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Update docs 

* bring homebrew install notes up-to-date
* update openkim docs
This commit is contained in:
Ryan S. Elliott 2019-07-21 15:17:53 -05:00
parent 03d26f6f6f
commit f2978475af
6 changed files with 30 additions and 45 deletions
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18
doc/src/Build_extras.txt
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@ -176,19 +176,13 @@ use with LAMMPS. If you want to use the "kim_query"_kim_commands.html
command, you also need to have libcurl installed with the matching
development headers and the curl-config tool.
Note that in LAMMPS jargon, a KIM model driver is a pair style
(e.g. EAM or Tersoff). A KIM model is a pair style for a particular
element or alloy and set of parameters, e.g. EAM for Cu with a
specific EAM potential file. Also note that when downloading and
installing from source
See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
learn how to install a pre-build binary of the OpenKIM Repository of Models.
See the list of all KIM models here: https://openkim.org/browse/models
(Also note that when downloading and installing from source
the KIM API library with all its models, may take a long time (tens of
minutes to hours) to build. Of course you only need to do that once.
See the list of KIM model drivers here:
https://openkim.org/browse/model-drivers/alphabetical
See the list of all KIM models here:
https://openkim.org/browse/models/by-model-drivers
minutes to hours) to build. Of course you only need to do that once.)
[CMake build]:

4
doc/src/Examples.txt
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@ -73,7 +73,7 @@ granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics
hyper: global and local hyperdynamics of diffusion on Pt surface
indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
kim: use of potentials from the "OpenKIM Repository"_openkim
latte: examples for using fix latte for DFTB via the LATTE library
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
@ -153,3 +153,5 @@ illustrate how to use the command(s) provided in that package. Many
of the sub-directories have their own README files which give further
instructions. See the "Packages_details"_Packages_details.html doc
page for more info on specific USER packages.
:link(openkim,https://openkim.org)

43
doc/src/Install_mac.txt
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@ -10,47 +10,34 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
Download an executable for Mac :h3
LAMMPS can be downloaded, built, and configured for OS X on a Mac with
"Homebrew"_homebrew. Only four of the LAMMPS packages are unavailable
at this time because of additional needs not yet met: KIM, GPU,
USER-INTEL, USER-ATC.
"Homebrew"_homebrew. The following LAMMPS packages are unavailable at this
time because of additional needs not yet met: GPU, KOKKOS, LATTE, MSCG,
MESSAGE, MPIIO POEMS VORONOI.
After installing Homebrew, you can install LAMMPS on your system with
the following commands:
% brew tap homebrew/science
% brew install lammps # serial version
% brew install lammps --with-mpi # mpi support :pre
% brew install lammps :pre
This will install the executable "lammps", a python module named
"lammps", and additional resources with all the standard packages. To
get the location of the additional resources type this:
% brew info lammps :pre
This command also tells you additional installation options available.
The user-packages are available as options, just install them like
this example for the USER-OMP package:
% brew install lammps --enable-user-omp :pre
It is usually best to install LAMMPS with the most up to date source
files, which can be done with the "--HEAD" option:
% brew install lammps --HEAD :pre
To re-install the LAMMPS HEAD, run this command occasionally (make sure
to use the desired options).
% brew install --force lammps --HEAD $\{options\} :pre
This will install the executables "lammps_serial" and "lammps_mpi", as well as
the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
Once LAMMPS is installed, you can test the installation with the
Lennard-Jones benchmark file:
% brew test lammps -v :pre
The LAMMPS binary is built with the "KIM package"_Build_extras#kim which
results in homebrew also installing the `kim-api` binaries when LAMMPS is
installed. In order to use potentials from "openkim.org"_openkim, you can
install the `openkim-models` package
% brew install openkim-models :pre
If you have problems with the installation you can post issues to
"this link"_homebrew.
Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
up the Homebrew capability.
:link(homebrew,https://github.com/Homebrew/homebrew-science/issues)
:link(homebrew,https://github.com/Homebrew/homebrew-core/issues)
:link(openkim,https://openkim.org)

4
doc/src/Intro_features.txt
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@ -92,8 +92,8 @@ commands)
implicit solvent potentials: hydrodynamic lubrication, Debye
force-field compatibility with common CHARMM, AMBER, DREIDING, \
OPLS, GROMACS, COMPASS options
access to "KIM archive"_http://openkim.org of potentials via \
"pair kim"_pair_kim.html
access to the "OpenKIM Repository"_http://openkim.org of potentials via \
"kim_init, kim_interactions, and kim_query"_kim_commands.html commands
hybrid potentials: multiple pair, bond, angle, dihedral, improper \
potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials :ul

3
doc/src/fix_adapt.txt
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@ -149,8 +149,7 @@ meaning of these parameters:
"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:
"table"_pair_table.html: table_cutoff: type pairs:
"ufm"_pair_ufm.html: epsilon,sigma: type pairs:
"soft"_pair_soft.html: a: type pairs:
"kim"_pair_kim.html: PARAM_FREE_*&#58i,j,...: global :tb(c=3,s=:)
"soft"_pair_soft.html: a: type pairs: :tb(c=3,s=:)
NOTE: It is easy to add new pairwise potentials and their parameters
to this list. All it typically takes is adding an extract() method to

3
doc/src/kim_commands.txt
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@ -116,6 +116,9 @@ See the "current list of KIM PMs and SMs archived in OpenKIM"_https://openkim.or
This list is sorted by species and can be filtered to display only
IMs for certain species combinations.
See "Obtaining KIM Models"_http://openkim.org/doc/usage/obtaining-models to
learn how to install a pre-build binary of the OpenKIM Repository of Models.
NOTE: It is also possible to locally install IMs not archived in OpenKIM,
in which case their names do not have to conform to the KIM ID format.