remove some more unneeded backslash escapes and fix up a few more doc links

doc/src/fix_atc.rst

@@ -143,97 +143,97 @@ Related commands
 
 After specifying this fix in your input script, several other :doc:`fix_modify <fix_modify>` commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.
 
-fix\_modify commands for setup:
+*fix\_modify* commands for setup:
 
-* `fix\_modify AtC mesh create <USER/atc/man_mesh_create.html>`_
+* `fix_modify AtC mesh create <USER/atc/man_mesh_create.html>`_
-* `fix\_modify AtC mesh quadrature <USER/atc/man_mesh_quadrature.html>`_
+* `fix_modify AtC mesh quadrature <USER/atc/man_mesh_quadrature.html>`_
-* `fix\_modify AtC mesh read <USER/atc/man_mesh_read.html>`_
+* `fix_modify AtC mesh read <USER/atc/man_mesh_read.html>`_
-* `fix\_modify AtC mesh write <USER/atc/man_mesh_write.html>`_
+* `fix_modify AtC mesh write <USER/atc/man_mesh_write.html>`_
-* `fix\_modify AtC mesh create\_nodeset <USER/atc/man_mesh_create_nodeset.html>`_
+* `fix_modify AtC mesh create_nodeset <USER/atc/man_mesh_create_nodeset.html>`_
-* `fix\_modify AtC mesh add\_to\_nodeset <USER/atc/man_mesh_add_to_nodeset.html>`_
+* `fix_modify AtC mesh add_to_nodeset <USER/atc/man_mesh_add_to_nodeset.html>`_
-* `fix\_modify AtC mesh create\_faceset box <USER/atc/man_mesh_create_faceset_box.html>`_
+* `fix_modify AtC mesh create_faceset box <USER/atc/man_mesh_create_faceset_box.html>`_
-* `fix\_modify AtC mesh create\_faceset plane <USER/atc/man_mesh_create_faceset_plane.html>`_
+* `fix_modify AtC mesh create_faceset plane <USER/atc/man_mesh_create_faceset_plane.html>`_
-* `fix\_modify AtC mesh create\_elementset <USER/atc/man_mesh_create_elementset.html>`_
+* `fix_modify AtC mesh create_elementset <USER/atc/man_mesh_create_elementset.html>`_
-* `fix\_modify AtC mesh delete\_elements <USER/atc/man_mesh_delete_elements.html>`_
+* `fix_modify AtC mesh delete_elements <USER/atc/man_mesh_delete_elements.html>`_
-* `fix\_modify AtC mesh nodeset\_to\_elementset <USER/atc/man_mesh_nodeset_to_elementset.html>`_
+* `fix_modify AtC mesh nodeset_to_elementset <USER/atc/man_mesh_nodeset_to_elementset.html>`_
-* `fix\_modify AtC boundary <USER/atc/man_boundary.html>`_
+* `fix_modify AtC boundary <USER/atc/man_boundary.html>`_
-* `fix\_modify AtC internal\_quadrature <USER/atc/man_internal_quadrature.html>`_
+* `fix_modify AtC internal_quadrature <USER/atc/man_internal_quadrature.html>`_
-* `fix\_modify AtC time\_integration (thermal) <USER/atc/man_thermal_time_integration.html>`_
+* `fix_modify AtC time_integration (thermal) <USER/atc/man_thermal_time_integration.html>`_
-* `fix\_modify AtC time\_integration (momentum) <USER/atc/man_momentum_time_integration.html>`_
+* `fix_modify AtC time_integration (momentum) <USER/atc/man_momentum_time_integration.html>`_
-* `fix\_modify AtC extrinsic electron\_integration <USER/atc/man_electron_integration.html>`_
+* `fix_modify AtC extrinsic electron_integration <USER/atc/man_electron_integration.html>`_
-* `fix\_modify AtC internal\_element\_set <USER/atc/man_internal_element_set.html>`_
+* `fix_modify AtC internal_element_set <USER/atc/man_internal_element_set.html>`_
-* `fix\_modify AtC decomposition <USER/atc/man_decomposition.html>`_
+* `fix_modify AtC decomposition <USER/atc/man_decomposition.html>`_
 
-fix\_modify commands for boundary and initial conditions:
+*fix\_modify* commands for boundary and initial conditions:
 
