general rename of files, styles, and keywords from "reax/c", "reax", or "reaxc" to "reaxff"

cmake/Modules/Packages/OPENMP.cmake

@@ -25,15 +25,15 @@
   endif()
 
   if(PKG_REAXFF)
-    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_forces_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
-                                 ${OPENMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxff_bond_orders_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_hydrogen_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_nonbonded_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_init_md_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_torsion_angles_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_forces_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_multi_body_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_valence_angles_omp.cpp)
   endif()
 
   target_sources(lammps PRIVATE ${OPENMP_SOURCES})

doc/src/Commands_fix.rst

@@ -179,14 +179,14 @@ OPT.
    * :doc:`qeq/dynamic <fix_qeq>`
    * :doc:`qeq/fire <fix_qeq>`
    * :doc:`qeq/point <fix_qeq>`
-   * :doc:`qeq/reax (ko) <fix_qeq_reax>`
+   * :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
    * :doc:`qeq/shielded <fix_qeq>`
    * :doc:`qeq/slater <fix_qeq>`
    * :doc:`qmmm <fix_qmmm>`
    * :doc:`qtb <fix_qtb>`
    * :doc:`rattle <fix_shake>`
-   * :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
-   * :doc:`reax/c/species (k) <fix_reaxc_species>`
+   * :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
+   * :doc:`reaxff/species (k) <fix_reaxff_species>`
    * :doc:`recenter <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
    * :doc:`rhok <fix_rhok>`

doc/src/Commands_pair.rst

@@ -235,7 +235,7 @@ OPT.
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
    * :doc:`rann <pair_rann>`
-   * :doc:`reax/c (ko) <pair_reaxc>`
+   * :doc:`reaxff (ko) <pair_reaxff>`
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`resquared (go) <pair_resquared>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

doc/src/Errors_warnings.rst

@@ -514,7 +514,7 @@ This will most likely cause errors in kinetic fluctuations.
    will integrate the body motion, but it would be more efficient to use
    fix rigid.
 
-*Not using real units with pair reax*
+*Not using real units with pair reaxff*
    This is most likely an error, unless you have created your own ReaxFF
    parameter file in a different set of units.
 
@@ -805,5 +805,3 @@ This will most likely cause errors in kinetic fluctuations.
 *Using pair tail corrections with pair_modify compute no*
    The tail corrections will thus not be computed.
 
-*pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c*
-   Self-explanatory.

doc/src/Packages_details.rst

@@ -2274,10 +2274,10 @@ for monitoring molecules as bonds are created and destroyed.
 
 * src/REAXFF: filenames -> commands
 * src/REAXFF/README
-* :doc:`pair_style reax/c <pair_reaxc>`
-* :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
-* :doc:`fix reax/c/species <fix_reaxc_species>`
-* examples/reax
+* :doc:`pair_style reaxff <pair_reaxff>`
+* :doc:`fix reaxff/bonds <fix_reaxff_bonds>`
+* :doc:`fix reaxff/species <fix_reaxff_species>`
+* examples/reaxff
 
 ----------
 

doc/src/Packages_list.rst

@@ -370,7 +370,7 @@ whether an extra library is needed to build and use the package:
      - no
    * - :ref:`REAXFF <PKG-REAXFF>`
      - ReaxFF potential (C/C++)
-     - :doc:`pair_style reaxc <pair_reaxc>`
+     - :doc:`pair_style reaxff <pair_reaxff>`
      - reax
      - no
    * - :ref:`REPLICA <PKG-REPLICA>`

doc/src/Tools.rst

@@ -76,7 +76,6 @@ Post-processing tools
    * :ref:`phonon <phonon>`
    * :ref:`pymol_asphere <pymol>`
    * :ref:`python <pythontools>`
-   * :ref:`reax <reax_tool>`
    * :ref:`replica <replica>`
    * :ref:`smd <smd>`
    * :ref:`spin <spin>`
@@ -947,20 +946,6 @@ while at the Shell lab at UC Santa Barbara. (tanmoy dot 7989 at gmail.com)
 
 ----------
 
-.. _reax_tool:
-
-reax tool
---------------------------
-
-The reax sub-directory contains stand-alone codes that can
-post-process the output of the :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
-command from a LAMMPS simulation using :doc:`ReaxFF <pair_reaxc>`.  See
-the README.txt file for more info.
-
-These tools were written by Aidan Thompson at Sandia.
-
-----------
-
 .. _smd:
 
 smd tool

doc/src/compute_pair.rst

@@ -24,7 +24,7 @@ Examples
    compute 1 all pair gauss
    compute 1 all pair lj/cut/coul/cut ecoul
    compute 1 all pair tersoff 2 epair
-   compute 1 all pair reax/c
+   compute 1 all pair reaxff
 
 Description
 """""""""""
@@ -64,7 +64,8 @@ is stored as a global scalar.
    :doc:`pair_modify <pair_modify>` command.
 
 Some pair styles tally additional quantities, e.g. a breakdown of
-potential energy into 14 components is tallied by the :doc:`pair_style reax/c <pair_reaxc>` command.  These values (1 or more)
+potential energy into 14 components is tallied by the
+:doc:`pair_style reaxff <pair_reaxff>` command.  These values (1 or more)
 are stored as a global vector by this compute.  See the doc page for
 :doc:`individual pair styles <pair_style>` for info on these values.
 

doc/src/fix.rst

@@ -322,14 +322,14 @@ accelerated styles exist.
 * :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method
 * :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
 * :doc:`qeq/point <fix_qeq>` - charge equilibration via point method
-* :doc:`qeq/reax <fix_qeq_reax>` - charge equilibration for ReaxFF potential
+* :doc:`qeq/reaxff <fix_qeq_reaxff>` - charge equilibration for ReaxFF potential
 * :doc:`qeq/shielded <fix_qeq>` - charge equilibration via shielded method
 * :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method
 * :doc:`qmmm <fix_qmmm>` - functionality to enable a quantum mechanics/molecular mechanics coupling
 * :doc:`qtb <fix_qtb>` - implement quantum thermal bath scheme
 * :doc:`rattle <fix_shake>` - RATTLE constraints on bonds and/or angles
-* :doc:`reax/c/bonds <fix_reaxc_bonds>` - write out ReaxFF bond information
-* :doc:`reax/c/species <fix_reaxc_species>` - write out ReaxFF molecule information
+* :doc:`reaxff/bonds <fix_reaxff_bonds>` - write out ReaxFF bond information
+* :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information
 * :doc:`recenter <fix_recenter>` - constrain the center-of-mass position of a group of atoms
 * :doc:`restrain <fix_restrain>` - constrain a bond, angle, dihedral
 * :doc:`rhok <fix_rhok>` - add bias potential for long-range ordered systems

doc/src/fix_adapt.rst

@@ -186,7 +186,7 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>`                           | E0,R0,m,n,coulombic_cutoff                       | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`reax/c <pair_reaxc>`                                                   | chi, eta, gamma                                  | type global |
+| :doc:`reaxff <pair_reaxff>`                                                  | chi, eta, gamma                                  | type global |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`snap <pair_snap>`                                                      | scale                                            | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+

doc/src/fix_gcmc.rst

@@ -374,7 +374,7 @@ in the context of NVT dynamics.
    has been reached.
 
 With some pair_styles, such as :doc:`Buckingham <pair_buck>`,
-:doc:`Born-Mayer-Huggins <pair_born>` and :doc:`ReaxFF <pair_reaxc>`, two
+:doc:`Born-Mayer-Huggins <pair_born>` and :doc:`ReaxFF <pair_reaxff>`, two
 atoms placed close to each other may have an arbitrary large, negative
 potential energy due to the functional form of the potential.  While
 these unphysical configurations are inaccessible to typical dynamical

doc/src/fix_qeq.rst

@@ -32,7 +32,7 @@ Syntax
 * cutoff = global cutoff for charge-charge interactions (distance unit)
 * tolerance = precision to which charges will be equilibrated
 * maxiter = maximum iterations to perform charge equilibration
-* qfile = a filename with QEq parameters or *coul/streitz* or *reax/c*
+* qfile = a filename with QEq parameters or *coul/streitz* or *reaxff*
 * zero or more keyword/value pairs may be appended
 * keyword = *alpha* or *qdamp* or *qstep* or *warn*
 
@@ -91,11 +91,11 @@ on the current atom configuration), then remove the fix via the
 
    The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used to
    perform charge equilibration with the :doc:`COMB potential
-   <pair_comb>`.  The :doc:`fix qeq/reax <fix_qeq_reax>` command can be
+   <pair_comb>`.  The :doc:`fix qeq/reaxff <fix_qeq_reaxff>` command can be
    used to perform charge equilibration with the :doc:`ReaxFF force
-   field <pair_reaxc>`, although fix qeq/shielded yields the same
-   results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
-   are the same.  Eventually the fix qeq/reax command will be
+   field <pair_reaxff>`, although fix qeq/shielded yields the same
+   results as fix qeq/reaxff if *Nevery*\ , *cutoff*\ , and *tolerance*
+   are the same.  Eventually the fix qeq/reaxff command will be
    deprecated.
 
 The QEq method minimizes the electrostatic energy of the system (or
@@ -150,11 +150,11 @@ interaction between a pair of charged particles.  Interaction through
 the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force
 field <vanDuin>` paper.  The shielding accounts for charge overlap
 between charged particles at small separation.  This style is the same
-as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with
-:doc:`pair_style reax/c <pair_reaxc>`.  Only the *chi*\ , *eta*\ , and
+as :doc:`fix qeq/reaxff <fix_qeq_reaxff>`, and can be used with
+:doc:`pair_style reaxff <pair_reaxff>`.  Only the *chi*\ , *eta*\ , and
 *gamma* parameters from the *qfile* file are used. When using the string
-*reax/c* as filename, these parameters are extracted directly from an
-active *reax/c* pair style.  This style solves partial charges on atoms
+*reaxff* as filename, these parameters are extracted directly from an
+active *reaxff* pair style.  This style solves partial charges on atoms
 via the matrix inversion method.  A tolerance of 1.0e-6 is usually a
 good number.
 
@@ -235,7 +235,7 @@ The qeq fixes are not compatible with the GPU and USER-INTEL packages.
 Related commands
 """"""""""""""""
 
-:doc:`fix qeq/reax <fix_qeq_reax>`, :doc:`fix qeq/comb <fix_qeq_comb>`
+:doc:`fix qeq/reaxff <fix_qeq_reaxff>`, :doc:`fix qeq/comb <fix_qeq_comb>`
 
 Default
 """""""

doc/src/fix_qeq_comb.rst

@@ -41,7 +41,7 @@ Perform charge equilibration (QeQ) in conjunction with the COMB
 equilibration portion of the calculation using the so-called QEq
 method, whereby the charge on each atom is adjusted to minimize the
 energy of the system.  This fix can only be used with the COMB
-potential; see the :doc:`fix qeq/reax <fix_qeq_reax>` command for a QeQ
+potential; see the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` command for a QeQ
 calculation that can be used with any potential.
 
 Only charges on the atoms in the specified group are equilibrated.

doc/src/fix_qeq_reaxff.rst

@@ -1,31 +1,31 @@
-.. index:: fix qeq/reax
-.. index:: fix qeq/reax/kk
-.. index:: fix qeq/reax/omp
+.. index:: fix qeq/reaxff
+.. index:: fix qeq/reaxff/kk
+.. index:: fix qeq/reaxff/omp
 
-fix qeq/reax command
-====================
+fix qeq/reaxff command
+======================
 
-Accelerator Variants: *qeq/reax/kk*, *qeq/reax/omp*
+Accelerator Variants: *qeq/reaxff/kk*, *qeq/reaxff/omp*
 
 Syntax
 """"""
 
 .. parsed-literal::
 
-   fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args
+   fix ID group-ID qeq/reaxff Nevery cutlo cuthi tolerance params args
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* qeq/reax = style name of this fix command
+* qeq/reaxff = style name of this fix command
 * Nevery = perform QEq every this many steps
 * cutlo,cuthi = lo and hi cutoff for Taper radius
 * tolerance = precision to which charges will be equilibrated
-* params = reax/c or a filename
+* params = reaxff or a filename
 * one or more keywords or keyword/value pairs may be appended
 
   .. parsed-literal::
 
      keyword = *dual* or *maxiter* or *nowarn*
-       *dual* = process S and T matrix in parallel (only for qeq/reax/omp)
+       *dual* = process S and T matrix in parallel (only for qeq/reaxff/omp)
        *maxiter* N = limit the number of iterations to *N*
        *nowarn* = do not print a warning message if the maximum number of iterations was reached
 
@@ -34,8 +34,8 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
-   fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq maxiter 500
+   fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
+   fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 param.qeq maxiter 500
 
 Description
 """""""""""
@@ -43,19 +43,19 @@ Description
 Perform the charge equilibration (QEq) method as described in
 :ref:`(Rappe and Goddard) <Rappe2>` and formulated in :ref:`(Nakano)
 <Nakano2>`.  It is typically used in conjunction with the ReaxFF force
-field model as implemented in the :doc:`pair_style reax/c <pair_reaxc>`
+field model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
 command, but it can be used with any potential in LAMMPS, so long as it
 defines and uses charges on each atom.  The :doc:`fix qeq/comb
 <fix_qeq_comb>` command should be used to perform charge equilibration
 with the :doc:`COMB potential <pair_comb>`.  For more technical details
-about the charge equilibration performed by fix qeq/reax, see the
+about the charge equilibration performed by fix qeq/reaxff, see the
 :ref:`(Aktulga) <qeq-Aktulga>` paper.
 
 The QEq method minimizes the electrostatic energy of the system by
 adjusting the partial charge on individual atoms based on interactions
 with their neighbors.  It requires some parameters for each atom type.
-If the *params* setting above is the word "reax/c", then these are
-extracted from the :doc:`pair_style reax/c <pair_reaxc>` command and
+If the *params* setting above is the word "reaxff", then these are
+extracted from the :doc:`pair_style reaxff <pair_reaxff>` command and
 the ReaxFF force field file it reads in.  If a file name is specified
 for *params*\ , then the parameters are taken from the specified file
 and the file must contain one line for each atom type.  The latter
@@ -76,7 +76,7 @@ of this fix are hard-coded to be A, eV, and electronic charge.
 
 The optional *dual* keyword allows to perform the optimization
 of the S and T matrices in parallel. This is only supported for
-the *qeq/reax/omp* style. Otherwise they are processed separately.
+the *qeq/reaxff/omp* style. Otherwise they are processed separately.
 
 The optional *maxiter* keyword allows changing the max number
 of iterations in the linear solver. The default value is 200.
@@ -119,7 +119,7 @@ periodic cell dimensions less than 10 angstroms.
 Related commands
 """"""""""""""""
 
-:doc:`pair_style reax/c <pair_reaxc>`
+:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`
 
 Default
 """""""

doc/src/fix_reaxff_bonds.rst

@@ -1,17 +1,17 @@
-.. index:: fix reax/c/bonds
-.. index:: fix reax/c/bonds/kk
+.. index:: fix reaxff/bonds
+.. index:: fix reaxff/bonds/kk
 
-fix reax/c/bonds command
+fix reaxff/bonds command
 ========================
 
-Accelerator Variants: *reax/c/bonds/kk*
+Accelerator Variants: *reaxff/bonds/kk*
 
 Syntax
 """"""
 
 .. parsed-literal::
 
-   fix ID group-ID reaxc/bonds Nevery filename
+   fix ID group-ID reaxff/bonds Nevery filename
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * reax/bonds = style name of this fix command
@@ -23,17 +23,17 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix 1 all reax/c/bonds 100 bonds.reaxc
+   fix 1 all reaxff/bonds 100 bonds.reaxff
 
 Description
 """""""""""
 
 Write out the bond information computed by the ReaxFF potential specified
-by :doc:`pair_style reax/c <pair_reaxc>` in the exact same format as the
+by :doc:`pair_style reaxff <pair_reaxff>` in the exact same format as the
 original stand-alone ReaxFF code of Adri van Duin.  The bond information
 is written to *filename* on timesteps that are multiples of *Nevery*\ ,
 including timestep 0.  For time-averaged chemical species analysis,
-please see the :doc:`fix reaxc/c/species <fix_reaxc_species>` command.
+please see the :doc:`fix reaxff/species <fix_reaxff_species>` command.
 
 The specified group-ID is ignored by this fix.
 
@@ -76,7 +76,7 @@ the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minim
 Restrictions
 """"""""""""
 
-The fix reax/c/bonds command requires that the :doc:`pair_style reax/c <pair_reaxc>` is invoked.  This fix is part of the
+The fix reaxff/bonds command requires that the :doc:`pair_style reaxff <pair_reaxff>` is invoked.  This fix is part of the
 REAXFF package.  It is only enabled if LAMMPS was built with that
 package.  See the :doc:`Build package <Build_package>` doc page for more
 info.
@@ -87,7 +87,7 @@ To write gzipped bond files, you must compile LAMMPS with the
 Related commands
 """"""""""""""""
 
-:doc:`pair_style reax/c <pair_reaxc>`, :doc:`fix reax/c/species <fix_reaxc_species>`
+:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix reaxff/species <fix_reaxff_species>`
 
 Default
 """""""

doc/src/fix_reaxff_species.rst

@@ -1,20 +1,20 @@
-.. index:: fix reax/c/species
-.. index:: fix reax/c/species/kk
+.. index:: fix reaxff/species
+.. index:: fix reaxff/species/kk
 
-fix reax/c/species command
+fix reaxff/species command
 ==========================
 
-Accelerator Variants: *reax/c/species/kk*
+Accelerator Variants: *reaxff/species/kk*
 
 Syntax
 """"""
 
 .. parsed-literal::
 
-   fix ID group-ID reax/c/species Nevery Nrepeat Nfreq filename keyword value ...
+   fix ID group-ID reaxff/species Nevery Nrepeat Nfreq filename keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* reax/c/species = style name of this command
+* reaxff/species = style name of this command
 * Nevery = sample bond-order every this many timesteps
 * Nrepeat = # of bond-order samples used for calculating averages
 * Nfreq = calculate average bond-order every this many timesteps
@@ -37,15 +37,15 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix 1 all reax/c/species 10 10 100 species.out
-   fix 1 all reax/c/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
-   fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
+   fix 1 all reaxff/species 10 10 100 species.out
+   fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
+   fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
 
 Description
 """""""""""
 
 Write out the chemical species information computed by the ReaxFF
-potential specified by :doc:`pair_style reax/c <pair_reaxc>`.
+potential specified by :doc:`pair_style reaxff <pair_reaxff>`.
 Bond-order values (either averaged or instantaneous, depending on
 value of *Nrepeat*\ ) are used to determine chemical bonds.  Every
 *Nfreq* timesteps, chemical species information is written to
@@ -73,7 +73,7 @@ symbol printed for each LAMMPS atom type. The number of symbols must
 match the number of LAMMPS atom types and each symbol must consist of
 1 or 2 alphanumeric characters. Normally, these symbols should be
 chosen to match the chemical identity of each LAMMPS atom type, as
-specified using the :doc:`reax/c pair_coeff <pair_reaxc>` command and
+specified using the :doc:`reaxff pair_coeff <pair_reaxff>` command and
 the ReaxFF force field file.
 
 The optional keyword *position* writes center-of-mass positions of
@@ -115,12 +115,12 @@ average bond-order for the species analysis output on timestep 100.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
-are relevant to this fix.
+No information about this fix is written to :doc:`binary restart files <restart>`.
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
 
-This fix computes both a global vector of length 2 and a per-atom
-vector, either of which can be accessed by various :doc:`output commands <Howto_output>`.  The values in the global vector are
-"intensive".
+This fix computes both a global vector of length 2 and a per-atom vector,
+either of which can be accessed by various :doc:`output commands <Howto_output>`.
+The values in the global vector are "intensive".
 
 The 2 values in the global vector are as follows:
 
@@ -134,7 +134,8 @@ will be the same and will be equal to the smallest atom ID of
 any atom in the molecule.
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.
+This fix is not invoked during :doc:`energy minimization <minimize>`.
 
 ----------
 
@@ -145,26 +146,20 @@ the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minim
 Restrictions
 """"""""""""
 
-The "fix reax/c/species" currently only works with :doc:`pair_style reax/c <pair_reaxc>` and it requires that the :doc:`pair_style reax/c <pair_reaxc>` be invoked.  This fix is part of the
-REAXFF package.  It is only enabled if LAMMPS was built with that
-package.  See the :doc:`Build package <Build_package>` doc page for more
-info.
+The "fix reaxff/species" requires that :doc:`pair_style reaxff <pair_reaxff>` is used.
+This fix is part of the REAXFF package.  It is only enabled if LAMMPS was built with that
+package.  See the :doc:`Build package <Build_package>` doc page for more info.
 
-To write gzipped species files, you must compile LAMMPS with the
--DLAMMPS_GZIP option.
-
-It should be possible to extend it to other reactive pair_styles (such as
-:doc:`rebo <pair_airebo>`, :doc:`airebo <pair_airebo>`,
-:doc:`comb <pair_comb>`, and :doc:`bop <pair_bop>`), but this has not yet been done.
+To write gzipped species files, you must compile LAMMPS with the -DLAMMPS_GZIP option.
 
 Related commands
 """"""""""""""""
 
-:doc:`pair_style reax/c <pair_reaxc>`, :doc:`fix reax/c/bonds <fix_reaxc_bonds>`
+:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`
 
 Default
 """""""
 
-The default values for bond-order cutoffs are 0.3 for all I-J pairs.  The
-default element symbols are C, H, O, N.  Position files are not written
-by default.
+The default values for bond-order cutoffs are 0.3 for all I-J pairs.
+The default element symbols are C, H, O, N.
+Position files are not written by default.

doc/src/kim_commands.rst

@@ -372,9 +372,9 @@ the *kim interactions* command executes the following LAMMPS input commands:
 
 .. code-block:: LAMMPS
 
-   pair_style reax/c lmp_control safezone 2.0 mincap 100
+   pair_style reaxff lmp_control safezone 2.0 mincap 100
    pair_coeff * * ffield.reax.rdx C H N O
-   fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq
+   fix reaxqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 param.qeq
 
 .. note::
 

doc/src/package.rst

@@ -448,7 +448,8 @@ does not require atomic operations in the calculation of pair forces. For
 that reason, *full* is the default setting for GPUs. However, when
 running on CPUs, a *half* neighbor list is the default because it are
 often faster, just as it is for non-accelerated pair styles. Similarly,
-the *neigh/qeq* keyword determines how neighbor lists are built for :doc:`fix qeq/reax/kk <fix_qeq_reax>`.
+the *neigh/qeq* keyword determines how neighbor lists are built for
+:doc:`fix qeq/reaxff/kk <fix_qeq_reaxff>`.
 
 If the *neigh/thread* keyword is set to *off*\ , then the KOKKOS package
 threads only over atoms. However, for small systems, this may not expose

doc/src/pair_reaxff.rst

@@ -1,18 +1,18 @@
-.. index:: pair_style reax/c
-.. index:: pair_style reax/c/kk
-.. index:: pair_style reax/c/omp
+.. index:: pair_style reaxff
+.. index:: pair_style reaxff/kk
+.. index:: pair_style reaxff/omp
 
-pair_style reax/c command
+pair_style reaxff command
 =========================
 
-Accelerator Variants: *reax/c/kk*, *reax/c/omp*
+Accelerator Variants: *reaxff/kk*, *reaxff/omp*
 
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   pair_style reax/c cfile keyword value
+   pair_style reaxff cfile keyword value
 
 * cfile = NULL or name of a control file
 * zero or more keyword/value pairs may be appended
@@ -20,7 +20,7 @@ Syntax
   .. parsed-literal::
 
      keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds*
-       *checkqeq* value = *yes* or *no* = whether or not to require qeq/reax fix
+       *checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff fix
        *enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
        *lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
        *safezone* = factor used for array allocation
@@ -32,37 +32,38 @@ Examples
 
 .. code-block:: LAMMPS
 
-   pair_style reax/c NULL
-   pair_style reax/c controlfile checkqeq no
-   pair_style reax/c NULL lgvdw yes
-   pair_style reax/c NULL safezone 1.6 mincap 100
+   pair_style reaxff NULL
+   pair_style reaxff controlfile checkqeq no
+   pair_style reaxff NULL lgvdw yes
+   pair_style reaxff NULL safezone 1.6 mincap 100
    pair_coeff * * ffield.reax C H O N
 
 Description
 """""""""""
 
-Style *reax/c* computes the ReaxFF potential of van Duin, Goddard and
+Style *reaxff* computes the ReaxFF potential of van Duin, Goddard and
 co-workers.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
 energy. There is more than one version of ReaxFF. The version
 implemented in LAMMPS uses the functional forms documented in the
-supplemental information of the following paper: :ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`.  The version integrated into LAMMPS matches
-the most up-to-date version of ReaxFF as of summer 2010.  For more
-technical details about the pair reax/c implementation of ReaxFF, see
-the :ref:`(Aktulga) <Aktulga>` paper. The *reax/c* style was initially
-implemented as a stand-alone C code and is now integrated into LAMMPS
-as a package.
+supplemental information of the following paper:
+:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`.  The version integrated
+into LAMMPS matches the version of ReaxFF From Summer 2010.  For more
+technical details about the pair reaxff implementation of ReaxFF, see
+the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style was initially
+implemented as a stand-alone C code and is now converted to C++ and
+integrated into LAMMPS as a package.
 
-The *reax/c/kk* style is a Kokkos version of the ReaxFF potential that
-is derived from the *reax/c* style. The Kokkos version can run on GPUs
+The *reaxff/kk* style is a Kokkos version of the ReaxFF potential that
+is derived from the *reaxff* style. The Kokkos version can run on GPUs
 and can also use OpenMP multithreading. For more information about the
 Kokkos package, see :doc:`Packages details <Packages_details>` and
 :doc:`Speed kokkos <Speed_kokkos>` doc pages.  One important
-consideration when using the *reax/c/kk* style is the choice of either
+consideration when using the *reaxff/kk* style is the choice of either
 half or full neighbor lists. This setting can be changed using the
 Kokkos :doc:`package <package>` command.
 
-The *reax/c* style differs from the (obsolete) "pair_style reax"
+The *reaxff* style differs from the (obsolete) "pair_style reax"
 command in the implementation details.  The *reax* style was a
 Fortran library, linked to LAMMPS.  The *reax* style has been removed
 from LAMMPS after the 12 December 2018 version.
@@ -73,7 +74,7 @@ documented in potentials/README.reax.  The default ffield.reax
 contains parameterizations for the following elements: C, H, O, N.
 
 The format of these files is identical to that used originally by van
-Duin.  We have tested the accuracy of *pair_style reax/c* potential
+Duin.  We have tested the accuracy of *pair_style reaxff* potential
 against the original ReaxFF code for the systems mentioned above.  You
 can use other ffield files for specific chemical systems that may be
 available elsewhere (but note that their accuracy may not have been
@@ -102,10 +103,11 @@ control variable.  The format of the control file is described below.
 
    The LAMMPS default values for the ReaxFF global parameters
    correspond to those used by Adri van Duin's stand-alone serial
-   code. If these are changed by setting control variables in the control
-   file, the results from LAMMPS and the serial code will not agree.
+   code.  If these are changed by setting control variables in the
+   control file, the results from LAMMPS and the serial code will
+   not agree.
 
-Examples using *pair_style reax/c* are provided in the examples/reax
+Examples using *pair_style reaxff* are provided in the examples/reax
 sub-directory.
 
 Use of this pair style requires that a charge be defined for every
@@ -115,25 +117,28 @@ charges.
 
 The ReaxFF parameter files provided were created using a charge
 equilibration (QEq) model for handling the electrostatic interactions.
-Therefore, by default, LAMMPS requires that the :doc:`fix qeq/reax <fix_qeq_reax>` command be used with *pair_style reax/c*
-when simulating a ReaxFF model, to equilibrate charge each timestep.
-Using the keyword *checkqeq* with the value *no*
-turns off the check for *fix qeq/reax*\ ,
-allowing a simulation to be run without charge equilibration.
-In this case, the static charges you
-assign to each atom will be used for computing the electrostatic
-interactions in the system.
-See the :doc:`fix qeq/reax <fix_qeq_reax>` command for details.
+Therefore, by default, LAMMPS requires that either the
+:doc:`fix qeq/reaxff <fix_qeq_reaxff>` or the
+:doc:`fix qeq/shielded <fix_qeq>` command be used with
+*pair_style reaxff* when simulating a ReaxFF model, to equilibrate
+the charges each timestep.
+
+Using the keyword *checkqeq* with the value *no* turns off the check
+for the QEq fixes, allowing a simulation to be run without charge
+equilibration. In this case, the static charges you assign to each
+atom will be used for computing the electrostatic interactions in
+the system. See the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or
+:doc:`fix qeq/shielded <fix_qeq>` command documentation for more details.
 
