| | | | Path |
|---|
| | A | | | .gitignore |
| | D | | | doc/html |
| | D | | | doc/html/.gitignore |
| | D | | | doc/html/2001 |
| | D | | | doc/html/2001/README.html |
| | D | | | doc/html/2001/basics.html |
| | D | | | doc/html/2001/data_format.html |
| | D | | | doc/html/2001/deficiencies.html |
| | D | | | doc/html/2001/force_fields.html |
| | D | | | doc/html/2001/history.html |
| | D | | | doc/html/2001/input_commands.html |
| | D | | | doc/html/2001/units.html |
| | D | | | doc/html/99 |
| | D | | | doc/html/99/README.html |
| | D | | | doc/html/99/basics.html |
| | D | | | doc/html/99/crib.html |
| | D | | | doc/html/99/data_format.html |
| | D | | | doc/html/99/force_fields.html |
| | D | | | doc/html/99/history.html |
| | D | | | doc/html/99/input_commands.html |
| | D | | | doc/html/99/units.html |
| | D | | | doc/html/Manual.html |
| | D | | | doc/html/PDF |
| | D | | | doc/html/PDF/PDLammps_EPS.pdf |
| | D | | | doc/html/PDF/PDLammps_VES.pdf |
| | D | | | doc/html/PDF/PDLammps_overview.pdf |
| | D | | | doc/html/PDF/SMD_LAMMPS_userguide.pdf |
| | D | | | doc/html/PDF/SPH_LAMMPS_userguide.pdf |
| | D | | | doc/html/PDF/colvars-refman-lammps.pdf |
| | D | | | doc/html/PDF/kspace.pdf |
| | D | | | doc/html/PDF/pair_gayberne_extra.pdf |
| | D | | | doc/html/PDF/pair_gayberne_extra.tex |
| | D | | | doc/html/PDF/pair_resquared_extra.pdf |
| | D | | | doc/html/PDF/pair_resquared_extra.tex |
| | D | | | doc/html/Section_accelerate.html |
| | D | | | doc/html/Section_commands.html |
| | D | | | doc/html/Section_errors.html |
| | D | | | doc/html/Section_example.html |
| | D | | | doc/html/Section_history.html |
| | D | | | doc/html/Section_howto.html |
| | D | | | doc/html/Section_intro.html |
| | D | | | doc/html/Section_modify.html |
| | D | | | doc/html/Section_packages.html |
| | D | | | doc/html/Section_perf.html |
| | D | | | doc/html/Section_python.html |
| | D | | | doc/html/Section_start.html |
| | D | | | doc/html/Section_tools.html |
| | D | | | doc/html/USER |
| | D | | | doc/html/USER/atc |
| | D | | | doc/html/USER/atc/man_add_molecule.html |
| | D | | | doc/html/USER/atc/man_add_species.html |
| | D | | | doc/html/USER/atc/man_atom_element_map.html |
| | D | | | doc/html/USER/atc/man_atom_weight.html |
| | D | | | doc/html/USER/atc/man_atomic_charge.html |
| | D | | | doc/html/USER/atc/man_boundary.html |
| | D | | | doc/html/USER/atc/man_boundary_dynamics.html |
| | D | | | doc/html/USER/atc/man_boundary_faceset.html |
| | D | | | doc/html/USER/atc/man_boundary_integral.html |
| | D | | | doc/html/USER/atc/man_consistent_fe_initialization.html |
| | D | | | doc/html/USER/atc/man_contour_integral.html |
| | D | | | doc/html/USER/atc/man_control.html |
| | D | | | doc/html/USER/atc/man_control_momentum.html |
| | D | | | doc/html/USER/atc/man_control_thermal.html |
| | D | | | doc/html/USER/atc/man_control_thermal_correction_max_iterations.html |
| | D | | | doc/html/USER/atc/man_decomposition.html |
| | D | | | doc/html/USER/atc/man_electron_integration.html |
| | D | | | doc/html/USER/atc/man_equilibrium_start.html |
| | D | | | doc/html/USER/atc/man_extrinsic_exchange.html |
| | D | | | doc/html/USER/atc/man_fe_md_boundary.html |
| | D | | | doc/html/USER/atc/man_fem_mesh.html |
| | D | | | doc/html/USER/atc/man_filter_scale.html |
| | D | | | doc/html/USER/atc/man_filter_type.html |
| | D | | | doc/html/USER/atc/man_fix_atc.html |
| | D | | | doc/html/USER/atc/man_fix_flux.html |
| | D | | | doc/html/USER/atc/man_fix_nodes.html |
| | D | | | doc/html/USER/atc/man_hardy_computes.html |
| | D | | | doc/html/USER/atc/man_hardy_fields.html |
| | D | | | doc/html/USER/atc/man_hardy_gradients.html |
| | D | | | doc/html/USER/atc/man_hardy_kernel.html |
| | D | | | doc/html/USER/atc/man_hardy_on_the_fly.html |
| | D | | | doc/html/USER/atc/man_hardy_rates.html |
| | D | | | doc/html/USER/atc/man_initial.html |
| | D | | | doc/html/USER/atc/man_internal_atom_integrate.html |
| | D | | | doc/html/USER/atc/man_internal_element_set.html |
| | D | | | doc/html/USER/atc/man_internal_quadrature.html |
| | D | | | doc/html/USER/atc/man_kernel_function.html |
| | D | | | doc/html/USER/atc/man_localized_lambda.html |
| | D | | | doc/html/USER/atc/man_lumped_lambda_solve.html |
| | D | | | doc/html/USER/atc/man_mask_direction.html |
| | D | | | doc/html/USER/atc/man_mass_matrix.html |
| | D | | | doc/html/USER/atc/man_material.html |
| | D | | | doc/html/USER/atc/man_mesh_add_to_nodeset.html |
| | D | | | doc/html/USER/atc/man_mesh_create.html |
| | D | | | doc/html/USER/atc/man_mesh_create_elementset.html |
| | D | | | doc/html/USER/atc/man_mesh_create_faceset_box.html |
| | D | | | doc/html/USER/atc/man_mesh_create_faceset_plane.html |
| | D | | | doc/html/USER/atc/man_mesh_create_nodeset.html |
| | D | | | doc/html/USER/atc/man_mesh_delete_elements.html |
| | D | | | doc/html/USER/atc/man_mesh_nodeset_to_elementset.html |
| | D | | | doc/html/USER/atc/man_mesh_output.html |
| | D | | | doc/html/USER/atc/man_mesh_quadrature.html |
| | D | | | doc/html/USER/atc/man_mesh_read.html |
| | D | | | doc/html/USER/atc/man_mesh_write.html |
| | D | | | doc/html/USER/atc/man_momentum_time_integration.html |
| | D | | | doc/html/USER/atc/man_output.html |
| | D | | | doc/html/USER/atc/man_output_elementset.html |
| | D | | | doc/html/USER/atc/man_output_nodeset.html |
| | D | | | doc/html/USER/atc/man_pair_interactions.html |
| | D | | | doc/html/USER/atc/man_poisson_solver.html |
| | D | | | doc/html/USER/atc/man_read_restart.html |
| | D | | | doc/html/USER/atc/man_remove_molecule.html |
| | D | | | doc/html/USER/atc/man_remove_source.html |
| | D | | | doc/html/USER/atc/man_remove_species.html |
| | D | | | doc/html/USER/atc/man_reset_atomic_reference_positions.html |
| | D | | | doc/html/USER/atc/man_reset_time.html |
| | D | | | doc/html/USER/atc/man_sample_frequency.html |
| | D | | | doc/html/USER/atc/man_set.html |
| | D | | | doc/html/USER/atc/man_source.html |
| | D | | | doc/html/USER/atc/man_source_integration.html |
| | D | | | doc/html/USER/atc/man_temperature_definition.html |
| | D | | | doc/html/USER/atc/man_thermal_time_integration.html |
| | D | | | doc/html/USER/atc/man_time_filter.html |
| | D | | | doc/html/USER/atc/man_track_displacement.html |
| | D | | | doc/html/USER/atc/man_unfix_flux.html |
| | D | | | doc/html/USER/atc/man_unfix_nodes.html |
| | D | | | doc/html/USER/atc/man_write_atom_weights.html |
| | D | | | doc/html/USER/atc/man_write_restart.html |
| | D | | | doc/html/_images |
| | D | | | doc/html/_images/angle_charmm.jpg |
| | D | | | doc/html/_images/angle_class2.jpg |
| | D | | | doc/html/_images/angle_cosine.jpg |
| | D | | | doc/html/_images/angle_cosine_delta.jpg |
| | D | | | doc/html/_images/angle_cosine_periodic.jpg |
| | D | | | doc/html/_images/angle_cosine_shift.jpg |
| | D | | | doc/html/_images/angle_cosine_shift_exp.jpg |
| | D | | | doc/html/_images/angle_cosine_squared.jpg |
| | D | | | doc/html/_images/angle_dipole_couple.jpg |
| | D | | | doc/html/_images/angle_dipole_gamma.jpg |
| | D | | | doc/html/_images/angle_dipole_potential.jpg |
| | D | | | doc/html/_images/angle_dipole_torque.jpg |
| | D | | | doc/html/_images/angle_fourier.jpg |
| | D | | | doc/html/_images/angle_fourier_simple.jpg |
| | D | | | doc/html/_images/angle_harmonic.jpg |
| | D | | | doc/html/_images/angle_quartic.jpg |
| | D | | | doc/html/_images/atc_nanotube.jpg |
| | D | | | doc/html/_images/balance_nonuniform.jpg |
| | D | | | doc/html/_images/balance_rcb.jpg |
| | D | | | doc/html/_images/balance_uniform.jpg |
| | D | | | doc/html/_images/bond_class2.jpg |
| | D | | | doc/html/_images/bond_fene.jpg |
| | D | | | doc/html/_images/bond_fene_expand.jpg |
| | D | | | doc/html/_images/bond_harmonic.jpg |
| | D | | | doc/html/_images/bond_harmonic_shift.jpg |
| | D | | | doc/html/_images/bond_harmonic_shift_cut.jpg |
| | D | | | doc/html/_images/bond_morse.jpg |
| | D | | | doc/html/_images/bond_nonlinear.jpg |
| | D | | | doc/html/_images/bond_quartic.jpg |
| | D | | | doc/html/_images/bondswap.jpg |
| | D | | | doc/html/_images/box.jpg |
| | D | | | doc/html/_images/box_inverse.jpg |
| | D | | | doc/html/_images/centro_symmetry.jpg |
| | D | | | doc/html/_images/cna_cutoff1.jpg |
| | D | | | doc/html/_images/cna_cutoff2.jpg |
| | D | | | doc/html/_images/compute_dpd.jpg |
| | D | | | doc/html/_images/compute_fep_bar.jpg |
| | D | | | doc/html/_images/compute_fep_fdti.jpg |
| | D | | | doc/html/_images/compute_fep_fep.jpg |
| | D | | | doc/html/_images/compute_fep_lambda.jpg |
| | D | | | doc/html/_images/compute_fep_ti.jpg |
| | D | | | doc/html/_images/compute_fep_u.jpg |
| | D | | | doc/html/_images/compute_fep_vol.jpg |
| | D | | | doc/html/_images/compute_gyration.jpg |
| | D | | | doc/html/_images/compute_msd_nongauss.jpg |
| | D | | | doc/html/_images/compute_saed1.jpg |
| | D | | | doc/html/_images/compute_saed2.jpg |
| | D | | | doc/html/_images/compute_saed3.jpg |
| | D | | | doc/html/_images/compute_sna_atom1.jpg |
| | D | | | doc/html/_images/compute_sna_atom2.jpg |
| | D | | | doc/html/_images/compute_sna_atom3.jpg |
| | D | | | doc/html/_images/compute_sna_atom4.jpg |
| | D | | | doc/html/_images/compute_sna_atom5.jpg |
| | D | | | doc/html/_images/compute_sna_atom6.jpg |
| | D | | | doc/html/_images/compute_xrd1.jpg |
| | D | | | doc/html/_images/compute_xrd2.jpg |
| | D | | | doc/html/_images/compute_xrd3.jpg |
| | D | | | doc/html/_images/compute_xrd4.jpg |
| | D | | | doc/html/_images/compute_xrd5.jpg |
| | D | | | doc/html/_images/coul_soft.jpg |
| | D | | | doc/html/_images/dihedral_charmm.jpg |
| | D | | | doc/html/_images/dihedral_class2.jpg |
| | D | | | doc/html/_images/dihedral_cosine_shift_exp.jpg |
| | D | | | doc/html/_images/dihedral_fourier.jpg |
| | D | | | doc/html/_images/dihedral_harmonic.jpg |
| | D | | | doc/html/_images/dihedral_helix.jpg |
| | D | | | doc/html/_images/dihedral_multi_harmonic.jpg |
| | D | | | doc/html/_images/dihedral_nharmonic.jpg |
| | D | | | doc/html/_images/dihedral_opls.jpg |
| | D | | | doc/html/_images/dihedral_quadratic.jpg |
| | D | | | doc/html/_images/dihedral_sign.jpg |
| | D | | | doc/html/_images/dihedral_spherical.jpg |
| | D | | | doc/html/_images/dihedral_spherical_angles.jpg |
| | D | | | doc/html/_images/dreiding_hbond.jpg |
| | D | | | doc/html/_images/dump1.jpg |
| | D | | | doc/html/_images/dump2.jpg |
| | D | | | doc/html/_images/eff_ECP1.jpg |
| | D | | | doc/html/_images/eff_ECP2.jpg |
| | D | | | doc/html/_images/eff_KE.jpg |
| | D | | | doc/html/_images/eff_NN.jpg |
| | D | | | doc/html/_images/eff_Ne.jpg |
| | D | | | doc/html/_images/eff_Pauli.jpg |
| | D | | | doc/html/_images/eff_ee.jpg |
| | D | | | doc/html/_images/eff_energy_expression.jpg |
| | D | | | doc/html/_images/fix_box_relax1.jpg |
| | D | | | doc/html/_images/fix_box_relax2.jpg |
| | D | | | doc/html/_images/fix_controller1.jpg |
| | D | | | doc/html/_images/fix_controller2.jpg |
| | D | | | doc/html/_images/fix_ehex_eom.jpg |
| | D | | | doc/html/_images/fix_ehex_f.jpg |
| | D | | | doc/html/_images/fix_eos-cv.jpg |
| | D | | | doc/html/_images/fix_eos_table_rx.jpg |
| | D | | | doc/html/_images/fix_gld1.jpg |
| | D | | | doc/html/_images/fix_lb_fluid_boltzmann.jpg |
| | D | | | doc/html/_images/fix_lb_fluid_fluidforce.jpg |
| | D | | | doc/html/_images/fix_lb_fluid_gammadefault.jpg |
| | D | | | doc/html/_images/fix_lb_fluid_navierstokes.jpg |
| | D | | | doc/html/_images/fix_lb_fluid_properties.jpg |
| | D | | | doc/html/_images/fix_lb_fluid_stress.jpg |
| | D | | | doc/html/_images/fix_lb_fluid_viscosity.jpg |
| | D | | | doc/html/_images/fix_nh1.jpg |
| | D | | | doc/html/_images/fix_nphug.jpg |
| | D | | | doc/html/_images/fix_orient_fcc.jpg |
| | D | | | doc/html/_images/fix_pimd.jpg |
| | D | | | doc/html/_images/fix_rattle_constraints.jpg |
| | D | | | doc/html/_images/fix_rattle_rij.jpg |
| | D | | | doc/html/_images/fix_rx.jpg |
| | D | | | doc/html/_images/fix_rx_localTemp.jpg |
| | D | | | doc/html/_images/fix_rx_localTemp2.jpg |
| | D | | | doc/html/_images/fix_rx_reaction.jpg |
| | D | | | doc/html/_images/fix_rx_reactionRate.jpg |
| | D | | | doc/html/_images/fix_spring_rg.jpg |
| | D | | | doc/html/_images/fix_ti_rs_force.jpg |
| | D | | | doc/html/_images/fix_ti_rs_function_1.jpg |
| | D | | | doc/html/_images/fix_ti_rs_function_2.jpg |
| | D | | | doc/html/_images/fix_ti_rs_function_3.jpg |
| | D | | | doc/html/_images/fix_ti_spring_force.jpg |
| | D | | | doc/html/_images/fix_ti_spring_function_1.jpg |
| | D | | | doc/html/_images/fix_ti_spring_function_2.jpg |
| | D | | | doc/html/_images/fix_ttm.jpg |
| | D | | | doc/html/_images/fix_ttm_blast.jpg |
| | D | | | doc/html/_images/fix_ttm_blast1.jpg |
| | D | | | doc/html/_images/fix_ttm_ce.jpg |
| | D | | | doc/html/_images/fix_ttm_mod.jpg |
| | D | | | doc/html/_images/fix_wall_colloid.jpg |
| | D | | | doc/html/_images/fix_wall_harmonic.jpg |
| | D | | | doc/html/_images/fix_wall_lj1043.jpg |
| | D | | | doc/html/_images/fix_wall_lj93.jpg |
| | D | | | doc/html/_images/fld.jpg |
| | D | | | doc/html/_images/fld2.jpg |
| | D | | | doc/html/_images/heat_flux_J.jpg |
| | D | | | doc/html/_images/heat_flux_k.jpg |
| | D | | | doc/html/_images/hexorder.jpg |
| | D | | | doc/html/_images/hop1.jpg |
| | D | | | doc/html/_images/hop2.jpg |
| | D | | | doc/html/_images/improper_class2.jpg |
| | D | | | doc/html/_images/improper_cossq.jpg |
| | D | | | doc/html/_images/improper_cvff.jpg |
| | D | | | doc/html/_images/improper_dist-1.jpg |
| | D | | | doc/html/_images/improper_distance.jpg |
| | D | | | doc/html/_images/improper_fourier.jpg |
| | D | | | doc/html/_images/improper_harmonic.jpg |
| | D | | | doc/html/_images/improper_ring.jpg |
| | D | | | doc/html/_images/improper_umbrella.jpg |
| | D | | | doc/html/_images/lj_soft.jpg |
| | D | | | doc/html/_images/min_energy.jpg |
| | D | | | doc/html/_images/offload_knc.png |
| | D | | | doc/html/_images/orientorder.jpg |
| | D | | | doc/html/_images/pair_adp.jpg |
| | D | | | doc/html/_images/pair_airebo.jpg |
| | D | | | doc/html/_images/pair_beck.jpg |
| | D | | | doc/html/_images/pair_bop.jpg |
| | D | | | doc/html/_images/pair_born.jpg |
| | D | | | doc/html/_images/pair_buck.jpg |
| | D | | | doc/html/_images/pair_charmm.jpg |
| | D | | | doc/html/_images/pair_class2.jpg |
| | D | | | doc/html/_images/pair_cmm.jpg |
| | D | | | doc/html/_images/pair_colloid_cc.jpg |
| | D | | | doc/html/_images/pair_colloid_cs.jpg |
| | D | | | doc/html/_images/pair_colloid_ss.jpg |
| | D | | | doc/html/_images/pair_comb1.jpg |
| | D | | | doc/html/_images/pair_comb2.jpg |
| | D | | | doc/html/_images/pair_coul_diel.jpg |
| | D | | | doc/html/_images/pair_coul_dsf.jpg |
| | D | | | doc/html/_images/pair_coul_soft.jpg |
| | D | | | doc/html/_images/pair_coul_wolf.jpg |
| | D | | | doc/html/_images/pair_coulomb.jpg |
| | D | | | doc/html/_images/pair_cs.jpg |
| | D | | | doc/html/_images/pair_debye.jpg |
