msmJAX

Contents:

  • User guide
    • Installation
      • CPU-only installation
      • CUDA installation
      • Optional dependencies
    • Setting up and running a calculation
  • API reference
    • msmjax.calculators
      • CustomJSONEncoder
        • CustomJSONEncoder.default()
      • CustomJSONDecoder
        • CustomJSONDecoder.object_hook()
      • MSMParams
        • MSMParams.p
        • MSMParams.mu
        • MSMParams.max_splitting_level
        • MSMParams.max_grid_level
        • MSMParams.cutoffs
        • MSMParams.cell
        • MSMParams.cell_mode
        • MSMParams.pbc
        • MSMParams.dynamic_cell
        • MSMParams.supercell_diag
        • MSMParams.use_neighborlist
        • MSMParams.neighborlist_prefactor
        • MSMParams.grids_defined_on_unitcube
        • MSMParams.grid_shapes
        • MSMParams.grid_spacings
        • MSMParams.stencil_extents_from_center
        • MSMParams.convolution_methods
        • MSMParams.n_dim
        • MSMParams.version
        • MSMParams.info
        • MSMParams.save_json()
        • MSMParams.load_json()
      • find_stencil_extents_all_levels()
      • set_up_msm_params()
      • create_msm()
      • check_cutoffs_and_get_actual_spacings()
    • msmjax.kernels
      • SoftenerOneOverR
      • split_one_over_r()
      • _get_distances()
      • _compute_one_stencil()
      • make_construct_stencils()
    • msmjax.bspline
      • msmjax.bspline.basis
        • characteristic()
        • evaluate_basis_element()
        • create_bspline_basis_element()
      • msmjax.bspline.coefficients
        • calc_Phi()
        • build_col_of_B()
        • build_col_of_B2()
        • build_Toeplitz_matrix()
        • build_Toeplitz_system()
        • compute_c_m()
        • generating_function()
        • calc_Mclaurin_coefficient()
        • calc_B_p_over_2()
        • calc_polynomials()
        • explode_Add()
        • coeff_dict_to_array()
        • compute_quasi_omega_prime()
        • compute_j_zeroplus()
      • msmjax.bspline.gridops
        • _find_n_gridpoints_1d()
        • set_up_grids_all_levels()
        • _arbitrary_dim_outer()
        • _multiindex_outer()
        • _ravel_multi_index_with_invalidation()
        • make_basis_evaluation_fn()
        • _make_restrict_1d()
        • make_restriction_operator()
        • _make_prolongate_1d()
        • make_prolongation_operator()
        • create_all_grid_to_grid_ops()
        • suggest_max_grid_level_nonperiodic()
        • find_spacings_and_max_level_periodic()
    • msmjax.core
      • msmjax.core.shortrange
        • _gen_supercell()
        • _displacement_free()
        • _displacement_ortho()
        • _displacement_general()
        • _concretize_displacement_fn()
        • make_eval_pair_pot()
        • make_eval_pair_pot_neighborlist()
        • make_compute_u_zero()
      • msmjax.core.longrange
        • _anterpolate()
        • _interpolate_energy()
        • _interpolate_energy_positions_gradient()
        • _interpolate_energy_charge_gradient()
        • special_periodic_convolve_scipy()
        • make_grid_pass_fn()
        • make_compute_u_oneplus()
    • msmjax.utils
      • msmjax.utils.benchmarking
        • dir_context()
        • write_lammps_data()
        • parse_energy_from_lammps_log()
        • parse_lammps_log()
        • make_lammps_input_text_pppm()
        • eval_lammps_pppm()
        • calc_rmse()
        • calc_relative_rmse_percent()
        • calc_relative_rmse()
        • make_timed_eval()
        • remove_duplicates_from_neighborlist()
        • build_duplicate_free_neighborlists()
        • coulomb_kernel()
        • calc_energy_nonperiodic_direct_summation()
        • calc_forces_nonperiodic_direct_summation()
        • calc_chargegrad_nonperiodic_direct_summation()
        • calc_stress_virial()
        • calc_nonperiodic_reference_results()
      • msmjax.utils.general
        • _divide_zero_safe()
        • _sqrt_jvp()
        • get_max_cutoff_for_mic()
        • find_covering_grid_extents()
msmJAX
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© Copyright 2025, Florian Buchner, Johannes Schörghuber, Nico Unglert, Jesús Carrete, Georg K. H. Madsen.

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