-* `fix\_modify AtC initial <USER/atc/man_initial.html>`_
+* `fix_modify AtC initial <USER/atc/man_initial.html>`_
-* `fix\_modify AtC fix <USER/atc/man_fix_nodes.html>`_
+* `fix_modify AtC fix <USER/atc/man_fix_nodes.html>`_
-* `fix\_modify AtC unfix <USER/atc/man_unfix_nodes.html>`_
+* `fix_modify AtC unfix <USER/atc/man_unfix_nodes.html>`_
-* `fix\_modify AtC fix\_flux <USER/atc/man_fix_flux.html>`_
+* `fix_modify AtC fix_flux <USER/atc/man_fix_flux.html>`_
-* `fix\_modify AtC unfix\_flux <USER/atc/man_unfix_flux.html>`_
+* `fix_modify AtC unfix_flux <USER/atc/man_unfix_flux.html>`_
-* `fix\_modify AtC source <USER/atc/man_source.html>`_
+* `fix_modify AtC source <USER/atc/man_source.html>`_
-* `fix\_modify AtC remove\_source <USER/atc/man_remove_source.html>`_
+* `fix_modify AtC remove_source <USER/atc/man_remove_source.html>`_
 
-fix\_modify commands for control and filtering:
+*fix\_modify* commands for control and filtering:
 
-* `fix\_modify AtC control <USER/atc/man_control.html>`_
+* `fix_modify AtC control <USER/atc/man_control.html>`_
-* `fix\_modify AtC control thermal <USER/atc/man_control_thermal.html>`_
+* `fix_modify AtC control thermal <USER/atc/man_control_thermal.html>`_
-* `fix\_modify AtC control thermal correction\_max\_iterations <USER/atc/man_control_thermal_correction_max_iterations.html>`_
+* `fix_modify AtC control thermal correction_max_iterations <USER/atc/man_control_thermal_correction_max_iterations.html>`_
-* `fix\_modify AtC control momentum <USER/atc/man_control_momentum.html>`_
+* `fix_modify AtC control momentum <USER/atc/man_control_momentum.html>`_
-* `fix\_modify AtC control localized\_lambda <USER/atc/man_localized_lambda.html>`_
+* `fix_modify AtC control localized_lambda <USER/atc/man_localized_lambda.html>`_
-* `fix\_modify AtC control lumped\_lambda\_solve <USER/atc/man_lumped_lambda_solve.html>`_
+* `fix_modify AtC control lumped_lambda_solve <USER/atc/man_lumped_lambda_solve.html>`_
-* `fix\_modify AtC control mask\_direction <USER/atc/man_mask_direction.html>`_ control
+* `fix_modify AtC control mask_direction <USER/atc/man_mask_direction.html>`_ control
-* `fix\_modify AtC filter <USER/atc/man_time_filter.html>`_
+* `fix_modify AtC filter <USER/atc/man_time_filter.html>`_
-* `fix\_modify AtC filter scale <USER/atc/man_filter_scale.html>`_
+* `fix_modify AtC filter scale <USER/atc/man_filter_scale.html>`_
-* `fix\_modify AtC filter type <USER/atc/man_filter_type.html>`_
+* `fix_modify AtC filter type <USER/atc/man_filter_type.html>`_
-* `fix\_modify AtC equilibrium\_start <USER/atc/man_equilibrium_start.html>`_
+* `fix_modify AtC equilibrium_start <USER/atc/man_equilibrium_start.html>`_
-* `fix\_modify AtC extrinsic exchange <USER/atc/man_extrinsic_exchange.html>`_
+* `fix_modify AtC extrinsic exchange <USER/atc/man_extrinsic_exchange.html>`_
-* `fix\_modify AtC poisson\_solver <USER/atc/man_poisson_solver.html>`_
+* `fix_modify AtC poisson_solver <USER/atc/man_poisson_solver.html>`_
 
-fix\_modify commands for output:
+*fix\_modify* commands for output:
 
-* `fix\_modify AtC output <USER/atc/man_output.html>`_
+* `fix_modify AtC output <USER/atc/man_output.html>`_
-* `fix\_modify AtC output nodeset <USER/atc/man_output_nodeset.html>`_
+* `fix_modify AtC output nodeset <USER/atc/man_output_nodeset.html>`_
-* `fix\_modify AtC output elementset <USER/atc/man_output_elementset.html>`_
+* `fix_modify AtC output elementset <USER/atc/man_output_elementset.html>`_
-* `fix\_modify AtC output boundary\_integral <USER/atc/man_boundary_integral.html>`_
+* `fix_modify AtC output boundary_integral <USER/atc/man_boundary_integral.html>`_
-* `fix\_modify AtC output contour\_integral <USER/atc/man_contour_integral.html>`_
+* `fix_modify AtC output contour_integral <USER/atc/man_contour_integral.html>`_
-* `fix\_modify AtC mesh output <USER/atc/man_mesh_output.html>`_
+* `fix_modify AtC mesh output <USER/atc/man_mesh_output.html>`_
-* `fix\_modify AtC write\_restart <USER/atc/man_write_restart.html>`_
+* `fix_modify AtC write_restart <USER/atc/man_write_restart.html>`_
-* `fix\_modify AtC read\_restart <USER/atc/man_read_restart.html>`_
+* `fix_modify AtC read_restart <USER/atc/man_read_restart.html>`_
 
-fix\_modify commands for post-processing:
+*fix\_modify* commands for post-processing:
 
-* `fix\_modify AtC kernel <USER/atc/man_hardy_kernel.html>`_
+* `fix_modify AtC kernel <USER/atc/man_hardy_kernel.html>`_
-* `fix\_modify AtC fields <USER/atc/man_hardy_fields.html>`_
+* `fix_modify AtC fields <USER/atc/man_hardy_fields.html>`_
-* `fix\_modify AtC grdients <USER/atc/man_hardy_gradients.html>`_
+* `fix_modify AtC grdients <USER/atc/man_hardy_gradients.html>`_
-* `fix\_modify AtC rates <USER/atc/man_hardy_rates.html>`_
+* `fix_modify AtC rates <USER/atc/man_hardy_rates.html>`_
-* `fix\_modify AtC computes <USER/atc/man_hardy_computes.html>`_
+* `fix_modify AtC computes <USER/atc/man_hardy_computes.html>`_
-* `fix\_modify AtC on\_the\_fly <USER/atc/man_hardy_on_the_fly.html>`_
+* `fix_modify AtC on_the_fly <USER/atc/man_hardy_on_the_fly.html>`_
-* `fix\_modify AtC pair\_interactions/bond\_interactions <USER/atc/man_pair_interactions.html>`_
+* `fix_modify AtC pair_interactions/bond_interactions <USER/atc/man_pair_interactions.html>`_
-* `fix\_modify AtC sample\_frequency <USER/atc/man_sample_frequency.html>`_
+* `fix_modify AtC sample_frequency <USER/atc/man_sample_frequency.html>`_
-* `fix\_modify AtC set <USER/atc/man_set.html>`_
+* `fix_modify AtC set <USER/atc/man_set.html>`_
 
-miscellaneous fix\_modify commands:
+miscellaneous *fix\_modify* commands:
 
-* `fix\_modify AtC atom\_element\_map <USER/atc/man_atom_element_map.html>`_
+* `fix_modify AtC atom_element_map <USER/atc/man_atom_element_map.html>`_
-* `fix\_modify AtC atom\_weight <USER/atc/man_atom_weight.html>`_
+* `fix_modify AtC atom_weight <USER/atc/man_atom_weight.html>`_
-* `fix\_modify AtC write\_atom\_weights <USER/atc/man_write_atom_weights.html>`_
+* `fix_modify AtC write_atom_weights <USER/atc/man_write_atom_weights.html>`_
-* `fix\_modify AtC reset\_time <USER/atc/man_reset_time.html>`_
+* `fix_modify AtC reset_time <USER/atc/man_reset_time.html>`_
-* `fix\_modify AtC reset\_atomic\_reference\_positions <USER/atc/man_reset_atomic_reference_positions.html>`_
+* `fix_modify AtC reset_atomic_reference_positions <USER/atc/man_reset_atomic_reference_positions.html>`_
-* `fix\_modify AtC fe\_md\_boundary <USER/atc/man_fe_md_boundary.html>`_
+* `fix_modify AtC fe_md_boundary <USER/atc/man_fe_md_boundary.html>`_
-* `fix\_modify AtC boundary\_faceset <USER/atc/man_boundary_faceset.html>`_
+* `fix_modify AtC boundary_faceset <USER/atc/man_boundary_faceset.html>`_
-* `fix\_modify AtC consistent\_fe\_initialization <USER/atc/man_consistent_fe_initialization.html>`_
+* `fix_modify AtC consistent_fe_initialization <USER/atc/man_consistent_fe_initialization.html>`_
-* `fix\_modify AtC mass\_matrix <USER/atc/man_mass_matrix.html>`_
+* `fix_modify AtC mass_matrix <USER/atc/man_mass_matrix.html>`_
-* `fix\_modify AtC material <USER/atc/man_material.html>`_
+* `fix_modify AtC material <USER/atc/man_material.html>`_
-* `fix\_modify AtC atomic\_charge <USER/atc/man_atomic_charge.html>`_
+* `fix_modify AtC atomic_charge <USER/atc/man_atomic_charge.html>`_
-* `fix\_modify AtC source\_integration <USER/atc/man_source_integration.html>`_
+* `fix_modify AtC source_integration <USER/atc/man_source_integration.html>`_
-* `fix\_modify AtC temperature\_definition <USER/atc/man_temperature_definition.html>`_
+* `fix_modify AtC temperature_definition <USER/atc/man_temperature_definition.html>`_
-* `fix\_modify AtC track\_displacement <USER/atc/man_track_displacement.html>`_
+* `fix_modify AtC track_displacement <USER/atc/man_track_displacement.html>`_
-* `fix\_modify AtC boundary\_dynamics <USER/atc/man_boundary_dynamics.html>`_
+* `fix_modify AtC boundary_dynamics <USER/atc/man_boundary_dynamics.html>`_
-* `fix\_modify AtC add\_species <USER/atc/man_add_species.html>`_
+* `fix_modify AtC add_species <USER/atc/man_add_species.html>`_
-* `fix\_modify AtC add\_molecule <USER/atc/man_add_molecule.html>`_
+* `fix_modify AtC add_molecule <USER/atc/man_add_molecule.html>`_
-* `fix\_modify AtC remove\_species <USER/atc/man_remove_species.html>`_
+* `fix_modify AtC remove_species <USER/atc/man_remove_species.html>`_
-* `fix\_modify AtC remove\_molecule <USER/atc/man_remove_molecule.html>`_
+* `fix_modify AtC remove_molecule <USER/atc/man_remove_molecule.html>`_
 
