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

This commit is contained in:
Axel Kohlmeyer 2018-12-10 14:51:21 -05:00
parent e2c39a1acd
commit 1933c2eb5f
8 changed files with 13 additions and 50 deletions
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1
doc/src/Commands_pair.txt
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@ -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,

40
doc/src/Packages_details.txt
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@ -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NOTE: the use of the REAX package is discouraged, as it is no longer
maintained.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
contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF
is universal reactive force field. See the src/USER-REAXC/README file
A pair style which implements the ReaxFF potential in C/C++. ReaxFF
is a 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

1
doc/src/Packages_standard.txt
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@ -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

2
doc/src/Tools.txt
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@ -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.

6
doc/src/compute_pair.txt
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@ -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
"pair_style reax"_pair_reax.html command. These values (1 or more)
potential energy into 14 components is tallied by the "pair_style
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.

2
doc/src/lammps.book
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@ -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

10
doc/src/pair_reaxc.txt
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@ -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
sub-directory, along with corresponding examples for
"pair_style reax"_pair_reax.html.
Examples using {pair_style reax/c} are provided in the examples/reax
sub-directory.
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}
pair style, any filename can be used.
The filename is the ReaxFF potential file.
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:]

1
doc/utils/sphinx-config/false_positives.txt
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@ -1522,6 +1522,7 @@ mdf
mdpd
mDPD
meam
meamc
MEAMC
meamf
meanDist