next chunk of documentation changes for the removal of REAX and MEAM

doc/src/Commands_pair.txt

@@ -193,7 +193,6 @@ OPT.
 "polymorphic"_pair_polymorphic.html,
 "python"_pair_python.html,
 "quip"_pair_quip.html,
-"reax"_pair_reax.html,
 "reax/c (ko)"_pair_reaxc.html,
 "rebo (io)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,

doc/src/Packages_details.txt

@@ -55,7 +55,6 @@ as contained in the file name.
 "POEMS"_#PKG-POEMS,
 "PYTHON"_#PKG-PYTHON,
 "QEQ"_#PKG-QEQ,
-"REAX"_#PKG-REAX,
 "REPLICA"_#PKG-REPLICA2,
 "RIGID"_#PKG-RIGID,
 "SHOCK"_#PKG-SHOCK,
@@ -802,38 +801,6 @@ examples/streitz :ul
 
 :line
 
-REAX package :link(PKG-REAX),h4
-
-[Contents:]
-
-NOTE: the use of the REAX package is discouraged, as it is no longer
-maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
-and possibly the KOKKOS enabled variant of that, which has a more robust
-memory management.
-
-A pair style which wraps a Fortran library which implements the ReaxFF
-potential, which is a universal reactive force field.  Also included is
-a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
-as bonds are created and destroyed.
-
-[Author:] Aidan Thompson (Sandia).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/REAX: filenames -> commands
-lib/reax/README
-"pair_style reax"_pair_reax.html
-"fix reax/bonds"_fix_reax_bonds.html
-examples/reax :ul
-
-:line
-
 REPLICA package :link(PKG-REPLICA2),h4
 
 [Contents:]
@@ -1861,9 +1828,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4
 
 [Contents:]
 
-A pair style which implements the ReaxFF potential in C/C++ (in
+A pair style which implements the ReaxFF potential in C/C++.  ReaxFF
-contrast to the "REAX package"_#PKG-REAX and its Fortran library).  ReaxFF
+is a universal reactive force field.  See the src/USER-REAXC/README file
-is universal reactive force field.  See the src/USER-REAXC/README file
 for more info on differences between the two packages.  Also two fixes
 for monitoring molecules as bonds are created and destroyed.
 
@@ -1874,7 +1840,7 @@ for monitoring molecules as bonds are created and destroyed.
 src/USER-REAXC: filenames -> commands
 src/USER-REAXC/README
 "pair_style reax/c"_pair_reaxc.html
-"fix reax/c/bonds"_fix_reax_bonds.html
+"fix reax/c/bonds"_fix_reaxc_bonds.html
 "fix reax/c/species"_fix_reaxc_species.html
 examples/reax :ul
 

doc/src/Packages_standard.txt

@@ -56,7 +56,6 @@ Package, Description, Doc page, Example, Library
 "POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
 "PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
 "QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
-"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
 "REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
 "RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
 "SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no

doc/src/Tools.txt

@@ -487,7 +487,7 @@ reax tool :h4,link(reax_tool)
 
 The reax sub-directory contains stand-alond codes that can
 post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
-command from a LAMMPS simulation using "ReaxFF"_pair_reax.html.  See
+command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html.  See
 the README.txt file for more info.
 
 These tools were written by Aidan Thompson at Sandia.

doc/src/compute_pair.txt

@@ -24,7 +24,7 @@ nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a
 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 :pre
+compute 1 all pair reax/c :pre
 
 [Description:]
 
@@ -60,8 +60,8 @@ corrections, even if they are enabled via the
 "pair_modify"_pair_modify.html command.
 
 Some pair styles tally additional quantities, e.g. a breakdown of
-potential energy into a dozen or so components is tallied by the
+potential energy into 14 components is tallied by the "pair_style
-"pair_style reax"_pair_reax.html command.  These values (1 or more)
+reax/c"_pair_reaxc.html command.  These values (1 or more)
 are stored as a global vector by this compute.  See the doc page for
 "individual pair styles"_pair_style.html for info on these values.
 

doc/src/lammps.book

@@ -356,7 +356,7 @@ fix_qeq_comb.html
 fix_qeq_reax.html
 fix_qmmm.html
 fix_qtb.html
-fix_reax_bonds.html
+fix_reaxc_bonds.html
 fix_reaxc_species.html
 fix_recenter.html
 fix_restrain.html

doc/src/pair_reaxc.txt

@@ -97,9 +97,8 @@ 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.
 
-Two examples using {pair_style reax/c} are provided in the examples/reax
+Examples using {pair_style reax/c} are provided in the examples/reax
-sub-directory, along with corresponding examples for
+sub-directory.
-"pair_style reax"_pair_reax.html.
 
 Use of this pair style requires that a charge be defined for every
 atom.  See the "atom_style"_atom_style.html and
@@ -192,8 +191,7 @@ where N is the number of LAMMPS atom types:
 filename
 N indices = ReaxFF elements :ul
 
-The filename is the ReaxFF potential file.  Unlike for the {reax}
+The filename is the ReaxFF potential file.
-pair style, any filename can be used.
 
 In the ReaxFF potential file, near the top, after the general
 parameters, is the atomic parameters section that contains element
@@ -336,7 +334,7 @@ appropriate units if your simulation doesn't use "real" units.
 [Related commands:]
 
 "pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html, "fix
-reax/c/bonds"_fix_reax_bonds.html, "fix
+reax/c/bonds"_fix_reaxc_bonds.html, "fix
 reax/c/species"_fix_reaxc_species.html
 
 [Default:]

doc/utils/sphinx-config/false_positives.txt

@@ -1522,6 +1522,7 @@ mdf
 mdpd
 mDPD
 meam
+meamc
 MEAMC
 meamf
 meanDist