AtomicAI

Getting Started

  • Installation
    • Requirements
    • Install from PyPI
    • Install from Source
    • Verify Installation
  • Quick Start
    • 1. Convert a structure file
    • 2. Compute atomic descriptors
    • 3. Generate force descriptors
    • 4. Radial Distribution Function
    • 5. Build a multilayer structure
    • 6. Generate surface slabs
    • 7. Dimensionality reduction

User Guide

  • File Format Conversion
    • VASP conversions
    • Conquest conversions
    • Trajectory conversions
    • Examples
  • Structure Building Tools
    • supercell
    • build_multilayers
    • build_constrained_multilayers
    • surfaces
    • build_interface
  • Atomic Descriptors
    • Command-line usage
      • Options
    • Descriptor types
      • ACSF_G2 — Radial symmetry functions
      • ACSF_G3 — Cosine basis functions
      • ACSF_G4 — Angular symmetry functions (with rjk)
      • ACSF_G5 — Angular symmetry functions (without rjk)
      • ACSF_G2G4 — Combined radial + angular (recommended)
      • ACSF_G2G4G5 — Full combined descriptor
      • SOAP — Smooth Overlap of Atomic Positions
      • MBSF — Many-body symmetry functions
    • Output
    • Running multiple types
  • Force Descriptors
    • Command-line usage
      • Options
    • Fingerprint types
      • BP2b — Behler-Parrinello 2-body
      • Split2b3b_ss — Split 2-body + 3-body (same species)
    • Output
  • Machine Learning Force Fields
    • Workflow
    • Step 1: Generate force descriptors
    • Step 2: Train the MLFF
    • Step 3: LAMMPS input files
    • VASP database inputs
  • Dimensionality Reduction
    • Available methods
    • Usage
    • TsLPP
  • Structure Analysis
    • Radial Distribution Function
    • Structure analysis
    • Molecular dynamics statistics
  • Visualization
    • RDF plots
    • MD statistics
    • Clustering

API Reference

  • Descriptors API
    • calculate_descriptors
      • calculate_descriptors()
    • generate_force_descriptor
      • force_descriptor()
      • generate_force_descriptors()
      • prepare_vforce()
      • writeout_fp()
    • laaf
      • AverageFingerprintCalculator
        • AverageFingerprintCalculator.compute_averaged_fingeprints_selection()
        • AverageFingerprintCalculator.compute_averaged_fingerprints_random()
      • calculate_average_fingerprint()
      • calculate_eta()
      • calculate_fingerprint_vector()
    • acsf
      • ACSF
        • ACSF.create()
      • ACSF_Force
        • ACSF_Force.create()
      • calculate_mirror_cubic()
      • get_g2()
      • get_g3()
      • get_g4()
      • get_g5()
      • get_v2b()
      • get_v3b()
      • random_vforce()
      • set_eta()
    • mbsf
      • MBSF
        • MBSF.create()
      • calculate_mirror_cubic()
      • get_ga_nblst()
      • get_gr()
      • get_gr_nblst()
      • get_grga()
      • get_neighbour_lst()
  • Tools API
    • build_multilayers
      • analyze_vectors()
      • build_multilayer()
      • build_multilayers()
      • calculate_stack_position()
      • create_supercell()
      • get_multiples_mapping()
      • get_nonredundant_permutations()
      • print_results()
      • read_vasp_files()
      • setup_logging()
    • surfaces
      • structures()
      • surfaces()
    • rdf
      • RDF()
      • available_pairs()
      • moving_average()
      • pairs()
      • predict_pairs()
      • supercell()
    • select_snapshots
      • select_snapshots()
    • structure_analysis
      • structure_analysis()
    • supercell
      • generate_supercell_vasp()
      • supercell()
  • MLFF API
    • mlff
      • get_mlff()
    • LassoLarCV
  • Dimensionality Reduction API
    • tslpp
      • compute_lpp()
      • new_centering()
      • perform_lpp()
      • tslpp()
    • lpp
      • compute_lpp()
      • lpp()
      • new_centering()
      • perform_lpp()

About

  • Changelog
    • 0.4.0 (2025)
    • 0.3.0
  • Citing AtomicAI
    • Software
    • Method references
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