Merge remote-tracking branch 'github/master' into adaptglok

# Conflicts:
#	doc/src/min_modify.rst

doc/src/Intro_features.rst

@@ -87,7 +87,7 @@ commands)
 * water potentials: TIP3P, TIP4P, SPC
 * implicit solvent potentials: hydrodynamic lubrication, Debye
 * force-field compatibility with common CHARMM, AMBER, DREIDING,     OPLS, GROMACS, COMPASS options
-* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim\_init, kim\_interactions, and kim\_query <kim_commands>` commands
+* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands
 * hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation
 * overlaid potentials: superposition of multiple pair potentials
 

doc/src/Packages_details.rst

@@ -927,7 +927,7 @@ Also several computes which calculate properties of rigid bodies.
 
 * src/RIGID: filenames -> commands
 * :doc:`compute erotate/rigid <compute_erotate_rigid>`
-* fix shake"_fix\_shake.html
+* :doc:`fix shake <fix_shake>`
 * :doc:`fix rattle <fix_shake>`
 * :doc:`fix rigid/\* <fix_rigid>`
 * examples/ASPHERE

doc/src/angle_cosine_buck6d.rst

@@ -46,9 +46,9 @@ internally.
 
 Additional to the cosine term the *cosine/buck6d* angle style computes
 the short range (vdW) interaction belonging to the
-:doc:`pair\_buck6d <pair_buck6d_coul_gauss>` between the end atoms of the
+:doc:`pair_style buck6d <pair_buck6d_coul_gauss>` between the end atoms of the
 angle.  For this reason this angle style only works in combination
-with the :doc:`pair\_buck6d <pair_buck6d_coul_gauss>` styles and needs
+with the :doc:`pair_style buck6d <pair_buck6d_coul_gauss>` styles and needs
 the :doc:`special_bonds <special_bonds>` 1-3 interactions to be weighted
 0.0 to prevent double counting.
 
@@ -61,7 +61,7 @@ Restrictions
 
 
 *cosine/buck6d* can only be used in combination with the
-:doc:`pair\_buck6d <pair_buck6d_coul_gauss>` style and with a
+:doc:`pair_style buck6d <pair_buck6d_coul_gauss>` style and with a
 :doc:`special_bonds <special_bonds>` 0.0 weighting of 1-3 interactions.
 
 This angle style can only be used if LAMMPS was built with the

doc/src/angle_cosine_shift.rst

@@ -83,6 +83,6 @@ Related commands
 """"""""""""""""
 
 :doc:`angle_coeff <angle_coeff>`,
-:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
+:doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>`
 
 **Default:** none

doc/src/angle_cosine_shift_exp.rst

@@ -94,7 +94,7 @@ Related commands
 """"""""""""""""
 
 :doc:`angle_coeff <angle_coeff>`,
-:doc:`angle\_cosine\_shift <angle_cosine_shift>`,
+:doc:`angle_style cosine/shift <angle_cosine_shift>`,
-:doc:`dihedral\_cosine\_shift\_exp <dihedral_cosine_shift_exp>`
+:doc:`dihedral_style cosine/shift/exp <dihedral_cosine_shift_exp>`
 
 **Default:** none

doc/src/bond_harmonic_shift_cut.rst

@@ -86,6 +86,6 @@ Related commands
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
 :doc:`bond_harmonic <bond_harmonic>`,
-:doc:`bond\_harmonic\_shift <bond_harmonic_shift>`
+:doc:`bond_style harmonic/shift <bond_harmonic_shift>`
 
 **Default:** none

doc/src/compute_fep.rst

@@ -301,7 +301,7 @@ Related commands
 """"""""""""""""
 
 :doc:`fix adapt/fep <fix_adapt_fep>`, :doc:`fix ave/time <fix_ave_time>`,
-:doc:`pair\_fep\_soft <pair_fep_soft>`
+:doc:`pair_style .../soft <pair_fep_soft>`
 
 Default
 """""""

doc/src/compute_hma.rst

@@ -54,19 +54,22 @@ effects, smaller timestep inaccuracy, faster equilibration and shorter
 decorrelation time.
 
 HMA should not be used if atoms are expected to diffuse.  It is also
-restricted to simulations in the NVT ensemble.  While this compute may be
+restricted to simulations in the NVT ensemble.  While this compute may
-used with any potential in LAMMPS, it will provide inaccurate results
+be used with any potential in LAMMPS, it will provide inaccurate results
 for potentials that do not go to 0 at the truncation distance;
-:doc:`pair\_lj\_smooth\_linear <pair_lj_smooth_linear>` and Ewald summation should
+:doc:`pair_style lj/smooth/linear <pair_lj_smooth_linear>` and Ewald
-work fine, while :doc:`pair_lj <pair_lj>` will perform poorly unless
+summation should work fine, while :doc:`pair_style lj/cut <pair_lj>`
-the potential is shifted (via :doc:`pair_modify <pair_modify>` shift) or the cutoff is large.  Furthermore, computation of the heat capacity with
+will perform poorly unless the potential is shifted (via
-this compute is restricted to those that implement the single\_hessian method
+:doc:`pair_modify <pair_modify>` shift) or the cutoff is large.
-in Pair.  Implementing single\_hessian in additional pair styles is simple.
+Furthermore, computation of the heat capacity with this compute is
-Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke (kofke at
+restricted to those that implement the *single\_hessian* method in Pair.
-buffalo.edu) if your desired pair style does not have this method.  This is
+Implementing *single\_hessian* in additional pair styles is simple.
-the list of pair styles that currently implement pair\_hessian:
+Please contact Andrew Schultz (ajs42 at buffalo.edu) and David Kofke
+(kofke at buffalo.edu) if your desired pair style does not have this
+method.  This is the list of pair styles that currently implement
+*single\_hessian*:
 
-* :doc:`lj\_smooth\_linear <pair_lj_smooth_linear>`
+* :doc:`pair_style lj/smooth/linear <pair_lj_smooth_linear>`
 
 
 In this method, the analytically known harmonic behavior of a crystal is removed from the traditional ensemble

doc/src/dihedral_cosine_shift_exp.rst

@@ -92,7 +92,7 @@ Related commands
 """"""""""""""""
 
 :doc:`dihedral_coeff <dihedral_coeff>`,
-:doc:`angle\_cosine\_shift\_exp <angle_cosine_shift_exp>`
+:doc:`angle_style cosine/shift/exp <angle_cosine_shift_exp>`
 
 **Default:** none
 

doc/src/fix_adapt_fep.rst

@@ -319,7 +319,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
+:doc:`compute fep <compute_fep>`, :doc:`fix adapt <fix_adapt>`, :doc:`compute ti <compute_ti>`, :doc:`pair_style \*/soft <pair_fep_soft>`
 
 Default
 """""""

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_bond_react.rst

@@ -390,7 +390,7 @@ the activation energy (:doc:`units <units>` of energy), and *seed* is a
 random number seed. The temperature is defined as the instantaneous
 temperature averaged over all atoms in the reaction site, and is
 calculated in the same manner as for example
-:doc:`compute\_temp\_chunk <compute_temp_chunk>`. Currently, there are no
+:doc:`compute temp/chunk <compute_temp_chunk>`. Currently, there are no
 options for additional temperature averaging or velocity-biased
 temperature calculations. A uniform random number between 0 and 1 is
 generated using *seed*\ ; if this number is less than the result of the

doc/src/fix_nh_uef.rst

@@ -89,14 +89,14 @@ in the LAMMPS frame. Only when the positions and velocities are
 updated is the system rotated to the flow frame, and it is rotated
 back to the LAMMPS frame immediately afterwards. For this reason, all
 vector-valued quantities (except for the tensors from
-:doc:`compute\_pressure/uef <compute_pressure_uef>` and
+:doc:`compute pressure/uef <compute_pressure_uef>` and
-:doc:`compute\_temp/uef <compute_temp_uef>`) will be computed in the
+:doc:`compute temp/uef <compute_temp_uef>`) will be computed in the
 LAMMPS frame. Rotationally invariant scalar quantities like the
 temperature and hydrostatic pressure are frame-invariant and will be
 computed correctly. Additionally, the system is in the LAMMPS frame
 during all of the output steps, and therefore trajectory files made
 using the dump command will be in the LAMMPS frame unless the
-:doc:`dump\_cfg/uef <dump_cfg_uef>` command is used.
+:doc:`dump cfg/uef <dump_cfg_uef>` command is used.
 
 
 ----------

doc/src/fix_precession_spin.rst

@@ -85,7 +85,7 @@ function for the same parameters.
 
 The temperature effects are accounted for by connecting the spin
 :math:`i` to a thermal bath using a Langevin thermostat (see
-:doc:`fix\_langevin\_spin <fix_langevin_spin>` for the definition of 
+:doc:`fix langevin/spin <fix_langevin_spin>` for the definition of 
 this thermostat).
 
 Style *anisotropy* is used to simulate an easy axis or an easy plane

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
+: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
+: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/min_modify.rst

@@ -121,7 +121,7 @@ quantities.
 
 The choice of a line search algorithm for the *spin/cg* and
 *spin/lbfgs* styles can be specified via the *line* keyword.  The
-*spin\_cubic* and *spin\_none* only make sense when one of those two
+*spin\_cubic* and *spin\_none* keywords only make sense when one of those two
 minimization styles is declared.  The *spin\_cubic* performs the line
 search based on a cubic interpolation of the energy along the search
 direction. The *spin\_none* keyword deactivates the line search
@@ -131,7 +131,7 @@ more robust if *spin\_cubic* line search is used.
 
 The Newton *integrator* used for *fire* minimization can be selected
 to be either the symplectic Euler (\ *eulerimplicit*\ ) or velocity
-Verlet (\ *verlet*\ ).  *tmax* define the maximum value for the
+Verlet (\ *verlet*\ ).  *tmax* defines the maximum value for the
 adaptive timestep during a *fire* minimization. It is a multiplication
 factor applied to the current :doc:`timestep <timestep>` (not in time
 unit). For example, *tmax* = 4.0 with a :doc:`timestep <timestep>` of
@@ -165,7 +165,7 @@ Restrictions
 
 
 For magnetic GNEB calculations, only *spin\_none* value for *line*
-keyword can be used when styles *spin/cg* and *spin/lbfgs* are
+keyword can be used when minimization styles *spin/cg* and *spin/lbfgs* are
 employed.  See :doc:`neb/spin <neb_spin>` for more explanation.
 
