forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13910 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
56d0caefcb
commit
cd861535f0
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@ -47,12 +47,13 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole fld gpu \
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python qeq reax replica rigid shock snap srd voronoi xtc
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PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \
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user-diffraction user-drude user-eff user-fep user-intel user-lb \
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user-diffraction user-drude user-eff user-fep user-h5md \
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user-intel user-lb \
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user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \
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user-quip user-reaxc user-smd user-sph
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PACKLIB = compress gpu kim kokkos meam poems python reax voronoi \
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user-atc user-awpmd user-colvars user-cuda user-molfile \
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user-atc user-awpmd user-colvars user-cuda user-h5md user-molfile \
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user-qmmm user-quip
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PACKALL = $(PACKAGE) $(PACKUSER)
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@ -0,0 +1,62 @@
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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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# 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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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 $1 = 1) then
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if (test -e ../Makefile.package) then
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sed -i -e 's/[^ \t]*ch5md[^ \t]* //g' ../Makefile.package
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sed -i -e 's|^PKG_INC =[ \t]*|&-I..\/..\/lib\/ch5md\/include |' ../Makefile.package
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sed -i -e 's|^PKG_PATH =[ \t]*|&-L..\/..\/lib\/ch5md |' ../Makefile.package
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sed -i -e 's|^PKG_LIB =[ \t]*|&-lch5md |' ../Makefile.package
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sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(ch5md_SYSINC) |' ../Makefile.package
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sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(ch5md_SYSLIB) |' ../Makefile.package
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sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(ch5md_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.*ch5md.*$/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\/ch5md\/Makefile.lammps
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' ../Makefile.package.settings
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fi
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elif (test $1 = 0) then
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if (test -e ../Makefile.package) then
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sed -i -e 's/[^ \t]*ch5md[^ \t]* //g' ../Makefile.package
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fi
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if (test -e ../Makefile.package.settings) then
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sed -i -e '/^include.*ch5md.*$/d' ../Makefile.package.settings
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fi
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fi
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@ -0,0 +1,9 @@
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This package provides the h5md dump style.
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See the doc page for the dump h5md command. This dump style requires
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building the bundled ch5md library in lib/h5md, and having HDF5 itself
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installed on your system (see lib/h5md/README).
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The person who created this package is Pierre de Buyl (KU Leuven); see
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http://pdebuyl.be for contact information. Please contact him directly
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if you have questions.
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@ -0,0 +1,555 @@
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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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Contributing author: Pierre de Buyl (KU Leuven)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "limits.h"
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#include "ch5md.h"
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#include "dump_h5md.h"
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#include "domain.h"
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#include "atom.h"
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#include "update.h"
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#include "group.h"
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#include "output.h"
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#include "error.h"
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#include "force.h"
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#include "memory.h"
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#include "version.h"
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using namespace LAMMPS_NS;
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#define MYMIN(a,b) ((a) < (b) ? (a) : (b))
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#define MYMAX(a,b) ((a) > (b) ? (a) : (b))
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/** Scan common options for the dump elements
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*/
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int element_args(int narg, char **arg, int *every)
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{
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int iarg=0;
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while (iarg<narg) {
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if (strcmp(arg[iarg], "every")==0) {
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if (narg<2) return -1;
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*every = atoi(arg[iarg+1]);
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iarg+=2;
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} else {
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break;
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}
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}
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return iarg;
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}
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/* ---------------------------------------------------------------------- */
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DumpH5MD::DumpH5MD(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
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{
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if (narg<6) error->all(FLERR,"Illegal dump h5md command");
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if (binary || compressed || multifile || multiproc)
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error->all(FLERR,"Invalid dump h5md filename");
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if (domain->triclinic!=0)
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error->all(FLERR,"Invalid domain for dump h5md. Only triclinic domains supported.");
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size_one = 6;
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sort_flag = 1;
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sortcol = 0;
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format_default = NULL;
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flush_flag = 0;
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unwrap_flag = 0;
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datafile_from_dump = -1;
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author_name=NULL;
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every_dump = force->inumeric(FLERR,arg[3]);
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every_position = every_image = -1;
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every_velocity = every_force = every_species = -1;
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every_charge = -1;
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do_box=true;
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create_group=true;
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bool box_is_set, create_group_is_set;
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box_is_set = create_group_is_set = false;
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int iarg=5;
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int n_parsed, default_every;
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size_one=0;
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if (every_dump==0) default_every=0; else default_every=1;
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while (iarg<narg) {
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if (strcmp(arg[iarg], "position")==0) {
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every_position=default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_position);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=domain->dimension;
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} else if (strcmp(arg[iarg], "image")==0) {
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if (every_position<0) error->all(FLERR, "Illegal dump h5md command");
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iarg+=1;
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size_one+=domain->dimension;
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every_image = every_position;
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} else if (strcmp(arg[iarg], "velocity")==0) {
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every_velocity = default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_velocity);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=domain->dimension;
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} else if (strcmp(arg[iarg], "force")==0) {
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every_force = default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_force);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=domain->dimension;
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} else if (strcmp(arg[iarg], "species")==0) {
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every_species=default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_species);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=1;
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} else if (strcmp(arg[iarg], "charge")==0) {
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if (!atom->q_flag)
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error->all(FLERR, "Requesting non-allocated quantity q in dump_h5md");
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every_charge = default_every;
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iarg+=1;
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n_parsed = element_args(narg-iarg, &arg[iarg], &every_charge);
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if (n_parsed<0) error->all(FLERR, "Illegal dump h5md command");
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iarg += n_parsed;
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size_one+=1;
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} else if (strcmp(arg[iarg], "file_from")==0) {
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if (iarg+1>=narg) {
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error->all(FLERR, "Invalid number of arguments in dump h5md");
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}
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if (box_is_set||create_group_is_set)
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error->all(FLERR, "Cannot set file_from in dump h5md after box or create_group");
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int idump;
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for (idump = 0; idump < output->ndump; idump++)
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if (strcmp(arg[iarg+1],output->dump[idump]->id) == 0) break;
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if (idump == output->ndump) error->all(FLERR,"Cound not find dump_modify ID");
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datafile_from_dump = idump;
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do_box=false;
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create_group=false;
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iarg+=2;
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} else if (strcmp(arg[iarg], "box")==0) {
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if (iarg+1>=narg) {
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error->all(FLERR, "Invalid number of arguments in dump h5md");
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}
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box_is_set = true;
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if (strcmp(arg[iarg+1], "yes")==0)
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do_box=true;
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else if (strcmp(arg[iarg+1], "no")==0)
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do_box=false;
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else
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error->all(FLERR, "Illegal dump h5md command");
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iarg+=2;
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} else if (strcmp(arg[iarg], "create_group")==0) {
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if (iarg+1>=narg) {
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error->all(FLERR, "Invalid number of arguments in dump h5md");
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}
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create_group_is_set = true;
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if (strcmp(arg[iarg+1], "yes")==0)
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create_group=true;
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else if (strcmp(arg[iarg+1], "no")==0) {
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create_group=false;
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}
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else
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error->all(FLERR, "Illegal dump h5md command");
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iarg+=2;
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} else if (strcmp(arg[iarg], "author")==0) {
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if (iarg+1>=narg) {
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error->all(FLERR, "Invalid number of arguments in dump h5md");
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}
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if (author_name==NULL) {
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author_name = new char[strlen(arg[iarg]+1)];
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strcpy(author_name, arg[iarg+1]);
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} else {
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error->all(FLERR, "Illegal dump h5md command: author argument repeated");
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}
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iarg+=2;
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} else {
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error->all(FLERR, "Invalid argument to dump h5md");
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}
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}
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// allocate global array for atom coords
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bigint n = group->count(igroup);
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natoms = static_cast<int> (n);
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if (every_position>=0)
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memory->create(dump_position,domain->dimension*natoms,"dump:position");
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if (every_image>=0)
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memory->create(dump_image,domain->dimension*natoms,"dump:image");
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if (every_velocity>=0)
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memory->create(dump_velocity,domain->dimension*natoms,"dump:velocity");
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if (every_force>=0)
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memory->create(dump_force,domain->dimension*natoms,"dump:force");
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if (every_species>=0)
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memory->create(dump_species,natoms,"dump:species");
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if (every_charge>=0)
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memory->create(dump_charge,natoms,"dump:charge");
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openfile();
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ntotal = 0;
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}
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/* ---------------------------------------------------------------------- */
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DumpH5MD::~DumpH5MD()
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{
