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Merge pull request #921 from lammps/doctweaks

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tweaks to doc pages
This commit is contained in:
Steve Plimpton
2018-05-22 10:02:01 -06:00
committed by GitHub
parent 94c6d2d546 cab602045e
commit 69903cb4aa
3 changed files with 36 additions and 31 deletions
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9
doc/src/pair_gw.txt
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@ -95,9 +95,9 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the USER-MISC package. It is only enabled
if LAMMPS was built with that package. See
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
This pair style is part of the MANYBODY package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.
@ -117,4 +117,5 @@ appropriate units if your simulation doesn't use "metal" units.
:line
:link(Gao)
[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics
Research B 191 (2012) 504.

54
doc/src/pair_reaxc.txt
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@ -47,13 +47,14 @@ the "(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.
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 and
can also use OpenMP multithreading. For more information about the Kokkos package,
see "Section 4"_Section_packages.html#kokkos and "Section 5.3.3"_accelerate_kokkos.html.
One important consideration when using the {reax/c/kk} style is the choice of either
half or full neighbor lists. This setting can be changed using the Kokkos "package"_package.html
command.
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
and can also use OpenMP multithreading. For more information about the
Kokkos package, see "Section 4"_Section_packages.html#kokkos and
"Section 5.3.3"_accelerate_kokkos.html. One important consideration
when using the {reax/c/kk} style is the choice of either half or full
neighbor lists. This setting can be changed using the Kokkos
"package"_package.html command.
The {reax/c} style differs from the "pair_style reax"_pair_reax.html
command in the lo-level implementation details. The {reax} style is a
@ -80,9 +81,8 @@ parameterizations for different classes of materials. You can submit
a contact request at the Materials Computation Center (MCC) website
"https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc,
describing the material(s) you are interested in modeling with ReaxFF.
They can tell
you what is currently available or what it would take to create a
suitable ReaxFF parameterization.
They can tell you what is currently available or what it would take to
create a suitable ReaxFF parameterization.
The {cfile} setting can be specified as NULL, in which case default
settings are used. A control file can be specified which defines
@ -120,28 +120,31 @@ assign to each atom will be used for computing the electrostatic
interactions in the system.
See the "fix qeq/reax"_fix_qeq_reax.html command for 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 "(Liu)"_#Liu_2011 paper. Force field
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 "(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
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 wrong ffield file generates an
error message.
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
potential energy and the per-atom energy of that atom. If the value
{no} is specified then the energy of atoms with no bonds is set to zero.
The latter behavior is usual not desired, as it causes discontinuities
in the potential energy when the bonding of an atom drops to zero.
{no} is specified then the energy of atoms with no bonds is set to
zero. The latter behavior is usual not desired, as it causes
discontinuities in the potential energy when the bonding of an atom
drops to zero.
Optional keywords {safezone} and {mincap} are used for allocating
reax/c arrays. Increasing these values can avoid memory problems, such
as segmentation faults and bondchk failed errors, that could occur under
certain conditions. These keywords aren't used by the Kokkos version, which
instead uses a more robust memory allocation scheme that checks if the sizes of
the arrays have been exceeded and automatically allocates more memory.
reax/c arrays. Increasing these values can avoid memory problems,
such as segmentation faults and bondchk failed errors, that could
occur under certain conditions. These keywords aren't used by the
Kokkos version, which instead uses a more robust memory allocation
scheme that checks if the sizes of the arrays have been exceeded and
automatically allocates more memory.
The thermo variable {evdwl} stores the sum of all the ReaxFF potential
energy contributions, with the exception of the Coulombic and charge
@ -153,7 +156,8 @@ This pair style tallies a breakdown of the total ReaxFF potential
energy into sub-categories, which can be accessed via the "compute
pair"_compute_pair.html 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):
names in italics match those used in the original FORTRAN ReaxFF
code):
{eb} = bond energy
{ea} = atom energy
@ -340,8 +344,8 @@ reax"_pair_reax.html
[Default:]
The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, safezone = 1.2,
mincap = 50.
The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no,
safezone = 1.2, mincap = 50.
:line

4
doc/src/pair_sw.txt
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@ -192,8 +192,8 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package. See
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
if LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
This pair style requires the "newton"_newton.html setting to be "on"
for pair interactions.