 Note: a set of example input files with the attendant material files are included with this package
 

doc/src/fix_wall_gran.rst

@@ -83,17 +83,18 @@ close enough to touch it.
 
 The nature of the wall/particle interactions are determined by the
 *fstyle* setting.  It can be any of the styles defined by the
-:doc:`pair_style gran/\* <pair_gran>` or the more general `pair\_style granular <pair_granular.html">`_ commands.  Currently the options are
+:doc:`pair_style gran/\* <pair_gran>` or the more general
-*hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and
+:doc:`pair_style granular <pair_granular>` commands.  Currently the
-*granular* with all the possible options of the associated
+options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the
+former, and *granular* with all the possible options of the associated
 *pair\_coeff* command for the latter.  The equation for the force
 between the wall and particles touching it is the same as the
 corresponding equation on the :doc:`pair_style gran/\* <pair_gran>` and
 :doc:`pair_style granular <pair_granular>` doc pages, in the limit of
-one of the two particles going to infinite radius and mass (flat
+one of the two particles going to infinite radius and mass (flat wall).
-wall).  Specifically, delta = radius - r = overlap of particle with
+Specifically, delta = radius - r = overlap of particle with wall, m\_eff
-wall, m\_eff = mass of particle, and the effective radius of contact =
+= mass of particle, and the effective radius of contact = RiRj/Ri+Rj is
-RiRj/Ri+Rj is set to the radius of the particle.
+set to the radius of the particle.
 
 The parameters *Kn*\ , *Kt*\ , *gamma\_n*, *gamma\_t*, *xmu* and *dampflag*
 have the same meaning and units as those specified with the

doc/src/fix_wall_gran_region.rst

@@ -154,15 +154,16 @@ corresponding manner.
 
 The nature of the wall/particle interactions are determined by the
 *fstyle* setting.  It can be any of the styles defined by the
-:doc:`pair_style gran/\* <pair_gran>` or the more general `pair\_style granular <pair_granular.html">`_ commands.  Currently the options are
+:doc:`pair_style gran/\* <pair_gran>` or the more general
-*hooke*\ , *hooke/history*\ , or *hertz/history* for the former, and
+:doc:`pair_style granular <pair_granular>` commands.  Currently the
-*granular* with all the possible options of the associated
+options are *hooke*\ , *hooke/history*\ , or *hertz/history* for the
+former, and *granular* with all the possible options of the associated
 *pair\_coeff* command for the latter.  The equation for the force
 between the wall and particles touching it is the same as the
 corresponding equation on the :doc:`pair_style gran/\* <pair_gran>` and
 :doc:`pair_style granular <pair_granular>` doc pages, but the effective
-radius is calculated using the radius of the particle and the radius
+radius is calculated using the radius of the particle and the radius of
-of curvature of the wall at the contact point.
+curvature of the wall at the contact point.
 
 Specifically, delta = radius - r = overlap of particle with wall,
 m\_eff = mass of particle, and RiRj/Ri+Rj is the effective radius, with

doc/src/rerun.rst

@@ -115,13 +115,13 @@ However if you specify a series of dump files in an incorrect order
 (with respect to the timesteps they contain), you may skip large
 numbers of snapshots
 
-Note that the dump files specified as part of the *dump* keyword can
+Note that the dump files specified as part of the *dump* keyword can be
-be parallel files, i.e. written as multiple files either per processor
+parallel files, i.e. written as multiple files either per processor
 and/or per snapshot.  If that is the case they will also be read in
 parallel which can make the rerun command operate dramatically faster
-for large systems.  See the doc page for the `read\_dump <read_dump>`_ and
+for large systems.  See the doc page for the :doc:`read_dump
-:doc:`dump <dump>` commands which describe how to read and write
+<read_dump>` and :doc:`dump <dump>` commands which describe how to read
-parallel dump files.
+and write parallel dump files.
 
 The *first*\ , *last*\ , *every*\ , *skip* keywords determine which
 snapshots are read from the dump file(s).  Snapshots are skipped until