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

2015-08-19 15:11:20 +00:00
parent 1c3e0dbfe9
commit c85a42ab6d
16 changed files with 948 additions and 2 deletions
--- a/src/COMPRESS/dump_atom_gz.cpp
+++ 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 <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);
+    }
+  }
+}
+