 Using the optional keyword *lgvdw* with the value *yes* turns on the
-low-gradient correction of the ReaxFF/C for long-range London
-Dispersion, as described in the :ref:`(Liu) <Liu_2011>` paper. Force field
-file *ffield.reax.lg* is designed for this correction, and is trained
-for several energetic materials (see "Liu"). When using lg-correction,
-recommended value for parameter *thb* is 0.01, which can be set in the
+low-gradient correction of ReaxFF for long-range London Dispersion,
+as described in the :ref:`(Liu) <Liu_2011>` paper. The bundled force
+field file *ffield.reax.lg* is designed for this correction, and is
+trained for several energetic materials (see "Liu"). When using *lgvdw yes*,
+the recommended value for parameter *thb* is 0.01, which can be set in the
 control file.  Note: Force field files are different for the original
-or lg corrected pair styles, using wrong ffield file generates an
-error message.
+or lg corrected pair styles, using the wrong ffield file generates an
+error.
 
 Using the optional keyword *enobonds* with the value *yes*\ , the energy
 of atoms with no bonds (i.e. isolated atoms) is included in the total
@@ -144,7 +149,7 @@ discontinuities in the potential energy when the bonding of an atom
 drops to zero.
 
 Optional keywords *safezone*\ , *mincap*\ , and *minhbonds* are used
-for allocating reax/c arrays.  Increasing these values can avoid memory
+for allocating reaxff arrays.  Increasing these values can avoid memory
 problems, such as segmentation faults and bondchk failed errors, that
 could occur under certain conditions. These keywords are not used by
 the Kokkos version, which instead uses a more robust memory allocation
@@ -158,7 +163,8 @@ equilibration contributions which are stored in the thermo variable
 :doc:`thermo <thermo>` command.
 
 This pair style tallies a breakdown of the total ReaxFF potential
-energy into sub-categories, which can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 14.
+energy into sub-categories, which can be accessed via the
+:doc:`compute pair <compute_pair>` command as a vector of values of length 14.
 The 14 values correspond to the following sub-categories (the variable
 names in italics match those used in the original FORTRAN ReaxFF
 code):
@@ -183,14 +189,14 @@ headings) the following commands could be included in an input script:
 
 .. code-block:: LAMMPS
 
-   compute reax all pair reax/c
+   compute reax all pair reaxff
    variable eb      equal c_reax[1]
    variable ea      equal c_reax[2]
    [...]
    variable eqeq    equal c_reax[14]
    thermo_style custom step temp epair v_eb v_ea [...] v_eqeq
 
-Only a single pair_coeff command is used with the *reax/c* style which
+Only a single pair_coeff command is used with the *reaxff* style which
 specifies a ReaxFF potential file with parameters for all needed
 elements.  These are mapped to LAMMPS atom types by specifying N
 additional arguments after the filename in the pair_coeff command,
@@ -209,7 +215,7 @@ to M. Each of the N indices you specify for the N atom types of LAMMPS
 atoms must be an integer from 1 to M.  Atoms with LAMMPS type 1 will
 be mapped to whatever element you specify as the first index value,
 etc.  If a mapping value is specified as NULL, the mapping is not
-performed.  This can be used when the *reax/c* style is used as part
+performed.  This can be used when the *reaxff* style is used as part
 of the *hybrid* pair style.  The NULL values are placeholders for atom
 types that will be used with other potentials.
 
@@ -241,7 +247,7 @@ brief description of their use and default values.
 
 
 *simulation_name*
-   Output files produced by *pair_style reax/c* carry
+   Output files produced by *pair_style reaxff* carry
    this name + extensions specific to their contents.  Partial energies
    are reported with a ".pot" extension, while the trajectory file has
    ".trj" extension.
@@ -286,8 +292,7 @@ brief description of their use and default values.
    to be considered in three body interactions. (default value = 0.00001)
 
 *write_freq*
-   Frequency of writes into the trajectory file. (default
-   value = 0)
+   Frequency of writes into the trajectory file. (default value = 0)
 
 *traj_title*
    Title of the trajectory - not the name of the trajectory file.
@@ -315,7 +320,8 @@ Mixing, shift, table, tail correction, restart, rRESPA info
 This pair style does not support the :doc:`pair_modify <pair_modify>`
 mix, shift, table, and tail options.
 
-This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+This pair style does not write its information to :doc:`binary restart files <restart>`,
+since it is stored in potential files.  Thus, you
 need to re-specify the pair_style and pair_coeff commands in an input
 script that reads a restart file.
 
@@ -333,18 +339,20 @@ Restrictions
 """"""""""""
 
 This pair style is part of the REAXFF package.  It is only enabled
-if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+if LAMMPS was built with that package.
+See the :doc:`Build package <Build_package>` doc page for more info.
 
 The ReaxFF potential files provided with LAMMPS in the potentials
-directory are parameterized for real :doc:`units <units>`.  You can use
-the ReaxFF potential with any LAMMPS units, but you would need to
+directory are parameterized for *real* :doc:`units <units>`.  You can use
+the ReaxFF pair style with any LAMMPS units, but you would need to
 create your own potential file with coefficients listed in the
 appropriate units if your simulation does not use "real" units.
 
