From c4801b6f5c22ecb201a6fdd6e331516d7e5ccab2 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 9 Feb 2007 23:41:45 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@289 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_errors.html | 2 +- doc/Section_history.html | 3 +-- doc/Section_history.txt | 3 +-- doc/Section_intro.html | 20 +++++++++++++++----- doc/Section_intro.txt | 22 +++++++++++++++++----- 5 files changed, 35 insertions(+), 15 deletions(-) diff --git a/doc/Section_errors.html b/doc/Section_errors.html index a27f2b6065..0f73e09ff8 100644 --- a/doc/Section_errors.html +++ b/doc/Section_errors.html @@ -73,7 +73,7 @@ of the following cases: allocated. Most reasonable MD runs are compute limited, not memory limited, so this shouldn't be a bottleneck on most platforms. Almost all large memory allocations in the code are done via C-style malloc's -which will generate an error message if you run out of memory. +prwhich will generate an error message if you run out of memory. Smaller chunks of memory are allocated via C++ "new" statements. If you are unlucky you could run out of memory just when one of these small requests is made, in which case the code will crash or hang (in diff --git a/doc/Section_history.html b/doc/Section_history.html index 881d419cd3..996c175d62 100644 --- a/doc/Section_history.html +++ b/doc/Section_history.html @@ -35,8 +35,7 @@ time or interest; others are just a lot of work!
  • torsional shear boundary conditions and temperature calculation
  • bond creation potentials
  • point dipole force fields -
  • many-body and bond-order potentials for materials like C, Si, or silica -
  • modified EAM (MEAM) potentials for metals +
  • REBO bond-order potential
  • ReaxFF force field from Bill Goddard's group
  • Parinello-Rahman non-rectilinear simulation box diff --git a/doc/Section_history.txt b/doc/Section_history.txt index 5ddf6b7cd3..2979a6cd01 100644 --- a/doc/Section_history.txt +++ b/doc/Section_history.txt @@ -32,8 +32,7 @@ Monte Carlo bond-swapping for polymers (was in Fortran LAMMPS) torsional shear boundary conditions and temperature calculation bond creation potentials point dipole force fields -many-body and bond-order potentials for materials like C, Si, or silica -modified EAM (MEAM) potentials for metals +REBO bond-order potential ReaxFF force field from Bill Goddard's group Parinello-Rahman non-rectilinear simulation box :ul diff --git a/doc/Section_intro.html b/doc/Section_intro.html index 81e6b50fbc..bbfd83cd43 100644 --- a/doc/Section_intro.html +++ b/doc/Section_intro.html @@ -28,8 +28,8 @@ the years.

    LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model -atomic, polymeric, biological, metallic, or granular systems using a -variety of force fields and boundary conditions. +atomic, polymeric, biological, metallic, granular, and coarse-grained +systems using a variety of force fields and boundary conditions.

    For examples of LAMMPS simulations, see the Publications page of the LAMMPS WWW Site. @@ -108,6 +108,7 @@ LAMMPS.

  • all-atom polymers, organic molecules, proteins, DNA
  • metals
  • granular materials +
  • coarse-grained mesoscale models
  • hybrid systems

    Force fields: @@ -117,8 +118,8 @@ LAMMPS. improper style, kspace style commands)

