diff --git a/doc/src/lammps.book b/doc/src/lammps.book new file mode 100644 index 000000000..620eee483 --- /dev/null +++ b/doc/src/lammps.book @@ -0,0 +1,622 @@ +#HTMLDOC 1.8.27 +-t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=1 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont helvetica --bodyfont times --headfootsize 11.0 --headfootfont helvetica --charset iso-8859-1 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow + +Manual.html +Section_intro.html +Section_start.html +Section_commands.html +Section_packages.html +Section_accelerate.html +accelerate_gpu.html +accelerate_intel.html +accelerate_kokkos.html +accelerate_omp.html +accelerate_opt.html +Section_howto.html +Section_example.html +Section_perf.html +Section_tools.html +Section_modify.html +Section_python.html +Section_errors.html +Section_history.html + +tutorial_drude.html +tutorial_github.html + +body.html +manifolds.html + +angle_coeff.html +angle_style.html +atom_modify.html +atom_style.html +balance.html +bond_coeff.html +bond_style.html +bond_write.html +boundary.html +box.html +change_box.html +clear.html +comm_modify.html +comm_style.html +compute.html +compute_modify.html +create_atoms.html +create_bonds.html +create_box.html +delete_atoms.html +delete_bonds.html +dielectric.html +dihedral_coeff.html +dihedral_style.html +dimension.html +displace_atoms.html +dump.html +dump_custom_vtk.html +dump_h5md.html +dump_image.html +dump_modify.html +dump_molfile.html +echo.html +fix.html +fix_modify.html +group.html +group2ndx.html +if.html +improper_coeff.html +improper_style.html +include.html +info.html +jump.html +kspace_modify.html +kspace_style.html +label.html +lattice.html +log.html +mass.html +min_modify.html +min_style.html +minimize.html +molecule.html +neb.html +neigh_modify.html +neighbor.html +newton.html +next.html +package.html +pair_coeff.html +pair_modify.html +pair_style.html +pair_write.html +partition.html +prd.html +print.html +processors.html +python.html +quit.html +read_data.html +read_dump.html +read_restart.html +region.html +replicate.html +rerun.html +reset_timestep.html +restart.html +run.html +run_style.html +set.html +shell.html +special_bonds.html +suffix.html +tad.html +temper.html +thermo.html +thermo_modify.html +thermo_style.html +timer.html +timestep.html +uncompute.html +undump.html +unfix.html +units.html +variable.html +velocity.html +write_coeff.html +write_data.html +write_dump.html +write_restart.html + +fix_adapt.html +fix_adapt_fep.html +fix_addforce.html +fix_addtorque.html +fix_append_atoms.html +fix_atc.html +fix_atom_swap.html +fix_ave_atom.html +fix_ave_chunk.html +fix_ave_correlate.html +fix_ave_correlate_long.html +fix_ave_histo.html +fix_ave_time.html +fix_aveforce.html +fix_balance.html +fix_bond_break.html +fix_bond_create.html +fix_bond_swap.html +fix_box_relax.html +fix_colvars.html +fix_controller.html +fix_deform.html +fix_deposit.html +fix_drag.html +fix_drude.html +fix_drude_transform.html +fix_dt_reset.html +fix_efield.html +fix_ehex.html +fix_enforce2d.html +fix_eos_cv.html +fix_eos_table.html +fix_eos_table_rx.html +fix_evaporate.html +fix_external.html +fix_flow_gauss.html +fix_freeze.html +fix_gcmc.html +fix_gld.html +fix_gle.html +fix_gravity.html +fix_heat.html +fix_imd.html +fix_indent.html +fix_ipi.html +fix_langevin.html +fix_langevin_drude.html +fix_langevin_eff.html +fix_lb_fluid.html +fix_lb_momentum.html +fix_lb_pc.html +fix_lb_rigid_pc_sphere.html +fix_lb_viscous.html +fix_lineforce.html +fix_manifoldforce.html +fix_meso.html +fix_meso_stationary.html +fix_momentum.html +fix_move.html +fix_msst.html +fix_neb.html +fix_nh.html +fix_nh_eff.html +fix_nph_asphere.html +fix_nph_body.html +fix_nph_sphere.html +fix_nphug.html +fix_npt_asphere.html +fix_npt_body.html +fix_npt_sphere.html +fix_nve.html +fix_nve_asphere.html +fix_nve_asphere_noforce.html +fix_nve_body.html +fix_nve_eff.html +fix_nve_limit.html +fix_nve_line.html +fix_nve_manifold_rattle.html +fix_nve_noforce.html +fix_nve_sphere.html +fix_nve_tri.html +fix_nvt_asphere.html +fix_nvt_body.html +fix_nvt_manifold_rattle.html +fix_nvt_sllod.html +fix_nvt_sllod_eff.html +fix_nvt_sphere.html +fix_oneway.html +fix_orient.html +fix_phonon.html +fix_pimd.html +fix_planeforce.html +fix_poems.html +fix_pour.html +fix_press_berendsen.html +fix_print.html +fix_property_atom.html +fix_qbmsst.html +fix_qeq.html +fix_qeq_comb.html +fix_qeq_reax.html +fix_qmmm.html +fix_qtb.html +fix_reax_bonds.html +fix_reaxc_species.html +fix_recenter.html +fix_restrain.html +fix_rigid.html +fix_rx.html +fix_saed_vtk.html +fix_setforce.html +fix_shake.html +fix_shardlow.html +fix_smd.html +fix_smd_adjust_dt.html +fix_smd_integrate_tlsph.html +fix_smd_integrate_ulsph.html +fix_smd_move_triangulated_surface.html +fix_smd_setvel.html +fix_smd_wall_surface.html +fix_spring.html +fix_spring_chunk.html +fix_spring_rg.html +fix_spring_self.html +fix_srd.html +fix_store_force.html +fix_store_state.html +fix_temp_berendsen.html +fix_temp_csvr.html +fix_temp_rescale.html +fix_temp_rescale_eff.html +fix_tfmc.html +fix_thermal_conductivity.html +fix_ti_spring.html +fix_tmd.html +fix_ttm.html +fix_tune_kspace.html +fix_vector.html +fix_viscosity.html +fix_viscous.html +fix_wall.html +fix_wall_gran.html +fix_wall_piston.html +fix_wall_reflect.html +fix_wall_region.html +fix_wall_srd.html + +compute_ackland_atom.html +compute_angle.html +compute_angle_local.html +compute_angmom_chunk.html +compute_basal_atom.html +compute_body_local.html +compute_bond.html +compute_bond_local.html +compute_centro_atom.html +compute_chunk_atom.html +compute_cluster_atom.html +compute_cna_atom.html +compute_com.html +compute_com_chunk.html +compute_contact_atom.html +compute_coord_atom.html +compute_damage_atom.html +compute_dihedral.html +compute_dihedral_local.html +compute_dilatation_atom.html +compute_dipole_chunk.html +compute_displace_atom.html +compute_dpd.html +compute_dpd_atom.html +compute_erotate_asphere.html +compute_erotate_rigid.html +compute_erotate_sphere.html +compute_erotate_sphere_atom.html +compute_event_displace.html +compute_fep.html +compute_group_group.html +compute_gyration.html +compute_gyration_chunk.html +compute_heat_flux.html +compute_hexorder_atom.html +compute_improper.html +compute_improper_local.html +compute_inertia_chunk.html +compute_ke.html +compute_ke_atom.html +compute_ke_atom_eff.html +compute_ke_eff.html +compute_ke_rigid.html +compute_meso_e_atom.html +compute_meso_rho_atom.html +compute_meso_t_atom.html +compute_msd.html +compute_msd_chunk.html +compute_msd_nongauss.html +compute_omega_chunk.html +compute_orientorder_atom.html +compute_pair.html +compute_pair_local.html +compute_pe.html +compute_pe_atom.html +compute_plasticity_atom.html +compute_pressure.html +compute_property_atom.html +compute_property_chunk.html +compute_property_local.html +compute_rdf.html +compute_reduce.html +compute_rigid_local.html +compute_saed.html +compute_slice.html +compute_smd_contact_radius.html +compute_smd_damage.html +compute_smd_hourglass_error.html +compute_smd_internal_energy.html +compute_smd_plastic_strain.html +compute_smd_plastic_strain_rate.html +compute_smd_rho.html +compute_smd_tlsph_defgrad.html +compute_smd_tlsph_dt.html +compute_smd_tlsph_num_neighs.html +compute_smd_tlsph_shape.html +compute_smd_tlsph_strain.html +compute_smd_tlsph_strain_rate.html +compute_smd_tlsph_stress.html +compute_smd_triangle_mesh_vertices.html +compute_smd_ulsph_num_neighs.html +compute_smd_ulsph_strain.html +compute_smd_ulsph_strain_rate.html +compute_smd_ulsph_stress.html +compute_smd_vol.html +compute_sna_atom.html +compute_stress_atom.html +compute_tally.html +compute_temp.html +compute_temp_asphere.html +compute_temp_body.html +compute_temp_chunk.html +compute_temp_com.html +compute_temp_cs.html +compute_temp_deform.html +compute_temp_deform_eff.html +compute_temp_drude.html +compute_temp_eff.html +compute_temp_partial.html +compute_temp_profile.html +compute_temp_ramp.html +compute_temp_region.html +compute_temp_region_eff.html +compute_temp_rotate.html +compute_temp_sphere.html +compute_ti.html +compute_torque_chunk.html +compute_vacf.html +compute_vcm_chunk.html +compute_voronoi_atom.html +compute_xrd.html + +pair_adp.html +pair_airebo.html +pair_awpmd.html +pair_beck.html +pair_body.html +pair_bop.html +pair_born.html +pair_brownian.html +pair_buck.html +pair_buck_long.html +pair_charmm.html +pair_class2.html +pair_colloid.html +pair_comb.html +pair_coul.html +pair_coul_diel.html +pair_cs.html +pair_dipole.html +pair_dpd.html +pair_dpd_fdt.html +pair_dsmc.html +pair_eam.html +pair_edip.html +pair_eff.html +pair_eim.html +pair_exp6_rx.html +pair_gauss.html +pair_gayberne.html +pair_gran.html +pair_gromacs.html +pair_hbond_dreiding.html +pair_hybrid.html +pair_kim.html +pair_lcbop.html +pair_line_lj.html +pair_list.html +pair_lj.html +pair_lj96.html +pair_lj_cubic.html +pair_lj_expand.html +pair_lj_long.html +pair_lj_sf.html +pair_lj_smooth.html +pair_lj_smooth_linear.html +pair_lj_soft.html +pair_lubricate.html +pair_lubricateU.html +pair_mdf.html +pair_meam.html +pair_meam_spline.html +pair_meam_sw_spline.html +pair_mgpt.html +pair_mie.html +pair_morse.html +pair_multi_lucy.html +pair_multi_lucy_rx.html +pair_nb3b_harmonic.html +pair_nm.html +pair_none.html +pair_peri.html +pair_polymorphic.html +pair_quip.html +pair_reax.html +pair_reax_c.html +pair_resquared.html +pair_sdk.html +pair_smd_hertz.html +pair_smd_tlsph.html +pair_smd_triangulated_surface.html +pair_smd_ulsph.html +pair_smtbq.html +pair_snap.html +pair_soft.html +pair_sph_heatconduction.html +pair_sph_idealgas.html +pair_sph_lj.html +pair_sph_rhosum.html +pair_sph_taitwater.html +pair_sph_taitwater_morris.html +pair_srp.html +pair_sw.html +pair_table.html +pair_table_rx.html +pair_tersoff.html +pair_tersoff_mod.html +pair_tersoff_zbl.html +pair_thole.html +pair_tri_lj.html +pair_vashishta.html +pair_yukawa.html +pair_yukawa_colloid.html +pair_zbl.html +pair_zero.html + +bond_class2.html +bond_fene.html +bond_fene_expand.html +bond_harmonic.html +bond_harmonic_shift.html +bond_harmonic_shift_cut.html +bond_hybrid.html +bond_morse.html +bond_none.html +bond_nonlinear.html +bond_quartic.html +bond_table.html +bond_zero.html + +angle_charmm.html +angle_class2.html +angle_cosine.html +angle_cosine_delta.html +angle_cosine_periodic.html +angle_cosine_shift.html +angle_cosine_shift_exp.html +angle_cosine_squared.html +angle_dipole.html +angle_fourier.html +angle_fourier_simple.html +angle_harmonic.html +angle_hybrid.html +angle_none.html +angle_quartic.html +angle_sdk.html +angle_table.html +angle_zero.html + +dihedral_charmm.html +dihedral_class2.html +dihedral_cosine_shift_exp.html +dihedral_fourier.html +dihedral_harmonic.html +dihedral_helix.html +dihedral_hybrid.html +dihedral_multi_harmonic.html +dihedral_nharmonic.html +dihedral_none.html +dihedral_opls.html +dihedral_quadratic.html +dihedral_spherical.html +dihedral_table.html +dihedral_zero.html + +improper_class2.html +improper_cossq.html +improper_cvff.html +improper_distance.html +improper_fourier.html +improper_harmonic.html +improper_hybrid.html +improper_none.html +improper_ring.html +improper_umbrella.html +improper_zero.html + +USER/atc/man_add_molecule.html +USER/atc/man_add_species.html +USER/atc/man_atom_element_map.html +USER/atc/man_atom_weight.html +USER/atc/man_atomic_charge.html +USER/atc/man_boundary.html +USER/atc/man_boundary_dynamics.html +USER/atc/man_boundary_faceset.html +USER/atc/man_boundary_integral.html +USER/atc/man_consistent_fe_initialization.html +USER/atc/man_contour_integral.html +USER/atc/man_control.html +USER/atc/man_control_momentum.html +USER/atc/man_control_thermal.html +USER/atc/man_control_thermal_correction_max_iterations.html +USER/atc/man_decomposition.html +USER/atc/man_electron_integration.html +USER/atc/man_equilibrium_start.html +USER/atc/man_extrinsic_exchange.html +USER/atc/man_fe_md_boundary.html +USER/atc/man_fem_mesh.html +USER/atc/man_filter_scale.html +USER/atc/man_filter_type.html +USER/atc/man_fix_atc.html +USER/atc/man_fix_flux.html +USER/atc/man_fix_nodes.html +USER/atc/man_hardy_computes.html +USER/atc/man_hardy_fields.html +USER/atc/man_hardy_gradients.html +USER/atc/man_hardy_kernel.html +USER/atc/man_hardy_on_the_fly.html +USER/atc/man_hardy_rates.html +USER/atc/man_initial.html +USER/atc/man_internal_atom_integrate.html +USER/atc/man_internal_element_set.html +USER/atc/man_internal_quadrature.html +USER/atc/man_kernel_function.html +USER/atc/man_localized_lambda.html +USER/atc/man_lumped_lambda_solve.html +USER/atc/man_mask_direction.html +USER/atc/man_mass_matrix.html +USER/atc/man_material.html +USER/atc/man_mesh_add_to_nodeset.html +USER/atc/man_mesh_create.html +USER/atc/man_mesh_create_elementset.html +USER/atc/man_mesh_create_faceset_box.html +USER/atc/man_mesh_create_faceset_plane.html +USER/atc/man_mesh_create_nodeset.html +USER/atc/man_mesh_delete_elements.html +USER/atc/man_mesh_nodeset_to_elementset.html +USER/atc/man_mesh_output.html +USER/atc/man_mesh_quadrature.html +USER/atc/man_mesh_read.html +USER/atc/man_mesh_write.html +USER/atc/man_momentum_time_integration.html +USER/atc/man_output.html +USER/atc/man_output_elementset.html +USER/atc/man_output_nodeset.html +USER/atc/man_pair_interactions.html +USER/atc/man_poisson_solver.html +USER/atc/man_read_restart.html +USER/atc/man_remove_molecule.html +USER/atc/man_remove_source.html +USER/atc/man_remove_species.html +USER/atc/man_reset_atomic_reference_positions.html +USER/atc/man_reset_time.html +USER/atc/man_sample_frequency.html +USER/atc/man_set.html +USER/atc/man_source.html +USER/atc/man_source_integration.html +USER/atc/man_temperature_definition.html +USER/atc/man_thermal_time_integration.html +USER/atc/man_time_filter.html +USER/atc/man_track_displacement.html +USER/atc/man_unfix_flux.html +USER/atc/man_unfix_nodes.html +USER/atc/man_write_atom_weights.html +USER/atc/man_write_restart.html