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if (every_position>=0) {
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memory->destroy(dump_position);
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if (me==0) {
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h5md_close_element(particles_data.position);
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if (do_box)
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h5md_close_element(particles_data.box_edges);
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}
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}
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if (every_image>=0) {
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memory->destroy(dump_image);
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if (me==0) h5md_close_element(particles_data.image);
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}
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if (every_velocity>=0) {
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memory->destroy(dump_velocity);
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if (me==0) h5md_close_element(particles_data.velocity);
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}
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if (every_force>=0) {
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memory->destroy(dump_force);
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if (me==0) h5md_close_element(particles_data.force);
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}
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if (every_species>=0) {
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memory->destroy(dump_species);
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if (me==0) h5md_close_element(particles_data.species);
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}
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if (every_charge>=0) {
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memory->destroy(dump_charge);
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if (me==0) h5md_close_element(particles_data.charge);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DumpH5MD::init_style()
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{
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if (sort_flag == 0 || sortcol != 0)
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error->all(FLERR,"Dump h5md requires sorting by atom ID");
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}
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/* ---------------------------------------------------------------------- */
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void DumpH5MD::openfile()
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{
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char *group_name;
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int group_name_length;
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int dims[2];
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char *boundary[3];
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for (int i=0; i<3; i++) {
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boundary[i] = new char[9];
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if (domain->periodicity[i]==1) {
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strcpy(boundary[i], "periodic");
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} else {
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strcpy(boundary[i], "none");
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}
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}
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if (me == 0) {
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if (datafile_from_dump<0) {
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if (author_name==NULL) {
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datafile = h5md_create_file(filename, "N/A", NULL, "lammps", LAMMPS_VERSION);
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} else {
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datafile = h5md_create_file(filename, author_name, NULL, "lammps", LAMMPS_VERSION);
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}
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group_name_length = strlen(group->names[igroup]);
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group_name = new char[group_name_length];
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strcpy(group_name, group->names[igroup]);
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if (create_group) {
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particles_data = h5md_create_particles_group(datafile, group_name);
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} else {
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particles_data.group = H5Gopen(datafile.particles, group_name, H5P_DEFAULT);
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}
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delete [] group_name;
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dims[0] = natoms;
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dims[1] = domain->dimension;
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if (every_position>0) {
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particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
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h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
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}
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if (every_image>0)
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particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
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if (every_velocity>0)
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particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
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if (every_force>0)
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particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
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if (every_species>0)
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particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
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if (every_charge>0) {
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particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
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h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
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}
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} else {
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DumpH5MD* other_dump;
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other_dump=(DumpH5MD*)output->dump[datafile_from_dump];
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datafile = other_dump->datafile;
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group_name_length = strlen(group->names[igroup]);
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group_name = new char[group_name_length];
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strcpy(group_name, group->names[igroup]);
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if (create_group) {
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particles_data = h5md_create_particles_group(datafile, group_name);
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} else {
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particles_data = other_dump->particles_data;
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||||
}
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||||
dims[0] = natoms;
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dims[1] = domain->dimension;
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if (every_position>0) {
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particles_data.position = h5md_create_time_data(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, NULL);
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h5md_create_box(&particles_data, dims[1], boundary, true, NULL, &particles_data.position);
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}
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if (every_image>0)
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particles_data.image = h5md_create_time_data(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, &particles_data.position);
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||||
if (every_velocity>0)
|
||||
particles_data.velocity = h5md_create_time_data(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
if (every_force>0)
|
||||
particles_data.force = h5md_create_time_data(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
if (every_species>0)
|
||||
particles_data.species = h5md_create_time_data(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, NULL);
|
||||
if (every_charge>0) {
|
||||
particles_data.charge = h5md_create_time_data(particles_data.group, "charge", 1, dims, H5T_NATIVE_DOUBLE, NULL);
|
||||
h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
if (author_name!=NULL) delete [] author_name;
|
||||
for (int i=0; i<3; i++) {
|
||||
delete [] boundary[i];
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::write_header(bigint nbig)
|
||||
{
|
||||
return;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::pack(tagint *ids)
|
||||
{
|
||||
int m,n;
|
||||
|
||||
tagint *tag = atom->tag;
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
int *species = atom->type;
|
||||
double *q = atom->q;
|
||||
imageint *image = atom->image;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int dim=domain->dimension;
|
||||
|
||||
double xprd = domain->xprd;
|
||||
double yprd = domain->yprd;
|
||||
double zprd = domain->zprd;
|
||||
|
||||
m = n = 0;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
if (every_position>=0) {
|
||||
int ix = (image[i] & IMGMASK) - IMGMAX;
|
||||
int iy = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
|
||||
int iz = (image[i] >> IMG2BITS) - IMGMAX;
|
||||
if (unwrap_flag == 1) {
|
||||
buf[m++] = (x[i][0] + ix * xprd);
|
||||
buf[m++] = (x[i][1] + iy * yprd);
|
||||
if (dim>2) buf[m++] = (x[i][2] + iz * zprd);
|
||||
} else {
|
||||
buf[m++] = x[i][0];
|
||||
buf[m++] = x[i][1];
|
||||
if (dim>2) buf[m++] = x[i][2];
|
||||
}
|
||||
if (every_image>=0) {
|
||||
buf[m++] = ix;
|
||||
buf[m++] = iy;
|
||||
if (dim>2) buf[m++] = iz;
|
||||
}
|
||||
}
|
||||
if (every_velocity>=0) {
|
||||
buf[m++] = v[i][0];
|
||||
buf[m++] = v[i][1];
|
||||
if (dim>2) buf[m++] = v[i][2];
|
||||
}
|
||||
if (every_force>=0) {
|
||||
buf[m++] = f[i][0];
|
||||
buf[m++] = f[i][1];
|
||||
if (dim>2) buf[m++] = f[i][2];
|
||||
}
|
||||
if (every_species>=0)
|
||||
buf[m++] = species[i];
|
||||
if (every_charge>=0)
|
||||
buf[m++] = q[i];
|
||||
ids[n++] = tag[i];
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::write_data(int n, double *mybuf)
|
||||
{
|
||||
// copy buf atom coords into global array
|
||||
|
||||
int m = 0;
|
||||
int dim = domain->dimension;
|
||||
int k = dim*ntotal;
|
||||
int k_image = dim*ntotal;
|
||||
int k_velocity = dim*ntotal;
|
||||
int k_force = dim*ntotal;
|
||||
int k_species = ntotal;
|
||||
int k_charge = ntotal;
|
||||
for (int i = 0; i < n; i++) {
|
||||
if (every_position>=0) {
|
||||
for (int j=0; j<dim; j++) {
|
||||
dump_position[k++] = mybuf[m++];
|
||||
}
|
||||
if (every_image>=0)
|
||||
for (int j=0; j<dim; j++) {
|
||||
dump_image[k_image++] = mybuf[m++];
|
||||
}
|
||||
}
|
||||
if (every_velocity>=0)
|
||||
for (int j=0; j<dim; j++) {
|
||||
dump_velocity[k_velocity++] = mybuf[m++];
|
||||
}
|
||||
if (every_force>=0)
|
||||
for (int j=0; j<dim; j++) {
|
||||
dump_force[k_force++] = mybuf[m++];
|
||||
}
|
||||
if (every_species>=0)
|
||||
dump_species[k_species++] = mybuf[m++];
|
||||
if (every_charge>=0)
|
||||
dump_charge[k_charge++] = mybuf[m++];
|
||||
ntotal++;
|
||||
}
|
||||
|
||||
// if last chunk of atoms in this snapshot, write global arrays to file
|
||||
|
||||
if (ntotal == natoms) {
|
||||
if (every_dump>0) {
|
||||
write_frame();
|
||||
ntotal = 0;
|
||||
} else {
|
||||
