diff --git a/doc/Manual.pdf b/doc/Manual.pdf index 9124db8a3b..2f395c578f 100644 Binary files a/doc/Manual.pdf and b/doc/Manual.pdf differ diff --git a/doc/lammps.book b/doc/lammps.book index e72adeb703..f7f96bf1b3 100644 --- a/doc/lammps.book +++ b/doc/lammps.book @@ -14,58 +14,96 @@ accelerate_omp.html accelerate_opt.html Section_howto.html Section_example.html -tutorial_drude.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 -box.html +bond_coeff.html +bond_style.html +bond_write.html boundary.html +box.html change_box.html clear.html -comm_style.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 -minimize.html -min_style.html min_modify.html +min_style.html +minimize.html molecule.html neb.html -neighbor.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 @@ -75,47 +113,32 @@ suffix.html tad.html temper.html thermo.html -thermo_style.html thermo_modify.html -timestep.html +thermo_style.html timer.html +timestep.html +uncompute.html +undump.html +unfix.html units.html variable.html velocity.html -read_data.html -write_data.html write_coeff.html -restart.html -read_restart.html -write_restart.html -dump.html -undump.html -dump_modify.html -dump_custom_vtk.html -dump_h5md.html -dump_image.html -dump_molfile.html -rerun.html -read_dump.html +write_data.html write_dump.html -atom_style.html -body.html -atom_modify.html -kspace_style.html -kspace_modify.html -fix.html -unfix.html -fix_modify.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_chunk.html fix_ave_histo.html fix_ave_time.html fix_aveforce.html @@ -128,14 +151,15 @@ fix_colvars.html fix_deform.html fix_deposit.html fix_drag.html -fix_drude_transform.html fix_drude.html -fix_eos_cv.html -fix_eos_table.html -fix_langevin_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_freeze.html @@ -145,9 +169,10 @@ fix_gle.html fix_gravity.html fix_heat.html fix_imd.html -fix_ipi.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 @@ -156,9 +181,6 @@ fix_lb_rigid_pc_sphere.html fix_lb_viscous.html fix_lineforce.html fix_manifoldforce.html -fix_nve_manifold_rattle.html -fix_nvt_manifold_rattle.html -manifolds.html fix_meso.html fix_meso_stationary.html fix_momentum.html @@ -175,22 +197,24 @@ fix_npt_asphere.html fix_npt_body.html fix_npt_sphere.html fix_nve.html -fix_nve_eff.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_fcc.html +fix_orient.html fix_phonon.html fix_pimd.html fix_planeforce.html @@ -205,14 +229,15 @@ fix_qeq_comb.html fix_qeq_reax.html fix_qmmm.html fix_qtb.html -fix_reaxc_bonds.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_saed_vtk.html fix_shardlow.html fix_smd.html fix_smd_adjust_dt.html @@ -223,6 +248,7 @@ fix_smd_setvel.html fix_smd_tlsph_reference_configuration.html fix_smd_wall_surface.html fix_spring.html +fix_spring_chunk.html fix_spring_rg.html fix_spring_self.html fix_srd.html @@ -237,135 +263,130 @@ fix_thermal_conductivity.html fix_ti_rs.html fix_ti_spring.html fix_tmd.html -fix_tune_kspace.html fix_ttm.html +fix_tune_kspace.html fix_vector.html fix_viscosity.html fix_viscous.html -fix_wall_gran.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.html -uncompute.html -compute_modify.html -compute_group_group.html -compute_pair.html -compute_angle.html -compute_bond.html -compute_dihedral.html -compute_improper.html -compute_pair_local.html -compute_body_local.html -compute_angle_local.html -compute_dihedral_local.html -compute_improper_local.html -compute_property_local.html -compute_chunk_atom.html -compute_angmom_chunk.html -compute_com_chunk.html -compute_dipole_chunk.html -compute_gyration_chunk.html -compute_inertia_chunk.html -compute_msd_chunk.html -compute_omega_chunk.html -compute_property_chunk.html -compute_temp_chunk.html -compute_torque_chunk.html -compute_vcm_chunk.html -compute_com.html -compute_dpd.html -compute_erotate_asphere.html -compute_erotate_sphere.html -compute_erotate_rigid.html -compute_event_displace.html -compute_fep.html -compute_gyration.html -compute_heat_flux.html -compute_ke.html -compute_msd.html -compute_pe.html -compute_msd_nongauss.html -compute_pressure.html -compute_rdf.html -compute_reduce.html -compute_slice.html -compute_saed.html -compute_property_atom.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_eff.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_sna_atom.html -compute_stress_atom.html -compute_voronoi_atom.html -compute_xrd.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_rate.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_rate.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_rate.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_temp_eff.html -compute_temp_deform_eff.html -compute_temp_region_eff.html compute_ti.html +compute_torque_chunk.html compute_vacf.html -pair_style.html -pair_modify.html -pair_write.html -pair_none.html -pair_zero.html +compute_vcm_chunk.html +compute_voronoi_atom.html +compute_xrd.html + pair_adp.html pair_airebo.html pair_awpmd.html @@ -378,7 +399,6 @@ pair_buck.html pair_buck_long.html pair_charmm.html pair_class2.html -pair_coeff.html pair_colloid.html pair_comb.html pair_coul.html @@ -392,6 +412,7 @@ 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 @@ -400,9 +421,9 @@ pair_hbond_dreiding.html pair_hybrid.html pair_kim.html pair_lcbop.html +pair_line_lj.html pair_list.html pair_lj.html -pair_line_lj.html pair_lj96.html pair_lj_cubic.html pair_lj_expand.html @@ -413,7 +434,6 @@ pair_lj_smooth_linear.html pair_lj_soft.html pair_lubricate.html pair_lubricateU.html -pair_nb3b_harmonic.html pair_mdf.html pair_meam.html pair_meam_spline.html @@ -422,20 +442,24 @@ 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_snap.html -pair_soft.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 @@ -445,6 +469,7 @@ 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 @@ -454,28 +479,24 @@ pair_vashishta.html pair_yukawa.html pair_yukawa_colloid.html pair_zbl.html -bond_style.html -bond_write.html -bond_none.html -bond_zero.html +pair_zero.html + bond_class2.html -bond_coeff.html -bond_fene_expand.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 -angle_style.html -angle_none.html -angle_zero.html +bond_zero.html + angle_charmm.html angle_class2.html -angle_coeff.html angle_cosine.html angle_cosine_delta.html angle_cosine_periodic.html @@ -487,15 +508,14 @@ 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 -dihedral_style.html -dihedral_none.html -dihedral_zero.html +angle_zero.html + dihedral_charmm.html dihedral_class2.html -dihedral_coeff.html dihedral_cosine_shift_exp.html dihedral_fourier.html dihedral_harmonic.html @@ -503,101 +523,102 @@ 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 -improper_style.html -improper_none.html -improper_zero.html +dihedral_zero.html + improper_class2.html -improper_coeff.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 -fix_atc.html -USER/atc/man_poisson_solver.html -USER/atc/man_atom_element_map.html -USER/atc/man_pair_interactions.html -USER/atc/man_output_nodeset.html -USER/atc/man_mesh_write.html -USER/atc/man_set.html -USER/atc/man_localized_lambda.html -USER/atc/man_mesh_delete_elements.html -USER/atc/man_internal_atom_integrate.html -USER/atc/man_mesh_create_faceset_plane.html -USER/atc/man_boundary_faceset.html -USER/atc/man_control.html -USER/atc/man_control_thermal.html -USER/atc/man_source.html -USER/atc/man_material.html -USER/atc/man_write_restart.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_track_displacement.html -USER/atc/man_unfix_flux.html -USER/atc/man_mesh_output.html -USER/atc/man_hardy_on_the_fly.html -USER/atc/man_contour_integral.html -USER/atc/man_fem_mesh.html -USER/atc/man_electron_integration.html -USER/atc/man_remove_source.html -USER/atc/man_time_filter.html -USER/atc/man_write_atom_weights.html -USER/atc/man_mesh_read.html -USER/atc/man_extrinsic_exchange.html -USER/atc/man_mesh_create_nodeset.html -USER/atc/man_source_integration.html -USER/atc/man_kernel_function.html -USER/atc/man_lumped_lambda_solve.html -USER/atc/man_reset_atomic_reference_positions.html -USER/atc/man_boundary_dynamics.html -USER/atc/man_mesh_nodeset_to_elementset.html -USER/atc/man_mass_matrix.html -USER/atc/man_atom_weight.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_boundary_integral.html -USER/atc/man_output.html -USER/atc/man_atomic_charge.html -USER/atc/man_read_restart.html -USER/atc/man_remove_species.html -USER/atc/man_control_momentum.html -USER/atc/man_filter_scale.html -USER/atc/man_sample_frequency.html -USER/atc/man_internal_quadrature.html -USER/atc/man_fe_md_boundary.html -USER/atc/man_add_species.html -USER/atc/man_mesh_quadrature.html -USER/atc/man_momentum_time_integration.html -USER/atc/man_thermal_time_integration.html -USER/atc/man_mesh_add_to_nodeset.html -USER/atc/man_internal_element_set.html -USER/atc/man_mesh_create_elementset.html -USER/atc/man_fix_atc.html -USER/atc/man_initial.html -USER/atc/man_equilibrium_start.html -USER/atc/man_unfix_nodes.html -USER/atc/man_reset_time.html -USER/atc/man_consistent_fe_initialization.html -USER/atc/man_mask_direction.html -USER/atc/man_mesh_create.html -USER/atc/man_temperature_definition.html -USER/atc/man_hardy_fields.html +USER/atc/man_hardy_on_the_fly.html USER/atc/man_hardy_rates.html -USER/atc/man_output_elementset.html -USER/atc/man_boundary.html -USER/atc/man_filter_type.html -USER/atc/man_hardy_computes.html -USER/atc/man_remove_molecule.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_decomposition.html -tutorial_github.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 + diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt index 07e11aa98e..dc2b0e3fa9 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/manifolds.txt @@ -6,11 +6,20 @@ :line -[Description:] +Manifolds (surfacse) :h3 -Below is a list of currently supported manifolds, their parameters and a short description of them. -The parameters listed here are in the same order as they should be passed to the relevant fixes. +[Overview:] +This doc page is not about a LAMMPS input script command, but about +manifolds, which are generalized surfaces, as defined and used by the +USER-MANIFOLD package, to track particle motion on the manifolds. See +the src/USER-MANIFOLD/README file for more details about the package +and its commands. + +Below is a list of currently supported manifolds by the USER-MANIFOLD +package, their parameters and a short description of them. The +parameters listed here are in the same order as they should be passed +to the relevant fixes. {manifold} || {parameters} || {equation} || {description} cylinder || R || x^2 + y^2 - R^2 = 0 || Cylinder along z-axis, axis going through (0,0,0) diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt index fba45f7f07..eb60c6b006 100644 --- a/doc/src/pair_modify.txt +++ b/doc/src/pair_modify.txt @@ -207,8 +207,6 @@ pair style be defined. :line -Use of {special} keyword :h5 - The {special} keyword allows to override the 1-2, 1-3, and 1-4 exclusion settings for individual sub-styles of a "hybrid pair style"_pair_hybrid.html. It requires 4 arguments similar diff --git a/doc/src/tutorial_github.txt b/doc/src/tutorial_github.txt index 941cabd6d0..06f15df874 100644 --- a/doc/src/tutorial_github.txt +++ b/doc/src/tutorial_github.txt @@ -6,19 +6,19 @@ :line -LAMMPS GitHub tutorial :h2 -written by Stefan Paquay :h3 +LAMMPS GitHub tutorial :h3 +[written by Stefan Paquay] :line -This document briefly describes how to use GitHub to merge changes -into LAMMPS using GitHub. It assumes that you are familiar with +This document briefly describes how to use GitHub to merge changes you +make into LAMMPS, using GitHub. It assumes that you are familiar with git. You may want to have a look at the "Git book"_http://git-scm.com/book/ to reacquaint yourself. :line -Making an account :h2 +[Making an account] First of all, you need a GitHub account. This is fairly simple, just go to "GitHub"_https://github.com and create an account by clicking @@ -28,7 +28,7 @@ username or e-mail address and password. :line -Forking the repository :h2 +[Forking the repository] To get changes into LAMMPS, you need to first fork the repository. At the time of writing, LAMMPS-ICMS is the preferred fork. Go to "LAMMPS @@ -49,12 +49,12 @@ can include changes from upstream into your repository. :line -Adding changes to your own fork :h2 +[Adding changes to your own fork] Before adding changes, it is better to first create a new branch that will contain these changes, a so-called feature branch. -Feature branches :h3 +[Feature branches] Since LAMMPS is such a big project and most user contributions come in small portions, the most ideal workflow for LAMMPS is the so-called @@ -111,7 +111,7 @@ After the files are added, the change should be comitted: The "-m" switch is used to add a message to the commit. Use this to indicate what type of change was commited. -Wisdom by Axel: :h4 +[Wisdom by Axel] {"Do not use "git commit -a". the -a flag will automatically include *all* modified or new files. mercurial does that and it find it @@ -176,7 +176,7 @@ request. :line -Additional changes :h2 +[Additional changes] Before the pull request is accepted, any additional changes you push into your repository will automatically become part of the pull @@ -184,7 +184,7 @@ request. :line -After a merge :h2 +[After a merge] When everything is fine the feature branch is merged into the LAMMPS repositories: