AGOX's modules are designed for usage of various structure search methods. Some basic modules are used everywhere, but do not need to be defined in the input script

Mandatory modules for an input script are:

Mandatory submodules (not directly passing to function) for an input script are:

Optional modules for an input script are:

Optional submodules for an input script are:

Command line tool






The feature vector is based on the local density of element Z around the central atom i

$$ \begin{array}{ccc} \rho _ i^Z(\lambda) = & \sum_{j \neq i, Z_j=Z} \dfrac{1}{\lambda}\text{exp}(-r_{ij}/\lambda) f_c(r_{ij}) \\ \\ f_c(r) = & \begin{cases} \dfrac{1}{2} \text{cos} (\pi \dfrac{r}{r_c}) + \dfrac{1}{2}, & r \le r_c \\ 0, & r > r_c \end{cases} \end{array} $$

where $\lambda$ is a hyperparameter and can have multiple values like 0.5Å, 1Å, 1.5Å, ...

Taking a silicate (Mg$_2$SiO$_4$)$_x$ system as an example, the whole feature vector is sorted by atomic numbers and is constructed as $$ \textbf{f}_i = [ \underbrace{\rho _ i^O(\lambda_1), \rho _ i^O(\lambda_2), \dots, \rho _ i^O(\lambda_n)} _ \text{Oxygen neighbors}, \underbrace{\rho _ i^{Mg}(\lambda_1), \rho _ i^{Mg}(\lambda_2), \dots, \rho _ i^{Mg}(\lambda_n)} _ \text{Magnesium neighbors}, \underbrace{\rho _ i^{Si}(\lambda_1), \rho _ i^{Si}(\lambda_2), \dots, \rho _ i^{Si}(\lambda_n)} _ \text{Silicon neighbors}, \underbrace{Z_i} _ \text{Atomic number}] $$

In practice, if the feature_matrix has a shape of (n_atoms, n_species, n_lambs), it can be flatten as feature_matrix.reshape(n_atoms, -1). For example, if there are 3 species and 5 lambdas, the feature matrix of one atom [O(1) means $\rho^O(\lambda_1)$]

O(1)    O(2)    O(3)   O(4)   O(5)
Mg(1)   Mg(2)   Mg(3)  Mg(4)  Mg(5)
Si(1)   Si(2)   Si(3)  Si(4)  Si(5)

will be reshaped into

O(1)    O(2)    O(3)   O(4)   O(5)  Mg(1)   Mg(2)   Mg(3)  Mg(4)  Mg(5)   Si(1)   Si(2)   Si(3)  Si(4)  Si(5)

Finally, the atomic numbers can be appended as the last column.


Ray ParallelCollector

Traceback (most recent call last):
  File "/scratch/10071999/run0/", line 175, in <module>
    post = ParallelRelaxPostprocess(model=model_calculator, 
  File "/home/tang/opt/agox/agox_gitlab/agox/postprocessors/", line 44, in __init__
    self.model_key = self.pool_add_module(model)
  File "/home/tang/opt/agox/agox_gitlab/agox/utils/", line 566, in pool_add_module
    return self.pool.add_module(module)
  File "/home/tang/opt/agox/agox_gitlab/agox/utils/", line 287, in add_module
    futures = [actor.add_module.remote(module, key) for actor in self.idle_actors]
  File "/home/tang/opt/agox/agox_gitlab/agox/utils/", line 287, in <listcomp>
    futures = [actor.add_module.remote(module, key) for actor in self.idle_actors]
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/", line 144, in remote
    return self._remote(args, kwargs)
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/_private/", line 24, in auto_init_wrapper
    return fn(*args, **kwargs)
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/util/tracing/", line 426, in _start_span
    return method(self, args, kwargs, *_args, **_kwargs)
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/", line 191, in _remote
    return invocation(args, kwargs)
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/", line 178, in invocation
    return actor._actor_method_call(
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/", line 1176, in _actor_method_call
    object_refs = worker.core_worker.submit_actor_task(
  File "python/ray/_raylet.pyx", line 3728, in ray._raylet.CoreWorker.submit_actor_task
  File "python/ray/_raylet.pyx", line 3733, in ray._raylet.CoreWorker.submit_actor_task
  File "python/ray/_raylet.pyx", line 694, in ray._raylet.prepare_args_and_increment_put_refs
  File "python/ray/_raylet.pyx", line 685, in ray._raylet.prepare_args_and_increment_put_refs
  File "python/ray/_raylet.pyx", line 732, in ray._raylet.prepare_args_internal
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/_private/", line 494, in serialize
    return self._serialize_to_msgpack(value)
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/_private/", line 472, in _serialize_to_msgpack
    pickle5_serialized_object = self._serialize_to_pickle5(
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/_private/", line 425, in _serialize_to_pickle5
    raise e
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/_private/", line 420, in _serialize_to_pickle5
    inband = pickle.dumps(
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/cloudpickle/", line 88, in dumps
  File "/home/tang/python-virtualenv/spk2/lib/python3.9/site-packages/ray/cloudpickle/", line 733, in dump
    return Pickler.dump(self, obj)
RuntimeError: Tried to serialize object __torch__.schnetpack.model.base.___torch_mangle_15.NeuralNetworkPotential which does not have a __getstate__ method defined!


LowerConfidenceBoundAcquisitor (sym_dev)