Modules

Tools

• Substrate (flake.substrate)
  • Coordinate convention
  • Substrate types
  • JIT notes
  • calc_en_gaussian()
  • calc_en_sin()
  • calc_en_tanh()
  • calc_matrices_bvect()
  • calc_matrices_square()
  • calc_matrices_triangle()
  • gaussian()
  • get_ks()
  • particle_en_gaussian()
  • particle_en_sin()
  • particle_en_tanh()
  • substrate_from_params()
• Cluster (flake.cluster)
  • add_basis()
  • calc_cluster_langevin()
  • cluster_from_params()
  • cluster_poly()
  • get_poly()
  • load_cluster()
  • make_cluster()
  • params_from_poscar()
  • rotate()
  • save_cluster()
  • save_xyz()
• String method (flake.string_method)
  • Two usage modes
  • Gradient and string step
  • Scale parameter
  • Algorithm
  • StringPath
  • StringPotential
  • find_mep()
• I/O (flake.io)
  • load_map()
  • load_params()
  • load_trajectory()
  • make_sin_params()
  • save_map()
  • save_params()
  • save_trajectory()
• Plotting (flake.plot)
  • Public API
  • get_brillouin_zone_2d()
  • plot_BZ2d()
  • plot_UC()
  • plot_lattice_vectors()
  • plt_cosmetic()

Static maps

• Static maps (flake.maps)
  • Grid coordinate convention
  • Parallelism
  • rotational_map()
  • rototrasl_map()
  • translational_map()

Dynamics

• Dynamics (flake.dynamics)
  • Physics
  • Integration
  • JIT path vs Python path
  • Public API
  • run_md()
• Sweep infrastructure (flake.sweep)
  • Public API
  • I/O convention
  • concat_sweeps()
  • drift_omega()
  • drift_velocity()
  • filter_sweep()
  • force_sweep()
  • grid_sweep()
  • last_state()
  • line_sweep()
  • load_sweep()
  • load_sweep_points()
  • mean_velocity()
  • sweep_md()