def train_mgp(self, skip=True):
t0 = time.time()
if self.l_bound < self.grid_params['bounds_2'][0, 0]:
self.grid_params['bounds_2'][0, 0] = self.l_bound - 0.01
self.grid_params['bounds_3'][
0, :2] = np.ones(2) * self.l_bound - 0.01
if skip and (self.curr_step in self.non_mapping_steps):
return 1
# set svd rank based on the training set, grid number and threshold 1000
train_size = len(self.gp.training_data)
rank_2 = np.min([1000, self.grid_params['grid_num_2'], train_size * 3])
rank_3 = np.min(
[1000, self.grid_params['grid_num_3'][0]**3, train_size * 3])
self.grid_params['svd_rank_2'] = rank_2
self.grid_params['svd_rank_3'] = rank_3
output.write_to_output('\ntraining set size: {}\n'.format(train_size),
self.output_name)
output.write_to_output('lower bound: {}\n'.format(self.l_bound))
output.write_to_output('mgp l_bound: {}\n'.format(
self.grid_params['bounds_2'][0, 0]))
output.write_to_output('Constructing mapped force field...\n',
self.output_name)
self.mgp = MappedGaussianProcess(self.gp, self.grid_params,
self.struc_params)
output.write_to_output(
'building mapping time: {}'.format(time.time() - t0),
self.output_name)
self.is_mgp_built = True
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
def update_gp(self, train_atoms, dft_frcs):
output.write_to_output('\nAdding atom {} to the training set.\n'
.format(train_atoms),
self.output_name)
output.write_to_output('Uncertainty: {}.\n'
.format(self.structure.stds[train_atoms[0]]),
self.output_name)
# update gp model
self.gp.update_db(self.structure, dft_frcs,
custom_range=train_atoms)
self.gp.set_L_alpha()
def write_mgp_header(self):
output.write_to_output('bounds 2:' + str(self.mgp_model.bounds_2),
self.output_name)
output.write_to_output('bounds 3:' + str(self.mgp_model.bounds_2),
self.output_name)
output.write_to_output('grid num 2:' + str(self.mgp_model.grid_num_2),
self.output_name)
output.write_to_output('grid num 3:' + str(self.mgp_model.grid_num_3),
self.output_name)
def predict_on_structure_mgp(structure,
mgp,
output=None,
output_name=None,
n_cpus=None,
write_to_structure=True,
selective_atoms: List[int] = None,
skipped_atom_value=0): # changed
"""
Assign forces to structure based on an mgp
"""
if output and output_name:
output.write_to_output('\npredict with mapping:\n', output_name)
forces = np.zeros(shape=(structure.nat, 3))
vars = np.zeros(shape=(structure.nat, 3))
if selective_atoms:
forces.fill(skipped_atom_value)
vars.fill(skipped_atom_value)
else:
selective_atoms = []
for n in range(structure.nat):
if n not in selective_atoms and selective_atoms:
continue
chemenv = AtomicEnvironment(structure, n, mgp.cutoffs)
force, var, _, _ = mgp.predict(chemenv)
if write_to_structure:
structure.forces[n][:] = force
structure.stds[n][:] = np.sqrt(np.absolute(var))
forces[n, :] = force
vars[n, :] = var
return forces, vars
def run_dft(self):
output.write_to_output('\nCalling Quantum Espresso...\n',
self.output_name)
# calculate DFT forces
forces = qe_util.run_espresso_par(self.qe_input, self.structure,
self.pw_loc, self.no_cpus)
self.structure.forces = forces
# write wall time of DFT calculation
self.dft_count += 1
output.write_to_output('QE run complete.\n', self.output_name)
time_curr = time.time() - self.start_time
output.write_to_output('number of DFT calls: %i \n' % self.dft_count,
self.output_name)
output.write_to_output('wall time from start: %.2f s \n' % time_curr,
self.output_name)
def run(self):
output.write_header(self.gp.cutoffs, self.gp.kernel_name, self.gp.hyps,
self.gp.algo, self.dt, self.number_of_steps,
self.structure, self.output_name,
self.std_tolerance)
counter = 0
self.start_time = time.time()
while self.curr_step < self.number_of_steps:
print('curr_step:', self.curr_step)
# run DFT and train initial model if first step and DFT is on
if self.curr_step == 0 and self.std_tolerance != 0:
# call dft and update positions
self.run_dft()
dft_frcs = copy.deepcopy(self.structure.forces)
new_pos = md.update_positions(self.dt, self.noa,
self.structure)
self.update_temperature(new_pos)
self.record_state()
# make initial gp model and predict forces
self.update_gp(self.init_atoms, dft_frcs)
if (self.dft_count-1) < self.freeze_hyps:
self.train_gp()
# after step 1, try predicting with GP model
else:
self.pred_func()
self.dft_step = False
new_pos = md.update_positions(self.dt, self.noa,
self.structure)
# get max uncertainty atoms
std_in_bound, target_atoms = self.is_std_in_bound()
if not std_in_bound:
# record GP forces
self.update_temperature(new_pos)
self.record_state()
gp_frcs = copy.deepcopy(self.structure.forces)
# run DFT and record forces
self.dft_step = True
self.run_dft()
dft_frcs = copy.deepcopy(self.structure.forces)
new_pos = md.update_positions(self.dt, self.noa,
self.structure)
self.update_temperature(new_pos)
self.record_state()
# compute mae and write to output
mae = np.mean(np.abs(gp_frcs - dft_frcs))
mac = np.mean(np.abs(dft_frcs))
output.write_to_output('\nmean absolute error:'
' %.4f eV/A \n'
% mae, self.output_name)
output.write_to_output('mean absolute dft component:'
' %.4f eV/A \n' % mac,
self.output_name)
# add max uncertainty atoms to training set
self.update_gp(target_atoms, dft_frcs)
if (self.dft_count-1) < self.freeze_hyps:
self.train_gp()
# write gp forces
if counter >= self.skip and not self.dft_step:
self.update_temperature(new_pos)
self.record_state()
counter = 0
counter += 1
self.update_positions(new_pos)
self.curr_step += 1
output.conclude_run(self.output_name)