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reax <fix_qeq_reax>`, :doc:`fix reax/c/bonds <fix_reaxc_bonds>`, :doc:`fix reax/c/species <fix_reaxc_species>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
+:doc:`fix reaxff/bonds <fix_reaxff_bonds>`, :doc:`fix reaxff/species <fix_reaxff_species>`
 
 Default
 """""""

doc/src/pair_style.rst

@@ -299,7 +299,7 @@ accelerated styles exist.
 * :doc:`python <pair_python>` -
 * :doc:`quip <pair_quip>` -
 * :doc:`rann <pair_rann>` -
-* :doc:`reax/c <pair_reaxc>` - ReaxFF potential in C
+* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
 * :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
 * :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
 * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions

doc/utils/check-styles.py

@@ -254,40 +254,27 @@ for command_type, entries in index.items():
 
 print("Total number of style index entries:", total_index)
 
+skip_fix = ('python', 'NEIGH_HISTORY/omp','qeq/reax','reax/c/bonds','reax/c/species')
+skip_pair = ('meam/c','lj/sf','reax/c')
+
 counter = 0
 
-counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",
-                       command,'Command',suffix=False)
-counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",
-                       compute,'Compute',suffix=True)
-counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",
-                       compute,'Compute',suffix=False)
-counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",
-                       fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=True)
-counter += check_style('fix.rst', doc_dir, ":doc:`(.+) <fix.+>` -",
-                       fix,'Fix',skip=('python', 'NEIGH_HISTORY/omp'),suffix=False)
-counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",
-                       pair,'Pair',skip=('meam/c','lj/sf'),suffix=True)
-counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",
-                       pair,'Pair',skip=('meam/c','lj/sf'),suffix=False)
-counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",
-                       bond,'Bond',suffix=True)
-counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",
-                       bond,'Bond',suffix=False)
-counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",
-                       angle,'Angle',suffix=True)
-counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",
-                       angle,'Angle',suffix=False)
-counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",
-                       dihedral,'Dihedral',suffix=True)
-counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",
-                       dihedral,'Dihedral',suffix=False)
-counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",
-                       improper,'Improper',suffix=True)
-counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",
-                       improper,'Improper',suffix=False)
-counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",
-                       kspace,'KSpace',suffix=True)
+counter += check_style('Commands_all.rst', doc_dir, ":doc:`(.+) <.+>`",command,'Command',suffix=False)
+counter += check_style('Commands_compute.rst', doc_dir, ":doc:`(.+) <compute.+>`",compute,'Compute',suffix=True)
+counter += check_style('compute.rst', doc_dir, ":doc:`(.+) <compute.+>` -",compute,'Compute',suffix=False)
+counter += check_style('Commands_fix.rst', doc_dir, ":doc:`(.+) <fix.+>`",fix,'Fix',skip=skip_fix,suffix=True)
+counter += check_style('fix.rst', doc_dir, ":doc:`(.+) <fix.+>` -",fix,'Fix',skip=skip_fix,suffix=False)
+counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",pair,'Pair',skip=skip_pair,suffix=True)
+counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",pair,'Pair',skip=skip_pair,suffix=False)
+counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",bond,'Bond',suffix=True)
+counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",bond,'Bond',suffix=False)
+counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',suffix=True)
+counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',suffix=False)
+counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",dihedral,'Dihedral',suffix=True)
+counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",dihedral,'Dihedral',suffix=False)
+counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",improper,'Improper',suffix=True)
+counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) <improper.+>` -",improper,'Improper',suffix=False)
+counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) <kspace_style>`",kspace,'KSpace',suffix=True)
 
 if counter:
     print(f"Found {counter} issue(s) with style lists")
@@ -295,13 +282,13 @@ if counter:
 counter = 0
 
 counter += check_style_index("compute", compute, index["compute"])
-counter += check_style_index("fix", fix, index["fix"], skip=['python'])
+counter += check_style_index("fix", fix, index["fix"], skip=['python','qeq/reax','reax/c/bonds','reax/c/species'])
 counter += check_style_index("angle_style", angle, index["angle_style"])
 counter += check_style_index("bond_style", bond, index["bond_style"])
 counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
 counter += check_style_index("improper_style", improper, index["improper_style"])
 counter += check_style_index("kspace_style", kspace, index["kspace_style"])
-counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf'])
+counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c'])
 
 if counter:
     print(f"Found {counter} issue(s) with style index")

examples/README

@@ -103,7 +103,7 @@ pour:     pouring of granular particles into a 3d box, then chute flow
 prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   use of PYTHON package to invoke Python code from input script
 qeq:      use of QEQ package for charge equilibration
-reax:     RDX and TATB and several other models using ReaxFF
+reaxff:   RDX and TATB and several other models using ReaxFF
 rerun:    use of rerun and read_dump commands
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void