FLARE: Fast Learning of Atomistic Rare Events

Contents

• Installation
  • Installation of FLARE
    • Requirements
    • Developer’s installation guide
    • Test FLARE installation
    • Trouble shooting
    • Acceleration with multiprocessing and MKL
      • Sparse Gaussian Process model
      • Full Gaussian Process model
  • Compile LAMMPS with FLARE
    • Compilation with CMake
      • Compilation for GPU with Kokkos
    • Basic usage
      • Running on a GPU with Kokkos
    • Notes on Newton (only relevant with Kokkos)
• Tutorials
  • FLARE: Active Learning Bayesian Force Fields
  • Training a 2+3-body Gaussian Process from an AIMD Run
    • Roadmap Figure
    • Step 1: Setting up a Gaussian Process Object
    • Step 2 (Optional): Extracting the Frames from a previous AIMD Run
    • Step 3: Training your Gaussian Process
    • Pre-Training arguments
  • Build 2+3-body Mapped GP
    • Parse OTF log file
    • Construct GP model from log file
    • Map the GP force field & Dump LAMMPS coefficient file
    • Run LAMMPS with MGP pair style
• 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
      • 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
      • nprandom()
    • Construct Atomic Environment
      • get_2_body_arrays()
      • get_3_body_arrays()
      • get_m2_body_arrays()
      • get_m3_body_arrays()
      • q3_value_mc()
    • NumpyEncoder
• C++ Code Documentation
  • Structures
  • Bayesian force fields
  • Descriptors
  • Kernels
• Frequently Asked Questions
  • Installation and Packages
  • Gaussian Processes
  • OTF (On-the-fly) Active-Learning
  • Offline-Learning
  • Production MD Simulations using a FLARE ML-FF
• Applications/Gallery
• How To Contribute
  • Git Workflow
    • General workflow
    • Master, development, and topic branches
    • Pushing changes to the MIR repo directly
    • Pushing changes from a forked repo
  • Code Standards
    • PEP 8
    • Docstrings
    • Tests
• How to Cite