├── .gitattributes ├── .github └── workflows │ ├── build-wheels.yml │ ├── meson-build.yml │ ├── run_tests.yml.disabled │ └── source-package.yml ├── .gitignore ├── .vscode └── settings.json ├── AUTHORS.md ├── ChangeLog.md ├── DEVELOPMENT.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── discover_version.py ├── doc ├── install.lammps.md ├── install.python.md ├── install.standalone.md ├── potentials.md ├── standalone.md └── unittests.md ├── docker ├── Dockerfile └── README.md ├── env.sh ├── examples ├── ASE │ ├── Au-Grochola-JCP05.eam.alloy │ ├── README │ ├── calcs.py │ ├── fcc.py │ ├── liquid_tools.py │ ├── quench.py │ ├── rho_2.9.traj │ ├── scc_dftb.py │ └── time_potentials.py ├── LAMMPS │ └── liquid_silicon │ │ ├── README │ │ ├── SiC.tersoff │ │ ├── atomistica.in │ │ ├── data.lammps.gz │ │ └── lammps.in └── STANDALONE │ ├── C60_with_DFTB │ ├── README.md │ ├── atoms.dat │ └── md.dat │ ├── C60_with_Rebo2 │ ├── atoms.dat │ └── md.dat │ ├── README.md │ ├── andersen_p │ ├── atoms.dat │ └── md.dat │ ├── spce_water │ ├── atoms.dat │ └── md.dat │ ├── variable_charge │ ├── atoms.dat │ ├── md.dat │ └── variable_charge.dat │ └── water_with_DFTB │ ├── README.md │ ├── atoms.dat │ └── md.dat ├── images └── logo.png ├── meson.build ├── pyproject.toml ├── rebuild-uv.sh ├── rebuild.sh ├── renovate.json ├── requirements.txt ├── src ├── core │ └── filter.f90 ├── filter.inc ├── gen_versioninfo.sh ├── lammps │ ├── MAKE │ │ └── Makefile.par │ ├── coulomb_dispatch.f90 │ ├── factory.template.c │ ├── factory.template.h │ ├── gen_factory.py │ ├── lammps_filter.f90 │ ├── lammps_neighbors.f90 │ ├── lammps_particles.f90 │ └── pair_style │ │ ├── pair_atomistica.cpp │ │ └── pair_atomistica.h ├── macros.inc ├── makefile.inc ├── notb │ ├── dense │ │ ├── analysis │ │ │ └── dense_bonds.f90 │ │ ├── c_dense_hamiltonian.cpp │ │ ├── dense_forces.f90 │ │ ├── dense_hamiltonian.f90 │ │ ├── dense_hamiltonian.h │ │ ├── dense_hamiltonian_type.f90 │ │ ├── dense_hs.f90 │ │ ├── dense_notb.f90 │ │ ├── dense_repulsion.f90 │ │ ├── dense_scc.f90 │ │ └── solver │ │ │ ├── dense_occupation.f90 │ │ │ ├── dense_solver_cp.f90 │ │ │ ├── dense_solver_dispatch.f90 │ │ │ └── dense_solver_lapack.f90 │ ├── materials.f90 │ └── materials.h ├── potentials │ ├── bop │ │ ├── bop_kernel.f90 │ │ ├── brenner │ │ │ ├── brenner.f90 │ │ │ ├── brenner_func.f90 │ │ │ ├── brenner_module.f90 │ │ │ ├── brenner_params.f90 │ │ │ ├── brenner_registry.f90 │ │ │ ├── brenner_scr.f90 │ │ │ └── brenner_type.f90 │ │ ├── default_bind_to_func.f90 │ │ ├── default_compute_func.f90 │ │ ├── default_cutoff.f90 │ │ ├── default_del_func.f90 │ │ ├── juslin │ │ │ ├── juslin.f90 │ │ │ ├── juslin_func.f90 │ │ │ ├── juslin_module.f90 │ │ │ ├── juslin_params.f90 │ │ │ ├── juslin_registry.f90 │ │ │ ├── juslin_scr.f90 │ │ │ └── juslin_type.f90 │ │ ├── kumagai │ │ │ ├── kumagai.f90 │ │ │ ├── kumagai_func.f90 │ │ │ ├── kumagai_module.f90 │ │ │ ├── kumagai_params.f90 │ │ │ ├── kumagai_registry.f90 │ │ │ ├── kumagai_scr.f90 │ │ │ └── kumagai_type.f90 │ │ ├── rebo2 │ │ │ ├── bop_kernel_rebo2.f90 │ │ │ ├── rebo2.f90 │ │ │ ├── rebo2_db.f90 │ │ │ ├── rebo2_default_tables.f90 │ │ │ ├── rebo2_func.f90 │ │ │ ├── rebo2_module.f90 │ │ │ ├── rebo2_registry.f90 │ │ │ ├── rebo2_scr.f90 │ │ │ └── rebo2_type.f90 │ │ └── tersoff │ │ │ ├── tersoff.f90 │ │ │ ├── tersoff_func.f90 │ │ │ ├── tersoff_module.f90 │ │ │ ├── tersoff_params.f90 │ │ │ ├── tersoff_registry.f90 │ │ │ ├── tersoff_scr.f90 │ │ │ └── tersoff_type.f90 │ ├── coulomb.inc │ ├── coulomb │ │ ├── coulomb_short_gamma.f90 │ │ ├── cutoff_coulomb.f90 │ │ ├── damp_short_gamma.f90 │ │ ├── direct_coulomb.f90 │ │ ├── fft3-public.f │ │ ├── fft_wrap.f │ │ ├── gaussian_charges.f90 │ │ ├── pme.f90 │ │ ├── pme_kernel.f90 │ │ └── slater_charges.f90 │ ├── dispersion │ │ └── dispdftd3.f90 │ ├── eam │ │ ├── tabulated_alloy_eam.f90 │ │ └── tabulated_eam.f90 │ └── pair_potentials │ │ ├── born_mayer.f90 │ │ ├── double_harmonic.f90 │ │ ├── harmonic.f90 │ │ ├── lj_cut.f90 │ │ └── r6.f90 ├── python │ ├── atomistica │ │ ├── __init__.py │ │ ├── _version.py │ │ ├── analysis.py │ │ ├── aseinterface.py │ │ ├── atomic_strain.py │ │ ├── deformation.py │ │ ├── hardware.py │ │ ├── io.py │ │ ├── join_calculators.py │ │ ├── logger.py │ │ ├── mdcore_io.py │ │ ├── native.py │ │ ├── parameters.py │ │ ├── snippets.py │ │ └── tests.py │ ├── c │ │ ├── analysis.c │ │ ├── analysis.h │ │ ├── atomisticamodule.c │ │ ├── atomisticamodule.h │ │ ├── coulomb.c │ │ ├── coulomb.h │ │ ├── coulomb_callback.c │ │ ├── coulomb_factory.template.c │ │ ├── coulomb_factory.template.h │ │ ├── factory.template.c │ │ ├── factory.template.h │ │ ├── neighbors.c │ │ ├── neighbors.h │ │ ├── numpy_compat.h │ │ ├── particles.c │ │ ├── particles.h │ │ ├── potential.c │ │ ├── potential.h │ │ ├── py_f.c │ │ └── py_f.h │ ├── f90 │ │ ├── coulomb_dispatch.f90 │ │ ├── neighbors_wrap.f90 │ │ ├── particles_wrap.f90 │ │ ├── python_helper.f90 │ │ ├── python_neighbors.f90 │ │ └── python_particles.f90 │ ├── gen_factory.py │ ├── mdcore │ │ └── __init__.py │ └── tools │ │ ├── a_angle_distribution.py │ │ ├── a_convert.py │ │ ├── a_fire.py │ │ ├── a_g2.py │ │ ├── a_run.py │ │ └── a_voro.py ├── special │ ├── anderson_mixer.f90 │ ├── extrapolation.f90 │ ├── table2d.f90 │ ├── table3d.f90 │ └── table4d.f90 ├── spline.inc ├── standalone │ ├── andersen_p.f90 │ ├── berendsen_p.f90 │ ├── berendsen_t.f90 │ ├── callables_dispatch.template.f90 │ ├── cfg.f90 │ ├── confinement.f90 │ ├── constant_force.f90 │ ├── constant_strain_rate.f90 │ ├── constant_velocity.f90 │ ├── constraints.f90 │ ├── coulomb_dispatch.template.f90 │ ├── cyclic.f90 │ ├── diffusion_coefficient.f90 │ ├── domain_decomposition.f90 │ ├── dynamics.f90 │ ├── factory.template.c │ ├── factory.template.h │ ├── ffm_tip.f90 │ ├── fire.f90 │ ├── freezer.f90 │ ├── gen_dispatch.py │ ├── gen_factory.py │ ├── harmonic_hook.f90 │ ├── heatflux.f90 │ ├── input_trajectory.f90 │ ├── integrators_dispatch.template.f90 │ ├── interpolation_kernels_dispatch.f90 │ ├── lammps_data.f90 │ ├── lucy.f90 │ ├── main.f90 │ ├── molecules.f90 │ ├── native_io.f90 │ ├── nc.f90 │ ├── neighbors.f90 │ ├── no_integration.f90 │ ├── output_cell.f90 │ ├── output_cfg.f90 │ ├── output_energy.f90 │ ├── output_nc.f90 │ ├── output_pdb.f90 │ ├── output_time.f90 │ ├── output_xyz.f90 │ ├── particles.f90 │ ├── pdb.f90 │ ├── peters_t.f90 │ ├── potentials_dispatch.template.f90 │ ├── r250.f │ ├── remove_rotation.f90 │ ├── rng.f90 │ ├── settle.f90 │ ├── signal_handler.f90 │ ├── slicing.f90 │ ├── sliding_p.f90 │ ├── sliding_t.f90 │ ├── square.f90 │ ├── symmetry.f90 │ ├── ufmc.f90 │ ├── variable_charge.f90 │ ├── verlet.f90 │ ├── verlet_global_langevin.f90 │ ├── verlet_global_langevin_1d.f90 │ ├── verlet_local_langevin.f90 │ ├── verlet_local_langevin_1d.f90 │ ├── verlet_support.f90 │ ├── vtk.f90 │ └── xyz_f90.f90 ├── support │ ├── MPI_context.f90 │ ├── PeriodicTable.f90 │ ├── System.f90 │ ├── Units.f90 │ ├── atomistica.f90 │ ├── c_f.f90 │ ├── c_linearalgebra.cpp │ ├── c_logging.c │ ├── c_ptrdict.c │ ├── complexcomp.h │ ├── cu_linearalgebra.cu │ ├── cu_mat.cu │ ├── cu_mat.h │ ├── cu_util.h │ ├── cu_vec.cu │ ├── cu_vec.h │ ├── cutoff.f90 │ ├── data.f90 │ ├── error.f90 │ ├── error.h │ ├── error.inc │ ├── f_linearalgebra.f90 │ ├── f_logging.f90 │ ├── f_ptrdict.f90 │ ├── histogram1d.f90 │ ├── io.f90 │ ├── linearalgebra.h │ ├── logging.h │ ├── mat.h │ ├── misc.f90 │ ├── nonuniform_spline.f90 │ ├── ptrdict.h │ ├── simple_spline.f90 │ ├── supplib.f90 │ ├── timer.f90 │ ├── tls.f90 │ └── vec.h └── unittests │ ├── LICENSE.txt │ ├── README │ ├── fruit.f90 │ ├── fruit_util.f90 │ ├── run_tests.f90 │ ├── test_cutoff.f90 │ ├── test_linearalgebra.f90 │ ├── test_table2d.f90 │ ├── test_table3d.f90 │ └── test_table4d.f90 ├── tests ├── Au-Grochola-JCP05.eam.alloy ├── Au_u3.eam ├── Cu_mishin1.eam.alloy ├── aC.cfg ├── aC_small.cfg ├── eam_crash1.poscar ├── eam_crash2.poscar ├── molecule_database │ ├── 1,2-pentadiene.xyz │ ├── 1,3-pentadiene.xyz │ ├── 1,4-pentadiene.xyz │ ├── 1-butene,2-methyl.xyz │ ├── 1-butene.xyz │ ├── 1-butyne.xyz │ ├── 2,3-pentadiene.xyz │ ├── 2-butene,2-methyl.xyz │ ├── 2-pentene.xyz │ ├── 2H2O.xyz │ ├── 3H2O.xyz │ ├── 4H2O.xyz │ ├── 5H2O.xyz │ ├── C2H.xyz │ ├── CH2=C=CH2.xyz │ ├── CH3CH=C=CH2.xyz │ ├── H3C2H2.xyz │ ├── cis-butene.xyz │ ├── cyclohexane.xyz │ ├── cyclopentane.xyz │ ├── cyclopentene.xyz │ ├── i-C4H9.xyz │ ├── isopentane.xyz │ ├── n-pentane.xyz │ ├── naphthalene.xyz │ ├── neopentane.xyz │ ├── propyne.xyz │ └── t-C4H9.xyz ├── test_bulk_properties.py ├── test_coulomb.py ├── test_dftb3.py ├── test_dimers.py ├── test_eam_special_cases.py ├── test_forces_and_virial.py ├── test_io.py ├── test_mask.py ├── test_mio.py ├── test_neighbor_list.py ├── test_pbc.py ├── test_rebo2_molecules.py ├── test_surface_properties.py ├── test_tb_stresses.py └── test_tersoff.py ├── tools ├── c_header.txt ├── f_header.txt ├── f_header_n.txt ├── fix_headers.sh ├── listclasses.py ├── meta.py └── py_header.txt └── uv.lock /.gitattributes: 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