    -
    • pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, Yukawa, embedded atom method (EAM, Finnis/Sinclair), frictional granular, -
    • Debye, soft, DPD, class 2 (COMPASS), tabulated, hybrid +
      • pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, Yukawa, frictional granular, Debye, soft, DPD, class 2 (COMPASS), tabulated, hybrid +
      • manybody potentials: EAM, Finnis/Sinclair, modified EAM (MEAM), Stillinger-Weber, Tersoff
      • bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable), hybrid
      • angle potentials: harmonic, CHARMM, cosine, cosine/squared, class 2 (COMPASS), hybrid
      • dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS, hybrid @@ -479,7 +480,16 @@ features in LAMMPS: DCD and XTC dump styles Naveen Michaud-Agrawal (Johns Hopkins U) breakable bond quartic potential Chris Lorenz and Mark Stevens (SNL) faster pair hybrid potential James Fischer (High Performance Technologies, Inc), Vincent Natoli and David Richie (Stone Ridge Technology) -POEMS coupled rigid body integrator Rudranarayan Mukherjee (RPI) +POEMS coupled rigid body integrator Rudranarayan Mukherjee (RPI) +OPLS dihedral potential Mark Stevens (Sandia) +multi-letter variable names Naveen Michaud-Agrawal (Johns Hopkins U) +fix momentum and recenter Naveen Michaud-Agrawal (Johns Hopkins U) +LJ tail corrections for energy/pressure Paul Crozier (Sandia) +region prism Pieter in't Veld (Sandia) +Stillinger-Weber and Tersoff potentials Aidan Thompson (Sandia) +fix wall/lj126 Mark Stevens (Sandia) +optimized pair potentials for lj/cut, charmm/long, eam, morse James Fischer (High Performance Tech), David Richie and Vincent Natol (Stone Ridge Technologies) +MEAM potential Greg Wagner (Sandia)

        Other CRADA partners involved in the design and testing of LAMMPS were diff --git a/doc/Section_intro.txt b/doc/Section_intro.txt index b7831926a9..8d988d6927 100644 --- a/doc/Section_intro.txt +++ b/doc/Section_intro.txt @@ -25,8 +25,8 @@ the years. LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model -atomic, polymeric, biological, metallic, or granular systems using a -variety of force fields and boundary conditions. +atomic, polymeric, biological, metallic, granular, and coarse-grained +systems using a variety of force fields and boundary conditions. For examples of LAMMPS simulations, see the Publications page of the "LAMMPS WWW Site"_lws. @@ -104,6 +104,7 @@ Kinds of systems LAMMPS can simulate: :h4 all-atom polymers, organic molecules, proteins, DNA metals granular materials + coarse-grained mesoscale models hybrid systems :ul Force fields: :h4 @@ -113,8 +114,10 @@ Force fields: :h4 commands) pairwise potentials: Lennard-Jones, Coulombic, Buckingham, Morse, \ - Yukawa, embedded atom method (EAM, Finnis/Sinclair), frictional granular, - Debye, soft, DPD, class 2 (COMPASS), tabulated, hybrid + Yukawa, frictional granular, Debye, soft, DPD, class 2 (COMPASS), \ + tabulated, hybrid + manybody potentials: EAM, Finnis/Sinclair, modified EAM (MEAM), \ + Stillinger-Weber, Tersoff bond potentials: harmonic, FENE, Morse, nonlinear, class 2, \ quartic (breakable), hybrid angle potentials: harmonic, CHARMM, cosine, cosine/squared, \ @@ -467,7 +470,16 @@ breakable bond quartic potential: Chris Lorenz and Mark Stevens (SNL) faster pair hybrid potential: James Fischer \ (High Performance Technologies, Inc), Vincent Natoli and \ David Richie (Stone Ridge Technology) -POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI) :tb(s=:) +POEMS coupled rigid body integrator: Rudranarayan Mukherjee (RPI) +OPLS dihedral potential: Mark Stevens (Sandia) +multi-letter variable names : Naveen Michaud-Agrawal (Johns Hopkins U) +fix momentum and recenter : Naveen Michaud-Agrawal (Johns Hopkins U) +LJ tail corrections for energy/pressure : Paul Crozier (Sandia) +region prism : Pieter in't Veld (Sandia) +Stillinger-Weber and Tersoff potentials : Aidan Thompson (Sandia) +fix wall/lj126 : Mark Stevens (Sandia) +optimized pair potentials for lj/cut, charmm/long, eam, morse : James Fischer (High Performance Tech), David Richie and Vincent Natol (Stone Ridge Technologies) +MEAM potential : Greg Wagner (Sandia) :tb(s=:) Other CRADA partners involved in the design and testing of LAMMPS were