git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15409 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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
+write_data.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_dump.html
-atom_style.html
+write_restart.html
-body.html
+
-atom_modify.html
-kspace_style.html
-kspace_modify.html
-fix.html
-unfix.html
-fix_modify.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_drude_transform.html
-fix_eos_table.html
-fix_langevin_drude.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_pressure.html
-compute_stress_atom.html
+compute_property_atom.html
-compute_voronoi_atom.html
+compute_property_chunk.html
-compute_xrd.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
+compute_vcm_chunk.html
-pair_modify.html
+compute_voronoi_atom.html
-pair_write.html
+compute_xrd.html
-pair_none.html
+
-pair_zero.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
+pair_zero.html
-bond_write.html
+
-bond_none.html
-bond_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
+bond_zero.html
-angle_none.html
+
-angle_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
+angle_zero.html
-dihedral_none.html
+
-dihedral_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
+dihedral_zero.html
-improper_none.html
+
-improper_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_hardy_computes.html
-USER/atc/man_unfix_flux.html
+USER/atc/man_hardy_fields.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_gradients.html
 USER/atc/man_hardy_kernel.html
-USER/atc/man_boundary_integral.html
+USER/atc/man_hardy_on_the_fly.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_rates.html
-USER/atc/man_output_elementset.html
+USER/atc/man_initial.html
-USER/atc/man_boundary.html
+USER/atc/man_internal_atom_integrate.html
-USER/atc/man_filter_type.html
+USER/atc/man_internal_element_set.html
-USER/atc/man_hardy_computes.html
+USER/atc/man_internal_quadrature.html
-USER/atc/man_remove_molecule.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
+USER/atc/man_mesh_create_faceset_plane.html
-tutorial_github.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
+
 

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.
+[Overview:]
-The parameters listed here are in the same order as they should be passed to the relevant fixes.
 
+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)

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

doc/src/tutorial_github.txt

@@ -6,19 +6,19 @@
 
 :line
 
-LAMMPS GitHub tutorial :h2
+LAMMPS GitHub tutorial :h3
-written by Stefan Paquay :h3
+[written by Stefan Paquay]
 
 :line
 
-This document briefly describes how to use GitHub to merge changes
+This document briefly describes how to use GitHub to merge changes you
-into LAMMPS using GitHub. It assumes that you are familiar with
+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: