git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13905 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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

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. 
+

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 <string.h>
+#include <zlib.h>
+
+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);
+    }
+  }
+}
+

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.
+
+*/

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 <string.h>
+#include <zlib.h>
+
+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);
+    }
+  }
+}
+

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.
+
+*/

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 <string.h>
+#include <zlib.h>
+
+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);
+    }
+  }
+}
+

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.
+
+*/

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 <string.h>
+#include <zlib.h>
+
+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);
+    }
+  }
+}

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.
+
+*/

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
 

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]);

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 
 

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;}
 

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);
+    }
+  }
 }
  
 /* ----------------------------------------------------------------------

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