| | D | | | doc/html/_images/pair_dipole.jpg |
| | D | | | doc/html/_images/pair_dipole_sf.jpg |
| | D | | | doc/html/_images/pair_dipole_sf2.jpg |
| | D | | | doc/html/_images/pair_dpd.jpg |
| | D | | | doc/html/_images/pair_dpd_conservative.jpg |
| | D | | | doc/html/_images/pair_dpd_omega.jpg |
| | D | | | doc/html/_images/pair_eam.jpg |
| | D | | | doc/html/_images/pair_eam_fs.jpg |
| | D | | | doc/html/_images/pair_edip.jpg |
| | D | | | doc/html/_images/pair_eim1.jpg |
| | D | | | doc/html/_images/pair_eim2.jpg |
| | D | | | doc/html/_images/pair_eim3.jpg |
| | D | | | doc/html/_images/pair_exp6_rx.jpg |
| | D | | | doc/html/_images/pair_exp6_rx_oneFluid.jpg |
| | D | | | doc/html/_images/pair_exp6_rx_oneFluid2.jpg |
| | D | | | doc/html/_images/pair_gauss.jpg |
| | D | | | doc/html/_images/pair_gauss_cut.jpg |
| | D | | | doc/html/_images/pair_gayberne.jpg |
| | D | | | doc/html/_images/pair_gayberne2.jpg |
| | D | | | doc/html/_images/pair_gran_hertz.jpg |
| | D | | | doc/html/_images/pair_gran_hooke.jpg |
| | D | | | doc/html/_images/pair_gromacs.jpg |
| | D | | | doc/html/_images/pair_hbond_dreiding.jpg |
| | D | | | doc/html/_images/pair_lj.jpg |
| | D | | | doc/html/_images/pair_lj96.jpg |
| | D | | | doc/html/_images/pair_lj_cubic.jpg |
| | D | | | doc/html/_images/pair_lj_expand.jpg |
| | D | | | doc/html/_images/pair_lj_sf.jpg |
| | D | | | doc/html/_images/pair_lj_smooth.jpg |
| | D | | | doc/html/_images/pair_lj_smooth_linear.jpg |
| | D | | | doc/html/_images/pair_lj_soft.jpg |
| | D | | | doc/html/_images/pair_lubricate.jpg |
| | D | | | doc/html/_images/pair_mdf-1.jpg |
| | D | | | doc/html/_images/pair_mdf-2.jpg |
| | D | | | doc/html/_images/pair_mdf-3.jpg |
| | D | | | doc/html/_images/pair_mdf-4.jpg |
| | D | | | doc/html/_images/pair_mdf-5.jpg |
| | D | | | doc/html/_images/pair_mdf-6.jpg |
| | D | | | doc/html/_images/pair_meam.jpg |
| | D | | | doc/html/_images/pair_meam_spline.jpg |
| | D | | | doc/html/_images/pair_meam_sw_spline.jpg |
| | D | | | doc/html/_images/pair_mgpt.jpg |
| | D | | | doc/html/_images/pair_mie.jpg |
| | D | | | doc/html/_images/pair_mie2.jpg |
| | D | | | doc/html/_images/pair_morse.jpg |
| | D | | | doc/html/_images/pair_morse_smooth_linear.jpg |
| | D | | | doc/html/_images/pair_morse_soft.jpg |
| | D | | | doc/html/_images/pair_multi_lucy.jpg |
| | D | | | doc/html/_images/pair_multi_lucy2.jpg |
| | D | | | doc/html/_images/pair_multi_lucy_energy.jpg |
| | D | | | doc/html/_images/pair_nb3b_harmonic.jpg |
| | D | | | doc/html/_images/pair_nm.jpg |
| | D | | | doc/html/_images/pair_resquared.jpg |
| | D | | | doc/html/_images/pair_resquared2.jpg |
| | D | | | doc/html/_images/pair_resquared3.jpg |
| | D | | | doc/html/_images/pair_resquared4.jpg |
| | D | | | doc/html/_images/pair_smtbq1.jpg |
| | D | | | doc/html/_images/pair_smtbq2.jpg |
| | D | | | doc/html/_images/pair_smtbq3.jpg |
| | D | | | doc/html/_images/pair_snap.jpg |
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