Merge pull request #907 from akohlmey/dump_maxfile

Implement 'dump_modify maxfiles' feature

doc/src/dump_modify.txt

@@ -15,7 +15,7 @@ dump_modify dump-ID keyword values ... :pre
 dump-ID = ID of dump to modify :ulb,l
 one or more keyword/value pairs may be appended :l
 these keywords apply to various dump styles :l
-keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
+keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {maxfiles} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l
   {append} arg = {yes} or {no}
   {at} arg = N
     N = index of frame written upon first dump
@@ -37,6 +37,8 @@ keyword = {append} or {at} or {buffer} or {delay} or {element} or {every} or {fi
   {image} arg = {yes} or {no}
   {label} arg = string
     string = character string (e.g. BONDS) to use in header of dump local file
+  {maxfiles} arg = Fmax
+    Fmax = keep only the most recent {Fmax} snapshots (one snapshot per file)
   {nfile} arg = Nf
     Nf = write this many files, one from each of Nf processors
   {pad} arg = Nchar = # of characters to convert timestep to
@@ -364,6 +366,20 @@ e.g. BONDS or ANGLES.
 
 :line
 
+The {maxfiles} keyword can only be used when a '*' wildcard is
+included in the dump file name, i.e. when writing a new file(s) for
+each snapshot.  The specified {Fmax} is how many snapshots will be
+kept.  Once this number is reached, the file(s) containing the oldest
+snapshot is deleted before a new dump file is written.  If the
+specified {Fmax} <= 0, then all files are retained.
+
+This can be useful for debugging, especially if you don't know on what
+timestep something bad will happen, e.g. when LAMMPS will exit with an
+error.  You can dump every timestep, and limit the number of dump
+files produced, even if you run for 1000s of steps.
+
+:line
+
 The {nfile} or {fileper} keywords can be used in conjunction with the
 "%" wildcard character in the specified dump file name, for all dump
 styles except the {dcd}, {image}, {movie}, {xtc}, and {xyz} styles
@@ -901,6 +917,7 @@ flush = yes
 format = %d and %g for each integer or floating point value
 image = no
 label = ENTRIES
+maxifiles = -1
 nfile = 1
 pad = 0
 pbc = no

lib/atc/Function.cpp

@@ -1,4 +1,6 @@
+#ifndef _WIN32
 #include <alloca.h>
+#endif
 #include "Function.h"
 #include "ATC_Error.h"
 #include "LammpsInterface.h"
@@ -59,7 +61,11 @@ namespace ATC {
   {
     string type = args[0];
     int narg = nargs -1;
+#ifdef _WIN32
+    double *dargs = (double *) _alloca(sizeof(double) * narg);
+#endif
     double *dargs = (double *) alloca(sizeof(double) * narg);
+#endif
     for (int i = 0; i < narg; ++i) dargs[i] = atof(args[i+1]);
   
     return function(type, narg, dargs);
@@ -193,7 +199,11 @@ XT_Function_Mgr * XT_Function_Mgr::myInstance_ = NULL;
   {
     string type = args[0];
     int narg = nargs -1;
+#ifdef _WIN32
+    double *dargs = (double *) _alloca(sizeof(double) * narg);
+#else
     double *dargs = (double *) alloca(sizeof(double) * narg);
+#endif
     for (int i = 0; i < narg; ++i) dargs[i] = atof(args[i+1]);
   
     return function(type, narg, dargs);

src/COMPRESS/dump_atom_gz.cpp

@@ -71,6 +71,19 @@ void DumpAtomGZ::openfile()
       sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
     }
     *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
   }
 
   // each proc with filewriter = 1 opens a file

src/COMPRESS/dump_cfg_gz.cpp

@@ -75,6 +75,19 @@ void DumpCFGGZ::openfile()
       sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
     }
     *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
   }
 
   // each proc with filewriter = 1 opens a file

src/COMPRESS/dump_custom_gz.cpp

@@ -73,6 +73,19 @@ void DumpCustomGZ::openfile()
       sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
     }
     *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
   }
 
   // each proc with filewriter = 1 opens a file

src/COMPRESS/dump_xyz_gz.cpp

@@ -73,6 +73,19 @@ void DumpXYZGZ::openfile()
       sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
     }
     *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
   }
 
   // each proc with filewriter = 1 opens a file

src/MPIIO/dump_atom_mpiio.cpp

@@ -77,6 +77,19 @@ void DumpAtomMPIIO::openfile()
       sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
     }
     *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
   }
 
   if (append_flag) { // append open

src/MPIIO/dump_cfg_mpiio.cpp

@@ -94,6 +94,19 @@ void DumpCFGMPIIO::openfile()
       sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
     }
     *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
   }
 
   if (append_flag) { // append open

src/MPIIO/dump_custom_mpiio.cpp

@@ -97,6 +97,19 @@ void DumpCustomMPIIO::openfile()
       sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
     }
     *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
   }
 
   if (append_flag) { // append open

src/MPIIO/dump_xyz_mpiio.cpp

@@ -97,6 +97,19 @@ void DumpXYZMPIIO::openfile()
       sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
     }
     *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
   }
 
   if (append_flag) { // append open

src/dump.cpp

@@ -91,6 +91,11 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   pbcflag = 0;
   delay_flag = 0;
 
+  maxfiles = -1;
+  numfiles = 0;
+  fileidx = 0;
+  nameslist = NULL;
+
   maxbuf = maxids = maxsort = maxproc = 0;
   buf = bufsort = NULL;
   ids = idsort = NULL;
@@ -187,6 +192,14 @@ Dump::~Dump()
 
   if (multiproc) MPI_Comm_free(&clustercomm);
 
+  // delete storage for caching file names
+
+  if (maxfiles > 0) {
+    for (int idx=0; idx < numfiles; ++idx)
+      delete[] nameslist[idx];
+    delete[] nameslist;
+  }
+
   // XTC style sets fp to NULL since it closes file in its destructor
 
   if (multifile == 0 && fp != NULL) {
@@ -549,6 +562,19 @@ void Dump::openfile()
       sprintf(filecurrent,pad,filestar,update->ntimestep,ptr+1);
     }
     *ptr = '*';
+    if (maxfiles > 0) {
+      if (numfiles < maxfiles) {
+        nameslist[numfiles] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[numfiles],filecurrent);
+        ++numfiles;
+      } else {
+        remove(nameslist[fileidx]);
+        delete[] nameslist[fileidx];
+        nameslist[fileidx] = new char[strlen(filecurrent)+1];
+        strcpy(nameslist[fileidx],filecurrent);
+        fileidx = (fileidx + 1) % maxfiles;
+      }
+    }
   }
 
   // each proc with filewriter = 1 opens a file
@@ -1003,6 +1029,27 @@ void Dump::modify_params(int narg, char **arg)
         iarg += n;
       }
 
+    } else if (strcmp(arg[iarg],"maxfiles") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
+      if (!multifile)
+        error->all(FLERR,"Cannot use dump_modify maxfiles "
+                   "without * in dump file name");
+      // wipe out existing storage
+      if (maxfiles > 0) {
+        for (int idx=0; idx < numfiles; ++idx)
+          delete[] nameslist[idx];
+        delete[] nameslist;
+      }
+      maxfiles = force->inumeric(FLERR,arg[iarg+1]);
+      if (maxfiles == 0) error->all(FLERR,"Illegal dump_modify command");
+      if (maxfiles > 0) {
+        nameslist = new char*[maxfiles];
+        numfiles = 0;
+        for (int idx=0; idx < maxfiles; ++idx)
+          nameslist[idx] = NULL;
+        fileidx = 0;
+      }
+      iarg += 2;
     } else if (strcmp(arg[iarg],"nfile") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal dump_modify command");
       if (!multiproc)

src/dump.h

@@ -106,6 +106,11 @@ class Dump : protected Pointers {
   double boxzlo,boxzhi;
   double boxxy,boxxz,boxyz;
 
+  int maxfiles;              // max number of files created, -1 == infinite
+  int numfiles;              // number of files in names list
+  int fileidx;               // index of file in names list
+  char **nameslist;          // list of history file names
+
   bigint ntotal;             // total # of per-atom lines in snapshot
   int reorderflag;           // 1 if OK to reorder instead of sort
   int ntotal_reorder;        // # of atoms that must be in snapshot