├── .gitignore ├── LICENSE ├── NOTICE ├── README.md ├── compile └── README.md ├── doc ├── Eqs │ ├── angle.png │ ├── angle.tex │ ├── angle_charmm.jpg │ ├── angle_charmm.tex │ ├── angle_class2.jpg │ ├── angle_class2.tex │ ├── angle_cosine.jpg │ ├── angle_cosine.tex │ ├── angle_cosine_delta.jpg │ ├── angle_cosine_delta.tex │ ├── angle_cosine_periodic.jpg │ ├── angle_cosine_periodic.tex │ ├── angle_cosine_shift.jpg │ ├── angle_cosine_shift.tex │ ├── angle_cosine_shift_exp.jpg │ ├── angle_cosine_shift_exp.tex │ ├── angle_cosine_squared.jpg │ ├── angle_cosine_squared.tex │ ├── angle_dipole_gamma.jpg │ ├── angle_dipole_gamma.tex │ ├── angle_dipole_potential.jpg │ ├── angle_dipole_potential.tex │ ├── angle_dipole_torque.jpg │ ├── angle_dipole_torque.tex │ ├── angle_fourier.jpg │ ├── angle_fourier.tex │ ├── angle_fourier_simple.jpg │ ├── angle_fourier_simple.tex │ ├── angle_harmonic.jpg │ ├── angle_harmonic.tex │ ├── angle_quartic.jpg │ ├── angle_quartic.tex │ ├── bond_class2.jpg │ ├── bond_class2.tex │ ├── bond_fene.jpg │ ├── bond_fene.tex │ ├── bond_fene_expand.jpg │ ├── bond_fene_expand.tex │ ├── bond_harmonic.jpg │ ├── bond_harmonic.tex │ ├── bond_harmonic_shift.jpg │ ├── bond_harmonic_shift.tex │ ├── bond_harmonic_shift_cut.jpg │ ├── bond_harmonic_shift_cut.tex │ ├── bond_morse.jpg │ ├── bond_morse.tex │ ├── bond_nonlinear.jpg │ ├── bond_nonlinear.tex │ ├── bond_quartic.jpg │ ├── bond_quartic.tex │ ├── box.jpg │ ├── box.tex │ ├── box_inverse.jpg │ ├── box_inverse.tex │ ├── centro_symmetry.jpg │ ├── centro_symmetry.tex │ ├── cna_cutoff1.jpg │ ├── cna_cutoff1.tex │ ├── cna_cutoff2.jpg │ ├── cna_cutoff2.tex │ ├── compute_gyration.jpg │ ├── compute_gyration.tex │ ├── compute_msd_nongauss.jpg │ ├── compute_msd_nongauss.tex │ ├── conduction_rate.png │ ├── dihedral_charmm.jpg │ ├── dihedral_charmm.tex │ ├── dihedral_class2.jpg │ ├── dihedral_class2.tex │ ├── dihedral_cosine_shift_exp.jpg │ ├── dihedral_cosine_shift_exp.tex │ ├── dihedral_fourier.jpg │ ├── dihedral_fourier.tex │ ├── dihedral_harmonic.jpg │ ├── dihedral_harmonic.tex │ ├── dihedral_helix.jpg │ ├── dihedral_helix.tex │ ├── dihedral_multi_harmonic.jpg │ ├── dihedral_multi_harmonic.tex │ ├── dihedral_nharmonic.jpg │ ├── dihedral_nharmonic.tex │ ├── dihedral_opls.jpg │ ├── dihedral_opls.tex │ ├── dihedral_quadratic.jpg │ ├── dihedral_quadratic.tex │ ├── dihedral_sign.jpg │ ├── dreiding_hbond.jpg │ ├── eff_ECP1.jpg │ ├── eff_ECP1.tex │ ├── eff_ECP2.jpg │ ├── eff_ECP2.tex │ ├── eff_KE.jpg │ ├── eff_KE.tex │ ├── eff_NN.jpg │ ├── eff_NN.tex │ ├── eff_Ne.jpg │ ├── eff_Ne.tex │ ├── eff_Pauli.jpg │ ├── eff_Pauli.tex │ ├── eff_ee.jpg │ ├── eff_ee.tex │ ├── eff_energy_expression.jpg │ ├── eff_energy_expression.tex │ ├── fix_box_relax1.jpg │ ├── fix_box_relax1.tex │ ├── fix_box_relax2.jpg │ ├── fix_box_relax2.tex │ ├── fix_gld1.jpg │ ├── fix_gld1.tex │ ├── fix_lb_fluid_boltzmann.jpg │ ├── fix_lb_fluid_boltzmann.tex │ ├── fix_lb_fluid_fluidforce.jpg │ ├── fix_lb_fluid_fluidforce.tex │ ├── fix_lb_fluid_gammadefault.jpg │ ├── fix_lb_fluid_gammadefault.tex │ ├── fix_lb_fluid_navierstokes.jpg │ ├── fix_lb_fluid_navierstokes.tex │ ├── fix_lb_fluid_properties.jpg │ ├── fix_lb_fluid_properties.tex │ ├── fix_lb_fluid_stress.jpg │ ├── fix_lb_fluid_stress.tex │ ├── fix_lb_fluid_viscosity.jpg │ ├── fix_lb_fluid_viscosity.tex │ ├── fix_nh1.jpg │ ├── fix_nh1.tex │ ├── fix_nphug.jpg │ ├── fix_nphug.tex │ ├── fix_orient_fcc.jpg │ ├── fix_orient_fcc.tex │ ├── fix_sph_density_continuity_eq1.gif │ ├── fix_sph_density_continuity_eq1.jpg │ ├── fix_sph_density_continuity_eq1.tex │ ├── fix_sph_density_continuity_eq2.gif │ ├── fix_sph_density_continuity_eq2.jpg │ ├── fix_sph_density_continuity_eq2.tex │ ├── fix_sph_density_corr_eq1.gif │ ├── fix_sph_density_corr_eq1.jpg │ ├── fix_sph_density_corr_eq1.tex │ ├── fix_sph_density_drift_corr_eq1.jpg │ ├── fix_sph_density_summation.jpg │ ├── fix_sph_density_summation.tex │ ├── fix_sph_density_summation_eq1.gif │ ├── fix_sph_integrity_eq1.jpg │ ├── fix_sph_mixidx_eq1.jpg │ ├── fix_sph_mixidx_eq2.jpg │ ├── fix_sph_mixidx_eq3.jpg │ ├── fix_sph_mixidx_eq4.jpg │ ├── fix_sph_mixidx_eq5.jpg │ ├── fix_sph_mixidx_eq6.jpg │ ├── fix_sph_pressure_abs.jpg │ ├── fix_sph_pressure_abs.tex │ ├── fix_sph_pressure_eq1.gif │ ├── fix_sph_pressure_eq2.gif │ ├── fix_sph_pressure_eq3.gif │ ├── fix_sph_pressure_rel.jpg │ ├── fix_sph_pressure_rel.tex │ ├── fix_sph_pressure_tait_eq1.jpg │ ├── fix_sph_pressure_tait_eq1.tex │ ├── fix_sph_pressure_tait_eq2.jpg │ ├── fix_sph_pressure_tait_eq2.tex │ ├── fix_sph_velgrad_eq1.jpg │ ├── fix_spring_rg.jpg │ ├── fix_spring_rg.tex │ ├── fix_ti_rs_force.jpg │ ├── fix_ti_rs_force.tex │ ├── fix_ti_rs_function_1.jpg │ ├── fix_ti_rs_function_1.tex │ ├── fix_ti_rs_function_2.jpg │ ├── fix_ti_rs_function_2.tex │ ├── fix_ti_rs_function_3.jpg │ ├── fix_ti_rs_function_3.tex │ ├── fix_ti_spring_force.jpg │ ├── fix_ti_spring_force.tex │ ├── fix_ti_spring_function_1.jpg │ ├── fix_ti_spring_function_1.tex │ ├── fix_ti_spring_function_2.jpg │ ├── fix_ti_spring_function_2.tex │ ├── fix_ttm.jpg │ ├── fix_ttm.tex │ ├── fix_wall_colloid.jpg │ ├── fix_wall_colloid.tex │ ├── fix_wall_harmonic.jpg │ ├── fix_wall_harmonic.tex │ ├── fix_wall_lj1043.jpg │ ├── fix_wall_lj1043.tex │ ├── fix_wall_lj93.jpg │ ├── fix_wall_lj93.tex │ ├── fix_wall_region_sph.jpg │ ├── fix_wall_region_sph.tex │ ├── fix_wall_region_sph_eq1.gif │ ├── fld.jpg │ ├── fld.tex │ ├── fld2.jpg │ ├── fld2.tex │ ├── gran_model_hooke_hysteresis_1.png │ ├── gran_model_hooke_hysteresis_1.tex │ ├── gran_model_hooke_hysteresis_2.png │ ├── gran_model_hooke_hysteresis_2.tex │ ├── heat_flux_J.jpg │ ├── heat_flux_J.tex │ ├── heat_flux_k.jpg │ ├── heat_flux_k.tex │ ├── heat_gran.jpg │ ├── heat_gran_radiation_bolzmann.png │ ├── improper_class2.jpg │ ├── improper_class2.tex │ ├── improper_cossq.jpg │ ├── improper_cossq.tex │ ├── improper_cvff.jpg │ ├── improper_cvff.tex │ ├── improper_fourier.jpg │ ├── improper_fourier.tex │ ├── improper_harmonic.jpg │ ├── improper_harmonic.tex │ ├── improper_ring.jpg │ ├── improper_ring.tex │ ├── improper_umbrella.jpg │ ├── improper_umbrella.tex │ ├── min_energy.jpg │ ├── min_energy.tex │ ├── model_A.png │ ├── model_C2_part_1.jpg │ ├── model_C2_part_1.png │ ├── model_C2_part_2.jpg │ ├── model_C3_part_1.jpg │ ├── model_C3_part_2.jpg │ ├── model_C_part_1.png │ ├── model_C_part_2.png │ ├── model_C_part_3.png │ ├── model_b1.png │ ├── model_b2_part1.png │ ├── model_b2_part2.png │ ├── modelb1.png │ ├── pair_adp.jpg │ ├── pair_adp.tex │ ├── pair_airebo.jpg │ ├── pair_airebo.tex │ ├── pair_beck.jpg │ ├── pair_beck.tex │ ├── pair_bop.jpg │ ├── pair_bop.tex │ ├── pair_born.jpg │ ├── pair_born.tex │ ├── pair_buck.jpg │ ├── pair_buck.tex │ ├── pair_charmm.jpg │ ├── pair_charmm.tex │ ├── pair_class2.jpg │ ├── pair_class2.tex │ ├── pair_cmm.jpg │ ├── pair_cmm.tex │ ├── pair_colloid_cc.jpg │ ├── pair_colloid_cc.tex │ ├── pair_colloid_cs.jpg │ ├── pair_colloid_cs.tex │ ├── pair_colloid_ss.jpg │ ├── pair_colloid_ss.tex │ ├── pair_comb1.jpg │ ├── pair_comb1.tex │ ├── pair_comb2.jpg │ ├── pair_comb2.tex │ ├── pair_coul_diel.jpg │ ├── pair_coul_diel.tex │ ├── pair_coul_dsf.jpg │ ├── pair_coul_dsf.tex │ ├── pair_coul_wolf.jpg │ ├── pair_coul_wolf.tex │ ├── pair_coulomb.jpg │ ├── pair_coulomb.tex │ ├── pair_debye.jpg │ ├── pair_debye.tex │ ├── pair_dipole.jpg │ ├── pair_dipole.tex │ ├── pair_dipole_sf.jpg │ ├── pair_dipole_sf.tex │ ├── pair_dipole_sf2.jpg │ ├── pair_dipole_sf2.tex │ ├── pair_dpd.jpg │ ├── pair_dpd.tex │ ├── pair_eam.jpg │ ├── pair_eam.tex │ ├── pair_eam_fs.jpg │ ├── pair_eam_fs.tex │ ├── pair_edip.jpg │ ├── pair_edip.tex │ ├── pair_eim1.jpg │ ├── pair_eim1.tex │ ├── pair_eim2.jpg │ ├── pair_eim2.tex │ ├── pair_eim3.jpg │ ├── pair_eim3.tex │ ├── pair_gauss.jpg │ ├── pair_gauss.tex │ ├── pair_gauss_cut.jpg │ ├── pair_gauss_cut.tex │ ├── pair_gayberne.jpg │ ├── pair_gayberne.tex │ ├── pair_gayberne2.jpg │ ├── pair_gayberne2.tex │ ├── pair_gran_hertz.jpg │ ├── pair_gran_hertz.tex │ ├── pair_gran_hooke.jpg │ ├── pair_gran_hooke.tex │ ├── pair_gran_hooke_eqEpsd1.gif │ ├── pair_gran_hooke_eqEpsd1.tex │ ├── pair_gran_hooke_eqEpsd2.gif │ ├── pair_gran_hooke_eqEpsd2.tex │ ├── pair_gran_hooke_eqEpsd3.gif │ ├── pair_gran_hooke_eqEpsd3.tex │ ├── pair_gran_hooke_eqEpsd4.gif │ ├── pair_gran_hooke_eqEpsd4.tex │ ├── pair_gran_hooke_eqEpsd5.gif │ ├── pair_gran_hooke_eqEpsd5.tex │ ├── pair_gran_html_147eaf38.png │ ├── pair_gran_html_60b8ced2 (copy).png │ ├── pair_gran_html_60b8ced2.png │ ├── pair_gran_html_m225ba7de.png │ ├── pair_gran_html_m4dff7906.png │ ├── pair_gran_html_m566a9984.png │ ├── pair_gran_html_m5aad056c.png │ ├── pair_gran_html_m76cd8bd9.png │ ├── pair_gromacs.jpg │ ├── pair_gromacs.tex │ ├── pair_hbond_dreiding.jpg │ ├── pair_hbond_dreiding.tex │ ├── pair_lj.jpg │ ├── pair_lj.tex │ ├── pair_lj96.jpg │ ├── pair_lj96.tex │ ├── pair_lj_cubic.jpg │ ├── pair_lj_cubic.tex │ ├── pair_lj_expand.jpg │ ├── pair_lj_expand.tex │ ├── pair_lj_sf.jpg │ ├── pair_lj_sf.tex │ ├── pair_lj_smooth.jpg │ ├── pair_lj_smooth.tex │ ├── pair_lj_smooth_linear.jpg │ ├── pair_lj_smooth_linear.tex │ ├── pair_lubricate.jpg │ ├── pair_lubricate.tex │ ├── pair_lubricate_GRM.jpg │ ├── pair_lubricate_GRM.tex │ ├── pair_meam.jpg │ ├── pair_meam.tex │ ├── pair_meam_spline.jpg │ ├── pair_meam_spline.tex │ ├── pair_meam_sw_spline.jpg │ ├── pair_meam_sw_spline.tex │ ├── pair_mie.jpg │ ├── pair_mie.tex │ ├── pair_mie2.jpg │ ├── pair_mie2.tex │ ├── pair_morse.jpg │ ├── pair_morse.tex │ ├── pair_nb3b_harmonic.jpg │ ├── pair_nb3b_harmonic.tex │ ├── pair_nm.jpg │ ├── pair_nm.tex │ ├── pair_resquared.jpg │ ├── pair_resquared.tex │ ├── pair_resquared2.jpg │ ├── pair_resquared2.tex │ ├── pair_resquared3.jpg │ ├── pair_resquared3.tex │ ├── pair_resquared4.jpg │ ├── pair_resquared4.tex │ ├── pair_soft.jpg │ ├── pair_soft.tex │ ├── pair_sph_artvisc_tenscorr_eq1.jpg │ ├── pair_sph_artvisc_tenscorr_eq1.tex │ ├── pair_sph_artvisc_tenscorr_eq2.jpg │ ├── pair_sph_artvisc_tenscorr_eq2.tex │ ├── pair_sph_artvisc_tenscorr_eq3.jpg │ ├── pair_sph_artvisc_tenscorr_eq3.tex │ ├── pair_sph_artvisc_tenscorr_eq4.jpg │ ├── pair_sph_artvisc_tenscorr_eq4.tex │ ├── pair_sph_artvisc_tenscorr_eq5.jpg │ ├── pair_sph_artvisc_tenscorr_eq5.tex │ ├── pair_sph_artvisc_tenscorr_eq6.jpg │ ├── pair_sph_artvisc_tenscorr_eq6.tex │ ├── pair_sph_artvisc_tenscorr_eq7.jpg │ ├── pair_sph_artvisc_tenscorr_eq7.tex │ ├── pair_sph_artvisc_tenscorr_eq8.jpg │ ├── pair_sph_artvisc_tenscorr_eq8.tex │ ├── pair_sph_ideal.jpg │ ├── pair_sph_ideal.tex │ ├── pair_sph_morris_tenscorr_eq1.jpg │ ├── pair_sph_morris_tenscorr_eq2.jpg │ ├── pair_sph_morris_tenscorr_eq3.jpg │ ├── pair_sph_morris_tenscorr_eq4.jpg │ ├── pair_sph_morris_tenscorr_eq5.jpg │ ├── pair_sph_morris_tenscorr_eq6.jpg │ ├── pair_sph_morris_tenscorr_eq7.jpg │ ├── pair_sph_tait.jpg │ ├── pair_sph_tait.tex │ ├── pair_sw.jpg │ ├── pair_sw.tex │ ├── pair_tersoff.jpg │ ├── pair_tersoff_1.jpg │ ├── pair_tersoff_1.tex │ ├── pair_tersoff_2.jpg │ ├── pair_tersoff_2.tex │ ├── pair_tersoff_mod.jpg │ ├── pair_tersoff_mod.tex │ ├── pair_tersoff_zbl.jpg │ ├── pair_tersoff_zbl.tex │ ├── pair_yukawa.jpg │ ├── pair_yukawa.tex │ ├── pair_yukawa_colloid.jpg │ ├── pair_yukawa_colloid.tex │ ├── pair_zbl.jpg │ ├── pair_zbl.tex │ ├── pressure.jpg │ ├── pressure.tex │ ├── pressure_tensor.jpg │ ├── pressure_tensor.tex │ ├── rotate.jpg │ ├── rotate.tex │ ├── roughnessLength.png │ ├── saturation_model.jpg │ ├── scsr.png │ ├── stress_tensor.jpg │ ├── stress_tensor.tex │ ├── stress_tensor_granular.png │ ├── stress_tensor_granular.tex │ ├── transform.jpg │ ├── transform.tex │ ├── umbrella.jpg │ ├── variables.png │ ├── vb.png │ ├── vbi.png │ ├── vbj.png │ ├── viblin.jpg │ ├── viblin.tex │ ├── vibrot.jpg │ └── vibrot.tex ├── JPG │ ├── atc_nanotube.jpg │ ├── balance.jpg │ ├── bondswap.jpg │ ├── dump1.jpg │ ├── dump1_small.jpg │ ├── dump2.jpg │ ├── dump2_small.jpg │ ├── hooke_hysteresis_luding1.png │ ├── hop1.jpg │ ├── hop1_small.jpg │ ├── hop2.jpg │ ├── hop2_small.jpg │ └── rhodo_staggered.jpg ├── LICENSE ├── LIGGGHTS_logo.png ├── Makefile ├── Manual.html ├── Manual.txt ├── PDF │ ├── PDLammps_VES.pdf │ ├── colvars-refman-lammps.pdf │ ├── kspace.pdf │ ├── pair_gayberne_extra.pdf │ ├── pair_gayberne_extra.tex │ ├── pair_resquared_extra.pdf │ └── pair_resquared_extra.tex ├── Scripts │ └── correlate.py ├── Section_commands.html ├── Section_commands.txt ├── Section_commands_LAMMPS.html ├── Section_commands_LAMMPS.txt ├── Section_errors.html ├── Section_errors.txt ├── Section_gran_howto.html ├── Section_gran_howto.txt ├── Section_gran_models.html ├── Section_gran_models.txt ├── Section_howto.html ├── Section_howto.txt ├── Section_input_script.html ├── Section_input_script.txt ├── Section_intro.html ├── Section_intro.txt ├── Section_mesh_modules.html ├── Section_mesh_modules.txt ├── Section_modify.html ├── Section_modify.txt ├── Section_packages.html ├── Section_packages.txt ├── Section_python.html ├── Section_python.txt ├── Section_start.html ├── Section_start.txt ├── _downloads │ └── yi_jing_01_chien.jpg ├── _images │ ├── LIGGGHTS_logo.png │ ├── balance.jpg │ ├── bond_harmonic.jpg │ ├── box.jpg │ ├── box_inverse.jpg │ ├── centro_symmetry.jpg │ ├── cna_cutoff1.jpg │ ├── cna_cutoff2.jpg │ ├── compute_gyration.jpg │ ├── compute_msd_nongauss.jpg │ ├── fix_box_relax1.jpg │ ├── fix_box_relax2.jpg │ ├── fix_sph_density_continuity_eq1.jpg │ ├── fix_sph_density_continuity_eq2.jpg │ ├── fix_sph_density_corr_eq1.jpg │ ├── fix_sph_density_summation.jpg │ ├── fix_sph_pressure_abs.jpg │ ├── fix_sph_pressure_rel.jpg │ ├── fix_sph_pressure_tait_eq1.jpg │ ├── fix_sph_pressure_tait_eq2.jpg │ ├── fix_spring_rg.jpg │ ├── fix_wall_colloid.jpg │ ├── fix_wall_harmonic.jpg │ ├── fix_wall_lj93.jpg │ ├── fix_wall_region_sph.jpg │ ├── heat_gran.jpg │ ├── pair_gran_hooke_eqEpsd1.gif │ ├── pair_gran_hooke_eqEpsd2.gif │ ├── pair_gran_hooke_eqEpsd3.gif │ ├── pair_gran_hooke_eqEpsd4.gif │ ├── pair_gran_hooke_eqEpsd5.gif │ ├── pair_gran_html_147eaf38.png │ ├── pair_gran_html_60b8ced2.png │ ├── pair_gran_html_m225ba7de.png │ ├── pair_gran_html_m566a9984.png │ ├── pair_gran_html_m5aad056c.png │ ├── pair_gran_html_m76cd8bd9.png │ ├── pair_lj.jpg │ ├── pair_soft.jpg │ ├── pair_sph_artvisc_tenscorr_eq1.jpg │ ├── pair_sph_artvisc_tenscorr_eq2.jpg │ ├── pair_sph_artvisc_tenscorr_eq3.jpg │ ├── pair_sph_artvisc_tenscorr_eq4.jpg │ ├── pair_sph_artvisc_tenscorr_eq5.jpg │ ├── pair_sph_artvisc_tenscorr_eq6.jpg │ ├── pair_sph_artvisc_tenscorr_eq7.jpg │ ├── pair_sph_artvisc_tenscorr_eq8.jpg │ ├── pressure.jpg │ ├── pressure_tensor.jpg │ ├── rotate.jpg │ ├── stress_tensor.jpg │ ├── stress_tensor_granular.png │ ├── transform.jpg │ ├── viblin.jpg │ ├── vibrot.jpg │ └── yi_jing_01_chien.jpg ├── _static │ ├── ajax-loader.gif │ ├── basic.css │ ├── comment-bright.png │ ├── comment-close.png │ ├── comment.png │ ├── css │ │ ├── badge_only.css │ │ └── theme.css │ ├── doctools.js │ ├── down-pressed.png │ ├── down.png │ ├── file.png │ ├── fonts │ │ ├── FontAwesome.otf │ │ ├── Inconsolata-Bold.ttf │ │ ├── Inconsolata-Regular.ttf │ │ ├── Lato-Bold.ttf │ │ ├── Lato-BoldItalic.ttf │ │ ├── Lato-Italic.ttf │ │ ├── Lato-Regular.ttf │ │ ├── RobotoSlab-Bold.ttf │ │ ├── RobotoSlab-Regular.ttf │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ └── fontawesome-webfont.woff2 │ ├── jquery.js │ ├── js │ │ ├── modernizr.min.js │ │ └── theme.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── underscore.js │ ├── up-pressed.png │ ├── up.png │ └── websupport.js ├── atom_modify.html ├── atom_modify.txt ├── atom_style.html ├── atom_style.txt ├── balance.html ├── balance.txt ├── bond_coeff.html ├── bond_coeff.txt ├── bond_harmonic.html ├── bond_harmonic.txt ├── bond_hybrid.html ├── bond_hybrid.txt ├── bond_none.html ├── bond_none.txt ├── bond_style.html ├── bond_style.txt ├── boundary.html ├── boundary.txt ├── box.html ├── box.txt ├── change_box.html ├── change_box.txt ├── clear.html ├── clear.txt ├── coarsegraining.html ├── coarsegraining.txt ├── communicate.html ├── communicate.txt ├── compute.html ├── compute.txt ├── compute_atom_molecule.html ├── compute_atom_molecule.txt ├── compute_bond_counter.html ├── compute_bond_counter.txt ├── compute_bond_local.html ├── compute_bond_local.txt ├── compute_centro_atom.html ├── compute_centro_atom.txt ├── compute_cluster_atom.html ├── compute_cluster_atom.txt ├── compute_cna_atom.html ├── compute_cna_atom.txt ├── compute_com.html ├── compute_com.txt ├── compute_com_molecule.html ├── compute_com_molecule.txt ├── compute_contact_atom.html ├── compute_contact_atom.txt ├── compute_coord_atom.html ├── compute_coord_atom.txt ├── compute_coord_gran.html ├── compute_coord_gran.txt ├── compute_crosssection.html ├── compute_crosssection.txt ├── compute_displace_atom.html ├── compute_displace_atom.txt ├── compute_erotate.html ├── compute_erotate.txt ├── compute_erotate_asphere.html ├── compute_erotate_asphere.txt ├── compute_erotate_multisphere.html ├── compute_erotate_multisphere.txt ├── compute_erotate_sphere.html ├── compute_erotate_sphere.txt ├── compute_erotate_sphere_atom.html ├── compute_erotate_sphere_atom.txt ├── compute_erotate_superquadric.html ├── compute_erotate_superquadric.txt ├── compute_group_group.html ├── compute_group_group.txt ├── compute_gyration.html ├── compute_gyration.txt ├── compute_gyration_molecule.html ├── compute_gyration_molecule.txt ├── compute_inertia_molecule.html ├── compute_inertia_molecule.txt ├── compute_ke.html ├── compute_ke.txt ├── compute_ke_atom.html ├── compute_ke_atom.txt ├── compute_ke_multisphere.html ├── compute_ke_multisphere.txt ├── compute_modify.html ├── compute_modify.txt ├── compute_msd.html ├── compute_msd.txt ├── compute_msd_molecule.html ├── compute_msd_molecule.txt ├── compute_msd_nongauss.html ├── compute_msd_nongauss.txt ├── compute_nparticles_tracer_region.html ├── compute_nparticles_tracer_region.txt ├── compute_pair_gran_local.html ├── compute_pair_gran_local.txt ├── compute_pe.html ├── compute_pe.txt ├── compute_pe_atom.html ├── compute_pe_atom.txt ├── compute_pressure.html ├── compute_pressure.txt ├── compute_property_atom.html ├── compute_property_atom.txt ├── compute_property_local.html ├── compute_property_local.txt ├── compute_property_molecule.html ├── compute_property_molecule.txt ├── compute_rdf.html ├── compute_rdf.txt ├── compute_reduce.html ├── compute_reduce.txt ├── compute_rigid.html ├── compute_rigid.txt ├── compute_slice.html ├── compute_slice.txt ├── compute_stress_atom.html ├── compute_stress_atom.txt ├── compute_surface.html ├── compute_surface.txt ├── compute_voronoi_atom.html ├── compute_voronoi_atom.txt ├── conf.py ├── create_atoms.html ├── create_atoms.txt ├── create_box.html ├── create_box.txt ├── create_particles.html ├── create_particles.txt ├── delete_atoms.html ├── delete_atoms.txt ├── delete_bonds.html ├── delete_bonds.txt ├── dielectric.html ├── dielectric.txt ├── dimension.html ├── dimension.txt ├── displace_atoms.html ├── displace_atoms.txt ├── dump.html ├── dump.txt ├── dump_custom_vtk.html ├── dump_custom_vtk.txt ├── dump_image.html ├── dump_image.txt ├── dump_local_gran_vtk.html ├── dump_local_gran_vtk.txt ├── dump_modify.html ├── dump_modify.txt ├── dump_modify_vtk.html ├── dump_modify_vtk.txt ├── echo.html ├── echo.txt ├── finnie-wear.pdf ├── fix.html ├── fix.txt ├── fix_adapt.html ├── fix_adapt.txt ├── fix_addforce.html ├── fix_addforce.txt ├── fix_ave_atom.html ├── fix_ave_atom.txt ├── fix_ave_correlate.html ├── fix_ave_correlate.txt ├── fix_ave_euler.html ├── fix_ave_euler.txt ├── fix_ave_histo.html ├── fix_ave_histo.txt ├── fix_ave_spatial.html ├── fix_ave_spatial.txt ├── fix_ave_time.html ├── fix_ave_time.txt ├── fix_aveforce.html ├── fix_aveforce.txt ├── fix_balance.html ├── fix_balance.txt ├── fix_bond_break.html ├── fix_bond_break.txt ├── fix_bond_create.html ├── fix_bond_create.txt ├── fix_box_relax.html ├── fix_box_relax.txt ├── fix_buoyancy.html ├── fix_buoyancy.txt ├── fix_check_timestep_gran.html ├── fix_check_timestep_gran.txt ├── fix_continuum_weighted.html ├── fix_continuum_weighted.txt ├── fix_couple_cfd.html ├── fix_couple_cfd.txt ├── fix_deform.html ├── fix_deform.txt ├── fix_drag.html ├── fix_drag.txt ├── fix_dragforce.html ├── fix_dragforce.txt ├── fix_dt_reset.html ├── fix_dt_reset.txt ├── fix_efield.html ├── fix_efield.txt ├── fix_enforce2d.html ├── fix_enforce2d.txt ├── fix_external.html ├── fix_external.txt ├── fix_freeze.html ├── fix_freeze.txt ├── fix_gravity.html ├── fix_gravity.txt ├── fix_heat_gran_conduction.html ├── fix_heat_gran_conduction.txt ├── fix_insert_fragments.html ├── fix_insert_fragments.txt ├── fix_insert_pack.html ├── fix_insert_pack.txt ├── fix_insert_rate_region.html ├── fix_insert_rate_region.txt ├── fix_insert_stream.html ├── fix_insert_stream.txt ├── fix_lineforce.html ├── fix_lineforce.txt ├── fix_massflow_mesh.html ├── fix_massflow_mesh.txt ├── fix_massflow_mesh_sieve.html ├── fix_massflow_mesh_sieve.txt ├── fix_mesh_surface.html ├── fix_mesh_surface.txt ├── fix_modify.html ├── fix_modify.txt ├── fix_momentum.html ├── fix_momentum.txt ├── fix_move.html ├── fix_move.txt ├── fix_move_mesh.html ├── fix_move_mesh.txt ├── fix_multicontact_halfspace.html ├── fix_multicontact_halfspace.txt ├── fix_multisphere.html ├── fix_multisphere.txt ├── fix_multisphere_advanced.html ├── fix_multisphere_advanced.txt ├── fix_multisphere_break.html ├── fix_multisphere_break.txt ├── fix_nve.html ├── fix_nve.txt ├── fix_nve_asphere.html ├── fix_nve_asphere.txt ├── fix_nve_asphere_noforce.html ├── fix_nve_asphere_noforce.txt ├── fix_nve_cfd_cn.html ├── fix_nve_cfd_cn.txt ├── fix_nve_limit.html ├── fix_nve_limit.txt ├── fix_nve_line.html ├── fix_nve_line.txt ├── fix_nve_noforce.html ├── fix_nve_noforce.txt ├── fix_nve_nonspherical.html ├── fix_nve_nonspherical.txt ├── fix_nve_sphere.html ├── fix_nve_sphere.txt ├── fix_nve_sphere_limit.html ├── fix_nve_sphere_limit.txt ├── fix_particledistribution_discrete.html ├── fix_particledistribution_discrete.txt ├── fix_particletemplate_multiplespheres.html ├── fix_particletemplate_multiplespheres.txt ├── fix_particletemplate_multisphere.html ├── fix_particletemplate_multisphere.txt ├── fix_particletemplate_sphere.html ├── fix_particletemplate_sphere.txt ├── fix_particletemplate_superquadric.html ├── fix_particletemplate_superquadric.txt ├── fix_planeforce.html ├── fix_planeforce.txt ├── fix_poems.html ├── fix_poems.txt ├── fix_print.html ├── fix_print.txt ├── fix_property.html ├── fix_property.txt ├── fix_property_atom_region_tracer_time.html ├── fix_property_atom_region_tracer_time.txt ├── fix_property_atom_tracer.html ├── fix_property_atom_tracer.txt ├── fix_property_atom_tracer_stream.html ├── fix_property_atom_tracer_stream.txt ├── fix_rigid.html ├── fix_rigid.txt ├── fix_set_vel.html ├── fix_set_vel.txt ├── fix_setforce.html ├── fix_setforce.txt ├── fix_sph_density_continuity.html ├── fix_sph_density_continuity.txt ├── fix_sph_density_corr.html ├── fix_sph_density_corr.txt ├── fix_sph_density_summation.html ├── fix_sph_density_summation.txt ├── fix_sph_pressure.html ├── fix_sph_pressure.txt ├── fix_spring.html ├── fix_spring.txt ├── fix_spring_rg.html ├── fix_spring_rg.txt ├── fix_spring_self.html ├── fix_spring_self.txt ├── fix_store_force.html ├── fix_store_force.txt ├── fix_store_state.html ├── fix_store_state.txt ├── fix_viscous.html ├── fix_viscous.txt ├── fix_wall_gran.html ├── fix_wall_gran.txt ├── fix_wall_reflect.html ├── fix_wall_reflect.txt ├── fix_wall_region.html ├── fix_wall_region.txt ├── fix_wall_region_sph.html ├── fix_wall_region_sph.txt ├── genindex.html ├── gran_cohesion_bond.html ├── gran_cohesion_bond.txt ├── gran_cohesion_easo_capillary_viscous.html ├── gran_cohesion_easo_capillary_viscous.txt ├── gran_cohesion_sjkr.html ├── gran_cohesion_sjkr.txt ├── gran_cohesion_sjkr2.html ├── gran_cohesion_sjkr2.txt ├── gran_cohesion_washino_capillary_viscous.html ├── gran_cohesion_washino_capillary_viscous.txt ├── gran_model_hertz.html ├── gran_model_hertz.txt ├── gran_model_hertz_stiffness.html ├── gran_model_hertz_stiffness.txt ├── gran_model_hooke.html ├── gran_model_hooke.txt ├── gran_model_hooke_stiffness.html ├── gran_model_hooke_stiffness.txt ├── gran_rolling_friction_cdt.html ├── gran_rolling_friction_cdt.txt ├── gran_rolling_friction_epsd.html ├── gran_rolling_friction_epsd.txt ├── gran_rolling_friction_epsd2.html ├── gran_rolling_friction_epsd2.txt ├── gran_rolling_friction_epsd3.html ├── gran_rolling_friction_epsd3.txt ├── gran_surface_multicontact.html ├── gran_surface_multicontact.txt ├── gran_surface_sphere.html ├── gran_surface_sphere.txt ├── gran_surface_superquadric.html ├── gran_surface_superquadric.txt ├── gran_tangential_history.html ├── gran_tangential_history.txt ├── gran_tangential_no_history.html ├── gran_tangential_no_history.txt ├── group.html ├── group.txt ├── howto_liggghts_4.X_tutorial.html ├── howto_liggghts_4.X_tutorial.txt ├── howto_superquadric_simulations.html ├── howto_superquadric_simulations.txt ├── if.html ├── if.txt ├── include.html ├── include.txt ├── info.html ├── info.txt ├── jump.html ├── jump.txt ├── label.html ├── label.txt ├── lattice.html ├── lattice.txt ├── liggghts_2.X_tutorial.html ├── liggghts_2.X_tutorial.txt ├── liggghts_3.X_tutorial.html ├── liggghts_3.X_tutorial.txt ├── log.html ├── log.txt ├── make.bat ├── mass.html ├── mass.txt ├── mesh_module_6dof.html ├── mesh_module_6dof.txt ├── mesh_module_liquidtransfer.html ├── mesh_module_liquidtransfer.txt ├── mesh_module_servo.html ├── mesh_module_servo.txt ├── mesh_module_stress.html ├── mesh_module_stress.txt ├── neigh_modify.html ├── neigh_modify.txt ├── neighbor.html ├── neighbor.txt ├── newton.html ├── newton.txt ├── next.html ├── next.txt ├── objects.inv ├── orient.html ├── orient.txt ├── origin.html ├── origin.txt ├── pair_coeff.html ├── pair_coeff.txt ├── pair_gran.html ├── pair_gran.txt ├── pair_hybrid.html ├── pair_hybrid.txt ├── pair_none.html ├── pair_none.txt ├── pair_soft.html ├── pair_soft.txt ├── pair_sph_artvisc_tenscorr.html ├── pair_sph_artvisc_tenscorr.txt ├── pair_style.html ├── pair_style.txt ├── partition.html ├── partition.txt ├── print.html ├── print.txt ├── processors.html ├── processors.txt ├── quit.html ├── quit.txt ├── read_data.html ├── read_data.txt ├── read_dump.html ├── read_dump.txt ├── read_restart.html ├── read_restart.txt ├── region.html ├── region.txt ├── replicate.html ├── replicate.txt ├── rerun.html ├── rerun.txt ├── reset_timestep.html ├── reset_timestep.txt ├── restart.html ├── restart.txt ├── run.html ├── run.txt ├── run_style.html ├── run_style.txt ├── search.html ├── searchindex.js ├── set.html ├── set.txt ├── shell.html ├── shell.txt ├── thermo.html ├── thermo.txt ├── thermo_modify.html ├── thermo_modify.txt ├── thermo_style.html ├── thermo_style.txt ├── timestep.html ├── timestep.txt ├── uncompute.html ├── uncompute.txt ├── undump.html ├── undump.txt ├── unfix.html ├── unfix.txt ├── units.html ├── units.txt ├── variable.html ├── variable.txt ├── velocity.html ├── velocity.txt ├── write_data.html ├── write_data.txt ├── write_dump.html ├── write_dump.txt ├── write_restart.html └── write_restart.txt ├── examples └── LIGGGHTS │ ├── INL │ ├── .gitignore │ ├── cohesive_bond │ │ ├── chain_bending_test │ │ │ └── in.chain_bending.lmp │ │ ├── chain_compression_test │ │ │ └── in.chain_compression.lmp │ │ ├── chain_test │ │ │ ├── in.chain_test │ │ │ ├── in.chain_test_2 │ │ │ ├── meshes │ │ │ │ ├── unit_plate.geo │ │ │ │ └── unit_plate.stl │ │ │ ├── post │ │ │ │ └── .gitignore │ │ │ └── postscript │ │ └── particle_replacement │ │ │ ├── data │ │ │ ├── particle3.txt │ │ │ └── particle3_fragments.txt │ │ │ ├── in.bonds_direct │ │ │ ├── in.bonds_from_ms │ │ │ ├── meshes │ │ │ ├── box.geo │ │ │ └── box.stl │ │ │ ├── postscript │ │ │ └── runscript │ ├── cohesive_bond_nonlinear_compression │ │ ├── chain_bending_mm_1 │ │ │ └── in.chain_bending.lmp │ │ ├── chain_bending_mm_2 │ │ │ └── in.chain_bending.lmp │ │ ├── chain_bending_um_1 │ │ │ └── in.chain_bending.lmp │ │ └── chain_bending_um_2 │ │ │ └── in.chain_bending.lmp │ ├── cohesive_bond_nonlinear_tension │ │ ├── 2_spheres │ │ │ ├── clump.txt │ │ │ ├── gold │ │ │ │ └── out.loading.csv │ │ │ └── in.particle_test │ │ ├── 3_spheres │ │ │ ├── clump.txt │ │ │ ├── gold │ │ │ │ └── out.loading.csv │ │ │ └── in.particle_test │ │ ├── 7_spheres │ │ │ ├── clump.txt │ │ │ ├── gold │ │ │ │ └── out.loading.csv │ │ │ └── in.particle_test │ │ ├── 9_spheres │ │ │ ├── clump.txt │ │ │ ├── gold │ │ │ │ └── out.loading.csv │ │ │ └── in.particle_test │ │ ├── README.md │ │ └── src │ │ │ └── cohesion_model_bond_nonlinear_tension.h │ ├── microstructure_compression │ │ ├── gold │ │ │ └── output.csv │ │ ├── in.microstructure_compression.lmp │ │ ├── mesh_plate.stl │ │ ├── post │ │ │ └── README │ │ ├── post2 │ │ │ └── README │ │ ├── prime_numbers.txt │ │ └── vox_1.lmp │ ├── multisphere_hopper_discharge │ │ ├── body_type1.dat │ │ ├── body_type2.dat │ │ ├── body_type3.dat │ │ ├── body_type4.dat │ │ ├── hopper.stl │ │ └── in.binflow │ ├── normal_contact_hysteretic_nonlinear1 │ │ ├── gold │ │ │ └── out_loading.csv │ │ └── input.lmp │ ├── normal_contact_hysteretic_nonlinear2 │ │ ├── gold │ │ │ └── out_loading.csv │ │ └── input.lmp │ └── rolling_resistance_cdtnonlinear2 │ │ ├── bottom.stl │ │ ├── gold │ │ └── out.loading.csv │ │ └── in.rolling_resistance_cdtnonlinear2 │ ├── INL_tutorials │ ├── README.md │ ├── figs │ │ ├── fig_staticAOR_MonoSphere.png │ │ └── fig_staticAOR_MultiSphere.png │ ├── t01a_static_angle_of_repose_monosphere │ │ ├── Cylinder_35cm_7cm.stl │ │ └── in.staticAOR_MonoSphere │ └── t01b_static_angle_of_repose_multisphere │ │ ├── Cylinder_35cm_7cm.stl │ │ ├── body_6mm_cube.dat │ │ └── in.staticAOR_MultiSphere │ ├── Tutorials_premium │ ├── 6dof_cube │ │ ├── in.6dof │ │ ├── in.6dof_modify │ │ ├── meshes │ │ │ └── cube.stl │ │ ├── octave │ │ │ └── postCoord.m │ │ ├── post │ │ │ └── restart │ │ │ │ └── .gitignore │ │ └── postscript │ ├── buyoancy │ │ ├── in.buoyancy_drag │ │ ├── in.buoyancy_nodrag │ │ ├── post │ │ │ └── .gitignore │ │ └── postscript │ ├── contact_test │ │ ├── data │ │ │ ├── particle3.txt │ │ │ └── particles.txt │ │ ├── in.contact │ │ ├── in.contact_2 │ │ ├── in.contact_ms │ │ ├── in.multisphere │ │ ├── meshes │ │ │ ├── box.stl │ │ │ └── insert.stl │ │ ├── post │ │ │ └── .gitignore │ │ └── postscript │ ├── dump_custom_vtk │ │ ├── in.dump_custom_vtk │ │ ├── in.dump_custom_vtk_mpi_np4 │ │ └── post │ │ │ └── .gitignore │ ├── mesh_force_eval │ │ ├── README │ │ ├── in.testmeshforce │ │ ├── in_nohistory.testmeshforce │ │ ├── meshes │ │ │ └── plate.stl │ │ ├── post │ │ │ └── .gitignore │ │ └── postscript │ ├── mix_sphere_multisphere │ │ ├── data │ │ │ ├── stone1.multisphere │ │ │ └── stone1.test │ │ ├── in.mix_sphere_ms │ │ ├── post │ │ │ └── .gitignore │ │ └── postscript │ ├── multisphere_coal │ │ ├── data │ │ │ ├── coal01_15_14.multisphere │ │ │ ├── coal01_15_14.vtk │ │ │ ├── coal02_0_20.multisphere │ │ │ ├── coal02_0_20.vtk │ │ │ ├── coal03_10_14.multisphere │ │ │ └── coal03_10_14.vtk │ │ ├── in.multisphere │ │ ├── in.multisphere_LB │ │ ├── post │ │ │ └── .gitignore │ │ └── postscript │ └── residence_time │ │ ├── in.residence_time │ │ ├── in.residence_time_and_dist_tracer │ │ ├── in.residence_time_ideal_periodic │ │ ├── in.residence_time_stream_multiple │ │ ├── in.residence_time_stream_once │ │ ├── in.residence_time_stream_once_restart │ │ ├── in.residence_time_stream_once_restart_re │ │ ├── in.residence_time_stream_rare │ │ ├── meshes │ │ └── face.stl │ │ ├── plot_octave.m │ │ ├── post │ │ ├── .gitignore │ │ └── restart │ │ │ └── .gitignore │ │ └── postscript │ └── Tutorials_public │ ├── ParScale │ ├── fluidizedBedTempParScale │ │ ├── README.md │ │ ├── cleanCase.sh │ │ ├── codeInfo.pascal │ │ ├── in.DEM │ │ ├── in.liggghts_init │ │ ├── in.liggghts_run │ │ ├── particle.data │ │ ├── particleFew.data │ │ ├── particleTemp.profile │ │ ├── pascal │ │ │ ├── 0 │ │ │ │ ├── heat.json │ │ │ │ ├── heat_fewParticle.json │ │ │ │ ├── heat_multiParticle.json │ │ │ │ ├── heat_singleParticle.json │ │ │ │ ├── radius.json │ │ │ │ ├── radius_fewParticle.json │ │ │ │ ├── radius_multiParticle.json │ │ │ │ └── radius_singleParticle.json │ │ │ ├── genPascalInput.m │ │ │ ├── in.pascal │ │ │ ├── plotMe.m │ │ │ └── settings │ │ │ │ ├── coupling_liggghts.json │ │ │ │ ├── integrator.json │ │ │ │ ├── model_heatCapacity_solid.json │ │ │ │ ├── model_heatDensity_solid.json │ │ │ │ └── model_heatThermalConductivity_solid.json │ │ ├── post │ │ │ ├── .gitignore │ │ │ └── restart │ │ │ │ ├── .dummy │ │ │ │ └── .gitignore │ │ └── settings │ │ │ └── parscale.json │ └── heatTransferBed_paScal │ │ ├── Allrun_convective │ │ ├── README.md │ │ ├── cleanscript │ │ ├── genInput.m │ │ ├── in.liggghts │ │ ├── pascal │ │ ├── 0 │ │ │ ├── heat.json │ │ │ └── radius.json │ │ ├── in.pascal │ │ ├── plotMe.m │ │ └── settings │ │ │ ├── coupling_liggghts.json │ │ │ ├── integrator.json │ │ │ ├── model_heatCapacity_solid.json │ │ │ ├── model_heatDensity_solid.json │ │ │ ├── model_heatThermalConductivity_solid.json │ │ │ └── model_heatTransferCoeff.json │ │ ├── post │ │ └── .gitignore │ │ └── settings │ │ └── parscale.json │ ├── chute_wear │ ├── in.chute_wear │ ├── meshes │ │ ├── insertion_face.stl │ │ └── simple_chute.stl │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── cohesion │ ├── in.cohesion │ ├── in.noCohesion │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── contactModels │ ├── in.newModels │ ├── in.oldModels │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── conveyor │ ├── in.conveyor │ ├── meshes │ │ ├── box.stl │ │ ├── conveyor.stl │ │ └── insertion_face.stl │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── heatTransfer_1 │ ├── in.heatGran │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── heatTransfer_2 │ ├── in.heatGran │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── hydrogel_multicontact │ ├── data │ │ └── input.data │ ├── force_comparison.plot │ ├── in.hydrogel_default │ ├── in.hydrogel_multicontact │ ├── meshes │ │ └── piston_hydrogel.stl │ └── post │ │ └── .gitignore │ ├── hysteresis │ ├── in.hysteresis │ ├── in.noHysteresis │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── insert_stream │ ├── in.insert_stream │ ├── in.insert_stream_reset_timestep │ ├── meshes │ │ └── face.stl │ ├── post │ │ └── .gitignore │ └── postscript │ ├── meshGran │ ├── in.meshGran │ ├── meshes │ │ ├── insertion_face.stl │ │ └── mesh.stl │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── mesh_tet │ ├── data │ │ └── test.vtk │ ├── in.mesh_tet │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── movingMeshGran │ ├── in.movingMeshGran │ ├── meshes │ │ └── bucket.stl │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── multisphere_stone_restitution │ ├── data │ │ ├── stone1.multisphere │ │ └── stone1.test │ ├── in.multisphere │ ├── post │ │ └── .gitignore │ └── postscript │ ├── packing │ ├── in.packing │ ├── post │ │ └── .gitignore │ ├── postscript │ └── runscript │ ├── sph_1 │ ├── in.sph_1 │ ├── post │ │ └── .gitignore │ └── postscript │ ├── sph_2 │ ├── in.sph_2 │ ├── post │ │ └── .gitignore │ └── postscript │ └── superquadric │ └── in.particle_particle ├── figs ├── fig_liggghts_inl_banner.png ├── fig_microstructure_compression.png ├── fig_nonlinear_contact.png ├── fig_string_mm.png ├── fig_string_um.png └── vtk │ ├── fig_cmake_1.png │ ├── fig_cmake_2.png │ ├── fig_cmake_3.png │ ├── fig_cmake_4.png │ └── fig_make.png ├── lib ├── README ├── atc │ ├── ATC_Coupling.cpp │ ├── ATC_Coupling.h │ ├── ATC_CouplingEnergy.cpp │ ├── ATC_CouplingEnergy.h │ ├── ATC_CouplingMass.cpp │ ├── ATC_CouplingMass.h │ ├── ATC_CouplingMomentum.cpp │ ├── ATC_CouplingMomentum.h │ ├── ATC_CouplingMomentumEnergy.cpp │ ├── ATC_CouplingMomentumEnergy.h │ ├── ATC_Error.h │ ├── ATC_Method.cpp │ ├── ATC_Method.h │ ├── ATC_Transfer.cpp │ ├── ATC_Transfer.h │ ├── ATC_TransferKernel.cpp │ ├── ATC_TransferKernel.h │ ├── ATC_TransferPartitionOfUnity.cpp │ ├── ATC_TransferPartitionOfUnity.h │ ├── ATC_TypeDefs.h │ ├── Array.h │ ├── Array2D.h │ ├── AtomToMoleculeTransfer.cpp │ ├── AtomToMoleculeTransfer.h │ ├── AtomicRegulator.cpp │ ├── AtomicRegulator.h │ ├── BodyForce.cpp │ ├── BodyForce.h │ ├── CBLattice.cpp │ ├── CBLattice.h │ ├── CG.h │ ├── CauchyBorn.cpp │ ├── CauchyBorn.h │ ├── CbEam.h │ ├── CbLjCut.h │ ├── CbLjSmoothLinear.h │ ├── CbPotential.cpp │ ├── CbPotential.h │ ├── ChargeRegulator.cpp │ ├── ChargeRegulator.h │ ├── CloneVector.h │ ├── ConcentrationRegulator.cpp │ ├── ConcentrationRegulator.h │ ├── DenseMatrix.h │ ├── DenseVector.h │ ├── DependencyManager.h │ ├── DiagonalMatrix.h │ ├── DislocationExtractor.h │ ├── ElasticTimeIntegrator.cpp │ ├── ElasticTimeIntegrator.h │ ├── ElectronChargeDensity.cpp │ ├── ElectronChargeDensity.h │ ├── ElectronDragPower.cpp │ ├── ElectronDragPower.h │ ├── ElectronFlux.cpp │ ├── ElectronFlux.h │ ├── ElectronHeatCapacity.cpp │ ├── ElectronHeatCapacity.h │ ├── ElectronHeatFlux.cpp │ ├── ElectronHeatFlux.h │ ├── ElectronPhononExchange.cpp │ ├── ElectronPhononExchange.h │ ├── ExtrinsicModel.cpp │ ├── ExtrinsicModel.h │ ├── ExtrinsicModelDriftDiffusion.cpp │ ├── ExtrinsicModelDriftDiffusion.h │ ├── ExtrinsicModelElectrostatic.cpp │ ├── ExtrinsicModelElectrostatic.h │ ├── ExtrinsicModelTwoTemperature.cpp │ ├── ExtrinsicModelTwoTemperature.h │ ├── FE_Element.cpp │ ├── FE_Element.h │ ├── FE_Engine.cpp │ ├── FE_Engine.h │ ├── FE_Interpolate.cpp │ ├── FE_Interpolate.h │ ├── FE_Mesh.cpp │ ├── FE_Mesh.h │ ├── FE_Quadrature.h │ ├── FieldEulerIntegrator.cpp │ ├── FieldEulerIntegrator.h │ ├── FieldManager.cpp │ ├── FieldManager.h │ ├── Function.cpp │ ├── Function.h │ ├── FundamentalAtomicQuantity.cpp │ ├── FundamentalAtomicQuantity.h │ ├── GMRES.h │ ├── GhostManager.cpp │ ├── GhostManager.h │ ├── ImplicitSolveOperator.cpp │ ├── ImplicitSolveOperator.h │ ├── InterscaleOperators.cpp │ ├── InterscaleOperators.h │ ├── KD_Tree.cpp │ ├── KD_Tree.h │ ├── KernelFunction.cpp │ ├── KernelFunction.h │ ├── KinetoThermostat.cpp │ ├── KinetoThermostat.h │ ├── Kinetostat.cpp │ ├── Kinetostat.h │ ├── LammpsInterface.cpp │ ├── LammpsInterface.h │ ├── LinearSolver.cpp │ ├── LinearSolver.h │ ├── MPI_Wrappers.cpp │ ├── MPI_Wrappers.h │ ├── Makefile.g++ │ ├── Makefile.icc │ ├── Makefile.lammps │ ├── Makefile.lammps.empty │ ├── Makefile.lammps.installed │ ├── Makefile.lammps.linalg │ ├── Makefile.mingw32-cross │ ├── Makefile.mingw32-cross-mpi │ ├── Makefile.mingw64-cross │ ├── Makefile.mingw64-cross-mpi │ ├── Makefile.mpic++ │ ├── Makefile.serial │ ├── Material.cpp │ ├── Material.h │ ├── Matrix.cpp │ ├── Matrix.h │ ├── MatrixDef.h │ ├── MatrixLibrary.h │ ├── MeshReader.cpp │ ├── MeshReader.h │ ├── MoleculeSet.cpp │ ├── MoleculeSet.h │ ├── NonLinearSolver.cpp │ ├── NonLinearSolver.h │ ├── OutputManager.cpp │ ├── OutputManager.h │ ├── PaqAtcUtility.cpp │ ├── PaqAtcUtility.h │ ├── ParDenseMatrix.h │ ├── ParDiagonalMatrix.cpp │ ├── ParDiagonalMatrix.h │ ├── ParSparseMatrix.cpp │ ├── ParSparseMatrix.h │ ├── PerAtomQuantity-inl.h │ ├── PerAtomQuantity.h │ ├── PerAtomQuantityLibrary.cpp │ ├── PerAtomQuantityLibrary.h │ ├── PerPairQuantity.cpp │ ├── PerPairQuantity.h │ ├── PhysicsModel.cpp │ ├── PhysicsModel.h │ ├── PoissonSolver.cpp │ ├── PoissonSolver.h │ ├── PolynomialSolver.cpp │ ├── PolynomialSolver.h │ ├── PrescribedDataManager.cpp │ ├── PrescribedDataManager.h │ ├── Quadrature.cpp │ ├── Quadrature.h │ ├── README │ ├── SchrodingerSolver.cpp │ ├── SchrodingerSolver.h │ ├── ShapeFunction.h │ ├── SparseMatrix-inl.h │ ├── SparseMatrix.h │ ├── SparseVector-inl.h │ ├── SparseVector.h │ ├── SpeciesTimeIntegrator.cpp │ ├── SpeciesTimeIntegrator.h │ ├── Stress.cpp │ ├── Stress.h │ ├── ThermalTimeIntegrator.cpp │ ├── ThermalTimeIntegrator.h │ ├── Thermostat.cpp │ ├── Thermostat.h │ ├── TimeFilter.cpp │ ├── TimeFilter.h │ ├── TimeIntegrator.cpp │ ├── TimeIntegrator.h │ ├── TransferLibrary.cpp │ ├── TransferLibrary.h │ ├── TransferOperator.cpp │ ├── TransferOperator.h │ ├── Utility.h │ ├── Vector.cpp │ ├── Vector.h │ ├── ViscousStress.cpp │ ├── ViscousStress.h │ ├── VoigtOperations.h │ ├── WeakEquation.h │ ├── WeakEquationChargeDiffusion.cpp │ ├── WeakEquationChargeDiffusion.h │ ├── WeakEquationDiffusion.cpp │ ├── WeakEquationDiffusion.h │ ├── WeakEquationElectronContinuity.cpp │ ├── WeakEquationElectronContinuity.h │ ├── WeakEquationElectronMomentum.cpp │ ├── WeakEquationElectronMomentum.h │ ├── WeakEquationElectronTemperature.cpp │ ├── WeakEquationElectronTemperature.h │ ├── WeakEquationMassDiffusion.cpp │ ├── WeakEquationMassDiffusion.h │ ├── WeakEquationMomentum.cpp │ ├── WeakEquationMomentum.h │ ├── WeakEquationPhononTemperature.cpp │ ├── WeakEquationPhononTemperature.h │ ├── WeakEquationPoisson.cpp │ ├── WeakEquationPoisson.h │ ├── WeakEquationSchrodinger.cpp │ └── WeakEquationSchrodinger.h ├── awpmd │ ├── Makefile.lammps.empty │ ├── Makefile.lammps.installed │ ├── Makefile.lammps.linalg │ ├── Makefile.mingw32-cross │ ├── Makefile.mingw32-cross-mpi │ ├── Makefile.mingw64-cross │ ├── Makefile.mingw64-cross-mpi │ ├── Makefile.openmpi │ ├── README │ ├── ivutils │ │ ├── include │ │ │ ├── cerf.h │ │ │ ├── cvector_3.h │ │ │ ├── erf.h │ │ │ ├── lapack_inter.h │ │ │ ├── logexc.h │ │ │ ├── pairhash.h │ │ │ ├── refobj.h │ │ │ ├── vector_3.h │ │ │ └── wavepacket.h │ │ └── src │ │ │ └── logexc.cpp │ ├── license │ │ ├── COPYING │ │ ├── awpmd_license.txt │ │ └── wx_license.txt │ └── systems │ │ └── interact │ │ └── TCP │ │ ├── tcpdefs.h │ │ ├── wpmd.cpp │ │ ├── wpmd.h │ │ ├── wpmd_split.cpp │ │ └── wpmd_split.h ├── colvars │ ├── Makefile.fermi │ ├── Makefile.g++ │ ├── Makefile.lammps.debug │ ├── Makefile.lammps.empty │ ├── Makefile.mingw32-cross │ ├── Makefile.mingw32-cross-mpi │ ├── Makefile.mingw64-cross │ ├── Makefile.mingw64-cross-mpi │ ├── README │ ├── colvar.cpp │ ├── colvar.h │ ├── colvaratoms.cpp │ ├── colvaratoms.h │ ├── colvarbias.cpp │ ├── colvarbias.h │ ├── colvarbias_abf.cpp │ ├── colvarbias_abf.h │ ├── colvarbias_meta.cpp │ ├── colvarbias_meta.h │ ├── colvarcomp.cpp │ ├── colvarcomp.h │ ├── colvarcomp_angles.cpp │ ├── colvarcomp_coordnums.cpp │ ├── colvarcomp_distances.cpp │ ├── colvarcomp_protein.cpp │ ├── colvarcomp_rotations.cpp │ ├── colvargrid.cpp │ ├── colvargrid.h │ ├── colvarmodule.cpp │ ├── colvarmodule.h │ ├── colvarparse.cpp │ ├── colvarparse.h │ ├── colvarproxy.h │ ├── colvartypes.h │ ├── colvarvalue.cpp │ └── colvarvalue.h ├── cuda │ ├── Makefile │ ├── Makefile.common │ ├── Makefile.cudalib │ ├── Makefile.defaults │ ├── Makefile.lammps │ ├── README │ ├── atom_vec_angle_cuda.cu │ ├── atom_vec_angle_cuda_cu.h │ ├── atom_vec_atomic_cuda.cu │ ├── atom_vec_atomic_cuda_cu.h │ ├── atom_vec_charge_cuda.cu │ ├── atom_vec_charge_cuda_cu.h │ ├── atom_vec_cuda.cu │ ├── atom_vec_cuda_cu.h │ ├── atom_vec_cuda_kernel.cu │ ├── atom_vec_full_cuda.cu │ ├── atom_vec_full_cuda_cu.h │ ├── comm_cuda.cu │ ├── comm_cuda_cu.h │ ├── comm_cuda_kernel.cu │ ├── compute_temp_cuda.cu │ ├── compute_temp_cuda_cu.h │ ├── compute_temp_cuda_kernel.cu │ ├── compute_temp_partial_cuda.cu │ ├── compute_temp_partial_cuda_cu.h │ ├── compute_temp_partial_cuda_kernel.cu │ ├── crm_cuda_utils.cu │ ├── cuda.cu │ ├── cuda_common.h │ ├── cuda_cu.h │ ├── cuda_data.cu │ ├── cuda_data_cu.h │ ├── cuda_data_kernel.cu │ ├── cuda_kernel.cu │ ├── cuda_pair.cu │ ├── cuda_pair_cu.h │ ├── cuda_pair_kernel.cu │ ├── cuda_pair_virial_kernel_nc.cu │ ├── cuda_precision.h │ ├── cuda_shared.h │ ├── cuda_wrapper.cu │ ├── cuda_wrapper_cu.h │ ├── cuda_wrapper_kernel.cu │ ├── domain.cu │ ├── domain_cu.h │ ├── domain_kernel.cu │ ├── fft3d_cuda.cu │ ├── fft3d_cuda_cu.h │ ├── fft3d_cuda_kernel.cu │ ├── fix_addforce_cuda.cu │ ├── fix_addforce_cuda_cu.h │ ├── fix_addforce_cuda_kernel.cu │ ├── fix_aveforce_cuda.cu │ ├── fix_aveforce_cuda_cu.h │ ├── fix_aveforce_cuda_kernel.cu │ ├── fix_enforce2d_cuda.cu │ ├── fix_enforce2d_cuda_cu.h │ ├── fix_enforce2d_cuda_kernel.cu │ ├── fix_freeze_cuda.cu │ ├── fix_freeze_cuda_cu.h │ ├── fix_freeze_cuda_kernel.cu │ ├── fix_gravity_cuda.cu │ ├── fix_gravity_cuda_cu.h │ ├── fix_gravity_cuda_kernel.cu │ ├── fix_nh_cuda.cu │ ├── fix_nh_cuda_cu.h │ ├── fix_nh_cuda_kernel.cu │ ├── fix_nve_cuda.cu │ ├── fix_nve_cuda_cu.h │ ├── fix_nve_cuda_kernel.cu │ ├── fix_set_force_cuda.cu │ ├── fix_set_force_cuda_cu.h │ ├── fix_set_force_cuda_kernel.cu │ ├── fix_shake_cuda.cu │ ├── fix_shake_cuda_cu.h │ ├── fix_shake_cuda_kernel.cu │ ├── fix_temp_berendsen_cuda.cu │ ├── fix_temp_berendsen_cuda_cu.h │ ├── fix_temp_berendsen_cuda_kernel.cu │ ├── fix_temp_rescale_cuda.cu │ ├── fix_temp_rescale_cuda_cu.h │ ├── fix_temp_rescale_cuda_kernel.cu │ ├── fix_temp_rescale_limit_cuda.cu │ ├── fix_temp_rescale_limit_cuda_cu.h │ ├── fix_temp_rescale_limit_cuda_kernel.cu │ ├── fix_viscous_cuda.cu │ ├── fix_viscous_cuda_cu.h │ ├── fix_viscous_cuda_kernel.cu │ ├── neighbor.cu │ ├── neighbor_cu.h │ ├── neighbor_kernel.cu │ ├── pair_born_coul_long_cuda.cu │ ├── pair_born_coul_long_cuda_cu.h │ ├── pair_born_coul_long_cuda_kernel_nc.cu │ ├── pair_buck_coul_cut_cuda.cu │ ├── pair_buck_coul_cut_cuda_cu.h │ ├── pair_buck_coul_long_cuda.cu │ ├── pair_buck_coul_long_cuda_cu.h │ ├── pair_buck_cuda.cu │ ├── pair_buck_cuda_cu.h │ ├── pair_buck_cuda_kernel_nc.cu │ ├── pair_cg_cmm_coul_cut_cuda.cu │ ├── pair_cg_cmm_coul_cut_cuda_cu.h │ ├── pair_cg_cmm_coul_debye_cuda.cu │ ├── pair_cg_cmm_coul_debye_cuda_cu.h │ ├── pair_cg_cmm_coul_long_cuda.cu │ ├── pair_cg_cmm_coul_long_cuda_cu.h │ ├── pair_cg_cmm_cuda.cu │ ├── pair_cg_cmm_cuda_cu.h │ ├── pair_cg_cmm_cuda_kernel_nc.cu │ ├── pair_eam_cuda.cu │ ├── pair_eam_cuda_cu.h │ ├── pair_eam_cuda_kernel_nc.cu │ ├── pair_gran_hooke_cuda.cu │ ├── pair_gran_hooke_cuda_cu.h │ ├── pair_gran_hooke_cuda_kernel_nc.cu │ ├── pair_lj96_cut_cuda.cu │ ├── pair_lj96_cut_cuda_cu.h │ ├── pair_lj96_cut_cuda_kernel_nc.cu │ ├── pair_lj_charmm_coul_charmm_cuda.cu │ ├── pair_lj_charmm_coul_charmm_cuda_cu.h │ ├── pair_lj_charmm_coul_charmm_cuda_kernel_nc.cu │ ├── pair_lj_charmm_coul_charmm_implicit_cuda.cu │ ├── pair_lj_charmm_coul_charmm_implicit_cuda_cu.h │ ├── pair_lj_charmm_coul_charmm_implicit_cuda_kernel_nc.cu │ ├── pair_lj_charmm_coul_long_cuda.cu │ ├── pair_lj_charmm_coul_long_cuda_cu.h │ ├── pair_lj_class2_coul_cut_cuda.cu │ ├── pair_lj_class2_coul_cut_cuda_cu.h │ ├── pair_lj_class2_coul_long_cuda.cu │ ├── pair_lj_class2_coul_long_cuda_cu.h │ ├── pair_lj_class2_cuda.cu │ ├── pair_lj_class2_cuda_cu.h │ ├── pair_lj_class2_cuda_kernel_nc.cu │ ├── pair_lj_cut_coul_cut_cuda.cu │ ├── pair_lj_cut_coul_cut_cuda_cu.h │ ├── pair_lj_cut_coul_debye_cuda.cu │ ├── pair_lj_cut_coul_debye_cuda_cu.h │ ├── pair_lj_cut_coul_long_cuda.cu │ ├── pair_lj_cut_coul_long_cuda_cu.h │ ├── pair_lj_cut_cuda.cu │ ├── pair_lj_cut_cuda_cu.h │ ├── pair_lj_cut_cuda_kernel_nc.cu │ ├── pair_lj_cut_experimental_cuda.cu │ ├── pair_lj_cut_experimental_cuda_cu.h │ ├── pair_lj_expand_cuda.cu │ ├── pair_lj_expand_cuda_cu.h │ ├── pair_lj_expand_cuda_kernel_nc.cu │ ├── pair_lj_gromacs_coul_gromacs_cuda.cu │ ├── pair_lj_gromacs_coul_gromacs_cuda_cu.h │ ├── pair_lj_gromacs_coul_gromacs_cuda_kernel_nc.cu │ ├── pair_lj_gromacs_cuda.cu │ ├── pair_lj_gromacs_cuda_cu.h │ ├── pair_lj_gromacs_cuda_kernel_nc.cu │ ├── pair_lj_sdk_coul_cut_cuda.cu │ ├── pair_lj_sdk_coul_cut_cuda_cu.h │ ├── pair_lj_sdk_coul_debye_cuda.cu │ ├── pair_lj_sdk_coul_debye_cuda_cu.h │ ├── pair_lj_sdk_coul_long_cuda.cu │ ├── pair_lj_sdk_coul_long_cuda_cu.h │ ├── pair_lj_sdk_cuda.cu │ ├── pair_lj_sdk_cuda_cu.h │ ├── pair_lj_sdk_cuda_kernel_nc.cu │ ├── pair_lj_smooth_cuda.cu │ ├── pair_lj_smooth_cuda_cu.h │ ├── pair_lj_smooth_cuda_kernel_nc.cu │ ├── pair_manybody_const.h │ ├── pair_morse_coul_long_cuda.cu │ ├── pair_morse_coul_long_cuda_cu.h │ ├── pair_morse_coul_long_cuda_kernel_nc.cu │ ├── pair_morse_cuda.cu │ ├── pair_morse_cuda_cu.h │ ├── pair_morse_cuda_kernel_nc.cu │ ├── pair_sw_cuda.cu │ ├── pair_sw_cuda_cu.h │ ├── pair_sw_cuda_kernel_nc.cu │ ├── pair_tersoff_cuda.cu │ ├── pair_tersoff_cuda_cu.h │ ├── pair_tersoff_cuda_kernel_nc.cu │ ├── pair_virial_compute_cu.h │ ├── pppm_cuda.cu │ ├── pppm_cuda_cu.h │ └── pppm_cuda_kernel.cu ├── gpu │ ├── Makefile.fermi │ ├── Makefile.lammps.mac_ocl │ ├── Makefile.lammps.mingw-cross │ ├── Makefile.lammps.opencl │ ├── Makefile.lammps.standard │ ├── Makefile.lens │ ├── Makefile.lincoln │ ├── Makefile.linux │ ├── Makefile.linux.double │ ├── Makefile.linux.mixed │ ├── Makefile.linux_opencl │ ├── Makefile.longhorn │ ├── Makefile.mac │ ├── Makefile.mac_opencl │ ├── Makefile.mingw32-cross │ ├── Makefile.mingw32-cross-mpi │ ├── Makefile.mingw64-cross │ ├── Makefile.mingw64-cross-mpi │ ├── Makefile.serial │ ├── Makefile.serial_opencl │ ├── Makefile.xk7 │ ├── Nvidia.makefile │ ├── Opencl.makefile │ ├── README │ ├── cudpp_mini │ │ ├── README │ │ ├── cta │ │ │ ├── radixsort_cta.cu │ │ │ └── scan_cta.cu │ │ ├── cudpp.cpp │ │ ├── cudpp.h │ │ ├── cudpp_globals.h │ │ ├── cudpp_maximal_launch.cpp │ │ ├── cudpp_maximal_launch.h │ │ ├── cudpp_plan.cpp │ │ ├── cudpp_plan.h │ │ ├── cudpp_plan_manager.cpp │ │ ├── cudpp_plan_manager.h │ │ ├── cudpp_radixsort.h │ │ ├── cudpp_scan.h │ │ ├── cudpp_util.h │ │ ├── cutil.h │ │ ├── kernel │ │ │ ├── radixsort_kernel.cu │ │ │ ├── scan_kernel.cu │ │ │ └── vector_kernel.cu │ │ ├── license.txt │ │ ├── radixsort_app.cu │ │ ├── scan_app.cu │ │ └── sharedmem.h │ ├── geryon │ │ ├── README │ │ ├── VERSION.txt │ │ ├── file_to_cstr.sh │ │ ├── nvd_device.h │ │ ├── nvd_kernel.h │ │ ├── nvd_macros.h │ │ ├── nvd_mat.h │ │ ├── nvd_memory.h │ │ ├── nvd_texture.h │ │ ├── nvd_timer.h │ │ ├── ocl_device.h │ │ ├── ocl_kernel.h │ │ ├── ocl_macros.h │ │ ├── ocl_mat.h │ │ ├── ocl_memory.h │ │ ├── ocl_texture.h │ │ ├── ocl_timer.h │ │ ├── ucl_arg_kludge.h │ │ ├── ucl_basemat.h │ │ ├── ucl_copy.h │ │ ├── ucl_d_mat.h │ │ ├── ucl_d_vec.h │ │ ├── ucl_get_devices.cpp │ │ ├── ucl_h_mat.h │ │ ├── ucl_h_vec.h │ │ ├── ucl_matrix.h │ │ ├── ucl_nv_kernel.h │ │ ├── ucl_print.h │ │ ├── ucl_s_obj_help.h │ │ ├── ucl_types.h │ │ └── ucl_vector.h │ ├── lal_answer.cpp │ ├── lal_answer.h │ ├── lal_atom.cpp │ ├── lal_atom.cu │ ├── lal_atom.h │ ├── lal_aux_fun1.h │ ├── lal_balance.h │ ├── lal_base_atomic.cpp │ ├── lal_base_atomic.h │ ├── lal_base_charge.cpp │ ├── lal_base_charge.h │ ├── lal_base_dipole.cpp │ ├── lal_base_dipole.h │ ├── lal_base_ellipsoid.cpp │ ├── lal_base_ellipsoid.h │ ├── lal_base_three.cpp │ ├── lal_base_three.h │ ├── lal_beck.cpp │ ├── lal_beck.cu │ ├── lal_beck.h │ ├── lal_beck_ext.cpp │ ├── lal_born.cpp │ ├── lal_born.cu │ ├── lal_born.h │ ├── lal_born_coul_long.cpp │ ├── lal_born_coul_long.cu │ ├── lal_born_coul_long.h │ ├── lal_born_coul_long_ext.cpp │ ├── lal_born_coul_wolf.cpp │ ├── lal_born_coul_wolf.cu │ ├── lal_born_coul_wolf.h │ ├── lal_born_coul_wolf_ext.cpp │ ├── lal_born_ext.cpp │ ├── lal_buck.cpp │ ├── lal_buck.cu │ ├── lal_buck.h │ ├── lal_buck_coul.cpp │ ├── lal_buck_coul.cu │ ├── lal_buck_coul.h │ ├── lal_buck_coul_ext.cpp │ ├── lal_buck_coul_long.cpp │ ├── lal_buck_coul_long.cu │ ├── lal_buck_coul_long.h │ ├── lal_buck_coul_long_ext.cpp │ ├── lal_buck_ext.cpp │ ├── lal_cg_cmm.cpp │ ├── lal_cg_cmm.cu │ ├── lal_cg_cmm.h │ ├── lal_cg_cmm_ext.cpp │ ├── lal_cg_cmm_long.cpp │ ├── lal_cg_cmm_long.cu │ ├── lal_cg_cmm_long.h │ ├── lal_cg_cmm_long_ext.cpp │ ├── lal_charmm_long.cpp │ ├── lal_charmm_long.cu │ ├── lal_charmm_long.h │ ├── lal_charmm_long_ext.cpp │ ├── lal_colloid.cpp │ ├── lal_colloid.cu │ ├── lal_colloid.h │ ├── lal_colloid_ext.cpp │ ├── lal_coul_dsf.cpp │ ├── lal_coul_dsf.cu │ ├── lal_coul_dsf.h │ ├── lal_coul_dsf_ext.cpp │ ├── lal_coul_long.cpp │ ├── lal_coul_long.cu │ ├── lal_coul_long.h │ ├── lal_coul_long_ext.cpp │ ├── lal_device.cpp │ ├── lal_device.cu │ ├── lal_device.h │ ├── lal_dipole_lj.cpp │ ├── lal_dipole_lj.cu │ ├── lal_dipole_lj.h │ ├── lal_dipole_lj_ext.cpp │ ├── lal_dipole_lj_sf.cpp │ ├── lal_dipole_lj_sf.cu │ ├── lal_dipole_lj_sf.h │ ├── lal_dipole_lj_sf_ext.cpp │ ├── lal_eam.cpp │ ├── lal_eam.cu │ ├── lal_eam.h │ ├── lal_eam_ext.cpp │ ├── lal_ellipsoid_extra.h │ ├── lal_ellipsoid_nbor.cu │ ├── lal_gauss.cpp │ ├── lal_gauss.cu │ ├── lal_gauss.h │ ├── lal_gauss_ext.cpp │ ├── lal_gayberne.cpp │ ├── lal_gayberne.cu │ ├── lal_gayberne.h │ ├── lal_gayberne_ext.cpp │ ├── lal_gayberne_lj.cu │ ├── lal_lj.cpp │ ├── lal_lj.cu │ ├── lal_lj.h │ ├── lal_lj96.cpp │ ├── lal_lj96.cu │ ├── lal_lj96.h │ ├── lal_lj96_ext.cpp │ ├── lal_lj_class2_long.cpp │ ├── lal_lj_class2_long.cu │ ├── lal_lj_class2_long.h │ ├── lal_lj_class2_long_ext.cpp │ ├── lal_lj_coul.cpp │ ├── lal_lj_coul.cu │ ├── lal_lj_coul.h │ ├── lal_lj_coul_debye.cpp │ ├── lal_lj_coul_debye.cu │ ├── lal_lj_coul_debye.h │ ├── lal_lj_coul_debye_ext.cpp │ ├── lal_lj_coul_ext.cpp │ ├── lal_lj_coul_long.cpp │ ├── lal_lj_coul_long.cu │ ├── lal_lj_coul_long.h │ ├── lal_lj_coul_long_ext.cpp │ ├── lal_lj_coul_msm.cpp │ ├── lal_lj_coul_msm.cu │ ├── lal_lj_coul_msm.h │ ├── lal_lj_coul_msm_ext.cpp │ ├── lal_lj_dsf.cpp │ ├── lal_lj_dsf.cu │ ├── lal_lj_dsf.h │ ├── lal_lj_dsf_ext.cpp │ ├── lal_lj_expand.cpp │ ├── lal_lj_expand.cu │ ├── lal_lj_expand.h │ ├── lal_lj_expand_ext.cpp │ ├── lal_lj_ext.cpp │ ├── lal_mie.cpp │ ├── lal_mie.cu │ ├── lal_mie.h │ ├── lal_mie_ext.cpp │ ├── lal_morse.cpp │ ├── lal_morse.cu │ ├── lal_morse.h │ ├── lal_morse_ext.cpp │ ├── lal_neighbor.cpp │ ├── lal_neighbor.h │ ├── lal_neighbor_cpu.cu │ ├── lal_neighbor_gpu.cu │ ├── lal_neighbor_shared.cpp │ ├── lal_neighbor_shared.h │ ├── lal_pppm.cpp │ ├── lal_pppm.cu │ ├── lal_pppm.h │ ├── lal_pppm_ext.cpp │ ├── lal_precision.h │ ├── lal_preprocessor.h │ ├── lal_re_squared.cpp │ ├── lal_re_squared.cu │ ├── lal_re_squared.h │ ├── lal_re_squared_ext.cpp │ ├── lal_re_squared_lj.cu │ ├── lal_soft.cpp │ ├── lal_soft.cu │ ├── lal_soft.h │ ├── lal_soft_ext.cpp │ ├── lal_sw.cpp │ ├── lal_sw.cu │ ├── lal_sw.h │ ├── lal_sw_ext.cpp │ ├── lal_table.cpp │ ├── lal_table.cu │ ├── lal_table.h │ ├── lal_table_ext.cpp │ ├── lal_yukawa.cpp │ ├── lal_yukawa.cu │ ├── lal_yukawa.h │ ├── lal_yukawa_colloid.cpp │ ├── lal_yukawa_colloid.cu │ ├── lal_yukawa_colloid.h │ ├── lal_yukawa_colloid_ext.cpp │ └── lal_yukawa_ext.cpp ├── hotint │ ├── Developers Documentation.pdf │ ├── HotInt_V1 │ │ ├── ElementsLib │ │ │ ├── ElementEDCauto.cpp │ │ │ ├── ElementsLib.vcproj │ │ │ ├── ElementsLib.vcxproj │ │ │ ├── ElementsLib.vcxproj.filters │ │ │ ├── IntegrationRule.cpp │ │ │ ├── IntegrationRule.h │ │ │ ├── PlaneSymmetricTensorComponents.cpp │ │ │ ├── PlaneSymmetricTensorComponents.h │ │ │ ├── XGProvider.h │ │ │ ├── beams │ │ │ │ ├── ANCFAxMovBeam2D.cpp │ │ │ │ ├── ANCFAxMovBeam2D.h │ │ │ │ ├── ANCFBeam2D.cpp │ │ │ │ ├── ANCFBeam2D.h │ │ │ │ ├── ANCFBeam3D.cpp │ │ │ │ ├── ANCFBeam3D.h │ │ │ │ ├── ANCFBeam3DTorsion.cpp │ │ │ │ ├── ANCFBeam3DTorsion.h │ │ │ │ ├── ANCFBeamBE2D.cpp │ │ │ │ ├── ANCFBeamBE2D.h │ │ │ │ ├── ANCFBeamShear2D.cpp │ │ │ │ ├── ANCFBeamShear2D.h │ │ │ │ ├── ANCFBeamShear3D.cpp │ │ │ │ ├── ANCFBeamShear3D.h │ │ │ │ ├── ANCFBeamShear3DGetddeidxidDiffVar.h │ │ │ │ ├── ANCFBeamShear3DGetdeidDiffVar.h │ │ │ │ ├── ANCFBeamShear3DGetdeidxi.h │ │ │ │ ├── ANCFBeamShear3DGetei.h │ │ │ │ ├── ANCFBeamShearFE2D.cpp │ │ │ │ ├── ANCFBeamShearFE2D.h │ │ │ │ ├── ANCFCable2D.cpp │ │ │ │ ├── ANCFCable2D.h │ │ │ │ ├── ANCFCable3D.cpp │ │ │ │ ├── ANCFCable3D.h │ │ │ │ ├── BEBeamGetDKappa1.h │ │ │ │ ├── BEBeamGetDKappa2.h │ │ │ │ ├── BEBeamGetDKappa3.h │ │ │ │ ├── BEBeamGetKappa1.h │ │ │ │ ├── BEBeamGetKappa2.h │ │ │ │ ├── BEBeamGetKappa3.h │ │ │ │ ├── BEBeamVectorOfTwistAndCurvature.h │ │ │ │ ├── BEBeamdRotdr.h │ │ │ │ ├── Beam2DFFRF.cpp │ │ │ │ ├── Beam2DFFRF.h │ │ │ │ ├── Beam2DaFFRF.cpp │ │ │ │ ├── Beam2DaFFRF.h │ │ │ │ ├── Beam3D.cpp │ │ │ │ ├── Beam3D.h │ │ │ │ ├── BeamBEdRotdrT.h │ │ │ │ ├── BeamShear2D.cpp │ │ │ │ ├── BeamShear2D.h │ │ │ │ ├── BeamSheardRotvdr_new.h │ │ │ │ ├── FiniteElementGenericBeam2D.cpp │ │ │ │ ├── FiniteElementGenericBeam2D.h │ │ │ │ ├── Truss3D.cpp │ │ │ │ └── Truss3D.h │ │ │ ├── body2D.h │ │ │ ├── body3D.h │ │ │ ├── constraints │ │ │ │ ├── AverageConstraint.cpp │ │ │ │ ├── AverageConstraint.h │ │ │ │ ├── KinematicPairs.cpp │ │ │ │ ├── KinematicPairs.h │ │ │ │ ├── RigidBodyJoints.cpp │ │ │ │ ├── RigidBodyJoints.h │ │ │ │ ├── SDA_constraints.cpp │ │ │ │ ├── SDA_constraints.h │ │ │ │ ├── SpecialConstraints.cpp │ │ │ │ ├── SpecialConstraints.h │ │ │ │ ├── constraint.cpp │ │ │ │ ├── constraint.h │ │ │ │ ├── contact2D.cpp │ │ │ │ ├── contact2D.h │ │ │ │ ├── contact3D.cpp │ │ │ │ ├── contact3D.h │ │ │ │ ├── contact_globalvariables.h │ │ │ │ ├── control.cpp │ │ │ │ └── control.h │ │ │ ├── deprecated_elements │ │ │ │ ├── KinematicPairsDeprecated.cpp │ │ │ │ ├── KinematicPairsDeprecated.h │ │ │ │ ├── sensor_old.cpp │ │ │ │ └── sensor_old.h │ │ │ ├── element.cpp │ │ │ ├── modal_reduction │ │ │ │ ├── BaseCMSElement.cpp │ │ │ │ ├── BaseCMSElement.h │ │ │ │ ├── CMSElement.cpp │ │ │ │ ├── CMSElement.h │ │ │ │ ├── CMSElement2D.cpp │ │ │ │ ├── CMSElement2D.h │ │ │ │ ├── GCMSElement.cpp │ │ │ │ ├── GCMSElement.h │ │ │ │ ├── GCMSRotorElement.cpp │ │ │ │ ├── GCMSRotorElement.h │ │ │ │ ├── referenceframe2D.cpp │ │ │ │ ├── referenceframe2D.h │ │ │ │ ├── referenceframe3D.cpp │ │ │ │ └── referenceframe3D.h │ │ │ ├── rigid │ │ │ │ ├── Rigid3DKardan.cpp │ │ │ │ ├── Rigid3DKardan.h │ │ │ │ ├── mass1D.cpp │ │ │ │ ├── mass1D.h │ │ │ │ ├── rigid2D.cpp │ │ │ │ ├── rigid2D.h │ │ │ │ ├── rigid3D.cpp │ │ │ │ └── rigid3D.h │ │ │ ├── shells │ │ │ │ ├── ANCFPlate3D.cpp │ │ │ │ ├── ANCFPlate3D.h │ │ │ │ ├── ANCFSimpleThinPlate3D.cpp │ │ │ │ ├── ANCFSimpleThinPlate3D.h │ │ │ │ ├── ANCFThinPlate3D.cpp │ │ │ │ ├── ANCFThinPlate3D.h │ │ │ │ ├── Plate2D.cpp │ │ │ │ └── Plate2D.h │ │ │ └── solidFE │ │ │ │ ├── FE2DTriQuad.cpp │ │ │ │ ├── FE2DTriQuad.h │ │ │ │ ├── FE3DHexTet.cpp │ │ │ │ ├── FE3DHexTet.h │ │ │ │ ├── FiniteElement2D.cpp │ │ │ │ ├── FiniteElement2D.h │ │ │ │ ├── FiniteElement3D.cpp │ │ │ │ ├── FiniteElement3D.h │ │ │ │ ├── FiniteElement3DFFRF.cpp │ │ │ │ ├── FiniteElement3DFFRF.h │ │ │ │ ├── FiniteElementGeneric.cpp │ │ │ │ └── FiniteElementGeneric.h │ │ ├── FEMesh │ │ │ ├── FEMesh.cpp │ │ │ ├── FEMesh.h │ │ │ ├── FEMesh.vcproj │ │ │ ├── FEMesh.vcxproj │ │ │ ├── FEMesh.vcxproj.filters │ │ │ ├── FEMesh_aux.cpp │ │ │ ├── FEMesh_aux.h │ │ │ └── FEMesh_generator.cpp │ │ ├── MBSElementsAndModels │ │ │ ├── MBSElementsAndModels.cpp │ │ │ ├── MBSElementsAndModels.vcproj │ │ │ ├── MBSElementsAndModels.vcxproj │ │ │ ├── MBSElementsAndModels.vcxproj.filters │ │ │ ├── MBSModelsLibrary.cpp │ │ │ ├── MBSModelsLibrary.h │ │ │ ├── MBSObjectFactory.cpp │ │ │ ├── MBSObjectFactory.h │ │ │ ├── models_include.cpp │ │ │ └── serviceFunctions.cpp │ │ ├── MBSKernelLib │ │ │ ├── MBSKernelLib.vcproj │ │ │ ├── MBSKernelLib.vcxproj │ │ │ ├── MBSKernelLib.vcxproj.filters │ │ │ ├── computeeigenmodes.cpp │ │ │ ├── drawsystem.cpp │ │ │ ├── femath.cpp │ │ │ ├── femath.h │ │ │ ├── initialize_system.cpp │ │ │ ├── mbs.cpp │ │ │ ├── mbs.h │ │ │ ├── mbs_communication.cpp │ │ │ ├── mbssolset_convert_auto.h │ │ │ ├── numnlsys_options.cpp │ │ │ ├── optimization.cpp │ │ │ ├── optimization.h │ │ │ ├── options_auto.h │ │ │ ├── options_mbs_auto.h │ │ │ ├── performcomp.cpp │ │ │ ├── performcomputation.h │ │ │ ├── sensitivity.cpp │ │ │ ├── sensitivity.h │ │ │ ├── ti_misc.cpp │ │ │ ├── timeint.cpp │ │ │ ├── timeint.h │ │ │ └── writesolution.cpp │ │ ├── MBS_Interface │ │ │ ├── ElementsAndModelsLibraryInterface.h │ │ │ ├── FEMeshInterface.h │ │ │ ├── GeomElements.h │ │ │ ├── MBSload.h │ │ │ ├── NumSolverInterface.h │ │ │ ├── element.h │ │ │ ├── finite_element_definitions.h │ │ │ ├── graphicsConstants.h │ │ │ ├── material.h │ │ │ ├── mbs_interface.h │ │ │ ├── node.h │ │ │ ├── options_class_auto.h │ │ │ ├── preprocessor_includes.h │ │ │ ├── renderContext.h │ │ │ ├── sensorProcessors.h │ │ │ ├── sensors.h │ │ │ ├── solversettings_auto.h │ │ │ ├── stepsettings.h │ │ │ ├── timeintlog.h │ │ │ └── useroutputinterface.h │ │ ├── ModelsLib │ │ │ ├── ModelsLib.vcproj │ │ │ ├── ModelsLib.vcxproj │ │ │ ├── ModelsLib.vcxproj.filters │ │ │ ├── ReadMe.txt │ │ │ ├── all_models.h │ │ │ └── open_source_examples │ │ │ │ ├── ANCFCable2D_contact │ │ │ │ ├── ANCFCable2D_contact.cpp │ │ │ │ └── ANCFCable2D_contact.txt │ │ │ │ ├── flexible_web_contact_3D │ │ │ │ ├── flexible_web_contact_3D.cpp │ │ │ │ ├── modeldata.txt │ │ │ │ └── obstacle.stl │ │ │ │ └── hourglass_rigid_contact_2D │ │ │ │ ├── hourglass_rigid_contact_2D.cpp │ │ │ │ └── hourglass_rigid_contact_2D.txt │ │ ├── Parser │ │ │ ├── Parser.vcproj │ │ │ ├── Parser.vcxproj │ │ │ ├── Parser.vcxproj.filters │ │ │ ├── command.cpp │ │ │ ├── command.h │ │ │ ├── mathobj.cpp │ │ │ ├── mathobj.h │ │ │ ├── parseobj.h │ │ │ ├── parseobjlist.cpp │ │ │ ├── parseobjlist.h │ │ │ ├── parser.cpp │ │ │ ├── parser.h │ │ │ ├── script_parser.cpp │ │ │ ├── script_parser.h │ │ │ ├── variable.cpp │ │ │ └── variable.h │ │ ├── ServiceObjectsLib │ │ │ ├── GeomElements.cpp │ │ │ ├── MBSload.cpp │ │ │ ├── ServiceObjectsLib.vcproj │ │ │ ├── ServiceObjectsLib.vcxproj │ │ │ ├── ServiceObjectsLib.vcxproj.filters │ │ │ ├── Sim2Hotint.cpp │ │ │ ├── Sim2Hotint.h │ │ │ ├── TcpIpRoutines.cpp │ │ │ ├── TcpIpRoutines.h │ │ │ ├── csg_geometry.cpp │ │ │ ├── csg_geometry.h │ │ │ ├── material.cpp │ │ │ ├── model_tools.cpp │ │ │ ├── model_tools.h │ │ │ ├── node.cpp │ │ │ ├── sensorProcessorsSpecific.cpp │ │ │ ├── sensorProcessorsSpecific.h │ │ │ ├── sensors.cpp │ │ │ ├── sensorsSpecific.cpp │ │ │ └── sensorsSpecific.h │ │ ├── SuperLU │ │ │ ├── ReadMe.txt │ │ │ ├── SuperLU.vcproj │ │ │ ├── SuperLU.vcxproj │ │ │ ├── SuperLU.vcxproj.filters │ │ │ ├── SuperLUmain.cpp │ │ │ ├── SuperLUmain.h │ │ │ ├── colamd.c │ │ │ ├── colamd.h │ │ │ ├── dasum.c │ │ │ ├── daxpy.c │ │ │ ├── dcolumn_bmod.c │ │ │ ├── dcolumn_dfs.c │ │ │ ├── dcopy.c │ │ │ ├── dcopy_to_ucol.c │ │ │ ├── ddot.c │ │ │ ├── dgemv.c │ │ │ ├── dger.c │ │ │ ├── dgscon.c │ │ │ ├── dgsequ.c │ │ │ ├── dgsrfs.c │ │ │ ├── dgssv.c │ │ │ ├── dgssvx.c │ │ │ ├── dgstrf.c │ │ │ ├── dgstrs.c │ │ │ ├── dlacon.c │ │ │ ├── dlamch.c │ │ │ ├── dlangs.c │ │ │ ├── dlaqgs.c │ │ │ ├── dmemory.c │ │ │ ├── dmyblas2.c │ │ │ ├── dnrm2.c │ │ │ ├── dpanel_bmod.c │ │ │ ├── dpanel_dfs.c │ │ │ ├── dpivotL.c │ │ │ ├── dpivotgrowth.c │ │ │ ├── dpruneL.c │ │ │ ├── dreadhb.c │ │ │ ├── drot.c │ │ │ ├── dscal.c │ │ │ ├── dsnode_bmod.c │ │ │ ├── dsnode_dfs.c │ │ │ ├── dsp_blas2.c │ │ │ ├── dsp_blas3.c │ │ │ ├── dsp_defs.h │ │ │ ├── dsymv.c │ │ │ ├── dsyr2.c │ │ │ ├── dtrsv.c │ │ │ ├── dutil.c │ │ │ ├── f2c.h │ │ │ ├── get_perm_c.c │ │ │ ├── heap_relax_snode.c │ │ │ ├── idamax.c │ │ │ ├── lib │ │ │ │ ├── SuperLU.lib │ │ │ │ ├── SuperLUd.lib │ │ │ │ ├── SuperLUx64.lib │ │ │ │ └── SuperLUx64d.lib │ │ │ ├── lsame.c │ │ │ ├── memory.c │ │ │ ├── mmd.c │ │ │ ├── relax_snode.c │ │ │ ├── slu_Cnames.h │ │ │ ├── slu_ddefs.h │ │ │ ├── slu_util.h │ │ │ ├── sp_coletree.c │ │ │ ├── sp_ienv.c │ │ │ ├── sp_preorder.c │ │ │ ├── superlu.c │ │ │ ├── superlu_f2c.h │ │ │ ├── superlu_timer.c │ │ │ ├── supermatrix.h │ │ │ ├── util.c │ │ │ └── xerbla.c │ │ ├── UtilityLib │ │ │ ├── FieldVariableDescriptor.cpp │ │ │ ├── FieldVariableDescriptor.h │ │ │ ├── UtilityLib.vcproj │ │ │ ├── UtilityLib.vcxproj │ │ │ ├── UtilityLib.vcxproj.filters │ │ │ ├── elementDataAccess.cpp │ │ │ ├── elementdata.cpp │ │ │ ├── elementdata.h │ │ │ ├── elementdataaccess.h │ │ │ ├── femathHelperFunctions.h │ │ │ ├── femathhelperfunctions.cpp │ │ │ ├── fft_utilities.cpp │ │ │ ├── fft_utilities.h │ │ │ ├── ioincludes.h │ │ │ ├── lapack_routines.cpp │ │ │ ├── lapack_routines.h │ │ │ ├── linalg.cpp │ │ │ ├── linalg.h │ │ │ ├── linalg3d.cpp │ │ │ ├── linalg3d.h │ │ │ ├── linalgeig.cpp │ │ │ ├── linalgeig.h │ │ │ ├── mathaux.h │ │ │ ├── mathfunc.cpp │ │ │ ├── mathfunc.h │ │ │ ├── mkl_includes.h │ │ │ ├── myfile.cpp │ │ │ ├── myfile.h │ │ │ ├── mystring.cpp │ │ │ ├── mystring.h │ │ │ ├── pardiso.h │ │ │ ├── release_assert.h │ │ │ └── tarray.h │ │ ├── WCDriver3D │ │ │ ├── CListDlg.cpp │ │ │ ├── CListDlg.h │ │ │ ├── ComputeEigenmodes.cpp │ │ │ ├── ComputeEigenmodes.h │ │ │ ├── CustomEditDialog.cpp │ │ │ ├── CustomEditDialog.h │ │ │ ├── DataStorage.cpp │ │ │ ├── DataStorage.h │ │ │ ├── DialogDataManager.cpp │ │ │ ├── DialogDataManager.h │ │ │ ├── DialogFramesRecording.cpp │ │ │ ├── DialogFramesRecording.h │ │ │ ├── DialogProgressBar.cpp │ │ │ ├── DialogProgressBar.h │ │ │ ├── DialogReadText.cpp │ │ │ ├── DialogReadText.h │ │ │ ├── DialogSaveSpecial.cpp │ │ │ ├── DialogSaveSpecial.h │ │ │ ├── DialogViewingOptions.cpp │ │ │ ├── DialogViewingOptions.h │ │ │ ├── DlgBodyJointOpt.cpp │ │ │ ├── DlgBodyJointOpt.h │ │ │ ├── DlgOneEditCtrl.cpp │ │ │ ├── DlgOneEditCtrl.h │ │ │ ├── DrawWindow2D.cpp │ │ │ ├── DrawWindow2D.h │ │ │ ├── FEDrawingOptions.cpp │ │ │ ├── FEDrawingOptions.h │ │ │ ├── GLDrawWnd.cpp │ │ │ ├── GLDrawWnd.h │ │ │ ├── MyBaseView.cpp │ │ │ ├── MyBaseView.h │ │ │ ├── OpenGLDlg.cpp │ │ │ ├── OpenGLDlg.h │ │ │ ├── OutputDialog.cpp │ │ │ ├── OutputDialog.h │ │ │ ├── PlotToolDlg.cpp │ │ │ ├── PlotToolDlg.h │ │ │ ├── PlotToolDlg_aux.cpp │ │ │ ├── PlotToolDlg_aux.h │ │ │ ├── RenderContext.cpp │ │ │ ├── RenderContext.h │ │ │ ├── Resource.h │ │ │ ├── StdAfx.cpp │ │ │ ├── StdAfx.h │ │ │ ├── TreeViewCustomEditDialog.cpp │ │ │ ├── TreeViewCustomEditDialog.h │ │ │ ├── WCDriver3D.cpp │ │ │ ├── WCDriver3D.h │ │ │ ├── WCDriver3D.rc │ │ │ ├── WCDriver3DDlg.cpp │ │ │ ├── WCDriver3DDlg.h │ │ │ ├── WCDriver3D_mbs - Template 2008.sln │ │ │ ├── WCDriver3D_mbs - Template 2010.sln │ │ │ ├── WCDriver3D_mbs.vcproj │ │ │ ├── WCDriver3D_mbs.vcxproj │ │ │ ├── WCDriver3D_mbs.vcxproj.filters │ │ │ ├── extgl.cpp │ │ │ ├── extgl.h │ │ │ ├── res │ │ │ │ ├── WCDriver3D.ico │ │ │ │ └── WCDriver3D.rc2 │ │ │ ├── resource.hm │ │ │ ├── savewindowbitmap.cpp │ │ │ ├── savewindowbitmap.h │ │ │ └── toolbar1.bmp │ │ ├── WorkingModule │ │ │ ├── StdAfx.h │ │ │ ├── UserOutput.h │ │ │ ├── WinCompDriverInterface.h │ │ │ ├── WorkingModule.cpp │ │ │ ├── WorkingModule.rc │ │ │ ├── WorkingModuleBaseClass.cpp │ │ │ ├── WorkingModuleBaseClass.h │ │ │ ├── WorkingModule_mbs.vcproj │ │ │ ├── WorkingModule_mbs.vcxproj │ │ │ ├── WorkingModule_mbs.vcxproj.filters │ │ │ ├── hotint_version.h │ │ │ ├── hotint_version_info.h │ │ │ └── resource.h │ │ ├── licenses │ │ │ └── License_Free.rtf │ │ └── tools │ │ │ ├── EDC_converter │ │ │ ├── EDC_converter.cpp │ │ │ ├── EDC_converter.vcproj │ │ │ ├── Release │ │ │ │ └── EDC_converter.bat │ │ │ ├── stdafx.cpp │ │ │ └── stdafx.h │ │ │ └── HOTINT_Log │ │ │ └── VC++ solution │ │ │ └── HOTINT_Log │ │ │ ├── AssemblyInfo.cpp │ │ │ ├── Form1.h │ │ │ ├── Form1.resX │ │ │ ├── HOTINT_Log.cpp │ │ │ ├── HOTINT_Log.vcproj │ │ │ ├── ReadMe.txt │ │ │ ├── app.ico │ │ │ ├── app.rc │ │ │ ├── log_tool_classes.h │ │ │ ├── resource.h │ │ │ ├── stdafx.cpp │ │ │ └── stdafx.h │ ├── documentation_1.2.196.Beta.pdf │ └── documentation_1.2.41.Beta.pdf ├── linalg │ ├── Makefile.gfortran │ ├── Makefile.mingw32-cross │ ├── Makefile.mingw32-cross-mpi │ ├── Makefile.mingw64-cross │ ├── Makefile.mingw64-cross-mpi │ ├── README │ ├── dasum.f │ ├── daxpy.f │ ├── dcopy.f │ ├── ddot.f │ ├── dgecon.f │ ├── dgemm.f │ ├── dgemv.f │ ├── dger.f │ ├── dgetf2.f │ ├── dgetrf.f │ ├── dgetri.f │ ├── disnan.f │ ├── dlabad.f │ ├── dlacn2.f │ ├── dlaisnan.f │ ├── dlamch.f │ ├── dlange.f │ ├── dlassq.f │ ├── dlaswp.f │ ├── dlatrs.f │ ├── drscl.f │ ├── dscal.f │ ├── dswap.f │ ├── dtrmm.f │ ├── dtrmv.f │ ├── dtrsm.f │ ├── dtrsv.f │ ├── dtrti2.f │ ├── dtrtri.f │ ├── idamax.f │ ├── ieeeck.f │ ├── ilaenv.f │ ├── iparmq.f │ ├── lsame.f │ ├── xerbla.f │ ├── zdotc.f │ ├── zdscal.f │ ├── zhpr.f │ ├── zpptrf.f │ ├── zpptri.f │ ├── zscal.f │ ├── ztpmv.f │ ├── ztpsv.f │ └── ztptri.f ├── meam │ ├── Makefile.g95 │ ├── Makefile.gfortran │ ├── Makefile.ifort │ ├── Makefile.lammps.gfortran │ ├── Makefile.lammps.glory │ ├── Makefile.lammps.ifort │ ├── Makefile.mingw32-cross │ ├── Makefile.mingw32-cross-mpi │ ├── Makefile.mingw64-cross │ ├── Makefile.mingw64-cross-mpi │ ├── Makefile.pgf90 │ ├── Makefile.tbird │ ├── README │ ├── meam_cleanup.F │ ├── meam_data.F │ ├── meam_dens_final.F │ ├── meam_dens_init.F │ ├── meam_force.F │ ├── meam_setup_done.F │ ├── meam_setup_global.F │ └── meam_setup_param.F ├── poems │ ├── Authors_List.txt │ ├── Copyright_Notice │ ├── Grants_List.txt │ ├── Makefile.g++ │ ├── Makefile.icc │ ├── Makefile.lammps │ ├── Makefile.lammps.empty │ ├── Makefile.mingw32-cross │ ├── Makefile.mingw32-cross-mpi │ ├── Makefile.mingw64-cross │ ├── Makefile.mingw64-cross-mpi │ ├── POEMSChain.h │ ├── POEMS_License.txt │ ├── README │ ├── SystemProcessor.h │ ├── bodies.h │ ├── body.cpp │ ├── body.h │ ├── body23joint.cpp │ ├── body23joint.h │ ├── colmatmap.cpp │ ├── colmatmap.h │ ├── colmatrix.cpp │ ├── colmatrix.h │ ├── defines.h │ ├── doc │ │ ├── Anderson_2007_POEMS_ParallelizableOpen-Source.pdf │ │ ├── Chun_MBOND_MultibodyMethodForLont-TimeMolecularDynamics.pdf │ │ └── interface_LIGGGHTS.md │ ├── eulerparameters.cpp │ ├── eulerparameters.h │ ├── fastmatrixops.cpp │ ├── fastmatrixops.h │ ├── fixedpoint.cpp │ ├── fixedpoint.h │ ├── freebodyjoint.cpp │ ├── freebodyjoint.h │ ├── ftm2v │ ├── inertialframe.cpp │ ├── inertialframe.h │ ├── joint.cpp │ ├── joint.h │ ├── joints.h │ ├── mat3x3.cpp │ ├── mat3x3.h │ ├── mat4x4.cpp │ ├── mat4x4.h │ ├── mat6x6.cpp │ ├── mat6x6.h │ ├── matrices.h │ ├── matrix.cpp │ ├── matrix.h │ ├── matrixfun.cpp │ ├── matrixfun.h │ ├── mixedjoint.cpp │ ├── mixedjoint.h │ ├── norm.cpp │ ├── norm.h │ ├── onbody.cpp │ ├── onbody.h │ ├── onfunctions.cpp │ ├── onfunctions.h │ ├── onsolver.cpp │ ├── onsolver.h │ ├── particle.cpp │ ├── particle.h │ ├── poemslist.h │ ├── poemsnodelib.h │ ├── poemsobject.cpp │ ├── poemsobject.h │ ├── poemstree.h │ ├── poemstreenode.cpp │ ├── poemstreenode.h │ ├── point.cpp │ ├── point.h │ ├── points.h │ ├── prismaticjoint.cpp │ ├── prismaticjoint.h │ ├── revolutejoint.cpp │ ├── revolutejoint.h │ ├── rigidbody.cpp │ ├── rigidbody.h │ ├── rowmatrix.cpp │ ├── rowmatrix.h │ ├── solver.cpp │ ├── solver.h │ ├── sphericalFlexiblejoint.cpp │ ├── sphericalFlexiblejoint.h │ ├── sphericaljoint.cpp │ ├── sphericaljoint.h │ ├── system.cpp │ ├── system.h │ ├── vect3.cpp │ ├── vect3.h │ ├── vect4.cpp │ ├── vect4.h │ ├── vect6.cpp │ ├── vect6.h │ ├── virtualcolmatrix.cpp │ ├── virtualcolmatrix.h │ ├── virtualmatrix.cpp │ ├── virtualmatrix.h │ ├── virtualrowmatrix.cpp │ ├── virtualrowmatrix.h │ ├── workspace.cpp │ └── workspace.h ├── reax │ ├── Makefile.g95 │ ├── Makefile.gfortran │ ├── Makefile.ifort │ ├── Makefile.lammps.gfortran │ ├── Makefile.lammps.ifort │ ├── Makefile.pgf90 │ ├── Makefile.redsky │ ├── Makefile.tbird │ ├── README │ ├── cbka.blk │ ├── cbkabo.blk │ ├── cbkatomcoord.blk │ ├── cbkbo.blk │ ├── cbkboncor.blk │ ├── cbkbopi.blk │ ├── cbkbopi2.blk │ ├── cbkbosi.blk │ ├── cbkc.blk │ ├── cbkch.blk │ ├── cbkcha.blk │ ├── cbkcharmol.blk │ ├── cbkchb.blk │ ├── cbkconst.blk │ ├── cbkcovbon.blk │ ├── cbkd.blk │ ├── cbkdbodc.blk │ ├── cbkdbopi2ndc.blk │ ├── cbkdbopidc.blk │ ├── cbkdbopindc.blk │ ├── cbkdcell.blk │ ├── cbkdhdc.blk │ ├── cbkdistan.blk │ ├── cbkdrdc.blk │ ├── cbkefield.blk │ ├── cbkenergies.blk │ ├── cbkeregime.blk │ ├── cbkff.blk │ ├── cbkfftorang.blk │ ├── cbkh.blk │ ├── cbkhbond.blk │ ├── cbkia.blk │ ├── cbkidbo.blk │ ├── cbkimove.blk │ ├── cbkinit.blk │ ├── cbklonpar.blk │ ├── cbkmolec.blk │ ├── cbknmolat.blk │ ├── cbknonbon.blk │ ├── cbknubon2.blk │ ├── cbknvlbo.blk │ ├── cbknvlown.blk │ ├── cbkpairs.blk │ ├── cbkpres.blk │ ├── cbkqa.blk │ ├── cbkrbo.blk │ ├── cbkrestr.blk │ ├── cbksrtbon1.blk │ ├── cbksrthb.blk │ ├── cbktorang.blk │ ├── cbktorsion.blk │ ├── cbktregime.blk │ ├── cbkvalence.blk │ ├── cbkvregime.blk │ ├── cellcoord.blk │ ├── control.blk │ ├── opt.blk │ ├── reax_charges.F │ ├── reax_connect.F │ ├── reax_defs.h │ ├── reax_inout.F │ ├── reax_lammps.F │ ├── reax_poten.F │ ├── reax_reac.F │ ├── small.blk │ └── valang.blk └── smd │ ├── .gitignore │ ├── Install.py │ ├── Makefile.lammps │ └── README ├── misc ├── comm_tiled.h ├── imbalance.h ├── imbalance_group.h ├── imbalance_neigh.h ├── imbalance_store.h ├── imbalance_time.h ├── imbalance_var.h └── rcb.h ├── python ├── README ├── examples │ ├── demo.py │ ├── gui.py │ ├── in.demo │ ├── in.gui │ ├── in.plot │ ├── in.simple │ ├── in.trivial │ ├── in.viz │ ├── pizza │ │ ├── dump.py │ │ ├── gl.py │ │ ├── gnu.py │ │ ├── pdbfile.py │ │ ├── vizinfo.py │ │ └── vmd.py │ ├── plot.py │ ├── simple.py │ ├── trivial.py │ ├── viz_atomeye.py │ ├── viz_gl.py │ ├── viz_pymol.py │ ├── viz_vmd.py │ ├── vizplotgui_atomeye.py │ ├── vizplotgui_gl.py │ ├── vizplotgui_pymol.py │ └── vizplotgui_vmd.py ├── install.py └── liggghts.py ├── release-notes.txt ├── src ├── .gitignore ├── CMakeLists.txt ├── Depend.sh ├── Doxyfile ├── Install.sh ├── LICENSE ├── MAKE │ ├── CMakeLists_Catalyst.txt │ ├── Makefile.auto │ ├── Makefile.dbg_gcc │ ├── Makefile.dbg_icc_mpich │ ├── Makefile.inl_macos │ ├── Makefile.lise_fpic │ ├── Makefile.mpi │ ├── Makefile.mpi_no_vtk │ ├── Makefile.mpi_ubuntu-18.04 │ ├── Makefile.mpi_ubuntu-20.04 │ ├── Makefile.mpi_ubuntu-22.04 │ ├── Makefile.mpi_vtk-7.1 │ ├── Makefile.opt_gcc │ ├── Makefile.opt_icc_mpich │ ├── Makefile.palmetto │ ├── Makefile.peregrine │ ├── Makefile.sawtooth │ ├── Makefile.sawtooth_novtk │ ├── Makefile.user_default │ ├── Makefile.user_default_patch_1.0 │ ├── Makefile.user_default_patch_1.1 │ ├── Makefile.user_default_patch_1.2 │ ├── Makefile.user_default_patch_1.3 │ └── deprecated │ │ ├── Makefile.altix │ │ ├── Makefile.bgl │ │ ├── Makefile.chama │ │ ├── Makefile.clang │ │ ├── Makefile.cygwin │ │ ├── Makefile.encanto │ │ ├── Makefile.fedora │ │ ├── Makefile.fedora_debug │ │ ├── Makefile.fedora_debug_opt │ │ ├── Makefile.fedora_fpic │ │ ├── Makefile.fedora_fpic_debug │ │ ├── Makefile.fedora_gp │ │ ├── Makefile.fedora_vtk_fpic │ │ ├── Makefile.fedora_vtk_fpic_debug │ │ ├── Makefile.fink │ │ ├── Makefile.g++ │ │ ├── Makefile.g++3 │ │ ├── Makefile.g++_mingw64 │ │ ├── Makefile.glory │ │ ├── Makefile.jaguar │ │ ├── Makefile.lam │ │ ├── Makefile.linux │ │ ├── Makefile.mac │ │ ├── Makefile.mac_mpi │ │ ├── Makefile.mingw │ │ ├── Makefile.mkl │ │ ├── Makefile.odin │ │ ├── Makefile.openmpi │ │ ├── Makefile.pgi │ │ ├── Makefile.power5 │ │ ├── Makefile.qed │ │ ├── Makefile.redsky │ │ ├── Makefile.sdsc │ │ ├── Makefile.seaborg │ │ ├── Makefile.serial_debug │ │ ├── Makefile.sgi │ │ ├── Makefile.solaris │ │ ├── Makefile.spirit │ │ ├── Makefile.storm │ │ ├── Makefile.tacc │ │ ├── Makefile.tbird │ │ ├── Makefile.tesla │ │ ├── Makefile.tunnison │ │ ├── Makefile.ubuntuVTK │ │ ├── Makefile.ubuntuVTK6 │ │ ├── Makefile.ubuntuVTKConvex │ │ ├── Makefile.ubuntuVTKConvex_debug │ │ ├── Makefile.ubuntuVTK_debug │ │ ├── Makefile.ubuntuVTK_fpic │ │ ├── Makefile.ubuntuVTK_fpic_debug │ │ ├── Makefile.xe6 │ │ ├── Makefile.xt3 │ │ ├── Makefile.xt5 │ │ └── _README ├── MOLECULE │ ├── atom_vec_bond.cpp │ ├── atom_vec_bond.h │ ├── atom_vec_full.cpp │ ├── atom_vec_full.h │ ├── atom_vec_molecular.cpp │ ├── atom_vec_molecular.h │ ├── bond_harmonic.cpp │ └── bond_harmonic.h ├── Make.py ├── Make.sh ├── Makedoxy ├── Makefile ├── Makefile.lib ├── Makefile.list ├── Makefile.package ├── Makefile.package.empty ├── Makefile.package.settings ├── Makefile.package.settings.empty ├── Makefile.shlib ├── PASCAL │ ├── Install.sh │ ├── fix_pascal_couple.cpp │ └── fix_pascal_couple.h ├── POEMS │ ├── Install.sh │ ├── fix_poems.cpp │ └── fix_poems.h ├── Package.sh ├── Purge.list ├── STUBS │ ├── Makefile │ ├── Makefile.mingw32-cross │ ├── Makefile.mingw64-cross │ ├── mpi.c │ └── mpi.h ├── VORONOI │ ├── Install.sh │ ├── Makefile.lammps │ ├── README │ ├── compute_voronoi_atom.cpp │ └── compute_voronoi_atom.h ├── WINDOWS │ ├── GenerateHeaders.bat │ └── extra │ │ ├── dirent.h │ │ ├── erf.h │ │ ├── erf_namd.c │ │ ├── fftw2 │ │ ├── FFTW2dll.dll │ │ ├── FFTW2dll.lib │ │ ├── FFTW2st.lib │ │ ├── RFFTW2dll.dll │ │ ├── RFFTW2dll.lib │ │ ├── RFFTW2st.lib │ │ ├── fftw.h │ │ └── x64 │ │ │ ├── FFTW2dll.dll │ │ │ ├── FFTW2dll.lib │ │ │ ├── FFTW2st.lib │ │ │ ├── RFFTW2dll.dll │ │ │ ├── RFFTW2dll.lib │ │ │ └── RFFTW2st.lib │ │ ├── inttypes.h │ │ ├── sleep.cpp │ │ ├── sleep.h │ │ ├── stdint.h │ │ ├── sys │ │ └── time.h │ │ └── unistd.h ├── abstract_mesh.h ├── accelerator_cuda.h ├── accelerator_omp.h ├── angle.cpp ├── angle.h ├── angle_hybrid.cpp ├── angle_hybrid.h ├── associative_pointer_array.h ├── associative_pointer_array_I.h ├── atom.cpp ├── atom.h ├── atom_map.cpp ├── atom_masks.h ├── atom_vec.cpp ├── atom_vec.h ├── atom_vec_atomic.cpp ├── atom_vec_atomic.h ├── atom_vec_charge.cpp ├── atom_vec_charge.h ├── atom_vec_convexhull.h ├── atom_vec_ellipsoid.cpp ├── atom_vec_ellipsoid.h ├── atom_vec_full.cpp ├── atom_vec_full.h ├── atom_vec_hybrid.cpp ├── atom_vec_hybrid.h ├── atom_vec_line.cpp ├── atom_vec_line.h ├── atom_vec_molecular.cpp ├── atom_vec_molecular.h ├── atom_vec_sph.cpp ├── atom_vec_sph.h ├── atom_vec_sph_var.cpp ├── atom_vec_sph_var.h ├── atom_vec_sphere.cpp ├── atom_vec_sphere.h ├── atom_vec_sphere_w.cpp ├── atom_vec_superquadric.cpp ├── atom_vec_superquadric.h ├── atom_vec_tri.cpp ├── atom_vec_tri.h ├── balance.cpp ├── balance.h ├── bond.cpp ├── bond.h ├── bond_harmonic.cpp ├── bond_harmonic.h ├── bond_hybrid.cpp ├── bond_hybrid.h ├── bounding_box.cpp ├── bounding_box.h ├── cfd_datacoupling.cpp ├── cfd_datacoupling.h ├── cfd_datacoupling_file.cpp ├── cfd_datacoupling_file.h ├── cfd_datacoupling_mpi.cpp ├── cfd_datacoupling_mpi.h ├── cfd_datacoupling_simple.h ├── cfd_regionmodel.h ├── cfd_regionmodel_none.cpp ├── cfd_regionmodel_none.h ├── change_box.cpp ├── change_box.h ├── citeme.cpp ├── citeme.h ├── cleanAllNonSpherical.sh ├── cleanAllParScale.sh ├── coarsegraining.cpp ├── coarsegraining.h ├── cohesion_model_base.h ├── cohesion_model_bond.h ├── cohesion_model_bond_nonlinear.h ├── cohesion_model_easo_capillary_viscous.h ├── cohesion_model_sjkr.h ├── cohesion_model_sjkr2.h ├── cohesion_model_washino_capillary_viscous.h ├── comm.cpp ├── comm.h ├── comm_brick.cpp ├── comm_brick.h ├── comm_tiled.h ├── compute.cpp ├── compute.h ├── compute_angmom.cpp ├── compute_angmom.h ├── compute_atom_molecule.cpp ├── compute_atom_molecule.h ├── compute_bond_counter.cpp ├── compute_bond_counter.h ├── compute_bond_local.cpp ├── compute_bond_local.h ├── compute_centro_atom.cpp ├── compute_centro_atom.h ├── compute_cluster_atom.cpp ├── compute_cluster_atom.h ├── compute_cna_atom.cpp ├── compute_cna_atom.h ├── compute_com.cpp ├── compute_com.h ├── compute_com_molecule.cpp ├── compute_com_molecule.h ├── compute_contact_atom.cpp ├── compute_contact_atom.h ├── compute_contact_atom_gran.cpp ├── compute_contact_atom_gran.h ├── compute_coord_atom.cpp ├── compute_coord_atom.h ├── compute_crosssection.cpp ├── compute_crosssection.h ├── compute_displace_atom.cpp ├── compute_displace_atom.h ├── compute_erotate.cpp ├── compute_erotate.h ├── compute_erotate_asphere.cpp ├── compute_erotate_asphere.h ├── compute_erotate_multisphere.cpp ├── compute_erotate_multisphere.h ├── compute_erotate_sphere.cpp ├── compute_erotate_sphere.h ├── compute_erotate_sphere_atom.cpp ├── compute_erotate_sphere_atom.h ├── compute_erotate_superquadric.cpp ├── compute_erotate_superquadric.h ├── compute_group_group.cpp ├── compute_group_group.h ├── compute_gyration.cpp ├── compute_gyration.h ├── compute_gyration_molecule.cpp ├── compute_gyration_molecule.h ├── compute_inertia_molecule.cpp ├── compute_inertia_molecule.h ├── compute_ke.cpp ├── compute_ke.h ├── compute_ke_atom.cpp ├── compute_ke_atom.h ├── compute_ke_multisphere.cpp ├── compute_ke_multisphere.h ├── compute_msd.cpp ├── compute_msd.h ├── compute_msd_molecule.cpp ├── compute_msd_molecule.h ├── compute_nparticles_tracer_region.cpp ├── compute_nparticles_tracer_region.h ├── compute_pair_gran_local.cpp ├── compute_pair_gran_local.h ├── compute_pair_gran_local_bond.cpp ├── compute_pair_gran_local_bond.h ├── compute_pe.cpp ├── compute_pe.h ├── compute_pe_atom.cpp ├── compute_pe_atom.h ├── compute_pressure.cpp ├── compute_pressure.h ├── compute_property_atom.cpp ├── compute_property_atom.h ├── compute_property_local.cpp ├── compute_property_local.h ├── compute_property_molecule.cpp ├── compute_property_molecule.h ├── compute_rdf.cpp ├── compute_rdf.h ├── compute_reduce.cpp ├── compute_reduce.h ├── compute_reduce_region.cpp ├── compute_reduce_region.h ├── compute_rigid.cpp ├── compute_rigid.h ├── compute_sauter_diameter.cpp ├── compute_sauter_diameter.h ├── compute_slice.cpp ├── compute_slice.h ├── compute_stress_atom.cpp ├── compute_stress_atom.h ├── compute_surface.cpp ├── compute_surface.h ├── compute_temp.cpp ├── compute_temp.h ├── compute_velocity_mesh.cpp ├── compute_velocity_mesh.h ├── contact_force_corrector.cpp ├── contact_force_corrector.h ├── contact_force_corrector_I.h ├── contact_interface.h ├── contact_model_base.h ├── contact_model_constants.h ├── contact_models.cpp ├── contact_models.h ├── container.h ├── container_base.cpp ├── container_base.h ├── container_base_I.h ├── create_atoms.cpp ├── create_atoms.h ├── create_box.cpp ├── create_box.h ├── create_particles.cpp ├── create_particles.h ├── custom_value_tracker.cpp ├── custom_value_tracker.h ├── custom_value_tracker_I.h ├── debug_liggghts.h ├── delete_atoms.cpp ├── delete_atoms.h ├── delete_bonds.cpp ├── delete_bonds.h ├── dihedral.cpp ├── dihedral.h ├── dihedral_hybrid.cpp ├── dihedral_hybrid.h ├── displace_atoms.cpp ├── displace_atoms.h ├── domain.cpp ├── domain.h ├── domain_I.h ├── domain_definitions.h ├── domain_wedge.h ├── domain_wedge_dummy.h ├── dump.cpp ├── dump.h ├── dump_atom_vtk.cpp ├── dump_atom_vtk.h ├── dump_custom.cpp ├── dump_custom.h ├── dump_custom_vtk.cpp ├── dump_custom_vtk.h ├── dump_custom_vtm.cpp ├── dump_custom_vtm.h ├── dump_decomposition_vtk.cpp ├── dump_decomposition_vtk.h ├── dump_euler_vtk.cpp ├── dump_euler_vtk.h ├── dump_image.cpp ├── dump_image.h ├── dump_local.cpp ├── dump_local.h ├── dump_local_gran.cpp ├── dump_local_gran.h ├── dump_local_gran_vtk.cpp ├── dump_local_gran_vtk.h ├── dump_mesh.cpp ├── dump_mesh.h ├── dump_mesh_stl.cpp ├── dump_mesh_stl.h ├── dump_mesh_vtk.cpp ├── dump_mesh_vtk.h ├── dump_mesh_vtm.cpp ├── dump_mesh_vtm.h ├── dump_movie.cpp ├── dump_movie.h ├── dump_particle.cpp ├── dump_particle.h ├── dump_vtk.cpp ├── dump_vtk.h ├── dump_xyz.cpp ├── dump_xyz.h ├── error.cpp ├── error.h ├── error_special.h ├── finish.cpp ├── finish.h ├── fix.cpp ├── fix.h ├── fix_adapt.cpp ├── fix_adapt.h ├── fix_addforce.cpp ├── fix_addforce.h ├── fix_ave_atom.cpp ├── fix_ave_atom.h ├── fix_ave_correlate.cpp ├── fix_ave_correlate.h ├── fix_ave_euler.cpp ├── fix_ave_euler.h ├── fix_ave_histo.cpp ├── fix_ave_histo.h ├── fix_ave_spatial.cpp ├── fix_ave_spatial.h ├── fix_ave_time.cpp ├── fix_ave_time.h ├── fix_aveforce.cpp ├── fix_aveforce.h ├── fix_balance.cpp ├── fix_balance.h ├── fix_base_liggghts.cpp ├── fix_base_liggghts.h ├── fix_box_relax.cpp ├── fix_box_relax.h ├── fix_buoyancy.cpp ├── fix_buoyancy.h ├── fix_calculate_energy_wall.h ├── fix_calculate_energy_wall_dissipated.h ├── fix_cfd_coupling.cpp ├── fix_cfd_coupling.h ├── fix_cfd_coupling_convection.cpp ├── fix_cfd_coupling_convection.h ├── fix_cfd_coupling_convection_impl.cpp ├── fix_cfd_coupling_convection_impl.h ├── fix_cfd_coupling_convection_species.cpp ├── fix_cfd_coupling_convection_species.h ├── fix_cfd_coupling_force.cpp ├── fix_cfd_coupling_force.h ├── fix_check_timestep_gran.cpp ├── fix_check_timestep_gran.h ├── fix_check_timestep_sph.cpp ├── fix_check_timestep_sph.h ├── fix_contact_atom_counter.h ├── fix_contact_atom_counter_dummy.h ├── fix_contact_atom_counter_wall.h ├── fix_contact_atom_counter_wall_dummy.h ├── fix_contact_history.cpp ├── fix_contact_history.h ├── fix_contact_history_mesh.cpp ├── fix_contact_history_mesh.h ├── fix_contact_history_mesh_I.h ├── fix_contact_property_atom.cpp ├── fix_contact_property_atom.h ├── fix_contact_property_atom_wall.cpp ├── fix_contact_property_atom_wall.h ├── fix_continuum_weighted.cpp ├── fix_continuum_weighted.h ├── fix_deform.cpp ├── fix_deform.h ├── fix_deform_check.cpp ├── fix_deform_check.h ├── fix_diam_max.cpp ├── fix_diam_max.h ├── fix_drag.cpp ├── fix_drag.h ├── fix_dragforce.cpp ├── fix_dragforce.h ├── fix_dt_reset.cpp ├── fix_dt_reset.h ├── fix_dummy.h ├── fix_dummy2.h ├── fix_efield.cpp ├── fix_efield.h ├── fix_enforce2d.cpp ├── fix_enforce2d.h ├── fix_external.cpp ├── fix_external.h ├── fix_fiber_spring_simple.cpp ├── fix_fiber_spring_simple.h ├── fix_freeze.cpp ├── fix_freeze.h ├── fix_gravity.cpp ├── fix_gravity.h ├── fix_heat_gran.cpp ├── fix_heat_gran.h ├── fix_heat_gran_conduction.cpp ├── fix_heat_gran_conduction.h ├── fix_insert.cpp ├── fix_insert.h ├── fix_insert_fragments.cpp ├── fix_insert_fragments.h ├── fix_insert_pack.cpp ├── fix_insert_pack.h ├── fix_insert_rate_region.cpp ├── fix_insert_rate_region.h ├── fix_insert_stream.cpp ├── fix_insert_stream.h ├── fix_insert_stream_predefined.h ├── fix_lb_coupling_onetoone.cpp ├── fix_lb_coupling_onetoone.h ├── fix_lineforce.cpp ├── fix_lineforce.h ├── fix_massflow_mesh.cpp ├── fix_massflow_mesh.h ├── fix_massflow_mesh_sieve.cpp ├── fix_massflow_mesh_sieve.h ├── fix_mesh.cpp ├── fix_mesh.h ├── fix_mesh_surface.cpp ├── fix_mesh_surface.h ├── fix_minimize.cpp ├── fix_minimize.h ├── fix_mixing.h ├── fix_momentum.cpp ├── fix_momentum.h ├── fix_move.cpp ├── fix_move.h ├── fix_move_mesh.cpp ├── fix_move_mesh.h ├── fix_multicontact_halfspace.cpp ├── fix_multicontact_halfspace.h ├── fix_multisphere.cpp ├── fix_multisphere.h ├── fix_multisphere_advanced.cpp ├── fix_multisphere_advanced.h ├── fix_multisphere_break.cpp ├── fix_multisphere_break.h ├── fix_multisphere_comm.cpp ├── fix_multisphere_comm_I.h ├── fix_neighlist_mesh.cpp ├── fix_neighlist_mesh.h ├── fix_nve.cpp ├── fix_nve.h ├── fix_nve_asphere.cpp ├── fix_nve_asphere.h ├── fix_nve_asphere_noforce.cpp ├── fix_nve_asphere_noforce.h ├── fix_nve_cfd_cn_sphere.cpp ├── fix_nve_cfd_cn_sphere.h ├── fix_nve_limit.cpp ├── fix_nve_limit.h ├── fix_nve_line.cpp ├── fix_nve_line.h ├── fix_nve_noforce.cpp ├── fix_nve_noforce.h ├── fix_nve_non_spherical.cpp ├── fix_nve_non_spherical.h ├── fix_nve_sph.cpp ├── fix_nve_sph.h ├── fix_nve_sph_stationary.cpp ├── fix_nve_sph_stationary.h ├── fix_nve_sphere.cpp ├── fix_nve_sphere.h ├── fix_nve_sphere_limit.cpp ├── fix_nve_sphere_limit.h ├── fix_particledistribution_discrete.cpp ├── fix_particledistribution_discrete.h ├── fix_planeforce.cpp ├── fix_planeforce.h ├── fix_print.cpp ├── fix_print.h ├── fix_property_atom.cpp ├── fix_property_atom.h ├── fix_property_atom_region_tracer.cpp ├── fix_property_atom_region_tracer.h ├── fix_property_atom_tracer.cpp ├── fix_property_atom_tracer.h ├── fix_property_atom_tracer_stream.cpp ├── fix_property_atom_tracer_stream.h ├── fix_property_global.cpp ├── fix_property_global.h ├── fix_read_restart.cpp ├── fix_read_restart.h ├── fix_region_variable.cpp ├── fix_region_variable.h ├── fix_relax_contacts.h ├── fix_remove.h ├── fix_respa.cpp ├── fix_respa.h ├── fix_rigid.cpp ├── fix_rigid.h ├── fix_scalar_transport_equation.cpp ├── fix_scalar_transport_equation.h ├── fix_set_vel.cpp ├── fix_set_vel.h ├── fix_setforce.cpp ├── fix_setforce.h ├── fix_sph.cpp ├── fix_sph.h ├── fix_sph_density_continuity.cpp ├── fix_sph_density_continuity.h ├── fix_sph_density_corr.cpp ├── fix_sph_density_corr.h ├── fix_sph_density_summation.cpp ├── fix_sph_density_summation.h ├── fix_sph_pressure.cpp ├── fix_sph_pressure.h ├── fix_spring.cpp ├── fix_spring.h ├── fix_spring_rg.cpp ├── fix_spring_rg.h ├── fix_spring_self.cpp ├── fix_spring_self.h ├── fix_store.cpp ├── fix_store.h ├── fix_store_force.cpp ├── fix_store_force.h ├── fix_store_state.cpp ├── fix_store_state.h ├── fix_template_multiplespheres.cpp ├── fix_template_multiplespheres.h ├── fix_template_multisphere.cpp ├── fix_template_multisphere.h ├── fix_template_sphere.cpp ├── fix_template_sphere.h ├── fix_template_superquadric.cpp ├── fix_template_superquadric.h ├── fix_viscous.cpp ├── fix_viscous.h ├── fix_wall.cpp ├── fix_wall.h ├── fix_wall_gran.cpp ├── fix_wall_gran.h ├── fix_wall_gran_base.h ├── fix_wall_region.cpp ├── fix_wall_region.h ├── fix_wall_region_sph.cpp ├── fix_wall_region_sph.h ├── fix_wall_sph.cpp ├── fix_wall_sph.h ├── force.cpp ├── force.h ├── genAutoExamplesWhitelist.sh ├── general_container.h ├── general_container_I.h ├── global_properties.cpp ├── global_properties.h ├── granular_pair_style.cpp ├── granular_pair_style.h ├── granular_styles.h ├── granular_wall.cpp ├── granular_wall.h ├── group.cpp ├── group.h ├── histogram.h ├── iloopcallbackcallable.h ├── iloopcallbackcaller.cpp ├── iloopcallbackcaller.h ├── image.cpp ├── image.h ├── imbalance.cpp ├── imbalance.h ├── imbalance_group.cpp ├── imbalance_group.h ├── imbalance_neigh.cpp ├── imbalance_neigh.h ├── imbalance_store.cpp ├── imbalance_store.h ├── imbalance_time.cpp ├── imbalance_time.h ├── imbalance_var.cpp ├── imbalance_var.h ├── improper.cpp ├── improper.h ├── improper_hybrid.cpp ├── improper_hybrid.h ├── info.cpp ├── info.h ├── input.cpp ├── input.h ├── input_mesh_tet.cpp ├── input_mesh_tet.h ├── input_mesh_tri.cpp ├── input_mesh_tri.h ├── input_multisphere.cpp ├── input_multisphere.h ├── integrate.cpp ├── integrate.h ├── irregular.cpp ├── irregular.h ├── kspace.cpp ├── kspace.h ├── lammps.cpp ├── lammps.h ├── lattice.cpp ├── lattice.h ├── library.cpp ├── library.h ├── library_cfd_coupling.cpp ├── library_cfd_coupling.h ├── lmptype.h ├── lmpwindows.h ├── main.cpp ├── math_complex.h ├── math_const.h ├── math_extra.cpp ├── math_extra.h ├── math_extra_liggghts.h ├── math_extra_liggghts_nonspherical.cpp ├── math_extra_liggghts_nonspherical.h ├── math_extra_liggghts_superquadric.cpp ├── math_extra_liggghts_superquadric.h ├── math_special.h ├── math_vector.h ├── memory.cpp ├── memory.h ├── memory_ns.h ├── mergesort.h ├── mesh_module.cpp ├── mesh_module.h ├── mesh_module_liquidtransfer.cpp ├── mesh_module_liquidtransfer.h ├── mesh_module_stress.cpp ├── mesh_module_stress.h ├── mesh_module_stress_6dof.cpp ├── mesh_module_stress_6dof.h ├── mesh_module_stress_servo.cpp ├── mesh_module_stress_servo.h ├── mesh_mover.h ├── mesh_mover_linear.cpp ├── mesh_mover_linear.h ├── mesh_mover_rotation.cpp ├── mesh_mover_rotation.h ├── min.cpp ├── min.h ├── min_cg.cpp ├── min_cg.h ├── min_linesearch.cpp ├── min_linesearch.h ├── minimize.cpp ├── minimize.h ├── modified_andrew.cpp ├── modified_andrew.h ├── modify.cpp ├── modify.h ├── modify_liggghts.cpp ├── mpi_liggghts.h ├── multi_node_mesh.h ├── multi_node_mesh_I.h ├── multi_node_mesh_parallel.h ├── multi_node_mesh_parallel_I.h ├── multi_node_mesh_parallel_buffer_I.h ├── multi_vector_container.h ├── multisphere.cpp ├── multisphere.h ├── multisphere_I.h ├── multisphere_parallel.cpp ├── multisphere_parallel.h ├── multisphere_parallel_I.h ├── my_page.h ├── my_pool_chunk.h ├── neigh_bond.cpp ├── neigh_bond.h ├── neigh_derive.cpp ├── neigh_derive.h ├── neigh_dummy.cpp ├── neigh_dummy.h ├── neigh_full.cpp ├── neigh_full.h ├── neigh_gran.cpp ├── neigh_gran.h ├── neigh_half_bin.cpp ├── neigh_half_bin.h ├── neigh_half_multi.cpp ├── neigh_half_multi.h ├── neigh_half_nsq.cpp ├── neigh_half_nsq.h ├── neigh_list.cpp ├── neigh_list.h ├── neigh_mlg_dummy.h ├── neigh_modify.h ├── neigh_multi_level_grid.h ├── neigh_request.cpp ├── neigh_request.h ├── neigh_respa.cpp ├── neigh_respa.h ├── neigh_stencil.cpp ├── neighbor.cpp ├── neighbor.h ├── normal_model_base.h ├── normal_model_c2.h ├── normal_model_edinburgh.h ├── normal_model_edinburgh_stiffness.h ├── normal_model_hertz.h ├── normal_model_hertz_stiffness.h ├── normal_model_hooke.h ├── normal_model_hooke_hysteresis.h ├── normal_model_hooke_stiffness.h ├── normal_model_hysteretic_nonlinear1.h ├── normal_model_hysteretic_nonlinear2.h ├── normal_model_luding.h ├── normal_model_thornton_ning.h ├── os_specific.h ├── output.cpp ├── output.h ├── pack.h ├── pair.cpp ├── pair.h ├── pair_gran.cpp ├── pair_gran.h ├── pair_gran_base.h ├── pair_gran_proxy.cpp ├── pair_gran_proxy.h ├── pair_hybrid.cpp ├── pair_hybrid.h ├── pair_hybrid_overlay.cpp ├── pair_hybrid_overlay.h ├── pair_line_lj.cpp ├── pair_line_lj.h ├── pair_soft.cpp ├── pair_soft.h ├── pair_sph.cpp ├── pair_sph.h ├── pair_sph_artvisc_tenscorr.cpp ├── pair_sph_artvisc_tenscorr.h ├── parallel_base.h ├── particleToInsert.cpp ├── particleToInsert.h ├── particleToInsertSuperquadric.cpp ├── particleToInsertSuperquadric.h ├── particleToInsert_multisphere.cpp ├── particleToInsert_multisphere.h ├── physicsheatconduction.cpp ├── physicsheatconduction.h ├── pointers.h ├── primitive_wall.h ├── primitive_wall_definitions.h ├── probability_distribution.h ├── procmap.cpp ├── procmap.h ├── properties.cpp ├── properties.h ├── property_registry.cpp ├── property_registry.h ├── property_type_base.h ├── property_type_constant.cpp ├── property_type_constant.h ├── property_type_lookup.h ├── random.cpp ├── random.h ├── random_mars.cpp ├── random_mars.h ├── random_park.cpp ├── random_park.h ├── rcb.h ├── read_data.cpp ├── read_data.h ├── read_dump.cpp ├── read_dump.h ├── read_restart.cpp ├── read_restart.h ├── reader.cpp ├── reader.h ├── reader_native.cpp ├── reader_native.h ├── reader_xyz.cpp ├── reader_xyz.h ├── region.cpp ├── region.h ├── region_block.cpp ├── region_block.h ├── region_cone.cpp ├── region_cone.h ├── region_cylinder.cpp ├── region_cylinder.h ├── region_intersect.cpp ├── region_intersect.h ├── region_mesh_tet.cpp ├── region_mesh_tet.h ├── region_mesh_tet_I.h ├── region_neighbor_list.cpp ├── region_neighbor_list.h ├── region_neighbor_list_I.h ├── region_neighbor_list_base.h ├── region_neighbor_list_definitions.h ├── region_plane.cpp ├── region_plane.h ├── region_prism.cpp ├── region_prism.h ├── region_sphere.cpp ├── region_sphere.h ├── region_union.cpp ├── region_union.h ├── region_wedge.cpp ├── region_wedge.h ├── replicate.cpp ├── replicate.h ├── rerun.cpp ├── rerun.h ├── respa.cpp ├── respa.h ├── rolling_model_base.h ├── rolling_model_cdt.h ├── rolling_model_cdtnonlinear2.h ├── rolling_model_epsd.h ├── rolling_model_epsd2.h ├── rolling_model_epsd3.h ├── rolling_model_luding.h ├── rotate.cpp ├── rotate.h ├── run.cpp ├── run.h ├── run_time.cpp ├── run_time.h ├── scalar_container.h ├── set.cpp ├── set.h ├── set_multisphere.cpp ├── set_multisphere.h ├── settings.h ├── signal_handling.cpp ├── signal_handling.h ├── sort_buffer.cpp ├── sort_buffer.h ├── special.cpp ├── special.h ├── sph_kernel_cubicspline.h ├── sph_kernel_cubicspline2D.h ├── sph_kernel_spiky.h ├── sph_kernel_spiky2D.h ├── sph_kernel_wendland.h ├── sph_kernel_wendland2D.h ├── sph_kernels.h ├── string_liggghts.h ├── suffix.h ├── superquadric.cpp ├── superquadric.h ├── surface_mesh.h ├── surface_mesh_I.h ├── surface_mesh_feature_remove.h ├── surface_mesh_feature_remove_I.h ├── surface_model_base.h ├── surface_model_default.h ├── surface_model_multicontact.h ├── surface_model_superquadric.h ├── surface_model_superquadric_orthogonal.h ├── tangential_model_base.h ├── tangential_model_history.h ├── tangential_model_hysteretic_nonlinear.h ├── tangential_model_luding_tn.h ├── tangential_model_no_history.h ├── tet_mesh.cpp ├── tet_mesh.h ├── tet_mesh_I.h ├── thermo.cpp ├── thermo.h ├── timer.cpp ├── timer.h ├── tracking_mesh.h ├── tracking_mesh_I.h ├── tri_line.h ├── tri_mesh.cpp ├── tri_mesh.h ├── tri_mesh_I.h ├── tri_mesh_I_superquadric.h ├── tri_mesh_deform.h ├── tri_mesh_planar.cpp ├── tri_mesh_planar.h ├── tri_mesh_planar_I.h ├── universe.cpp ├── universe.h ├── update.cpp ├── update.h ├── update_wall_clock_time.h ├── utils.h ├── variable.cpp ├── variable.h ├── vector_container.h ├── vector_liggghts.h ├── velocity.cpp ├── velocity.h ├── verlet.cpp ├── verlet.h ├── version.h ├── version_liggghts.txt ├── version_liggghts_branch.txt ├── version_struct.h ├── volume_mesh.h ├── volume_mesh_I.h ├── wear_model_archard.h ├── write_data.cpp ├── write_data.h ├── write_dump.cpp ├── write_dump.h ├── write_restart.cpp └── write_restart.h └── tools ├── FIJI ├── README.md └── figs │ ├── fig_fiji_step01.png │ ├── fig_fiji_step02.png │ ├── fig_fiji_step03.png │ ├── fig_fiji_step04.png │ ├── fig_fiji_step05.png │ ├── fig_fiji_step06.png │ ├── fig_fiji_step07.png │ ├── fig_fiji_step08.png │ ├── fig_fiji_step09.png │ ├── fig_fiji_step10.png │ └── fig_fiji_step11.png ├── NVIDIA_CUDA_Installation_Guide_for_Linux └── README.md └── PorosityAnalysis3D ├── Example_1 ├── BW_images.zip ├── Loose_5_Dimensional_porosity.mat ├── Loose_packing.mat ├── Loose_porosity_5.mat ├── Sub_Loose_packing.mat ├── fig_2a0.png ├── fig_directional_porosity_x.png ├── fig_directional_porosity_y.png ├── fig_directional_porosity_z.png ├── fig_local_porosity.png ├── fig_local_porosity_x.png ├── fig_local_porosity_y.png ├── fig_local_porosity_z.png └── vox_list.lmp ├── Example_2 ├── BW_images.zip ├── Raw_images.zip ├── Steel_packing.mat ├── Sub_Steel_5_Dimensional_porosity.mat ├── Sub_Steel_packing.mat ├── Sub_Steel_porosity_5.mat ├── fig_2a.png ├── fig_local_porosity_distribution.png ├── fig_local_porosity_x.png ├── fig_local_porosity_y.png ├── fig_local_porosity_z.png ├── fig_x_directional_porosity.png ├── fig_y_directional_porosity.png ├── fig_z_directional_porosity.png └── vox_list.lmp ├── README.md ├── Step2a_import_bw_slices.m ├── Step2b_crop_subchunk.m ├── Step3_local_porosity.m ├── Step4_directional_porosity.m ├── Step5_plot_local_porosity.m ├── Step6_plot_directional_porosity.m ├── Step7_export_voxel_list.m ├── fig_banner.png └── imshow3Dfull.m /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/idaholab/LIGGGHTS-INL/HEAD/.gitignore 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