hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation - overlaid potentials: superposition of multiple pair potentials -
(read_data, lattice, diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index 65ceac8fdc..aae41e9728 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -154,13 +154,14 @@ commands) polymer potentials: all-atom, united-atom, bead-spring, breakable water potentials: TIP3P, TIP4P, SPC implicit solvent potentials: hydrodynamic lubrication, Debye + "KIM archive"_http://openkim.org of potentials long-range Coulombics and dispersion: Ewald, Wolf, \ PPPM (similar to particle-mesh Ewald), Ewald/N for long-range Lennard-Jones force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options - handful of GPU-enabled pair styles :ul + handful of GPU-enabled pair styles hybrid potentials: multiple pair, bond, angle, dihedral, improper \ potentials can be used in one simulation - overlaid potentials: superposition of multiple pair potentials + overlaid potentials: superposition of multiple pair potentials :ul Atom creation :h4 ("read_data"_read_data.html, "lattice"_lattice.html, diff --git a/doc/Section_packages.html b/doc/Section_packages.html index 8acc522a82..f14415221b 100644 --- a/doc/Section_packages.html +++ b/doc/Section_packages.html @@ -50,7 +50,8 @@ packages, more details are provided.
(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott, +and Ellad Tadmor (U Minn). +
The "Doc page" column links to either a portion of the Section_howto of the manual, or an input script command implemented as part of the package. diff --git a/doc/Section_packages.txt b/doc/Section_packages.txt index 334355e740..47b03c559b 100644 --- a/doc/Section_packages.txt +++ b/doc/Section_packages.txt @@ -46,6 +46,7 @@ DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dip FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, - GPU, GPU-enabled potentials, Mike Brown (ORNL), "Section accelerate"_Section_accelerate.html#acc_3, gpu, lib/gpu GRANULAR, granular systems, -, "howto"_Section_howto.html#howto_6, pour, - +KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), pair_style kim"_pair_kim.html, kim, lib/kim KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, - MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, - MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam @@ -71,6 +72,9 @@ Jonathan Higdon's group at UIUC. Technologies), David Richie, and Vincent Natoli (Stone Ridge Technolgy). +(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott, +and Ellad Tadmor (U Minn). + The "Doc page" column links to either a portion of the "Section_howto"_Section_howto.html of the manual, or an input script command implemented as part of the package. diff --git a/doc/Section_start.html b/doc/Section_start.html index d0108c5d19..ba02ba91c0 100644 --- a/doc/Section_start.html +++ b/doc/Section_start.html @@ -637,10 +637,10 @@ type "make package" to see all of the package-related make options.
A few of the standard and user packages require additional auxiliary libraries to be compiled first. If you get a LAMMPS build error about -a missing library, this is likely the reason. The source code for -these libraries is included in the LAMMPS distribution under the "lib" -directory. Look at the lib/README file for a list of these or see -Section_packages of the doc pages. +a missing library, this is likely the reason. The source code or +hooks to these libraries is included in the LAMMPS distribution under +the "lib" directory. Look at the lib/README file for a list of these +or see Section_packages of the doc pages.
Each lib directory has a README file (e.g. lib/reax/README) with instructions on how to build that library. Typically this is done @@ -649,13 +649,16 @@ in this manner:
make -f Makefile.g++
in the appropriate directory, e.g. in lib/reax. Some of the libraries -do not build this way. Again, see the libary README file for details. +do not build this way. Some of the directories do not even have +source code for the library, since you are expected to download and +build it separately. Again, see the libary README file for details.
-In any event, you will need to use a Makefile that is a match for your -system. If one of the provided Makefiles is not appropriate for your -system you will need to edit or add one. For example, in the case of -Fortran-based libraries, your system must have a Fortran compiler, the -settings for which will need to be listed in the Makefile. +
If you are building the library, you will need to use a Makefile that +is a match for your system. If one of the provided Makefiles is not +appropriate for your system you will need to edit or add one. For +example, in the case of Fortran-based libraries, your system must have +a Fortran compiler, the settings for which will need to be listed in +the Makefile.
When you have built one of these libraries, there are 2 things to check: diff --git a/doc/Section_start.txt b/doc/Section_start.txt index 882a16f9cc..b5e65e4b0a 100644 --- a/doc/Section_start.txt +++ b/doc/Section_start.txt @@ -631,10 +631,10 @@ type "make package" to see all of the package-related make options. A few of the standard and user packages require additional auxiliary libraries to be compiled first. If you get a LAMMPS build error about -a missing library, this is likely the reason. The source code for -these libraries is included in the LAMMPS distribution under the "lib" -directory. Look at the lib/README file for a list of these or see -"Section_packages"_Section_packages.html of the doc pages. +a missing library, this is likely the reason. The source code or +hooks to these libraries is included in the LAMMPS distribution under +the "lib" directory. Look at the lib/README file for a list of these +or see "Section_packages"_Section_packages.html of the doc pages. Each lib directory has a README file (e.g. lib/reax/README) with instructions on how to build that library. Typically this is done @@ -643,13 +643,16 @@ in this manner: make -f Makefile.g++ :pre in the appropriate directory, e.g. in lib/reax. Some of the libraries -do not build this way. Again, see the libary README file for details. +do not build this way. Some of the directories do not even have +source code for the library, since you are expected to download and +build it separately. Again, see the libary README file for details. -In any event, you will need to use a Makefile that is a match for your -system. If one of the provided Makefiles is not appropriate for your -system you will need to edit or add one. For example, in the case of -Fortran-based libraries, your system must have a Fortran compiler, the -settings for which will need to be listed in the Makefile. +If you are building the library, you will need to use a Makefile that +is a match for your system. If one of the provided Makefiles is not +appropriate for your system you will need to edit or add one. For +example, in the case of Fortran-based libraries, your system must have +a Fortran compiler, the settings for which will need to be listed in +the Makefile. When you have built one of these libraries, there are 2 things to check: