Merge pull request #3115 from rbberger/pylammps_update

PyLammps update

src/error.cpp

@@ -213,8 +213,7 @@ void Error::one(const std::string &file, int line, const std::string &str)
 
   throw LAMMPSAbortException(mesg, world);
 #else
-  if (screen) fflush(screen);
-  if (logfile) fflush(logfile);
+  utils::flush_buffers(lmp);
   KokkosLMP::finalize();
   MPI_Abort(world,1);
   exit(1); // to trick "smart" compilers into believing this does not return

src/library.cpp

@@ -5439,6 +5439,21 @@ void lammps_fix_external_set_vector(void *handle, const char *id, int idx, doubl
 
 /* ---------------------------------------------------------------------- */
 
+/** Flush output buffers
+
+\verbatim embed:rst
+This function can be used to force output to be written to screen and logfiles
+to simplify capturing output from LAMMPS library calls.
+\endverbatim
+ *
+ * \param  handle    pointer to a previously created LAMMPS instance cast to ``void *``.
+ */
+void lammps_flush_buffers(void *handle) {
+  utils::flush_buffers((LAMMPS *) handle);
+}
+
+/* ---------------------------------------------------------------------- */
+
 /** Free memory buffer allocated by LAMMPS.
  *
 \verbatim embed:rst

src/library.h

@@ -246,6 +246,8 @@ void lammps_fix_external_set_virial_peratom(void *handle, const char *id, double
 void lammps_fix_external_set_vector_length(void *handle, const char *id, int len);
 void lammps_fix_external_set_vector(void *handle, const char *id, int idx, double val);
 
+void lammps_flush_buffers(void *ptr);
+
 void lammps_free(void *ptr);
 
 int lammps_is_running(void *handle);

src/thermo.cpp

@@ -375,8 +375,7 @@ void Thermo::compute(int flag)
 
   if (me == 0) {
     utils::logmesg(lmp,line);
-    if (screen && flushflag) fflush(screen);
-    if (logfile && flushflag) fflush(logfile);
+    if (flushflag) utils::flush_buffers(lmp);
   }
 
   // set to 1, so that subsequent invocations of CPU time will be non-zero

src/utils.cpp

@@ -24,6 +24,7 @@
 #include "text_file_reader.h"
 #include "tokenizer.h"
 #include "update.h"
+#include "universe.h"
 
 #include <algorithm>
 #include <cctype>
@@ -138,6 +139,14 @@ void utils::fmtargs_logmesg(LAMMPS *lmp, fmt::string_view format, fmt::format_ar
   }
 }
 
+void utils::flush_buffers(LAMMPS *lmp)
+{
+  if (lmp->screen) fflush(lmp->screen);
+  if (lmp->logfile) fflush(lmp->logfile);
+  if (lmp->universe->uscreen)  fflush(lmp->universe->uscreen);
+  if (lmp->universe->ulogfile) fflush(lmp->universe->ulogfile);
+}
+
 /* define this here, so we won't have to include the headers
    everywhere and utils.h will more likely be included anyway. */
 

src/utils.h

@@ -74,6 +74,14 @@ namespace utils {
 
   void logmesg(LAMMPS *lmp, const std::string &mesg);
 
+  /*! Flush output buffers
+   *
+   *  This function calls fflush on screen and logfile FILE pointers
+   *  if available
+   */
+
+  void flush_buffers(LAMMPS *lmp);
+
   /*! Return a string representing the current system error status
    *
    *  This is a wrapper around calling strerror(errno).