git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10491 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/citeme.cpp

@@ -0,0 +1,72 @@
+/* ----------------------------------------------------------------------
+   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 "citeme.h"
+#include "version.h"
+#include "universe.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+static const char cite_header[] = 
+  "This LAMMPS simulation made specific use of work described in the\n"
+  "following references.  See http://lammps.sandia.gov/cite.html\n"
+  "for details.\n\n";
+
+static const char cite_nagline[] = "\nPlease see the log.cite file "
+  "for references relevant to this simulation\n\n";
+
+/* ---------------------------------------------------------------------- */
+
+CiteMe::CiteMe(LAMMPS *lmp) : Pointers(lmp)
+{
+  fp = NULL;
+  cs = new citeset();
+}
+
+/* ---------------------------------------------------------------------- 
+   write out nag-line at the end of the regular output and clean up
+------------------------------------------------------------------------- */
+
+CiteMe::~CiteMe()
+{
+  if (universe->me) return;
+  if (cs->size() == 0) return;
+
+  if (screen) fprintf(screen,cite_nagline);
+  if (logfile) fprintf(logfile,cite_nagline);
+
+  delete cs;
+  if (fp) fclose(fp);
+}
+
+/* ----------------------------------------------------------------------
+   write out and register a citation so it will be written only once
+------------------------------------------------------------------------- */
+
+void CiteMe::add(const char *ref)
+{
+  if (universe->me) return;
+  if (cs->find(ref) != cs->end()) return;
+  cs->insert(ref);
+
+  if (!fp) {
+    fp = fopen("log.cite","w");
+    if (!fp) error->universe_one(FLERR,"Could not open log.cite file");
+    fprintf(fp,cite_header);
+    fflush(fp);
+  }
+
+  fprintf(fp,ref);
+  fflush(fp);
+}

src/citeme.h

@@ -0,0 +1,42 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_CITEME_H
+#define LMP_CITEME_H
+
+#include "pointers.h"
+#include "stdio.h"
+#include <set>
+
+namespace LAMMPS_NS {
+
+class CiteMe : protected Pointers {
+ public:
+  CiteMe(class LAMMPS *);
+  virtual ~CiteMe();
+  void add(const char *);       // print out and register publication
+
+ private:
+  FILE *fp;                    // opaque pointer to log.cite file object
+  typedef std::set<const char *> citeset;
+  citeset *cs;                // registered set of publications
+};
+
+}
+
+#endif
+
+/* ERROR/WARNING messages:
+
+
+*/

src/lammps.cpp

@@ -39,6 +39,7 @@
 #include "modify.h"
 #include "group.h"
 #include "output.h"
+#include "citeme.h"
 #include "accelerator_cuda.h"
 #include "accelerator_omp.h"
 #include "timer.h"
@@ -73,7 +74,9 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
   int partscreenflag = 0;
   int partlogflag = 0;
   int cudaflag = -1;
+  int citeflag = 1;
   int helpflag = 0;
+
   suffix = NULL;
   suffix_enable = 0;
 
@@ -156,6 +159,10 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
         error->universe_all(FLERR,"Cannot use -reorder after -partition");
       universe->reorder(arg[iarg+1],arg[iarg+2]);
       iarg += 3;
+    } else if (strcmp(arg[iarg],"-nocite") == 0 ||
+               strcmp(arg[iarg],"-nc") == 0) {
+      citeflag = 0;
+      iarg++;
     } else if (strcmp(arg[iarg],"-help") == 0 ||
                strcmp(arg[iarg],"-h") == 0) {
       if (iarg+1 > narg)
@@ -393,6 +400,11 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
   MPI_Comm_rank(world,&me);
   if (cuda && me == 0) error->message(FLERR,"USER-CUDA mode is enabled");
 
+  // allocate CiteMe class if enabled
+
+  if (citeflag) citeme = new CiteMe(this);
+  else citeme = NULL;
+
   // allocate input class now that MPI is fully setup
 
   input = new Input(this,narg,arg);
@@ -422,6 +434,8 @@ LAMMPS::~LAMMPS()
 {
   destroy();
 
+  delete citeme;
+
   if (universe->nworlds == 1) {
     if (logfile) fclose(logfile);
   } else {

src/lammps.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -44,8 +44,11 @@ class LAMMPS {
 
   char *suffix;                  // suffix to add to input script style names
   int suffix_enable;             // 1 if suffix enabled, 0 if disabled
+  int cite_enable;               // 1 if generating log.cite, 0 if disabled
   class Cuda *cuda;              // CUDA accelerator class
 
+  class CiteMe *citeme;          // citation info
+
   LAMMPS(int, char **, MPI_Comm);
   ~LAMMPS();
   void create();

src/neighbor.cpp

@@ -36,6 +36,7 @@
 #include "update.h"
 #include "respa.h"
 #include "output.h"
+#include "citeme.h"
 #include "memory.h"
 #include "error.h"
 
@@ -51,6 +52,19 @@ using namespace LAMMPS_NS;
 
 enum{NSQ,BIN,MULTI};     // also in neigh_list.cpp
 
+static const char cite_neigh_multi[] =
+  "neighbor multi command:\n\n"
+  "@Article{intveld08,\n"
+  " author =  {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton"
+  " and G.{\\,}S.~Grest},\n"
+  " title =   {Accurate and Efficient Methods for Modeling Colloidal\n"
+  "            Mixtures in an Explicit Solvent using Molecular Dynamics},\n"
+  " journal = {Comp.~Phys.~Comm.},\n"
+  " year =    2008,\n"
+  " volume =  179,\n"
+  " pages =   {320--329}\n"
+  "}\n\n";
+
 //#define NEIGH_LIST_DEBUG 1
 
 /* ---------------------------------------------------------------------- */
@@ -1644,6 +1658,8 @@ void Neighbor::set(int narg, char **arg)
   else if (strcmp(arg[1],"bin") == 0) style = BIN;
   else if (strcmp(arg[1],"multi") == 0) style = MULTI;
   else error->all(FLERR,"Illegal neighbor command");
+
+  if (style == MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi);
 }
 
 /* ----------------------------------------------------------------------