 Related commands

doc/src/min_spin.rst

@@ -70,14 +70,13 @@ discretization factor *discrete\_factor*.
 By default, style *spin/cg* does not employ the line search procedure 
 and uses the adaptive time-step technique in the same way as style *spin*\ .
 
-Style *spin/lbfgs* defines an orthogonal spin optimization
+Style *spin/lbfgs* defines an orthogonal spin optimization (OSO)
-(OSO) combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno 
+combined to a limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS)
-(L-BFGS) algorithm.
+algorithm.  By default, style *spin/lbfgs* does not employ line search
-By default, style *spin/lbfgs* does not employ line search procedure.
+procedure.  If the line search procedure is not used then the discrete
-If the line search procedure is not used then the discrete factor defines
+factor defines the maximum root mean squared rotation angle of spins by
-the maximum root mean squared rotation angle of spins by equation *pi/(5\*Kappa)*.
+equation *pi/(5\*Kappa)*.  The default value for Kappa is 10.  The
-The default value for Kappa is 10.
+*spin\_cubic* line search option can improve the convergence of the
-The *spin\_cubic* line search can improve the convergence of the 
 *spin/lbfgs* algorithm.
 
 The :doc:`min_modify <min_modify>` command can be used to

doc/src/neb_spin.rst

@@ -389,8 +389,9 @@ This command can only be used if LAMMPS was built with the SPIN
 package.  See the :doc:`Build package <Build_package>` doc
 page for more info.
 
-For magnetic GNEB calculations, only *spin\_none* value for *line* keyword can be used
+For magnetic GNEB calculations, only the *spin\_none* value for the
-when styles *spin/cg* and *spin/lbfgs* are employed.
+*line* keyword can be used when minimization styles *spin/cg* and
+*spin/lbfgs* are employed.
 
 
 ----------

doc/src/pair_class2.rst

@@ -133,7 +133,7 @@ cutoff distance.
 
 A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
 free energy calculations, is part of the USER-FEP package and is documented with
-the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
+the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is
 only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
 
 
@@ -203,7 +203,7 @@ LAMMPS was built with that package.  See the :doc:`Build package <Build_package>
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style */soft <pair_fep_soft>`
 
 **Default:** none
 

doc/src/pair_coul.rst

@@ -392,7 +392,7 @@ info.
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`pair\_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style, hybrid/overlay <pair_hybrid>`, :doc:`kspace_style <kspace_style>`
 
 **Default:** none
 

doc/src/pair_fep_soft.rst

@@ -193,7 +193,7 @@ and Coulomb potentials modified by a soft core, with the functional form
 The *lj/class2/soft* style is a 9-6 potential with the exponent of the
 denominator of the first term in brackets taking the value 1.5 instead of 2
 (other details differ, see the form of the potential in
-:doc:`pair\_class2 <pair_class2>`).
+:doc:`pair_style lj/class2 <pair_class2>`).
 
 Coulomb interactions can also be damped with a soft core at short distance,
 
@@ -255,14 +255,14 @@ optional cutoffs.
 
 Style *lj/charmm/coul/long/soft* implements a soft-core version of the modified
 12-6 LJ potential used in CHARMM and documented in the
-:doc:`pair\_lj\_charmm <pair_charmm>` style. In the soft version the parameters n,
+:doc:`pair_style lj/charmm/coul/long <pair_charmm>` style. In the soft version the parameters n,
 alpha\_LJ and alpha\_C are set in the :doc:`pair_style <pair_style>` command, before
 the global cutoffs. The activation parameter lambda is introduced as an argument
 of the :doc:`pair_coeff <pair_coeff>` command, after epsilon and sigma and
 before the optional eps14 and sigma14.
 
 Style *lj/class2/soft* implements a soft-core version of the 9-6 potential in
-:doc:`pair\_class2 <pair_class2>`. In the soft version the parameters n, alpha\_LJ
+:doc:`pair_style lj/class2 <pair_class2>`. In the soft version the parameters n, alpha\_LJ
 and alpha\_C are set in the :doc:`pair_style <pair_style>` command, before the
 global cutoffs. The activation parameter lambda is introduced as an argument of
 the the :doc:`pair_coeff <pair_coeff>` command, after epsilon and sigma and before

doc/src/pair_lj.rst

@@ -348,7 +348,7 @@ pair\_style command.
 
 A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
 free energy calculations, is part of the USER-FEP package and is documented with
-the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
+the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is
 only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
 
 

doc/src/pair_lj_long.rst

@@ -180,7 +180,7 @@ specified in the pair\_style command.
 