write_fixed_frame();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int DumpH5MD::modify_param(int narg, char **arg)
|
||||
{
|
||||
if (strcmp(arg[0],"unwrap") == 0) {
|
||||
if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
|
||||
if (strcmp(arg[1],"yes") == 0) unwrap_flag = 1;
|
||||
else if (strcmp(arg[1],"no") == 0) unwrap_flag = 0;
|
||||
else error->all(FLERR,"Illegal dump_modify command");
|
||||
return 2;
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DumpH5MD::write_frame()
|
||||
{
|
||||
int local_step;
|
||||
double local_time;
|
||||
double edges[3];
|
||||
local_step = update->ntimestep;
|
||||
local_time = local_step * update->dt;
|
||||
edges[0] = boxxhi - boxxlo;
|
||||
edges[1] = boxyhi - boxylo;
|
||||
edges[2] = boxzhi - boxzlo;
|
||||
if (every_position>0) {
|
||||
if (local_step % (every_position*every_dump) == 0) {
|
||||
h5md_append(particles_data.position, dump_position, local_step, local_time);
|
||||
h5md_append(particles_data.box_edges, edges, local_step, local_time);
|
||||
if (every_image>0)
|
||||
h5md_append(particles_data.image, dump_image, local_step, local_time);
|
||||
}
|
||||
} else {
|
||||
if (do_box) h5md_append(particles_data.box_edges, edges, local_step, local_time);
|
||||
}
|
||||
if (every_velocity>0 && local_step % (every_velocity*every_dump) == 0) {
|
||||
h5md_append(particles_data.velocity, dump_velocity, local_step, local_time);
|
||||
}
|
||||
if (every_force>0 && local_step % (every_force*every_dump) == 0) {
|
||||
h5md_append(particles_data.force, dump_force, local_step, local_time);
|
||||
}
|
||||
if (every_species>0 && local_step % (every_species*every_dump) == 0) {
|
||||
h5md_append(particles_data.species, dump_species, local_step, local_time);
|
||||
}
|
||||
if (every_charge>0 && local_step % (every_charge*every_dump) == 0) {
|
||||
h5md_append(particles_data.charge, dump_charge, local_step, local_time);
|
||||
}
|
||||
}
|
||||
|
||||
void DumpH5MD::write_fixed_frame()
|
||||
{
|
||||
double edges[3];
|
||||
int dims[2];
|
||||
char *boundary[3];
|
||||
|
||||
for (int i=0; i<3; i++) {
|
||||
boundary[i] = new char[9];
|
||||
if (domain->periodicity[i]==1) {
|
||||
strcpy(boundary[i], "periodic");
|
||||
} else {
|
||||
strcpy(boundary[i], "none");
|
||||
}
|
||||
}
|
||||
|
||||
dims[0] = natoms;
|
||||
dims[1] = domain->dimension;
|
||||
|
||||
edges[0] = boxxhi - boxxlo;
|
||||
edges[1] = boxyhi - boxylo;
|
||||
edges[2] = boxzhi - boxzlo;
|
||||
if (every_position==0) {
|
||||
particles_data.position = h5md_create_fixed_data_simple(particles_data.group, "position", 2, dims, H5T_NATIVE_DOUBLE, dump_position);
|
||||
h5md_create_box(&particles_data, dims[1], boundary, false, edges, NULL);
|
||||
if (every_image==0)
|
||||
particles_data.image = h5md_create_fixed_data_simple(particles_data.group, "image", 2, dims, H5T_NATIVE_INT, dump_image);
|
||||
}
|
||||
if (every_velocity==0)
|
||||
particles_data.velocity = h5md_create_fixed_data_simple(particles_data.group, "velocity", 2, dims, H5T_NATIVE_DOUBLE, dump_velocity);
|
||||
if (every_force==0)
|
||||
particles_data.force = h5md_create_fixed_data_simple(particles_data.group, "force", 2, dims, H5T_NATIVE_DOUBLE, dump_force);
|
||||
if (every_species==0)
|
||||
particles_data.species = h5md_create_fixed_data_simple(particles_data.group, "species", 1, dims, H5T_NATIVE_INT, dump_species);
|
||||
if (every_charge==0) {
|
||||
particles_data.charge = h5md_create_fixed_data_simple(particles_data.group, "charge", 1, dims, H5T_NATIVE_INT, dump_charge);
|
||||
h5md_write_string_attribute(particles_data.group, "charge", "type", "effective");
|
||||
}
|
||||
|
||||
for (int i=0; i<3; i++) {
|
||||
delete [] boundary[i];
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,107 @@
|
|||
/* -*- 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.
|
||||
Contributing author: Pierre de Buyl (KU Leuven)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef DUMP_CLASS
|
||||
|
||||
DumpStyle(h5md,DumpH5MD)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_DUMP_H5MD_H
|
||||
#define LMP_DUMP_H5MD_H
|
||||
|
||||
#include "dump.h"
|
||||
#include "ch5md.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class DumpH5MD : public Dump {
|
||||
public:
|
||||
DumpH5MD(class LAMMPS *, int, char**);
|
||||
virtual ~DumpH5MD();
|
||||
|
||||
private:
|
||||
int natoms,ntotal;
|
||||
int nevery_save;
|
||||
int unwrap_flag; // 1 if atom coords are unwrapped, 0 if no
|
||||
h5md_file datafile;
|
||||
int datafile_from_dump;
|
||||
h5md_particles_group particles_data;
|
||||
char *author_name;
|
||||
|
||||
bool do_box;
|
||||
bool create_group;
|
||||
|
||||
// data arrays and intervals
|
||||
int every_dump;
|
||||
double *dump_position;
|
||||
int every_position;
|
||||
int *dump_image;
|
||||
int every_image;
|
||||
double *dump_velocity;
|
||||
int every_velocity;
|
||||
double *dump_force;
|
||||
int every_force;
|
||||
int *dump_species;
|
||||
int every_species;
|
||||
int *dump_charge;
|
||||
int every_charge;
|
||||
|
||||
void init_style();
|
||||
int modify_param(int, char **);
|
||||
void openfile();
|
||||
void write_header(bigint);
|
||||
void pack(tagint *);
|
||||
void write_data(int, double *);
|
||||
|
||||
void write_frame();
|
||||
void write_fixed_frame();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#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.
|
||||
|
||||
E: Invalid number of arguments in dump h5md
|
||||
|
||||
Make sure that each data item (position, etc.) is followed by a dump
|
||||
interval.
|
||||
|
||||
E: Dump h5md requires sorting by atom ID
|
||||
|
||||
Use the dump_modify sort command to enable this.
|
||||
|
||||
E: Cannot use variable every setting for dump xtc
|
||||
|
||||
The format of this file requires snapshots at regular intervals.
|
||||
|
||||
E: Cannot change dump_modify every for dump xtc
|
||||
|
||||
The frequency of writing dump xtc snapshots cannot be changed.
|
||||
|
||||
E: Cannot set file_from in dump h5md after box or create_group
|
||||
|
||||
The file_from option modifies the box and create_group options and
|
||||
they must appear after file_from if used.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue