forked from lijiext/lammps
initial dummy version of fix_latte.cpp
This commit is contained in:
Steve Plimpton
parent
a23b287a7a
commit
6f23f6535c
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@ -0,0 +1,5 @@
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# Settings that the LAMMPS build will import when this package is installed
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latte_SYSINC =
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latte_SYSLIB = -lgfortran
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latte_SYSPATH =
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@ -0,0 +1,5 @@
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# Settings that the LAMMPS build will import when this package library is used
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latte_SYSINC =
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latte_SYSLIB = -lifcore -lsvml -lompstub -limf
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latte_SYSPATH = -L/opt/intel/fce/10.0.023/lib
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@ -0,0 +1,33 @@
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This directory contains build settings for the LATTE library which
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is required to use the LATTE package and its fix latte command in a
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LAMMPS input script.
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Information about the LATTE DFTB code can be found at ... The LATTE
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developement effort is led by Anders Niklasson, etc at LANLS.
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To download, build, and install LATTE as a library on your system,
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follow these steps. We are working on scripts that will automate this
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process.
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Go to this web site: https://??? and download a current tarball. The
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tarball you download is "latte-??.tgz", which can be unpacked in this
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directory or wherever you wish:
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tar xvfz latte*tgz
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Note that if you unpack and build LATTE in this directory, when you
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download a new LAMMPS tarball, the files you have added here will be
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lost. So you likely want to build it somewhere else.
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Build instructions for LATTE library ...
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When you have successully built the LATTE library, you can build
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LAMMPS with the LATTE package installed:
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$ cd lammps/src
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$ make yes-latte
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$ make g++ (or whatever target you wish)
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Note that the Makefile.lammps file in this directory is required to
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allow the LAMMPS build to find the necessary LATTE files. You should
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not normally need to edit this file.
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@ -0,0 +1,67 @@
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# Install/unInstall package files in LAMMPS
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# mode = 0/1/2 for uninstall/install/update
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mode=$1
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# enforce using portable C locale
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LC_ALL=C
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export LC_ALL
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# arg1 = file, arg2 = file it depends on
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action () {
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if (test $mode = 0) then
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rm -f ../$1
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elif (! cmp -s $1 ../$1) then
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if (test -z "$2" || test -e ../$2) then
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cp $1 ..
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if (test $mode = 2) then
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echo " updating src/$1"
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fi
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fi
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elif (test -n "$2") then
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if (test ! -e ../$2) then
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rm -f ../$1
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fi
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fi
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}
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# all package files with no dependencies
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for file in *.cpp *.h; do
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action $file
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done
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# edit 2 Makefile.package files to include/exclude package info
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if (test $1 = 1) then
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if (test -e ../Makefile.package) then
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sed -i -e 's/[^ \t]*latte[^ \t]* //' ../Makefile.package
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sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/latte |' ../Makefile.package
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sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/latte |' ../Makefile.package
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#sed -i -e 's|^PKG_LIB =[ \t]*|&-llatte |' ../Makefile.package
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sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(latte_SYSINC) |' ../Makefile.package
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sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(latte_SYSLIB) |' ../Makefile.package
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sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(latte_SYSPATH) |' ../Makefile.package
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fi
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if (test -e ../Makefile.package.settings) then
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sed -i -e '/^include.*latte.*$/d' ../Makefile.package.settings
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# multiline form needed for BSD sed on Macs
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sed -i -e '4 i \
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include ..\/..\/lib\/latte\/Makefile.lammps
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' ../Makefile.package.settings
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fi
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elif (test $1 = 0) then
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if (test -e ../Makefile.package) then
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sed -i -e 's/[^ \t]*latte[^ \t]* //' ../Makefile.package
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fi
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if (test -e ../Makefile.package.settings) then
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sed -i -e '/^include.*latte.*$/d' ../Makefile.package.settings
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fi
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fi
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This package provides a fix latte command which is a wrapper on the
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LATTE DFTB code, so that molecular dynamics can be run with LAMMPS
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using density-functional tight-binding quantum forces calculated by
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LATTE. More information on LATTE can be found at "web site". Its
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authors are Anders Niklasson, etc at LANL.
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Using this package requires the LATTE code to be downloaded and built
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as a library on your system. The library can be downloaded and built
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in lib/latte or elsewhere on your system, which must be done before
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building LAMMPS with this package. Details of the download, build, and
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install process for LATTE are given in the lib/latte/README file, and
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scripts are provided to help automate the process.
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Also see the LAMMPS manual for general information on building LAMMPS
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with external libraries. The settings in the Makefile.lammps file in
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lib/latte must be correct for LAMMPS to build correctly with this
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package installed. However, the default settings should be correct in
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most cases and the Makefile.lammps file usually will not need to be
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changed.
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Once you have successfully built LAMMPS with this package and the
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LATTE library you can test it using an input file from the examples
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dir:
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./lmp_serial < lammps/examples/latte/in.latte
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This pair style was written in collaboration with the LATTE
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developers.
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@ -0,0 +1,283 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include <stdio.h>
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#include <string.h>
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#include "fix_latte.h"
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "neighbor.h"
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#include "neigh_request.h"
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#include "neigh_list.h"
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#include "modify.h"
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#include "compute.h"
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#include "comm.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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#define INVOKED_PERATOM 8
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/* ---------------------------------------------------------------------- */
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FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg != 4) error->all(FLERR,"Illegal fix latte command");
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// store pe/atom ID used for input of Coulomb potential to LATTE
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// insure it is valid for these computations
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int n = strlen(arg[3]) + 1;
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id_pe = new char[n];
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strcpy(id_pe,arg[3]);
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int ipe = modify->find_compute(id_pe);
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if (ipe < 0) error->all(FLERR,"Could not find fix latte compute ID");
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if (modify->compute[ipe]->peatomflag == 0)
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error->all(FLERR,"Fix latte compute ID does not compute pe/atom");
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// initialize LATTE with LAMMPS info about box, atoms, atom types, etc ?
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// may need to be done in init() ??
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// any per-atom quantities to allocate/initialize for LAMMPS?
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// i.e. quantities carried with atoms across timesteps ??
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}
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/* ---------------------------------------------------------------------- */
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FixLatte::~FixLatte()
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{
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delete [] id_pe;
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}
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/* ---------------------------------------------------------------------- */
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int FixLatte::setmask()
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{
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int mask = 0;
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mask |= INITIAL_INTEGRATE;
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mask |= FINAL_INTEGRATE;
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mask |= POST_FORCE;
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mask |= MIN_POST_FORCE;
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mask |= THERMO_ENERGY;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixLatte::init()
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{
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// error checks
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int ipe = modify->find_compute(id_pe);
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if (ipe < 0) error->all(FLERR,"Could not find fix latte compute ID");
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c_pe = modify->compute[ipe];
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// warn if any integrate fix comes after this one
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// is it actually necessary for q(n) update to come after x,v update ??
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int after = 0;
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int flag = 0;
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for (int i = 0; i < modify->nfix; i++) {
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if (strcmp(id,modify->fix[i]->id) == 0) after = 1;
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else if ((modify->fmask[i] & INITIAL_INTEGRATE) && after) flag = 1;
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}
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if (flag && comm->me == 0)
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error->warning(FLERR,"Fix latte should come after all other "
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"integration fixes");
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// need a full neighbor list
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// perpetual list, built whenever re-neighboring occurs
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->pair = 0;
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neighbor->requests[irequest]->fix = 1;
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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// integrator timesteps
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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// any more LATTE initialization to do ?
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}
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/* ---------------------------------------------------------------------- */
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void FixLatte::init_list(int id, NeighList *ptr)
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{
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list = ptr;
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}
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/* ---------------------------------------------------------------------- */
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void FixLatte::setup(int vflag)
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{
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post_force(vflag);
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}
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/* ---------------------------------------------------------------------- */
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void FixLatte::min_setup(int vflag)
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{
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// for minimize, what about charge DOFs ??
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post_force(vflag);
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}
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/* ----------------------------------------------------------------------
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integrate electronic degrees of freedom
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------------------------------------------------------------------------- */
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void FixLatte::initial_integrate(int vflag)
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{
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// what do I do here for q(n) update?
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// is it the same variable as LAMMPS q, I think so
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// is it an Euler update or VV update ??
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/*
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double dtfm;
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// update v and x of atoms in group
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double *mass = atom->mass;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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x[i][0] += dtv * v[i][0];
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x[i][1] += dtv * v[i][1];
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x[i][2] += dtv * v[i][2];
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}
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*/
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}
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/* ---------------------------------------------------------------------- */
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void FixLatte::post_force(int vflag)
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{
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// what should cutoffs be for passing neighlist info to LATTE ??
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// do cutoffs include many self image atoms for tiny periodic system ??
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int i,j,ii,jj,inum,jnum;
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int *ilist,*jlist,*numneigh,**firstneigh;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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// enforce a different cutoff than pair style?
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// what are optimal cutoffs for pair/Kspace for tiny system?
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// operations on I/J pairs if necessary
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}
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}
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// invoke compute pe/atom
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// wrap with clear/add and trigger pe/atom calculation every step
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// Coulomb potential should just be pe[i]/q[i] ??
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modify->clearstep_compute();
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if (!(c_pe->invoked_flag & INVOKED_PERATOM)) {
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c_pe->compute_peratom();
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c_pe->invoked_flag |= INVOKED_PERATOM;
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}
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double *pe = c_pe->vector_atom;
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modify->addstep_compute(update->ntimestep+1);
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// construct H0,S,Z
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// setup full Hamiltonian H(R,n)
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// calculate density matrix D and charge q(n)
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// calculate DFTB forces via LATTE = F(R,H0,S,Z,D,q,n)
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// how to pass neighbor list and Coulomb potential to LATTE ??
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// HERE is where main call to LATTE goes to get forces
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// simply add the returned forces to atom->f
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// how to request/get global or per-atom energy back from LATTE ??
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// how to request/get global or per-atom virial back from LATTE ??
|
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}
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|
||||
/* ----------------------------------------------------------------------
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integrate electronic degrees of freedom
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------------------------------------------------------------------------- */
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void FixLatte::final_integrate()
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{
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// possibly nothing to do here if Euler step of q(n) ??
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/*
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double dtfm;
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// update v of atoms in group
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double **v = atom->v;
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double **f = atom->f;
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double *mass = atom->mass;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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if (igroup == atom->firstgroup) nlocal = atom->nfirst;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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dtfm = dtf / mass[type[i]];
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v[i][0] += dtfm * f[i][0];
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v[i][1] += dtfm * f[i][1];
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v[i][2] += dtfm * f[i][2];
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}
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*/
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}
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||||
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||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixLatte::reset_dt()
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{
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||||
// will we ever auto-adjust the timestep ??
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dtv = update->dt;
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dtf = 0.5 * update->dt * force->ftm2v;
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||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
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||||
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double FixLatte::compute_scalar()
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{
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||||
// return DFTB global energy
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||||
return 0.0;
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||||
}
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||||
|
||||
|
|
@ -0,0 +1,63 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
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||||
|
||||
FixStyle(latte,FixLatte)
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||||
|
||||
#else
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||||
|
||||
#ifndef LMP_FIX_LATTE_H
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||||
#define LMP_FIX_LATTE_H
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||||
|
||||
#include "fix.h"
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||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixLatte : public Fix {
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||||
public:
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||||
FixLatte(class LAMMPS *, int, char **);
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||||
virtual ~FixLatte();
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||||
int setmask();
|
||||
void init();
|
||||
void init_list(int, class NeighList *);
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void initial_integrate(int);
|
||||
void post_force(int);
|
||||
void final_integrate();
|
||||
void reset_dt();
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||||
double compute_scalar();
|
||||
|
||||
protected:
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||||
double dtv,dtf;
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||||
char *id_pe;
|
||||
|
||||
class NeighList *list;
|
||||
class Compute *c_pe;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
*/
|
||||
|
|
@ -44,8 +44,8 @@ endif
|
|||
# Package variables
|
||||
|
||||
PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
|
||||
granular kim \
|
||||
kokkos kspace manybody mc meam misc molecule mpiio opt peri poems \
|
||||
granular kim kokkos kspace latte manybody mc meam misc \
|
||||
molecule mpiio opt peri poems \
|
||||
python qeq reax replica rigid shock snap srd voronoi
|
||||
|
||||
PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars \
|
||||
|
|
@ -55,7 +55,7 @@ PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars \
|
|||
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
|
||||
user-vtk
|
||||
|
||||
PACKLIB = compress gpu kim kokkos meam mpiio poems python reax voronoi \
|
||||
PACKLIB = compress gpu kim kokkos latte meam mpiio poems python reax voronoi \
|
||||
user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
|
||||
user-nc-dump user-qmmm user-quip user-smd user-vtk
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue