Python Code Documentation

• Bayesian Force Fields
  • Gaussian Process Force Fields
    • Predict
    • Helper functions for GP
    • FLARE ASE Calculator
    • GaussianProcess
  • Mapped Gaussian Process
    • Splines Methods
    • Formulation of Mapped Gaussian Process
    • MappedGaussianProcess
  • Sparse Gaussian Process Force Fields
    • ASE Calculator of Sparse GP
    • SGP_Wrapper
    • compute_negative_likelihood()
    • compute_negative_likelihood_grad()
    • compute_negative_likelihood_grad_stable()
    • optimize_hyperparameters()
• Bayesian Active Learning
  • On-the-Fly Training
    • OTF
  • On-the-Fly Training in LAMMPS
    • LMPOTF
  • GP From AIMD
    • Seed frames
    • parse_trajectory_trainer_output()
    • structures_from_gpfa_output()
  • Conditions to add training data
    • get_max_cutoff()
    • is_force_in_bound_per_species()
    • is_std_in_bound()
    • is_std_in_bound_per_species()
    • subset_of_frame_by_element()
• ASE MD Engine
  • Fake MD
    • FakeDFT
    • FakeMD
  • LAMMPS Calculator and MD
    • LAMMPS_MD
    • LAMMPS_MOD
    • add_single_atom_energies()
    • check_sgp_match()
    • get_kinetic_stress()
  • NoseHoover (NVT Ensemble)
    • NoseHoover
• Descriptors
  • Atomic Environments
    • AtomicEnvironment
• Kernels
  • Single-element Kernels
    • many_body()
    • many_body_en()
    • many_body_en_jit()
    • many_body_force_en()
    • many_body_force_en_jit()
    • many_body_grad()
    • many_body_grad_jit()
    • many_body_jit()
    • three_body()
    • three_body_en()
    • three_body_en_jit()
    • three_body_force_en()
    • three_body_force_en_jit()
    • three_body_grad()
    • three_body_grad_jit()
    • three_body_jit()
    • two_body()
    • two_body_en()
    • two_body_en_jit()
    • two_body_force_en()
    • two_body_force_en_jit()
    • two_body_grad()
    • two_body_grad_jit()
    • two_body_jit()
    • two_plus_many_body()
    • two_plus_many_body_en()
    • two_plus_many_body_force_en()
    • two_plus_many_body_grad()
    • two_plus_three_body()
    • two_plus_three_body_grad()
    • two_plus_three_en()
    • two_plus_three_force_en()
    • two_plus_three_plus_many_body()
    • two_plus_three_plus_many_body_en()
    • two_plus_three_plus_many_body_force_en()
    • two_plus_three_plus_many_body_grad()
  • Multi-element Kernels (simple)
    • many_body_mc()
    • many_body_mc_en()
    • many_body_mc_en_jit()
    • many_body_mc_force_en()
    • many_body_mc_force_en_jit()
    • many_body_mc_grad()
    • many_body_mc_grad_jit()
    • many_body_mc_jit()
    • three_body_mc()
    • three_body_mc_en()
    • three_body_mc_en_jit()
    • three_body_mc_force_en()
    • three_body_mc_force_en_jit()
    • three_body_mc_grad()
    • three_body_mc_grad_jit()
    • three_body_mc_jit()
    • three_body_se_jit()
    • three_body_sf_jit()
    • three_body_ss_jit()
    • two_body_mc()
    • two_body_mc_en()
    • two_body_mc_en_jit()
    • two_body_mc_force_en()
    • two_body_mc_force_en_jit()
    • two_body_mc_grad()
    • two_body_mc_grad_jit()
    • two_body_mc_jit()
    • two_body_mc_stress_en_jit()
    • two_body_mc_stress_force_jit()
    • two_body_mc_stress_stress_jit()
    • two_plus_many_body_mc()
    • two_plus_many_body_mc_en()
    • two_plus_many_body_mc_force_en()
    • two_plus_many_body_mc_grad()
    • two_plus_three_body_mc()
    • two_plus_three_body_mc_grad()
    • two_plus_three_mc_en()
    • two_plus_three_mc_force_en()
    • two_plus_three_plus_many_body_mc()
    • two_plus_three_plus_many_body_mc_en()
    • two_plus_three_plus_many_body_mc_force_en()
    • two_plus_three_plus_many_body_mc_grad()
  • Multi-element Kernels (Separate Parameters)
    • many_body_mc()
    • many_body_mc_en()
    • many_body_mc_force_en()
    • many_body_mc_grad()
    • three_body_mc()
    • three_body_mc_en()
    • three_body_mc_force_en()
    • three_body_mc_force_en_jit()
    • three_body_mc_grad()
    • three_body_mc_grad_jit()
    • two_body_mc()
    • two_body_mc_en()
    • two_body_mc_en_jit()
    • two_body_mc_force_en()
    • two_body_mc_force_en_jit()
    • two_body_mc_grad()
    • two_body_mc_grad_jit()
    • two_body_mc_jit()
    • two_plus_three_body_mc()
    • two_plus_three_body_mc_grad()
    • two_plus_three_mc_en()
    • two_plus_three_mc_force_en()
    • two_three_many_body_mc()
    • two_three_many_body_mc_grad()
    • two_three_many_mc_en()
    • two_three_many_mc_force_en()
    • three_body_mc_force_en_sepcut_jit()
    • three_body_mc_grad_sepcut_jit()
    • many_body_mc_en_sepcut_jit()
    • many_body_mc_force_en_sepcut_jit()
    • many_body_mc_grad_sepcut_jit()
    • many_body_mc_sepcut_jit()
  • Cutoff Functions
    • cosine_cutoff()
    • cubic_cutoff()
    • hard_cutoff()
    • quadratic_cutoff()
    • quadratic_cutoff_bound()
  • Helper Functions
    • coordination_number()
    • force_helper()
    • k_sq_exp_dev()
    • k_sq_exp_double_dev()
    • mb_grad_helper_ls()
    • mb_grad_helper_ls_()
    • q_value()
    • q_value_mc()
• File Input and Output
  • Output
    • Output
    • add_file()
    • add_stream()
    • set_logger()
  • OTF Parser
    • OtfAnalysis
    • append_atom_lists()
    • extract_gp_info()
    • parse_frame_line()
    • parse_header_information()
    • parse_snapshot()
    • strip_and_split()
• Utility
  • Advanced Hyperparameters Set Up
    • ParameterHelper
  • Construct Atomic Environment
    • get_2_body_arrays()
    • get_3_body_arrays()
    • get_m2_body_arrays()
    • get_m3_body_arrays()
    • q3_value_mc()
  • NumpyEncoder