 2, 3]:
assert np.all(
the_gp.predict(x_t=test_env, d=d) == new_gp.predict(x_t=test_env,
d=d))
for f in glob(f"meth_test*"):
remove(f)
def predict_on_atom_en_std(param):
"""Predict local energy and predictive std of a chemical environment."""
structure, atom, gp = param
chemenv = AtomicEnvironment(structure, atom, gp.cutoffs, cutoffs_mask=gp.hyps_mask)
# predict local energy
loc_en, loc_en_var = gp.predict_local_energy_and_var(chemenv)
loc_en_std = np.sqrt(np.abs(loc_en_var))
return loc_en, loc_en_std
def predict_on_atom_mgp(atom, structure, cutoffs, mgp):
chemenv = AtomicEnvironment(structure, atom, cutoffs)
# predict force components and standard deviations
force, var = mgp.predict(chemenv)
comps = force
stds = np.sqrt(np.absolute(var))
# predict local energy
# local_energy = self.gp.predict_local_energy(chemenv)
local_energy = 0
return comps, stds, local_energy
def get_forces(self, atoms):
nat = len(atoms)
struc_curr = struc.Structure(atoms.cell, ['A'] * nat, atoms.positions)
forces = np.zeros((nat, 3))
for n in range(nat):
chemenv = AtomicEnvironment(struc_curr, n,
self.mff_model.GP.cutoffs)
force, _ = self.mff_model.predict(chemenv, mean_only=True)
return forces
def test_env_methods(cutoff):
cell = np.eye(3)
species = [1, 2, 3]
positions = np.array([[0, 0, 0], [0.5, 0.5, 0.5], [0.1, 0.1, 0.1]])
struc_test = Structure(cell, species, positions)
env_test = AtomicEnvironment(struc_test, 0, np.array([1, 1]))
assert str(env_test) == 'Atomic Env. of Type 1 surrounded by 12 atoms' \
' of Types [2, 3]'
the_dict = env_test.as_dict()
assert isinstance(the_dict, dict)
for key in ['positions', 'cell', 'atom', 'cutoffs', 'species']:
assert key in the_dict.keys()
remade_env = AtomicEnvironment.from_dict(the_dict)
assert isinstance(remade_env, AtomicEnvironment)
assert np.array_equal(remade_env.bond_array_2, env_test.bond_array_2)
assert np.array_equal(remade_env.bond_array_3, env_test.bond_array_3)
assert np.array_equal(remade_env.bond_array_mb, env_test.bond_array_mb)
def test_species_count(cutoff):
cell = np.eye(3)
species = [1, 2, 3]
positions = np.array([[0, 0, 0], [0.5, 0.5, 0.5], [0.1, 0.1, 0.1]])
struc_test = Structure(cell, species, positions)
env_test = AtomicEnvironment(structure=struc_test,
atom=0,
cutoffs=np.array([1, 1]))
assert (len(struc_test.positions) == len(struc_test.coded_species))
assert (len(env_test.bond_array_2) == len(env_test.etypes))
assert (isinstance(env_test.etypes[0], np.int8))
def predict_on_structure_mgp(self): # changed
"""
Assign forces to self.structure based on self.gp
"""
output.write_to_output('\npredict with mapping:\n', self.output_name)
for n in range(self.structure.nat):
chemenv = AtomicEnvironment(self.structure, n, self.gp.cutoffs)
force, var = self.mgp.predict(chemenv)
self.structure.forces[n][:] = force
self.structure.stds[n][:] = np.sqrt(np.absolute(var))
self.structure.dft_forces = False