From c85a42ab6d62018b20b02714252eb2e98f120e40 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 19 Aug 2015 15:11:20 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13905 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/COMPRESS/Install.sh | 60 +++++++++++++ src/COMPRESS/README | 13 +++ src/COMPRESS/dump_atom_gz.cpp | 145 ++++++++++++++++++++++++++++++ src/COMPRESS/dump_atom_gz.h | 55 ++++++++++++ src/COMPRESS/dump_cfg_gz.cpp | 154 ++++++++++++++++++++++++++++++++ src/COMPRESS/dump_cfg_gz.h | 55 ++++++++++++ src/COMPRESS/dump_custom_gz.cpp | 145 ++++++++++++++++++++++++++++++ src/COMPRESS/dump_custom_gz.h | 55 ++++++++++++ src/COMPRESS/dump_xyz_gz.cpp | 125 ++++++++++++++++++++++++++ src/COMPRESS/dump_xyz_gz.h | 55 ++++++++++++ src/GPU/Install.sh | 6 ++ src/GPU/fix_gpu.cpp | 1 + src/Makefile | 5 +- src/compute.h | 4 + src/pair.cpp | 63 +++++++++++++ src/pair.h | 9 ++ 16 files changed, 948 insertions(+), 2 deletions(-) create mode 100644 src/COMPRESS/Install.sh create mode 100644 src/COMPRESS/README create mode 100644 src/COMPRESS/dump_atom_gz.cpp create mode 100644 src/COMPRESS/dump_atom_gz.h create mode 100644 src/COMPRESS/dump_cfg_gz.cpp create mode 100644 src/COMPRESS/dump_cfg_gz.h create mode 100644 src/COMPRESS/dump_custom_gz.cpp create mode 100644 src/COMPRESS/dump_custom_gz.h create mode 100644 src/COMPRESS/dump_xyz_gz.cpp create mode 100644 src/COMPRESS/dump_xyz_gz.h diff --git a/src/COMPRESS/Install.sh b/src/COMPRESS/Install.sh new file mode 100644 index 0000000000..49bc09f709 --- /dev/null +++ b/src/COMPRESS/Install.sh @@ -0,0 +1,60 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# all package files with no dependencies + +for file in *.cpp *.h; do + action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*compress[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(compress_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(compress_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(compress_SYSPATH) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*compress.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/compress\/Makefile.lammps +' ../Makefile.package.settings + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*compress[^ \t]* //' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*compress.*$/d' ../Makefile.package.settings + fi + +fi diff --git a/src/COMPRESS/README b/src/COMPRESS/README new file mode 100644 index 0000000000..31f30d9e6a --- /dev/null +++ b/src/COMPRESS/README @@ -0,0 +1,13 @@ +This package provides alternative styles that allow compressed file I/O +via compression libraries. This is similar to what is enabled through +using the -DLAMMPS_GZIP preprocessor flag, but it does not open a pipe +to an external executable that handles the compression. These styles +use library calls to libraries like zlib instead and thus have to be +compiled using the library header files and linked to the respective +library. This provides an alternative for compressed file I/O on systems +where using a pipe can cause problems, e.g. when using RDMA communication +with pinned memory like clusters with infiniband or myrinet. + +At the moment a few selected dump styles are supported +for writing via this packaging. + diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp new file mode 100644 index 0000000000..ccbc8ecb6d --- /dev/null +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -0,0 +1,145 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "dump_atom_gz.h" +#include "domain.h" +#include "error.h" +#include "update.h" + +#include +#include + +using namespace LAMMPS_NS; + +DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : + DumpAtom(lmp, narg, arg) +{ + gzFp = NULL; + + if (!compressed) + error->all(FLERR,"Dump atom/gz only writes compressed files"); +} + +/* ---------------------------------------------------------------------- */ + +DumpAtomGZ::~DumpAtomGZ() +{ + if (gzFp) gzclose(gzFp); + gzFp = NULL; + fp = NULL; +} + +/* ---------------------------------------------------------------------- + generic opening of a dump file + ASCII or binary or gzipped + some derived classes override this function +------------------------------------------------------------------------- */ + +void DumpAtomGZ::openfile() +{ + // single file, already opened, so just return + + if (singlefile_opened) return; + if (multifile == 0) singlefile_opened = 1; + + // if one file per timestep, replace '*' with current timestep + + char *filecurrent = filename; + if (multiproc) filecurrent = multiname; + + if (multifile) { + char *filestar = filecurrent; + filecurrent = new char[strlen(filestar) + 16]; + char *ptr = strchr(filestar,'*'); + *ptr = '\0'; + if (padflag == 0) + sprintf(filecurrent,"%s" BIGINT_FORMAT "%s", + filestar,update->ntimestep,ptr+1); + else { + char bif[8],pad[16]; + strcpy(bif,BIGINT_FORMAT); + sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]); + sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1); + } + *ptr = '*'; + } + + // each proc with filewriter = 1 opens a file + + if (filewriter) { + if (append_flag) { + gzFp = gzopen(filecurrent,"ab9"); + } else { + gzFp = gzopen(filecurrent,"wb9"); + } + + if (gzFp == NULL) error->one(FLERR,"Cannot open dump file"); + } else gzFp = NULL; + + // delete string with timestep replaced + + if (multifile) delete [] filecurrent; +} + +/* ---------------------------------------------------------------------- */ + +void DumpAtomGZ::write_header(bigint ndump) +{ + if ((multiproc) || (!multiproc && me == 0)) { + if (domain->triclinic == 0) { + gzprintf(gzFp,"ITEM: TIMESTEP\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); + gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); + gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); + gzprintf(gzFp,"%g %g\n",boxxlo,boxxhi); + gzprintf(gzFp,"%g %g\n",boxylo,boxyhi); + gzprintf(gzFp,"%g %g\n",boxzlo,boxzhi); + gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); + } else { + gzprintf(gzFp,"ITEM: TIMESTEP\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); + gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); + gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); + gzprintf(gzFp,"%g %g %g\n",boxxlo,boxxhi,boxxy); + gzprintf(gzFp,"%g %g %g\n",boxylo,boxyhi,boxxz); + gzprintf(gzFp,"%g %g %g\n",boxzlo,boxzhi,boxyz); + gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); + } + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpAtomGZ::write_data(int n, double *mybuf) +{ + gzwrite(gzFp,mybuf,sizeof(char)*n); +} + +/* ---------------------------------------------------------------------- */ + +void DumpAtomGZ::write() +{ + DumpAtom::write(); + if (filewriter) { + if (multifile) { + gzclose(gzFp); + gzFp = NULL; + } else { + if (flush_flag) + gzflush(gzFp,Z_SYNC_FLUSH); + } + } +} + diff --git a/src/COMPRESS/dump_atom_gz.h b/src/COMPRESS/dump_atom_gz.h new file mode 100644 index 0000000000..3a91844de6 --- /dev/null +++ b/src/COMPRESS/dump_atom_gz.h @@ -0,0 +1,55 @@ +/* -*- 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 DUMP_CLASS + +DumpStyle(atom/gz,DumpAtomGZ) + +#else + +#ifndef LMP_DUMP_ATOM_GZ_H +#define LMP_DUMP_ATOM_GZ_H + +#include "dump_atom.h" + +// forward definition from zlib.h +typedef struct gzFile_s *gzFile; + +namespace LAMMPS_NS { + +class DumpAtomGZ : public DumpAtom { + public: + DumpAtomGZ(class LAMMPS *, int, char **); + virtual ~DumpAtomGZ(); + + protected: + gzFile gzFp; // file pointer for the compressed output stream + + virtual void openfile(); + virtual void write_header(bigint); + virtual void write_data(int, double *); + virtual void write(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Dump atom/gz only writes compressed files + +The dump atom/gz output file name must have a .gz suffix. + +*/ diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp new file mode 100644 index 0000000000..0a5f1a6314 --- /dev/null +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -0,0 +1,154 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "dump_cfg_gz.h" +#include "atom.h" +#include "domain.h" +#include "error.h" +#include "update.h" + +#include +#include + +using namespace LAMMPS_NS; +#define UNWRAPEXPAND 10.0 + +DumpCFGGZ::DumpCFGGZ(LAMMPS *lmp, int narg, char **arg) : + DumpCFG(lmp, narg, arg) +{ + gzFp = NULL; + + if (!compressed) + error->all(FLERR,"Dump cfg/gz only writes compressed files"); +} + + +/* ---------------------------------------------------------------------- */ + +DumpCFGGZ::~DumpCFGGZ() +{ + if (gzFp) gzclose(gzFp); + gzFp = NULL; + fp = NULL; +} + + +/* ---------------------------------------------------------------------- + generic opening of a dump file + ASCII or binary or gzipped + some derived classes override this function +------------------------------------------------------------------------- */ + +void DumpCFGGZ::openfile() +{ + // single file, already opened, so just return + + if (singlefile_opened) return; + if (multifile == 0) singlefile_opened = 1; + + // if one file per timestep, replace '*' with current timestep + + char *filecurrent = filename; + if (multiproc) filecurrent = multiname; + + if (multifile) { + char *filestar = filecurrent; + filecurrent = new char[strlen(filestar) + 16]; + char *ptr = strchr(filestar,'*'); + *ptr = '\0'; + if (padflag == 0) + sprintf(filecurrent,"%s" BIGINT_FORMAT "%s", + filestar,update->ntimestep,ptr+1); + else { + char bif[8],pad[16]; + strcpy(bif,BIGINT_FORMAT); + sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]); + sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1); + } + *ptr = '*'; + } + + // each proc with filewriter = 1 opens a file + + if (filewriter) { + if (append_flag) { + gzFp = gzopen(filecurrent,"ab9"); + } else { + gzFp = gzopen(filecurrent,"wb9"); + } + + if (gzFp == NULL) error->one(FLERR,"Cannot open dump file"); + } else gzFp = NULL; + + // delete string with timestep replaced + + if (multifile) delete [] filecurrent; +} + +/* ---------------------------------------------------------------------- */ + +void DumpCFGGZ::write_header(bigint n) +{ + // set scale factor used by AtomEye for CFG viz + // default = 1.0 + // for peridynamics, set to pre-computed PD scale factor + // so PD particles mimic C atoms + // for unwrapped coords, set to UNWRAPEXPAND (10.0) + // so molecules are not split across periodic box boundaries + + double scale = 1.0; + if (atom->peri_flag) scale = atom->pdscale; + else if (unwrapflag == 1) scale = UNWRAPEXPAND; + + char str[64]; + sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT); + gzprintf(gzFp,str,n); + gzprintf(gzFp,"A = %g Angstrom (basic length-scale)\n",scale); + gzprintf(gzFp,"H0(1,1) = %g A\n",domain->xprd); + gzprintf(gzFp,"H0(1,2) = 0 A \n"); + gzprintf(gzFp,"H0(1,3) = 0 A \n"); + gzprintf(gzFp,"H0(2,1) = %g A \n",domain->xy); + gzprintf(gzFp,"H0(2,2) = %g A\n",domain->yprd); + gzprintf(gzFp,"H0(2,3) = 0 A \n"); + gzprintf(gzFp,"H0(3,1) = %g A \n",domain->xz); + gzprintf(gzFp,"H0(3,2) = %g A \n",domain->yz); + gzprintf(gzFp,"H0(3,3) = %g A\n",domain->zprd); + gzprintf(gzFp,".NO_VELOCITY.