 A version of these styles with a soft core, *lj/cut/soft*\ , suitable for use in
 free energy calculations, is part of the USER-FEP package and is documented with
-the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is
+the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is
 only available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
 
 

doc/src/pair_modify.rst

@@ -13,18 +13,14 @@ Syntax
 
 * one or more keyword/value pairs may be listed
 * keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner*
-  or *tabinner/disp* or *tail* or *compute* or *nofdotr*
+  or *tabinner/disp* or *tail* or *compute* or *nofdotr* or *special* or 
+  *compute/tally*
   
   .. parsed-literal::
   
-       *pair* values = sub-style N *special* which wt1 wt2 wt3
+       *pair* value = sub-style N
-                    or sub-style N *compute/tally* flag
          sub-style = sub-style of :doc:`pair hybrid <pair_hybrid>`
-         N = which instance of sub-style (only if sub-style is used multiple times)
+         N = which instance of sub-style (1 to M), only specify if sub-style is used multiple times
-           *special* which wt1 wt2 wt3 = override *special_bonds* settings (optional)
-             which = *lj/coul* or *lj* or *coul*
-             w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
-           *compute/tally* flag = *yes* or *no*
        *mix* value = *geometric* or *arithmetic* or *sixthpower*
        *shift* value = *yes* or *no*
        *table* value = N
@@ -37,8 +33,11 @@ Syntax
          cutoff = inner cutoff at which to begin table (distance units)
        *tail* value = *yes* or *no*
        *compute* value = *yes* or *no*
-       *nofdotr*
+       *nofdotr* value = none
-
+       *special* values = which wt1 wt2 wt3
+          which = *lj/coul* or *lj* or *coul*
+          w1,w2,w3 = 1-2, 1-3, 1-4 weights from 0.0 to 1.0 inclusive
+       *compute/tally* value = *yes* or *no*
 
 
 Examples
@@ -53,47 +52,41 @@ Examples
    pair_modify pair lj/cut compute no
    pair_modify pair tersoff compute/tally no
    pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0
+   pair_modify pair lj/cut/coul/long special lj 0.0 0.0 0.5 special coul 0.0 0.0 0.8333333
 
 Description
 """""""""""
 
-Modify the parameters of the currently defined pair style.  Not all
+Modify the parameters of the currently defined pair style.  If the
-parameters are relevant to all pair styles.
+pair style is :doc:`hybrid or hybrid/overlay <pair_hybrid>`, then the
+specified parameters are by default modified for all the hybrid sub-styles.
 
-If used, the *pair* keyword must appear first in the list of keywords.
+.. note::
-It can only be used with the :doc:`hybrid and hybrid/overlay <pair_hybrid>` pair styles.  It means that all the
-following parameters will only be modified for the specified
-sub-style.  If the sub-style is defined multiple times, then an
-additional numeric argument *N* must also be specified, which is a
-number from 1 to M where M is the number of times the sub-style was
-listed in the :doc:`pair_style hybrid <pair_hybrid>` command.  The extra
-number indicates which instance of the sub-style the remaining
-keywords will be applied to.  Note that if the *pair* keyword is not
-used, and the pair style is *hybrid* or *hybrid/overlay*\ , then all the
-specified keywords will be applied to all sub-styles.
 
-The *special* and *compute/tally* keywords can **only** be used in
+  The behavior for hybrid pair styles can be changed by using the *pair*
-conjunction with the *pair* keyword and must directly follow it.
+  keyword, which allows selection of a specific sub-style to apply all
-*special* allows to override the
+  remaining keywords to.
-:doc:`special_bonds <special_bonds>` settings for the specified sub-style.
+  The *special* and *compute/tally* keywords can **only** be
-*compute/tally* allows to disable or enable registering
+  used in conjunction with the *pair* keyword.  See further details about
-:doc:`compute \*/tally <compute_tally>` computes for a given sub-style.
+  these 3 keywords below.
-More details are given below.
 
 The *mix* keyword affects pair coefficients for interactions between
 atoms of type I and J, when I != J and the coefficients are not
 explicitly set in the input script.  Note that coefficients for I = J
 must be set explicitly, either in the input script via the
-"pair\_coeff" command or in the "Pair Coeffs" section of the :doc:`data file <read_data>`.  For some pair styles it is not necessary to
+:doc:`pair_coeff <pair_coeff>` command or in the "Pair Coeffs" section of the
-specify coefficients when I != J, since a "mixing" rule will create
+:doc:`data file <read_data>`.  For some pair styles it is not
-them from the I,I and J,J settings.  The pair\_modify *mix* value
+necessary to specify coefficients when I != J, since a "mixing" rule
-determines what formulas are used to compute the mixed coefficients.
+will create them from the I,I and J,J settings.  The pair\_modify
-In each case, the cutoff distance is mixed the same way as sigma.
+*mix* value determines what formulas are used to compute the mixed
+coefficients.  In each case, the cutoff distance is mixed the same way
+as sigma.
 
-Note that not all pair styles support mixing.  Also, some mix options
+Note that not all pair styles support mixing and some mix options
-are not available for certain pair styles.  See the doc page for
+are not available for certain pair styles. Also, there are additional
-individual pair styles for those restrictions.  Note also that the
+restrictions when using :doc:`pair style hybrid or hybrid/overlay <pair_hybrid>`.
-:doc:`pair_coeff <pair_coeff>` command also can be to directly set
+See the doc page for individual pair styles for those restrictions.  Note also that the
+:doc:`pair_coeff <pair_coeff>` command also can be used to directly set
 coefficients for a specific I != J pairing, in which case no mixing is
 performed.
 
@@ -135,10 +128,11 @@ see the doc page for individual styles to see which potentials support
 these options.  If N is non-zero, a table of length 2\^N is
 pre-computed for forces and energies, which can shrink their
 computational cost by up to a factor of 2.  The table is indexed via a
-bit-mapping technique :ref:`(Wolff) <Wolff1>` and a linear interpolation is
+bit-mapping technique :ref:`(Wolff) <Wolff1>` and a linear
-performed between adjacent table values.  In our experiments with
+interpolation is performed between adjacent table values.  In our
-different table styles (lookup, linear, spline), this method typically
+experiments with different table styles (lookup, linear, spline), this
-gave the best performance in terms of speed and accuracy.
+method typically gave the best performance in terms of speed and
+accuracy.
 
 The choice of table length is a tradeoff in accuracy versus speed.  A
 larger N yields more accurate force computations, but requires more
@@ -162,27 +156,28 @@ pairwise interactions are computed via table lookup for simulations
 with "real" units, but some close pairs may be computed directly
 (non-table) for simulations with "lj" units.
 
-When the *tail* keyword is set to *yes*\ , certain pair styles will add
+When the *tail* keyword is set to *yes*\ , certain pair styles will
-a long-range VanderWaals tail "correction" to the energy and pressure.
+add a long-range VanderWaals tail "correction" to the energy and
-These corrections are bookkeeping terms which do not affect dynamics,
+pressure.  These corrections are bookkeeping terms which do not affect
-unless a constant-pressure simulation is being performed.  See the doc
+dynamics, unless a constant-pressure simulation is being performed.
-page for individual styles to see which support this option.  These
+See the doc page for individual styles to see which support this
-corrections are included in the calculation and printing of
+option.  These corrections are included in the calculation and
-thermodynamic quantities (see the :doc:`thermo_style <thermo_style>`
+printing of thermodynamic quantities (see the :doc:`thermo_style
-command).  Their effect will also be included in constant NPT or NPH
+<thermo_style>` command).  Their effect will also be included in
-simulations where the pressure influences the simulation box
+constant NPT or NPH simulations where the pressure influences the
-dimensions (e.g. the :doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`
+simulation box dimensions (e.g. the :doc:`fix npt <fix_nh>` and
-commands).  The formulas used for the long-range corrections come from
+:doc:`fix nph <fix_nh>` commands).  The formulas used for the
-equation 5 of :ref:`(Sun) <Sun>`.
+long-range corrections come from equation 5 of :ref:`(Sun) <Sun>`.
 
 .. note::
 
    The tail correction terms are computed at the beginning of each
    run, using the current atom counts of each atom type.  If atoms are
-   deleted (or lost) or created during a simulation, e.g. via the :doc:`fix gcmc <fix_gcmc>` command, the correction factors are not
+   deleted (or lost) or created during a simulation, e.g. via the
-   re-computed.  If you expect the counts to change dramatically, you can
+   :doc:`fix gcmc <fix_gcmc>` command, the correction factors are not
-   break a run into a series of shorter runs so that the correction
+   re-computed.  If you expect the counts to change dramatically, you
-   factors are re-computed more frequently.
+   can break a run into a series of shorter runs so that the
+   correction factors are re-computed more frequently.
 
 Several additional assumptions are inherent in using tail corrections,
 including the following:
@@ -191,26 +186,27 @@ including the following:
   should not be used for systems that are non-liquid, 2d, have a slab
   geometry (only 2d periodic), or inhomogeneous.
 * G(r), the radial distribution function (rdf), is unity beyond the
-  cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
+  cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for
-  LJ fluid), and it is probably a good idea to verify this assumption by
+  an LJ fluid), and it is probably a good idea to verify this
-  checking the rdf.  The rdf is not exactly unity beyond the cutoff for
+  assumption by checking the rdf.  The rdf is not exactly unity beyond
-  each pair of interaction types, so the tail correction is necessarily
+  the cutoff for each pair of interaction types, so the tail
-  an approximation.
+  correction is necessarily an approximation.
 
-  The tail corrections are computed at the beginning of each simulation
+  The tail corrections are computed at the beginning of each
-  run.  If the number of atoms changes during the run, e.g. due to atoms
+  simulation run.  If the number of atoms changes during the run,
-  leaving the simulation domain, or use of the :doc:`fix gcmc <fix_gcmc>`
+  e.g. due to atoms leaving the simulation domain, or use of the
-  command, then the corrections are not updated to reflect the changed
+  :doc:`fix gcmc <fix_gcmc>` command, then the corrections are not
-  atom count.  If this is a large effect in your simulation, you should
+  updated to reflect the changed atom count.  If this is a large
-  break the long run into several short runs, so that the correction
+  effect in your simulation, you should break the long run into
-  factors are re-computed multiple times.
+  several short runs, so that the correction factors are re-computed
+  multiple times.
 
-* Thermophysical properties obtained from calculations with this option
+* Thermophysical properties obtained from calculations with this
-  enabled will not be thermodynamically consistent with the truncated
+  option enabled will not be thermodynamically consistent with the
-  force-field that was used.  In other words, atoms do not feel any LJ
+  truncated force-field that was used.  In other words, atoms do not
-  pair interactions beyond the cutoff, but the energy and pressure
+  feel any LJ pair interactions beyond the cutoff, but the energy and
-  reported by the simulation include an estimated contribution from
+  pressure reported by the simulation include an estimated
-  those interactions.
+  contribution from those interactions.
 
 
 The *compute* keyword allows pairwise computations to be turned off,
@@ -225,53 +221,73 @@ a simulation with :doc:`pair_style hybrid <pair_hybrid>` with only a
 subset of the hybrid sub-styles enabled.  Second, this option allows
 you to perform a simulation with only long-range interactions but no
 short-range pairwise interactions.  Doing this by simply not defining
-a pair style will not work, because the
+a pair style will not work, because the :doc:`kspace_style
-:doc:`kspace_style <kspace_style>` command requires a Kspace-compatible
+<kspace_style>` command requires a Kspace-compatible pair style be
-pair style be defined.
+defined.
 
 The *nofdotr* keyword allows to disable an optimization that computes
-the global stress tensor from the total forces and atom positions rather
+the global stress tensor from the total forces and atom positions
-than from summing forces between individual pairs of atoms.
+rather than from summing forces between individual pairs of atoms.
 
 
 ----------
 
+The *pair* keyword can only be used with the :doc:`hybrid and
+hybrid/overlay <pair_hybrid>` pair styles.  If used, it must appear
+first in the list of keywords.
 
-The *special* keyword allows to override the 1-2, 1-3, and 1-4
+Its meaning is that all the following parameters will only be modified
-exclusion settings for individual sub-styles of a
+for the specified sub-style.  If the sub-style is defined multiple
-:doc:`hybrid pair style <pair_hybrid>`. It requires 4 arguments similar
+times, then an additional numeric argument *N* must also be specified,
-to the :doc:`special_bonds <special_bonds>` command, *which* and
+which is a number from 1 to M where M is the number of times the
-wt1,wt2,wt3.  The *which* argument can be *lj* to change the
+sub-style was listed in the :doc:`pair_style hybrid <pair_hybrid>`
-Lennard-Jones settings, *coul* to change the Coulombic settings,
+command.  The extra number indicates which instance of the sub-style
-or *lj/coul* to change both to the same set of 3 values.  The wt1,wt2,wt3
+the remaining keywords will be applied to.
-values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
+
-1-3, and 1-4 bond topology neighbors, respectively. The *special*
+The *special* and *compute/tally* keywords can **only** be used in
-keyword can only be used in conjunction with the *pair* keyword
+conjunction with the *pair* keyword and they must directly follow it.
-and has to directly follow it.  This option is not compatible with
+I.e. any other keyword, must appear after *pair*, *special*, and
-pair styles from the GPU or the USER-INTEL package and attempting
+*compute/tally*.
-it will cause an error.
+
+The *special* keyword overrides the global :doc:`special_bonds <special_bonds>`
+1-2, 1-3, 1-4 exclusion settings (weights) for the sub-style selected
+by the *pair* keyword.
+
+Similar to the :doc:`special_bonds <special_bonds>` command, it takes
+4 arguments.  The *which* argument can be *lj* to change only the
+non-Coulomb weights (e.g. Lennard-Jones or Buckingham), *coul* to change
+only the Coulombic settings, or *lj/coul* to change both to the same
+values.  The *wt1,wt2,wt3* values are numeric weights from 0.0 to 1.0
+inclusive, for the 1-2, 1-3, and 1-4 bond topology neighbors, respectively.
+The *special* keyword can be used multiple times, e.g. to set the *lj*
+and *coul* settings to different values.
 
 .. note::
 
-   The global settings specified by the
+   The *special* keyword is not compatible with pair styles from the
-   :doc:`special_bonds <special_bonds>` command affect the construction of
+   GPU or the USER-INTEL package and attempting to use it will cause
-   neighbor lists.  Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
+   an error.
-   exclude those pairs from the neighbor list entirely.  Weights of 1.0
-   store the neighbor with no weighting applied. Thus only global values
-   different from exactly 0.0 or 1.0 can be overridden and an error is
-   generated if the requested setting is not compatible with the global
-   setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
-   usually a sufficient workaround in this case without causing a
-   significant error.
-
-The *compute/tally* keyword takes exactly 1 argument (\ *no* or *yes*\ ),
-and allows to selectively disable or enable processing of the various
-:doc:`compute \*/tally <compute_tally>` styles for a given
-:doc:`pair hybrid or hybrid/overlay <pair_hybrid>` sub-style.
 
 .. note::
 
-   Any "pair\_modify pair compute/tally" command must be issued
+   Weights of exactly 0.0 or 1.0 in the :doc:`special_bonds <special_bonds>`
+   command have implications on the neighbor list construction, which
+   means that they cannot be overridden by using the *special* keyword.
+   One workaround for this restriction is to use the :doc:`special_bonds <special_bonds>`
+   command with weights like 1.0e-10 or 0.999999999 instead of 0.0 or 1.0,
+   respectively, which enables to reset each them to any value between 0.0
+   and 1.0 inclusively.  Otherwise you can set **all** global weights to
+   an arbitrary number between 0.0 or 1.0, like 0.5, and then you have
+   to override **all** *special* settings for **all** sub-styles which use
+   the 1-2, 1-3, and 1-4 exclusion weights in their force/energy computation.
+
+The *compute/tally* keyword disables or enables registering :doc:`compute
+\*/tally <compute_tally>` computes for the sub-style specified by
+the *pair* keyword.  Use *no* to disable, or *yes* to enable.
+
+.. note::
+
+   The "pair_modify pair compute/tally" command must be issued
    **before** the corresponding compute style is defined.
 
 
@@ -290,7 +306,7 @@ Related commands
 """"""""""""""""
 
 :doc:`pair_style <pair_style>`, :doc:`pair_style hybrid <pair_hybrid>`,
-pair\_coeff"_pair\_coeff.html, :doc:`thermo_style <thermo_style>`,
+:doc:`pair_coeff <pair_coeff>`, :doc:`thermo_style <thermo_style>`,
 :doc:`compute \*/tally <compute_tally>`
 
 Default

doc/src/pair_morse.rst

@@ -95,7 +95,7 @@ the *morse* and *morse/smooth/linear* styles.
 
 A version of the *morse* style with a soft core, *morse/soft*\ , suitable for use in
 free energy calculations, is part of the USER-FEP package and is documented with
-the :doc:`pair\_fep\_soft <pair_fep_soft>` styles. The version with soft core is only
+the :doc:`pair_style */soft <pair_fep_soft>` styles. The version with soft core is only
 available if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
 
 
@@ -160,7 +160,7 @@ built with the USER-MISC package.  See the :doc:`Build package <Build_package>`
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`pair\_fep\_soft <pair_fep_soft>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style */soft <pair_fep_soft>`
 
 **Default:** none
 

doc/src/pair_spin_exchange.rst

@@ -55,7 +55,7 @@ in :ref:`(Tranchida) <Tranchida3>`.
 
 From this exchange interaction, each spin :math:`i` will be submitted
 to a magnetic torque :math:`\vec{\omega}`, and its associated atom can be submitted to a
-force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
+force :math:`\vec{F}` for spin-lattice calculations (see :doc:`fix nve/spin <fix_nve_spin>`),
 such as:
 
 .. math::

doc/src/pair_spin_magelec.rst

@@ -41,7 +41,7 @@ direction of a screened dielectric atomic polarization (in eV).
 
 From this magneto-electric interaction, each spin i will be submitted
 to a magnetic torque omega, and its associated atom can be submitted to a
-force F for spin-lattice calculations (see :doc:`fix\_nve\_spin <fix_nve_spin>`),
+force F for spin-lattice calculations (see :doc:`fix nve/spin <fix_nve_spin>`),
 such as:
 
 .. image:: Eqs/pair_spin_me_forces.jpg
@@ -68,7 +68,7 @@ Related commands
 """"""""""""""""
 
 :doc:`atom_style spin <atom_style>`, :doc:`pair_coeff <pair_coeff>`,
-:doc:`pair\_spin\_exchange <pair_spin_exchange>`, :doc:`pair_eam <pair_eam>`,
+:doc:`pair_style spin/exchange <pair_spin_exchange>`, :doc:`pair_eam <pair_eam>`,
 
 **Default:** none
 

doc/src/pair_thole.rst

@@ -53,7 +53,7 @@ describes how to use the :doc:`thermalized Drude oscillator model <Howto_drude>`
 discussed on the :doc:`Howto polarizable <Howto_polarizable>` doc page.
 
 The *thole* pair style should be used as a sub-style within in the
-:doc:`pair\_hybrid/overlay <pair_hybrid>` command, in conjunction with a
+:doc:`pair_style hybrid/overlay <pair_hybrid>` command, in conjunction with a
 main pair style including Coulomb interactions, i.e. any pair style
 containing *coul/cut* or *coul/long* in its style name.
 

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

doc/src/set.rst

@@ -359,9 +359,9 @@ particles must be ellipsoids as defined by the :doc:`atom_style ellipsoid <atom_
 of the particles is set to the 3 specified components.
 
 Keyword *omega* sets the angular velocity of selected atoms.  The
-particles must be spheres as defined by the "atom\_style sphere"_
+particles must be spheres as defined by the
-atom\_style.html command.  The angular velocity vector of the particles
+:doc:`atom_style sphere <atom_style>` command.  The angular velocity
-is set to the 3 specified components.
+vector of the particles is set to the 3 specified components.
 
 Keyword *mass* sets the mass of all selected particles.  The particles
 must have a per-atom mass attribute, as defined by the

doc/src/temper_grem.rst

@@ -14,7 +14,7 @@ Syntax
 * N = total # of timesteps to run
 * M = attempt a tempering swap every this many steps
 * lambda = initial lambda for this ensemble
-* fix-ID = ID of fix\_grem
+* fix-ID = ID of *fix grem*
 * thermostat-ID = ID of the thermostat that controls kinetic temperature
 * seed1 = random # seed used to decide on adjacent temperature to partner with
 * seed2 = random # seed for Boltzmann factor in Metropolis swap

src/USER-CGDNA/bond_oxdna_fene.cpp

@@ -221,7 +221,7 @@ void BondOxdnaFene::compute(int eflag, int vflag)
               TAGINT_FORMAT " " TAGINT_FORMAT " %g",
               update->ntimestep,atom->tag[a],atom->tag[b],r);
       error->warning(FLERR,str,0);
-      if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
+      if (rlogarg <= -8.0) error->one(FLERR,"Bad FENE bond");
     }
 
