autoplex.fitting.common.utils

Utility functions for fitting jobs.

Functions

calculate_delta_2b	Calculate the delta parameter and average number of triplets for gap-fitting.
check_convergence	Check the convergence of the fit.
compute_num_of_descriptor	Compute the number of two-body or three-body descriptors within a specified cutoff radius.
convert_xyz_to_structure	Convert extxyz to pymatgen Structure format.
energy_remain	Plot the distribution of energy per atom on the output vs.
extract_gap_label	Extract GAP label.
flatten	Flatten an iterable fully, but excluding Atoms objects.
gap_fitting	Perform the GAP (Gaussian approximation potential) model fitting.
gap_hyperparameter_constructor	Construct a list of arguments needed to execute gap potential from the parameters' dict.
gcm3_to_Vm	Convert gcm3 to Vm.
get_atomic_numbers	Get atomic numbers.
get_list_of_vasp_calc_dirs	Return a list of vasp_calc_dirs from PhononDFTMLDataGenerationFlow output.
jace_fitting	Perform the ACE (Atomic Cluster Expansion) potential fitting.
m3gnet_fitting	Perform the M3GNet potential fitting.
mace_fitting	Perform the MACE potential fitting.
mace_virial_format_conversion	Convert the format of virial vector (9,) into a format (3x3) recognizable by MACE.
nep_fitting	Perform the NEP (Neural evolution Potential) model fitting.
nequip_fitting	Perform the NequIP potential fitting.
plot_convex_hull	Plot convex hull.
prepare_fit_environment	Prepare the environment for the fit.
run_ace	Julia-ACE script runner.
run_ase_gap	ASE-GAP runner.
run_gap	GAP runner.
run_mace	MACE runner.
run_nep	NEP runner.
run_nequip	Nequip runner.
vaspoutput_2_extended_xyz	Parse all VASP output files (vasprun.xml/OUTCAR) and generates a vasp_ref.extxyz.
write_after_distillation_data_split	Write train.extxyz and test.extxyz after data distillation and split.

Classes

CustomPotential	A custom potential class that modifies the outputs of potentials.
chemical_symbols	Built-in mutable sequence.