\n"); + gzprintf(gzFp,"entry_count = %d\n",nfield-2); + for (int i = 0; i < nfield-5; i++) + gzprintf(gzFp,"auxiliary[%d] = %s\n",i,auxname[i]); +} + +/* ---------------------------------------------------------------------- */ + +void DumpCFGGZ::write_data(int n, double *mybuf) +{ + gzwrite(gzFp,mybuf,sizeof(char)*n); +} + +/* ---------------------------------------------------------------------- */ + +void DumpCFGGZ::write() +{ + DumpCFG::write(); + if (filewriter) { + if (multifile) { + gzclose(gzFp); + gzFp = NULL; + } else { + if (flush_flag) + gzflush(gzFp,Z_SYNC_FLUSH); + } + } +} + diff --git a/src/COMPRESS/dump_cfg_gz.h b/src/COMPRESS/dump_cfg_gz.h new file mode 100644 index 0000000000..3b15cc8b14 --- /dev/null +++ b/src/COMPRESS/dump_cfg_gz.h @@ -0,0 +1,55 @@ +/* -*- 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 DUMP_CLASS + +DumpStyle(cfg/gz,DumpCFGGZ) + +#else + +#ifndef LMP_DUMP_CFG_GZ_H +#define LMP_DUMP_CFG_GZ_H + +#include "dump_cfg.h" + +// forward definition from zlib.h +typedef struct gzFile_s *gzFile; + +namespace LAMMPS_NS { + +class DumpCFGGZ : public DumpCFG { + public: + DumpCFGGZ(class LAMMPS *, int, char **); + virtual ~DumpCFGGZ(); + + protected: + gzFile gzFp; // file pointer for the compressed output stream + + virtual void openfile(); + virtual void write_header(bigint); + virtual void write_data(int, double *); + virtual void write(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Dump cfg/gz only writes compressed files + +The dump cfg/gz output file name must have a .gz suffix. + +*/ diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp new file mode 100644 index 0000000000..27ac968bed --- /dev/null +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -0,0 +1,145 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "dump_custom_gz.h" +#include "domain.h" +#include "error.h" +#include "update.h" + +#include +#include + +using namespace LAMMPS_NS; + +DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) : + DumpCustom(lmp, narg, arg) +{ + gzFp = NULL; + + if (!compressed) + error->all(FLERR,"Dump custom/gz only writes compressed files"); +} + + +/* ---------------------------------------------------------------------- */ + +DumpCustomGZ::~DumpCustomGZ() +{ + if (gzFp) gzclose(gzFp); + gzFp = NULL; + fp = NULL; +} + + +/* ---------------------------------------------------------------------- + generic opening of a dump file + ASCII or binary or gzipped + some derived classes override this function +------------------------------------------------------------------------- */ + +void DumpCustomGZ::openfile() +{ + // single file, already opened, so just return + + if (singlefile_opened) return; + if (multifile == 0) singlefile_opened = 1; + + // if one file per timestep, replace '*' with current timestep + + char *filecurrent = filename; + if (multiproc) filecurrent = multiname; + + if (multifile) { + char *filestar = filecurrent; + filecurrent = new char[strlen(filestar) + 16]; + char *ptr = strchr(filestar,'*'); + *ptr = '\0'; + if (padflag == 0) + sprintf(filecurrent,"%s" BIGINT_FORMAT "%s", + filestar,update->ntimestep,ptr+1); + else { + char bif[8],pad[16]; + strcpy(bif,BIGINT_FORMAT); + sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]); + sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1); + } + *ptr = '*'; + } + + // each proc with filewriter = 1 opens a file + + if (filewriter) { + if (append_flag) { + gzFp = gzopen(filecurrent,"ab9"); + } else { + gzFp = gzopen(filecurrent,"wb9"); + } + + if (gzFp == NULL) error->one(FLERR,"Cannot open dump file"); + } else gzFp = NULL; + + // delete string with timestep replaced + + if (multifile) delete [] filecurrent; +} + +void DumpCustomGZ::write_header(bigint ndump) +{ + if ((multiproc) || (!multiproc && me == 0)) { + if (domain->triclinic == 0) { + gzprintf(gzFp,"ITEM: TIMESTEP\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); + gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); + gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); + gzprintf(gzFp,"%g %g\n",boxxlo,boxxhi); + gzprintf(gzFp,"%g %g\n",boxylo,boxyhi); + gzprintf(gzFp,"%g %g\n",boxzlo,boxzhi); + gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); + } else { + gzprintf(gzFp,"ITEM: TIMESTEP\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); + gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); + gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); + gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); + gzprintf(gzFp,"%g %g %g\n",boxxlo,boxxhi,boxxy); + gzprintf(gzFp,"%g %g %g\n",boxylo,boxyhi,boxxz); + gzprintf(gzFp,"%g %g %g\n",boxzlo,boxzhi,boxyz); + gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); + } + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustomGZ::write_data(int n, double *mybuf) +{ + gzwrite(gzFp,mybuf,sizeof(char)*n); +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustomGZ::write() +{ + DumpCustom::write(); + if (filewriter) { + if (multifile) { + gzclose(gzFp); + gzFp = NULL; + } else { + if (flush_flag) + gzflush(gzFp,Z_SYNC_FLUSH); + } + } +} + diff --git a/src/COMPRESS/dump_custom_gz.h b/src/COMPRESS/dump_custom_gz.h new file mode 100644 index 0000000000..0d7fa96a0c --- /dev/null +++ b/src/COMPRESS/dump_custom_gz.h @@ -0,0 +1,55 @@ +/* -*- 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 DUMP_CLASS + +DumpStyle(custom/gz,DumpCustomGZ) + +#else + +#ifndef LMP_DUMP_CUSTOM_GZ_H +#define LMP_DUMP_CUSTOM_GZ_H + +#include "dump_custom.h" + +// forward definition from zlib.h +typedef struct gzFile_s *gzFile; + +namespace LAMMPS_NS { + +class DumpCustomGZ : public DumpCustom { + public: + DumpCustomGZ(class LAMMPS *, int, char **); + virtual ~DumpCustomGZ(); + + protected: + gzFile gzFp; // file pointer for the compressed output stream + + virtual void openfile(); + virtual void write_header(bigint); + virtual void write_data(int, double *); + virtual void write(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Dump custom/gz only writes compressed files + +The dump custom/gz output file name must have a .gz suffix. + +*/ diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp new file mode 100644 index 0000000000..0bf0f15209 --- /dev/null +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -0,0 +1,125 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include "dump_xyz_gz.h" +#include "domain.h" +#include "error.h" +#include "update.h" + +#include +#include + +using namespace LAMMPS_NS; + +DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) : + DumpXYZ(lmp, narg, arg) +{ + gzFp = NULL; + + if (!compressed) + error->all(FLERR,"Dump xyz/gz only writes compressed files"); +} + + +/* ---------------------------------------------------------------------- */ + +DumpXYZGZ::~DumpXYZGZ() +{ + if (gzFp) gzclose(gzFp); + gzFp = NULL; + fp = NULL; +} + + +/* ---------------------------------------------------------------------- + generic opening of a dump file + ASCII or binary or gzipped + some derived classes override this function +------------------------------------------------------------------------- */ + +void DumpXYZGZ::openfile() +{ + // single file, already opened, so just return + + if (singlefile_opened) return; + if (multifile == 0) singlefile_opened = 1; + + // if one file per timestep, replace '*' with current timestep + + char *filecurrent = filename; + if (multiproc) filecurrent = multiname; + + if (multifile) { + char *filestar = filecurrent; + filecurrent = new char[strlen(filestar) + 16]; + char *ptr = strchr(filestar,'*'); + *ptr = '\0'; + if (padflag == 0) + sprintf(filecurrent,"%s" BIGINT_FORMAT "%s", + filestar,update->ntimestep,ptr+1); + else { + char bif[8],pad[16]; + strcpy(bif,BIGINT_FORMAT); + sprintf(pad,"%%s%%0%d%s%%s",padflag,&bif[1]); + sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1); + } + *ptr = '*'; + } + + // each proc with filewriter = 1 opens a file + + if (filewriter) { + if (append_flag) { + gzFp = gzopen(filecurrent,"ab9"); + } else { + gzFp = gzopen(filecurrent,"wb9"); + } + + if (gzFp == NULL) error->one(FLERR,"Cannot open dump file"); + } else gzFp = NULL; + + // delete string with timestep replaced + + if (multifile) delete [] filecurrent; +} + +void DumpXYZGZ::write_header(bigint ndump) +{ + if (me == 0) { + gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); + gzprintf(gzFp,"Atoms. Timestep: " BIGINT_FORMAT "\n",update->ntimestep); + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpXYZGZ::write_data(int n, double *mybuf) +{ + gzwrite(gzFp,mybuf,sizeof(char)*n); +} + +/* ---------------------------------------------------------------------- */ + +void DumpXYZGZ::write() +{ + DumpXYZ::write(); + if (filewriter) { + if (multifile) { + gzclose(gzFp); + gzFp = NULL; + } else { + if (flush_flag) + gzflush(gzFp,Z_SYNC_FLUSH); + } + } +} diff --git a/src/COMPRESS/dump_xyz_gz.h b/src/COMPRESS/dump_xyz_gz.h new file mode 100644 index 0000000000..b647334395 --- /dev/null +++ b/src/COMPRESS/dump_xyz_gz.h @@ -0,0 +1,55 @@ +/* -*- 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 DUMP_CLASS + +DumpStyle(xyz/gz,DumpXYZGZ) + +#else + +#ifndef LMP_DUMP_XYZ_GZ_H +#define LMP_DUMP_XYZ_GZ_H + +#include "dump_xyz.h" + +// forward definition from zlib.h +typedef struct gzFile_s *gzFile; + +namespace LAMMPS_NS { + +class DumpXYZGZ : public DumpXYZ { + public: + DumpXYZGZ(class LAMMPS *, int, char **); + virtual ~DumpXYZGZ(); + + protected: + gzFile gzFp; // file pointer for the compressed output stream + + virtual void openfile(); + virtual void write_header(bigint); + virtual void write_data(int, double *); + virtual void write(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Dump xyz/gz only writes compressed files + +The dump xyz/gz output file name must have a .gz suffix. + +*/ diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh index fe96620110..e4f901c329 100644 --- a/src/GPU/Install.sh +++ b/src/GPU/Install.sh @@ -77,6 +77,8 @@ action pair_lj_class2_coul_long_gpu.cpp pair_lj_class2_coul_long.cpp action pair_lj_class2_coul_long_gpu.h pair_lj_class2_coul_long.cpp action pair_lj_class2_gpu.cpp pair_lj_class2.cpp action pair_lj_class2_gpu.h pair_lj_class2.cpp +action pair_lj_cubic_gpu.cpp +action pair_lj_cubic_gpu.h action pair_lj_cut_coul_cut_gpu.cpp action pair_lj_cut_coul_cut_gpu.h action pair_lj_cut_coul_debye_gpu.cpp @@ -109,10 +111,14 @@ action pair_sw_gpu.cpp pair_sw.cpp action pair_sw_gpu.h pair_sw.h action pair_table_gpu.cpp pair_table.cpp action pair_table_gpu.h pair_table.cpp +action pair_tersoff_gpu.cpp pair_tersoff.cpp +action pair_tersoff_gpu.h pair_tersoff.cpp action pair_yukawa_colloid_gpu.cpp pair_yukawa_colloid.cpp action pair_yukawa_colloid_gpu.h pair_yukawa_colloid.cpp action pair_yukawa_gpu.cpp pair_yukawa.cpp action pair_yukawa_gpu.h pair_yukawa.cpp +action pair_zbl_gpu.cpp +action pair_zbl_gpu.h action pppm_gpu.cpp pppm.cpp action pppm_gpu.h pppm.cpp diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 86a4996ae9..6135a1f754 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -115,6 +115,7 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg+1],"off") == 0) newtonflag = 0; else if (strcmp(arg[iarg+1],"on") == 0) newtonflag = 1; else error->all(FLERR,"Illegal package gpu command"); + iarg += 2; } else if (strcmp(arg[iarg],"binsize") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal package gpu command"); binsize = force->numeric(FLERR,arg[iarg+1]); diff --git a/src/Makefile b/src/Makefile index 8136f36ad5..20c66c126d 100755 --- a/src/Makefile +++ b/src/Makefile @@ -41,7 +41,8 @@ endif # Package variables -PACKAGE = asphere body class2 colloid coreshell dipole fld gpu granular kim \ +PACKAGE = asphere body class2 colloid compress coreshell dipole fld gpu \ + granular kim \ kokkos kspace manybody mc meam misc molecule mpiio opt peri poems \ python qeq reax replica rigid shock snap srd voronoi xtc @@ -50,7 +51,7 @@ PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \ user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \ user-quip user-reaxc user-smd user-sph -PACKLIB = gpu kim kokkos meam poems python reax voronoi \ +PACKLIB = compress gpu kim kokkos meam poems python reax voronoi \ user-atc user-awpmd user-colvars user-cuda user-molfile \ user-qmmm user-quip diff --git a/src/compute.h b/src/compute.h index ba3835a34d..732ced15da 100644 --- a/src/compute.h +++ b/src/compute.h @@ -131,6 +131,10 @@ class Compute : protected Pointers { virtual double memory_usage() {return 0.0;} + virtual void pair_tally_callback(int, int, int, int, + double, double, double, + double, double, double) {} + virtual int unsigned data_mask() {return datamask;} virtual int unsigned data_mask_ext() {return datamask_ext;} diff --git a/src/pair.cpp b/src/pair.cpp index 75f1e6aa06..31fa8edad4 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -32,6 +32,8 @@ #include "force.h" #include "kspace.h" #include "update.h" +#include "modify.h" +#include "compute.h" #include "accelerator_cuda.h" #include "suffix.h" #include "atom_masks.h" @@ -96,6 +98,9 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) eatom = NULL; vatom = NULL; + num_tally_compute = 0; + list_tally_compute = NULL; + // CUDA and KOKKOS per-fix data masks datamask = ALL_MASK; @@ -112,6 +117,9 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) Pair::~Pair() { + num_tally_compute = 0; + memory->sfree((void *)list_tally_compute); + if (copymode) return; memory->destroy(eatom); @@ -685,6 +693,53 @@ void Pair::compute_dummy(int eflag, int vflag) else evflag = 0; } +/* ------------------------------------------------------------------- + register a callback to a compute, so it can compute and accumulate + additional properties during the pair computation from within + Pair::ev_tally(). ensure each compute instance is registered only once +---------------------------------------------------------------------- */ +void Pair::add_tally_callback(Compute *ptr) +{ + int i,found=-1; + + for (i=0; i < num_tally_compute; ++i) { + if (list_tally_compute[i] == ptr) + found = i; + } + + if (found < 0) { + found = num_tally_compute; + ++num_tally_compute; + void *p = memory->srealloc((void *)list_tally_compute, + sizeof(Compute **) * num_tally_compute, + "pair:list_tally_compute"); + list_tally_compute = (Compute **) p; + list_tally_compute[num_tally_compute-1] = ptr; + } +} + +/* ------------------------------------------------------------------- + unregister a callback to a fix for additional pairwise tallying +---------------------------------------------------------------------- */ +void Pair::del_tally_callback(Compute *ptr) +{ + int i,found=-1; + + for (i=0; i < num_tally_compute; ++i) { + if (list_tally_compute[i] == ptr) + found = i; + } + + if (found < 0) + return; + + // compact the list of active computes + --num_tally_compute; + for (i=found; i < num_tally_compute; ++i) { + list_tally_compute[i] = list_tally_compute[i+1]; + } +} + /* ---------------------------------------------------------------------- setup for energy, virial computation see integrate::ev_set() for values of eflag (0-3) and vflag (0-6) @@ -866,6 +921,14 @@ void Pair::ev_tally(int i, int j, int nlocal, int newton_pair, } } } + + if (num_tally_compute > 0) { + for (int k=0; k < num_tally_compute; ++k) { + Compute *c = list_tally_compute[k]; + c->pair_tally_callback(i, j, nlocal, newton_pair, + evdwl, ecoul, fpair, delx, dely, delz); + } + } } /* ---------------------------------------------------------------------- diff --git a/src/pair.h b/src/pair.h index 2378dd567c..3d73fc1a93 100644 --- a/src/pair.h +++ b/src/pair.h @@ -186,6 +186,15 @@ class Pair : protected Pointers { virtual unsigned int data_mask() {return datamask;} virtual unsigned int data_mask_ext() {return datamask_ext;} + // management of callbacks to be run from ev_tally() + + private: + int num_tally_compute; + class Compute **list_tally_compute; + public: + void add_tally_callback(class Compute *); + void del_tally_callback(class Compute *); + protected: int instance_me; // which Pair class instantiation I am