def get_init_configs(system, init_configs=None, n=10, method_name=None):
"""Generate a set of initial configurations to use for active learning"""
if init_configs is not None:
if all(cfg.energy is not None for cfg in init_configs):
logger.info(f'Initialised with {len(init_configs)} configurations '
f'all with defined energy')
return init_configs
# Initial configurations are not defined, so make some - will use random
# with the largest maximum distance between molecules possible
max_vdw = max(get_vdw_radius(symbol) for symbol in system.atom_symbols())
ideal_dist = 2*max_vdw - 0.5 # Desired minimum distance in Å
# Reduce the distance until there is a probability at least 0.1 that a
# random configuration can be generated with that distance threshold
p_acc, dist = 0, ideal_dist+0.2
while p_acc < 0.1:
n_generated_configs = 0
dist -= 0.2 # Reduce the minimum distance requirement
for _ in range(10):
try:
_ = system.random(min_dist_threshold=dist)
n_generated_configs += 1
except ex.RandomiseFailed:
continue
p_acc = n_generated_configs / 10
logger.info(f'Generated configurations with p={p_acc:.2f} with a '
f'minimum distance of {dist:.2f}')
init_configs = gt.Data(name='init_configs')
# Finally generate the initial configurations
while len(init_configs) < n:
try:
init_configs += system.random(min_dist_threshold=dist,
with_intra=True)
except ex.RandomiseFailed:
continue
logger.info(f'Added {len(init_configs)} configurations with min dist = '
f'{dist:.3f} Å')
if method_name is None:
logger.warning('Have no method - not evaluating energies')
return init_configs
# And run the desired method in parallel across them
method = getattr(init_configs, f'parallel_{method_name.lower()}')
method()
init_configs.save()
return init_configs
def test_gap_train():
system = gt.System(box_size=[10, 10, 10])
training_data = gt.Data(name='test')
training_data.load(system=system,
filename=os.path.join(here, 'data', 'rnd_training.xyz'))
assert len(training_data) == 10
assert len(training_data[0].atoms) == 31
if 'GT_GAP' not in os.environ or not os.environ['GT_GAP'] == 'True':
return
# Run GAP train with the training data
gap = gt.GAP(name='test', system=system)
gap.train(training_data)
def grid_configs(n_to_cube):
"""
:param n_to_cube: (int) Generate n^3 configurations
:return: (gt.Configuration)
"""
configs = gt.Data(name=f'grid_{n_to_cube}-cubed')
# Also add the minimum energy strucutre
minimum = get_h2o(r1=1.0, r2=1.0, r3=1.5)
minimum.run_gpaw(max_force=0.01, n_cores=4)
configs += minimum
for r1 in np.linspace(0.8, 1.5, n_to_cube):
for r2 in np.linspace(0.8, 1.5, n_to_cube):
for r3 in np.linspace(1.0, 2.5, n_to_cube):
h2o = get_h2o(r1, r2, r3)
configs += h2o
return configs
def test_load_no_box():
data = gt.Data()
data.load(filename=os.path.join(here, 'data', 'rnd_training.xyz'))
assert len(data) > 0
for config in data:
assert config.energy is not None
assert config.charge == 0
assert config.mult == 1
with open('tmp.xyz', 'w') as test_xyz:
print('1\nLattice=""', file=test_xyz)
with pytest.raises(LoadingFailed):
configs = ConfigurationSet()
configs.load(filename='tmp.xyz')
os.remove('tmp.xyz')
def grid_configs(n_to_cube):
"""
:param n_to_cube: (int) Generate n^3 configurations
:return: (gt.Configuration)
"""
configs = gt.Data(name=f'grid_{n_to_cube}-cubed')
# Also add the minimum energy strucutre
minimum = gt.Configuration('h2o_min_revPBE0.xyz', box=gt.Box([8, 8, 8]))
assert minimum.atoms is not None
configs += minimum
for r1 in np.linspace(0.8, 1.5, n_to_cube):
for r2 in np.linspace(0.8, 1.5, n_to_cube):
for r3 in np.linspace(1.0, 2.5, n_to_cube):
h2o = get_h2o(r1, r2, r3)
configs += h2o
configs.parallel_cp2k()
return configs
import gaptrain as gt
gt.GTConfig.n_cores = 4
if __name__ == '__main__':
system = gt.System(box_size=[12.42, 12.42, 12.42])
system.add_molecules(gt.Molecule('znh2o6.xyz', charge=2))
system.add_solvent('h2o', n=58)
intra_h2o_gap = gt.gap.SolventIntraGAP(name='water_intra_gap',
system=system)
intra_znh2o6_gap = gt.gap.SoluteIntraGAP(
name='intra_znh2o6', system=system, molecule=gt.Molecule('znh2o6.xyz'))
inter_gap = gt.InterGAP(name='inter', system=system, default_params=False)
# Run 30 ps of dynamics from an equilibrated point
traj = gt.md.run_gapmd(configuration=gt.Data('eqm_final_frame.xyz')[0],
gap=gt.gap.SSGAP(solute_intra=intra_znh2o6_gap,
solvent_intra=intra_h2o_gap,
inter=inter_gap),
temp=300,
dt=0.5,
interval=5,
ps=30,
n_cores=4)
traj.save(filename=f'zn_h2o_traj')
# Run 1 ps molecular dynamics using the GAP at 300 K using a 0.5 fs time-step.
# The initial configuration is methane located at a random position in the box
traj = gt.md.run_gapmd(
configuration=methane.random(),
gap=gap,
temp=500, # Kelvin
dt=0.5, # fs
interval=1, # frames
fs=50,
n_cores=4)
# save the trajectory with no energies
traj.save(filename='traj.xyz')
# create sets of data from the trajectory containing predicted & true energies
pred = gt.Data('traj.xyz')
pred.parallel_gap(gap=gap)
true = gt.Data('traj.xyz')
true.parallel_orca()
# and plot the energies over time ---------------------------------------------
import numpy as np
import matplotlib.pyplot as plt
plt.plot(
np.linspace(0, 50, len(pred)), # 0 -> 50 fs
pred.energies() - np.min(true.energies()), # rel energies
label='GAP',
lw=2)
def train(system: gt.System,
method_name: str,
gap=None,
max_time_active_fs=1000,
min_time_active_fs=0,
n_configs_iter=10,
temp=300,
active_e_thresh=None,
active_method='diff',
max_energy_threshold=None,
validate=False,
tau=None,
tau_max=None,
val_interval=None,
max_active_iters=50,
n_init_configs=10,
init_configs=None,
remove_intra_init_configs=True,
fix_init_config=False,
bbond_energy=None,
fbond_energy=None,
init_active_temp=None):
"""
Train a system using active learning, by propagating dynamics using ML
driven molecular dynamics (MD) and adding configurations where the error
is above a threshold. Loop looks something like
Generate configurations -> train a GAP -> run GAP-MD -> frames with error
^ |
|________ calc true ___________
Active learning will loop until either (1) the iteration > max_active_iters
or (2) no configurations are found to add or (3) if calculated τ = max(τ)
where the loop will break out
--------------------------------------------------------------------------
:param system: (gt.system.System)
:param method_name: (str) Name of a method to use as the ground truth e.g.
dftb, orca, gpaw
:param gap: (gt.gap.GAP) GAP to train with the active learnt data, if
None then one will be initialised by placing SOAPs on each
heavy atom and defining the 'other' atom types included in the
neighbour density by their proximity. Distance cutoffs default
to 3.5 Å for all atoms
:param max_time_active_fs: (float) Maximum propagation time in the active
learning loop. Default = 1 ps
:param min_time_active_fs: (float) Minimum propagation time for an
active learnt configuration. Will be updated
so the error is only calculated where the GAP
is unlikely to be accurate
:param n_configs_iter: (int) Number of configurations to generate per
active learning cycle
:param temp: (float) Temperature in K to propagate active learning at -
higher is better for stability but requires more training
:param active_method: (str) Method used to generate active learnt
configurations. One of ['diff', 'qbc', 'gp_var']
:param active_e_thresh: (float) Threshold in eV (E_t) above which a
configuration is added to the potential. If None
then will use 1 kcal mol-1 molecule-1
1. active_method='diff': |E_0 - E_GAP| > E_t
2. active_method='qbc': σ(E_GAP1, E_GAP2...) > E_t
3. active_method='gp_var': σ^2_GAP(predicted) > E_t
:param max_energy_threshold: (float) Maximum relative energy threshold for
configurations to be added to the training
data
:param validate: (bool) Whether or not to validate the potential during
the training. Will, by default run a τ calculation with
an interval max_time_active_fs / 100, so that a maximum of
50 calculations are run and a maximum time of
max(τ) = 5 x max_time_active_fs
:param tau: (gt.loss.Tau) A instance of the τ error metric, unused if no
validation is performed. Otherwise
:param tau_max: (float | None) Maximum τ_acc in fs if float, will break out
of the active learning loop if this value is reached. If
None then won't break out
:param val_interval: (int) Interval in the active training loop at which to
run the validation. Defaults to max_active_iters // 10
if validation is requested
:param max_active_iters: (int) Maximum number of active learning
iterations to perform. Will break if we hit the
early stopping criteria
:param n_init_configs: (int) Number of initial configurations to generate,
will be ignored if init_configs is not None
:param init_configs: (gt.ConfigurationSet) A set of configurations from
which to start the active learning from
:param remove_intra_init_configs: (bool) Whether the intramolecular
component of the energy/force needs to
be removed prior to training with
init_configs. only applies for IIGAP
and init_configs != None
:param fix_init_config: (bool) Always start from the same initial
configuration for the active learning loop, if
False then the minimum energy structure is used.
Useful for TS learning, where dynamics should be
propagated from a saddle point not the minimum
:param bbond_energy: (dict | None) Additional energy to add to a breaking
bond. e.g. bbond_energy={(0, 1), 0.1} Adds 0.1 eV
to the 'bond' between atoms 0 and 1 as velocities
shared between the atoms in the breaking bond direction
:param fbond_energy: (dict | None) As bbond_energy but in the direction to
form a bond
:param init_active_temp: (float | None) Initial temperature for velocities
in the 'active' MD search for configurations
:return: (gt.Data, gt.GAP)
"""
init_configs = get_init_configs(init_configs=init_configs,
n=n_init_configs,
method_name=method_name,
system=system)
# Remove the intra-molecular energy if an intra+inter (II) GAP is being
# trained
do_remove_intra = isinstance(gap, gt.IIGAP)
if do_remove_intra and remove_intra_init_configs:
remove_intra(init_configs, gap=gap)
# Initial configuration must have energies
assert all(cfg.energy is not None for cfg in init_configs)
if gap is None:
gap = gt.GAP(name=unique_name('active_gap'), system=system)
# Initialise a τ metric with default parameters
if validate and tau is None:
# 1 ps default maximum tau
tau = gt.loss.Tau(configs=get_init_configs(system, n=5),
e_lower=0.043363 * len(system.molecules),
max_fs=tau_max if tau_max is not None else 1000)
# Default to validating 10 times through the training
if validate and val_interval is None:
val_interval = max(max_active_iters // 10, 1)
# Initialise training data
train_data = gt.Data(name=gap.name)
train_data += init_configs
# and train an initial GAP
gap.train(init_configs)
if active_e_thresh is None:
if active_method.lower() == 'diff':
# 1 kcal mol-1 molecule-1
active_e_thresh = 0.043363 * len(system.molecules)
if active_method.lower() == 'qbc':
# optimised on a small box of water. std dev. for total energy
active_e_thresh = 1E-6 * len(system.molecules)
if active_method.lower() == 'gp_var':
# Threshold for maximum per-atom GP variance (eV atom^-1)
active_e_thresh = 5E-5
# Initialise the validation output file
if validate:
tau_file = open(f'{gap.name}_tau.txt', 'w')
print('Iteration n_evals τ_acc / fs', file=tau_file)
# Run the active learning loop, running iterative GAP-MD
for iteration in range(max_active_iters):
# Set the configuration from which GAP-MD will be run
min_idx = int(np.argmin(train_data.energies()))
init_config = train_data[0] if fix_init_config else train_data[min_idx]
configs = get_active_configs(init_config,
gap=gap,
ref_method_name=method_name,
method=str(active_method),
n_configs=n_configs_iter,
temp=temp,
e_thresh=active_e_thresh,
max_time_fs=max_time_active_fs,
min_time_fs=min_time_active_fs,
bbond_energy=bbond_energy,
fbond_energy=fbond_energy,
init_temp=init_active_temp)
# Active learning finds no configurations,,
if len(configs) == 0:
# Calculate the final tau if we're running with validation
if validate:
tau.calculate(gap=gap, method_name=method_name)
print(iteration, tau.value, sep='\t\t\t', file=tau_file)
logger.info('No configs to add. Active learning = DONE')
break
min_time_active_fs = min(config.t0 for config in configs)
logger.info(f'All active configurations reached t = '
f'{min_time_active_fs} fs before an error exceeded the '
f'threshold of {active_e_thresh:.3f} eV')
if do_remove_intra:
remove_intra(configs, gap=gap)
train_data += configs
# If required remove high-lying energy configuration from the data
if max_energy_threshold is not None:
train_data.remove_above_e(max_energy_threshold)
# Retrain on these new data
gap.train(train_data)
# Print the accuracy
if validate and iteration % val_interval == 0:
tau.calculate(gap=gap, method_name=method_name)
print(f'{iteration:<13g}'
f'{sum(config.n_evals for config in train_data):<13g}'
f'{tau.value}', sep='\t', file=tau_file)
if np.abs(tau.value - tau.max_time) < 1:
logger.info('Reached the maximum tau. Active learning = DONE')
break
return train_data, gap
def get_active_configs(config, gap, ref_method_name, method='diff',
max_time_fs=1000, n_configs=10, temp=300, e_thresh=0.1,
min_time_fs=0, **kwargs):
"""
Generate n_configs using on-the-fly active learning parallelised over
GTConfig.n_cores
--------------------------------------------------------------------------
:param config: (gt.Configuration) Initial configuration to propagate from
:param gap: (gt.gap.GAP) GAP to run MD with
:param ref_method_name: (str) Name of the method to use as the ground truth
:param method: (str) Name of the strategy used to generate new configurations
:param max_time_fs: (float) Maximum propagation time in the active learning
loop. Default = 1 ps
:param n_configs: (int) Number of configurations to generate
:param temp: (float) Temperature in K to run the intermediate MD with
:param e_thresh: (float) Energy threshold in eV above which the MD frame
is returned by the active learning function i.e
E_t < |E_GAP - E_true| method='diff'
:param min_time_fs: (float) Minimum propagation time in the active learning
loop. If non-zero then will run this amount of time
initially then look for a configuration with a
|E_0 - E_GAP| > e_thresh
:param kwargs: Additional keyword arguments passed to the GAP MD function
:return:(gt.ConfigurationSet)
"""
if int(n_configs) < int(gt.GTConfig.n_cores):
raise NotImplementedError('Active learning is only implemented using '
'one core for each process. Please use '
'n_configs >= gt.GTConfig.n_cores')
results = []
configs = gt.Data()
logger.info('Searching for "active" configurations with a threshold of '
f'{e_thresh:.6f} eV')
if method.lower() == 'diff':
function = get_active_config_diff
args = (config, gap, temp, e_thresh, max_time_fs, ref_method_name,
0, 0, min_time_fs)
elif method.lower() == 'qbc':
function = get_active_config_qbc
# Train a few GAPs on the same data
gap = gt.gap.GAPEnsemble(name=f'{gap.name}_ensemble', gap=gap)
gap.train()
args = (config, gap, temp, e_thresh, max_time_fs)
elif method.lower() == 'gp_var':
function = get_active_config_gp_var
args = (config, gap, temp, e_thresh, max_time_fs)
else:
raise ValueError('Unsupported active method')
logger.info(f'Using {gt.GTConfig.n_cores} processes')
with Pool(processes=int(gt.GTConfig.n_cores)) as pool:
for _ in range(n_configs):
result = pool.apply_async(func=function, args=args, kwds=kwargs)
results.append(result)
for result in results:
try:
config = result.get(timeout=None)
if config is not None and config.energy is not None:
configs.add(config)
# Lots of different exceptions can be raised when trying to
# generate an active config, continue regardless..
except Exception as err:
logger.error(f'Raised an exception in calculating the energy\n'
f'{err}')
continue
if method.lower() != 'diff':
logger.info('Running reference calculations on configurations '
f'generated by {method}')
configs.single_point(method_name=ref_method_name)
# Set the number of ground truth function calls for each iteration
for config in configs:
config.n_evals = 1
return configs