     fbond = -k[type]*rr0/rlogarg/Deltasq/r;
@@ -421,7 +421,7 @@ double BondOxdnaFene::single(int type, double rsq, int /*i*/, int /*j*/,
     sprintf(str,"FENE bond too long: " BIGINT_FORMAT " %g",
             update->ntimestep,sqrt(rsq));
     error->warning(FLERR,str,0);
-    if (rlogarg <= -3.0) error->one(FLERR,"Bad FENE bond");
+    if (rlogarg <= -8.0) error->one(FLERR,"Bad FENE bond");
   }
 
   double eng = -0.5 * k[type]*log(rlogarg);

src/kspace.cpp

@@ -286,7 +286,7 @@ void KSpace::qsum_qsq(int warning_flag)
   double qsum_local(0.0), qsqsum_local(0.0);
 
 #if defined(_OPENMP)
-#pragma omp parallel for default(none) reduction(+:qsum_local,qsqsum_local)
+#pragma omp parallel for default(shared) reduction(+:qsum_local,qsqsum_local)
 #endif
   for (int i = 0; i < nlocal; i++) {
     qsum_local += q[i];

src/neighbor.cpp

@@ -402,13 +402,6 @@ void Neighbor::init()
     }
   }
 
-  // maxwt = max multiplicative factor on atom indices stored in neigh list
-
-  maxwt = 0;
-  if (special_flag[1] == 2) maxwt = 2;
-  if (special_flag[2] == 2) maxwt = 3;
-  if (special_flag[3] == 2) maxwt = 4;
-
   // ------------------------------------------------------------------
   // xhold array
 

src/neighbor.h

@@ -166,7 +166,6 @@ class Neighbor : protected Pointers {
 
   int maxatom;                     // max size of atom-based NeighList arrays
   int maxrequest;                  // max size of NeighRequest list
-  int maxwt;                       // max weighting factor applied + 1
 
   // info for other Neigh classes: NBin,NStencil,NPair,NTopo
 

src/pair_hybrid.cpp

@@ -859,14 +859,17 @@ void PairHybrid::modify_params(int narg, char **arg)
       iarg = 3;
     }
 
-    // if 2nd keyword (after pair) is special:
+    // keywords "special" and "compute/tally" have to be listed directly
-    // invoke modify_special() for the sub-style
+    // after "pair" but can be given multiple times
+
+again:
 
     if (iarg < narg && strcmp(arg[iarg],"special") == 0) {
       if (narg < iarg+5)
         error->all(FLERR,"Illegal pair_modify special command");
       modify_special(m,narg-iarg,&arg[iarg+1]);
       iarg += 5;
+      goto again;
     }
 
     // if 2nd keyword (after pair) is compute/tally:
@@ -881,11 +884,13 @@ void PairHybrid::modify_params(int narg, char **arg)
         compute_tally[m] = 0;
       } else error->all(FLERR,"Illegal pair_modify compute/tally command");
       iarg += 2;
+      goto again;
     }
 
-    // apply the remaining keywords to the base pair style itself and the
+    // apply the remaining keywords to the base pair style itself and
-    // sub-style except for "pair" and "special".
+    // the sub-style except for "pair" and "special" or "compute/tally"
-    // the former is important for some keywords like "tail" or "compute"
+    // and their arguments. the former is important for some keywords
+    // like "tail" or "compute"
 
     if (narg-iarg > 0) {
       Pair::modify_params(narg-iarg,&arg[iarg]);

src/random_mars.cpp

@@ -183,7 +183,7 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
   int mode,index,oldindex,newvalue,nflip,which,niter;
   int active[2],first[2],last[2];
   int newactive[2],newfirst[2],newlast[2];
-  bigint nmark,nactive,nactiveall,nflipall,bnflip;
+  bigint nmark,nflipall;
   bigint activeall[2],bsum[3],bsumall[3];
   double thresh;
 
@@ -210,15 +210,12 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
 
     // choose to ADD or SUBTRACT from current nmark
     // thresh = desired flips / size of active set
-    // nactive = size of current active set, only for debug output below
 
     if (ntarget-nmark > 0) {
       mode = ADD;
-      // nactive = active[mode];
       thresh = 1.0 * (ntarget-nmark) / activeall[mode];
     } else {
       mode = SUBTRACT;
-      // nactive = active[mode];
       thresh = 1.0 * (nmark-ntarget) / activeall[mode];
     }
 
@@ -278,12 +275,10 @@ void RanMars::select_subset(bigint ntarget, int nmine, int *mark, int *next)
     bsum[0] = nflip;
     bsum[1] = active[0];
     bsum[2] = active[1];
-    bsum[3] = nactive;
+    MPI_Allreduce(&bsum,&bsumall,3,MPI_LMP_BIGINT,MPI_SUM,world);
-    MPI_Allreduce(&bsum,&bsumall,4,MPI_LMP_BIGINT,MPI_SUM,world);
     nflipall = bsumall[0];
     activeall[0] = bsumall[1];
     activeall[1] = bsumall[2];
-    nactiveall = bsumall[3];
 
     if (mode == ADD) nmark += nflipall;
     else if (mode == SUBTRACT) nmark -= nflipall;