From d39edd80b8d6351703e35e3502ca1e90cb9c8745 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 31 Jan 2012 22:57:34 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7626 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_intro.html | 8 ++++---- doc/Section_intro.txt | 5 +++-- doc/Section_packages.html | 6 +++++- doc/Section_packages.txt | 4 ++++ doc/Section_start.html | 23 +++++++++++++---------- doc/Section_start.txt | 23 +++++++++++++---------- 6 files changed, 42 insertions(+), 27 deletions(-) diff --git a/doc/Section_intro.html b/doc/Section_intro.html index b4b158029d..434b0a226a 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -155,13 +155,13 @@ commands)
  • polymer potentials: all-atom, united-atom, bead-spring, breakable
  • water potentials: TIP3P, TIP4P, SPC
  • implicit solvent potentials: hydrodynamic lubrication, Debye +
  • KIM archive 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 +
  • 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 -

    hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation - overlaid potentials: superposition of multiple pair potentials -

    Atom creation

    (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. DIPOLE point dipole particles - pair_style dipole/cut dipole - FLD Fast Lubrication Dynamics Kumar & Bybee & Higdon (1) pair_style lubricateU - - GPU GPU-enabled potentials Mike Brown (ORNL) Section accelerate gpu lib/gpu -GRANULAR granular systems - howto pour - +GRANULAR granular systems - >howto pour - +KIM openKIM potentials Smirichinski & Elliot & Tadmor (3) pair_style kim kim lib/kim KSPACE long-range Coulombic solvers - kspace_style peptide - MANYBODY many-body potentials - pair_style tersoff shear - MEAM modified EAM potential Greg Wagner (Sandia) pair_style meam meam lib/meam @@ -77,6 +78,9 @@ 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 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: