initial attempt to refactor the citation logging in LAMMPS

this implements the basic features and flow of control.
to be done are the specific texts and the documentation.

src/citeme.cpp

@@ -12,6 +12,7 @@
 ------------------------------------------------------------------------- */
 
 #include "citeme.h"
+#include "comm.h"
 #include "universe.h"
 
 using namespace LAMMPS_NS;
@@ -21,55 +22,99 @@ static const char cite_header[] =
   "following references.  See https://lammps.sandia.gov/cite.html\n"
   "for details.\n\n";
 
-static const char cite_nagline[] = "\nPlease see the log.cite file "
+static const char cite_nagline[] = "Please see the log.cite file "
   "for references relevant to this simulation\n\n";
 
+static const char cite_seefile[] = "Please see the citation file "
+  "for references relevant to this simulation\n\n";
+
+static const char cite_separator[] =
+  "\nCITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE\n\n";
+
 /* ---------------------------------------------------------------------- */
 
-CiteMe::CiteMe(LAMMPS *lmp) : Pointers(lmp)
+CiteMe::CiteMe(LAMMPS *lmp, int _screen, int _logfile, const char *_file)
+  : Pointers(lmp)
 {
   fp = nullptr;
   cs = new citeset();
+
+  screen_flag = _screen;
+  scrbuffer.clear();
+  
+  logfile_flag = _logfile;
+  logbuffer.clear();
+  
+  if (_file && universe->me == 0) {
+    fp = fopen(_file,"w");
+    if (fp) {
+      fputs(cite_header,fp);
+      fflush(fp);
+    } else {
+      utils::logmesg(lmp, "Unable to open citation file '" + std::string(_file)
+                     + "': " + utils::getsyserror() + "\n");
+    }
+  }
 }
 
 /* ----------------------------------------------------------------------
-   write out nag-line at the end of the regular output and clean up
+   write out remaining citations at end of the regular output and clean up
 ------------------------------------------------------------------------- */
 
 CiteMe::~CiteMe()
 {
-  if (universe->me || cs->size() == 0) {
+  flush();
-    delete cs;
-    return;
-  }
-
   delete cs;
 
-  if (fp) {
+  if (fp) fclose(fp);
-    if (screen) fprintf(screen,cite_nagline);
-    if (logfile) fprintf(logfile,cite_nagline);
-
-    fclose(fp);
-  }
 }
 
 /* ----------------------------------------------------------------------
-   write out and register a citation so it will be written only once
+   process an added citation so it will be shown only once and as requested
 ------------------------------------------------------------------------- */
 
 void CiteMe::add(const char *ref)
 {
-  if (universe->me) return;
+  if (comm->me != 0) return;
   if (cs->find(ref) != cs->end()) return;
   cs->insert(ref);
 
-  if (!fp) {
+  if (fp) {
-    fp = fopen("log.cite","w");
+    fputs(ref,fp);
-    if (!fp) return;
-    fputs(cite_header,fp);
     fflush(fp);
   }
 
-  fputs(ref,fp);
+  if (scrbuffer.empty()) {
-  fflush(fp);
+    scrbuffer += cite_separator;
+    if (screen_flag == VERBOSE) scrbuffer += cite_header;
+    if (screen_flag == TERSE) scrbuffer += cite_nagline;
+  }
+  
+  if (logbuffer.empty()) {
+    logbuffer += cite_separator;
+    if (logfile_flag == VERBOSE) logbuffer += cite_header;
+    if (logfile_flag == TERSE) logbuffer += cite_nagline;
+  }
+
+  std::string reference = ref;
+  std::size_t found = reference.find_first_of("\n");
+  std::string header = reference.substr(0,found+1);
+  if (screen_flag == VERBOSE) scrbuffer += reference;
+  if (screen_flag == TERSE) scrbuffer += header;
+  if (logfile_flag == VERBOSE) logbuffer += reference;
+  if (logfile_flag == TERSE) logbuffer += header;
 }
+
+void CiteMe::flush()
+{
+  if (comm->me == 0) {
+    scrbuffer += cite_separator;
+    logbuffer += cite_separator;
+    if (screen) fputs(scrbuffer.c_str(),screen);
+    if (logfile) fputs(logbuffer.c_str(),logfile);
+    scrbuffer.clear();
+    logbuffer.clear();
+  }
+  return;
+}
+

src/citeme.h

@@ -21,27 +21,32 @@ namespace LAMMPS_NS {
 
 class CiteMe : protected Pointers {
  public:
-  CiteMe(class LAMMPS *);
+  CiteMe(class LAMMPS *, int, int, const char *);
   virtual ~CiteMe();
-  void add(const char *);       // print out and register publication
+  void add(const char *);       // register publication for output
+  void flush();                 // flush buffers to screen and logfile
+  enum {VERBOSE, TERSE};
 
  private:
-  FILE *fp;                    // opaque pointer to log.cite file object
+  FILE *fp;                    // explicit citation file pointer or NULL
+  int screen_flag;             // determine whether verbose or terse output
+  int logfile_flag;            // determine whether verbose or terse output
+  std::string scrbuffer;       // output buffer for screen
+  std::string logbuffer;       // output buffer for logfile
   typedef std::set<const char *> citeset;
   citeset *cs;                 // registered set of publications
 };
-
 }
 
 #endif
 
 /* ERROR/WARNING messages:
 
-E: Cannot open log.cite file
+E: Cannot open citation file
 
 This file is created when you use some LAMMPS features, to indicate
 what paper you should cite on behalf of those who implemented
-the feature.  Check that you have write privileges into the directory
+the feature.  Check that you have write privileges in the directory
 you are running in.
 
 */

src/integrate.cpp

@@ -12,12 +12,14 @@
 ------------------------------------------------------------------------- */
 
 #include "integrate.h"
-#include "update.h"
+
+#include "citeme.h"
+#include "compute.h"
 #include "force.h"
-#include "pair.h"
 #include "kspace.h"
 #include "modify.h"
-#include "compute.h"
+#include "pair.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 
@@ -45,6 +47,7 @@ Integrate::~Integrate()
 
 void Integrate::init()
 {
+  if (lmp->citeme) lmp->citeme->flush();
   update->atimestep = update->ntimestep;
 
   // allow pair and Kspace compute() to be turned off via modify flags

src/lammps.cpp

@@ -171,6 +171,9 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
   int restart2dump = 0;
   int restartremap = 0;
   int citeflag = 1;
+  int citescreen = CiteMe::TERSE;
+  int citelogfile = CiteMe::VERBOSE;
+  char *citefile = nullptr;
   int helpflag = 0;
 
   suffix = suffix2 = suffixp = nullptr;
@@ -190,7 +193,35 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
   iarg = 1;
   while (iarg < narg) {
 
-    if (strcmp(arg[iarg],"-echo") == 0 ||
+    if (strcmp(arg[iarg],"-cite") == 0 ||
+               strcmp(arg[iarg],"-c") == 0) {
+      if (iarg+2 > narg)
+        error->universe_all(FLERR,"Invalid command-line argument");
+
+      if (strcmp(arg[iarg+1],"both") == 0) {
+        citescreen = CiteMe::VERBOSE;
+        citelogfile = CiteMe::VERBOSE;
+        citefile = nullptr;
+      } else if (strcmp(arg[iarg+1],"none") == 0) {
+        citescreen = CiteMe::TERSE;
+        citelogfile = CiteMe::TERSE;
+        citefile = nullptr;
+      } else if (strcmp(arg[iarg+1],"screen") == 0) {
+        citescreen = CiteMe::VERBOSE;
+        citelogfile = CiteMe::TERSE;
+        citefile = nullptr;
+      } else if (strcmp(arg[iarg+1],"log") == 0) {
+        citescreen = CiteMe::TERSE;
+        citelogfile = CiteMe::VERBOSE;
+        citefile = nullptr;
+      } else {
+        citescreen = CiteMe::TERSE;
+        citelogfile = CiteMe::TERSE;
+        citefile = arg[iarg+1];
+      }
+      iarg += 2;
+
+    } else if (strcmp(arg[iarg],"-echo") == 0 ||
                strcmp(arg[iarg],"-e") == 0) {
       if (iarg+2 > narg)
         error->universe_all(FLERR,"Invalid command-line argument");
@@ -605,7 +636,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
 
   // allocate CiteMe class if enabled
 
-  if (citeflag) citeme = new CiteMe(this);
+  if (citeflag) citeme = new CiteMe(this,citescreen,citelogfile,citefile);
   else citeme = nullptr;
 
   // allocate input class now that MPI is fully setup
@@ -669,8 +700,8 @@ LAMMPS::~LAMMPS()
 {
   const int me = comm->me;
 
-  destroy();
   delete citeme;
+  destroy();
 
   if (num_package) {
     for (int i = 0; i < num_package; i++) {

src/lammps.h

@@ -56,7 +56,6 @@ class LAMMPS {
   char *exename;                 // pointer to argv[0]
   char ***packargs;              // arguments for cmdline package commands
   int num_package;               // number of cmdline package commands
-  int cite_enable;               // 1 if generating log.cite, 0 if disabled
 
   int clientserver;              // 0 = neither, 1 = client, 2 = server
   void *cslib;                   // client/server messaging via CSlib
@@ -66,9 +65,9 @@ class LAMMPS {
   class AtomKokkos *atomKK;      // KOKKOS version of Atom class
   class MemoryKokkos *memoryKK;  // KOKKOS version of Memory class
 
-  class Python * python;         // Python interface
+  class Python *python;          // Python interface
 
-  class CiteMe *citeme;          // citation info
+  class CiteMe *citeme;          // handle citation info
 
   const char *match_style(const char *style, const char *name);
   static const char * installed_packages[];

src/minimize.cpp

@@ -13,6 +13,7 @@
 
 #include "minimize.h"
 
+#include "citeme.h"
 #include "domain.h"
 #include "error.h"
 #include "finish.h"
@@ -46,6 +47,7 @@ void Minimize::command(int narg, char **arg)
   if (update->etol < 0.0 || update->ftol < 0.0)
     error->all(FLERR,"Illegal minimize command");
 
+  if (lmp->citeme) lmp->citeme->flush();
   update->whichflag = 2;
   update->beginstep = update->firststep = update->ntimestep;
   update->endstep = update->laststep = update->firststep + update->nsteps;