use mutex to avoid race condition when accessing thermo data during run

src/finish.cpp

@@ -121,9 +121,9 @@ void Finish::end(int flag)
     MPI_Allreduce(&cpu_loop,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
     cpu_loop = tmp/nprocs;
     if (time_loop > 0.0) cpu_loop = cpu_loop/time_loop*100.0;
+    output->thermo->footer();
 
     if (me == 0) {
-      output->thermo->footer();
       int ntasks = nprocs * nthreads;
       utils::logmesg(lmp,"Loop time of {:.6g} on {} procs for {} steps with {} atoms\n\n",
                      time_loop,ntasks,update->nsteps,atom->natoms);

src/library.cpp

@@ -853,7 +853,11 @@ This differs from :cpp:func:`lammps_get_thermo` in that it does **not**
 trigger an evaluation.  Instead it provides direct access to a read-only
 location of the last thermo output data and the corresponding keyword
 strings.  How to handle the return value depends on the value of the *what*
-argument string.
+argument string.  When accessing the data from a concurrent thread while
+LAMMPS is running, the cache needs to be locked first and then unlocked
+after the data is obtained, so that the data is not corrupted while
+reading in case LAMMPS wants to update it at the same time.  Outside
+of a run, the lock/unlock calls have no effect.
 
 .. note::
 
@@ -902,6 +906,14 @@ argument string.
      - actual field data for column
      - pointer to int, int64_t or double
      - yes
+   * - lock
+     - acquires lock to thermo data cache
+     - NULL pointer
+     - no
+   * - unlock
+     - releases lock to thermo data cache
+     - NULL pointer
+     - no
 
 \endverbatim
  *
@@ -957,8 +969,14 @@ void *lammps_last_thermo(void *handle, const char *what, int index)
       } else if (field.type == multitype::LAMMPS_DOUBLE) {
         val = (void *) &field.data.d;
       }
-
+    } else if (strcmp(what, "lock") == 0) {
+      th->lock_cache();
+      val = nullptr;
+    } else if (strcmp(what, "unlock") == 0) {
+      th->unlock_cache();
+      val = nullptr;
     } else val = nullptr;
+
   }
   END_CAPTURE
   return val;

src/thermo.cpp

@@ -48,6 +48,7 @@
 
 #include <cmath>
 #include <cstring>
+#include <mutex>
 #include <stdexcept>
 
 using namespace LAMMPS_NS;
@@ -100,8 +101,8 @@ static char fmtbuf[512];
 /* ---------------------------------------------------------------------- */
 
 Thermo::Thermo(LAMMPS *_lmp, int narg, char **arg) :
-    Pointers(_lmp), style(nullptr), vtype(nullptr), field2index(nullptr), argindex1(nullptr),
-    argindex2(nullptr), temperature(nullptr), pressure(nullptr), pe(nullptr)
+    Pointers(_lmp), style(nullptr), vtype(nullptr), cache_mutex(nullptr), field2index(nullptr),
+    argindex1(nullptr), argindex2(nullptr), temperature(nullptr), pressure(nullptr), pe(nullptr)
 {
   style = utils::strdup(arg[0]);
 
@@ -208,6 +209,7 @@ void Thermo::init()
   ValueTokenizer *format_line = nullptr;
   if (format_line_user.size()) format_line = new ValueTokenizer(format_line_user);
 
+  lock_cache();
   field_data.clear();
   field_data.resize(nfield);
   std::string format_this, format_line_user_def;
@@ -277,6 +279,7 @@ void Thermo::init()
         format[i] += fmt::format("{:<8} = {} ", keyword[i], format_this);
     }
   }
+  unlock_cache();
 
   // chop off trailing blank or add closing bracket if needed and then add newline
   if (lineflag == ONELINE)
@@ -320,6 +323,9 @@ void Thermo::init()
   if (index_press_scalar >= 0) pressure = computes[index_press_scalar];
   if (index_press_vector >= 0) pressure = computes[index_press_vector];
   if (index_pe >= 0) pe = computes[index_pe];
+
+  // create mutex to protect access to cached thermo data
+  cache_mutex = new std::mutex;
 }
 
 /* ----------------------------------------------------------------------
@@ -366,11 +372,19 @@ void Thermo::header()
 
 /* ---------------------------------------------------------------------- */
 
+// called at the end of a run from Finish class
+
 void Thermo::footer()
 {
+  if (comm->me == 0) {
     if (lineflag == YAMLLINE) utils::logmesg(lmp, "...\n");
   }
 
+  // no more locking for cached thermo data access needed
+  delete cache_mutex;
+  cache_mutex = nullptr;
+}
+
 /* ---------------------------------------------------------------------- */
 
 void Thermo::compute(int flag)
@@ -422,6 +436,7 @@ void Thermo::compute(int flag)
   }
 
   // add each thermo value to line with its specific format
+  lock_cache();
   field_data.clear();
   field_data.resize(nfield);
 
@@ -441,6 +456,7 @@ void Thermo::compute(int flag)
       field_data[ifield] = bivalue;
     }
   }
+  unlock_cache();
 
   // print line to screen and logfile
 
@@ -579,7 +595,8 @@ void Thermo::modify_params(int narg, char **arg)
       if (iarg + 2 > narg) error->all(FLERR, "Illegal thermo_modify command");
       triclinic_general = utils::logical(FLERR, arg[iarg + 1], false, lmp);
       if (triclinic_general && !domain->triclinic_general)
-        error->all(FLERR,"Thermo_modify triclinic/general cannot be used "
+        error->all(FLERR,
+                   "Thermo_modify triclinic/general cannot be used "
                    "if simulation box is not general triclinic");
       iarg += 2;
 
@@ -1566,6 +1583,26 @@ int Thermo::evaluate_keyword(const std::string &word, double *answer)
   return 0;
 }
 
+/* ---------------------------------------------------------------------- */
+
+// lock cache for current thermo data
+
+void Thermo::lock_cache()
+{
+  // no locking outside of a run
+  if (!cache_mutex) return;
+  cache_mutex->lock();
+}
+
+// unlock cache for current thermo data
+
+void Thermo::unlock_cache()
+{
+  // no locking outside of a run
+  if (!cache_mutex) return;
+  cache_mutex->unlock();
+}
+
 /* ----------------------------------------------------------------------
    extraction of Compute, Fix, Variable results
    compute/fix are normalized by atoms if returning extensive value

src/thermo.h

@@ -17,6 +17,10 @@
 #include "pointers.h"
 #include <map>
 
+namespace std {
+class mutex;
+}
+
 namespace LAMMPS_NS {
 
 class Thermo : protected Pointers {
@@ -43,6 +47,8 @@ class Thermo : protected Pointers {
   int evaluate_keyword(const std::string &, double *);
 
   // for accessing cached thermo and related data
+  void lock_cache();
+  void unlock_cache();
   const int *get_line() const { return &nline; }
   const char *get_image_fname() const { return image_fname.c_str(); }
 
@@ -82,6 +88,9 @@ class Thermo : protected Pointers {
   int nline;
   std::string image_fname;
 
+  // mutex for locking the cache
+  std::mutex *cache_mutex;
+
   // data used by routines that compute single values
 
   int ivalue;          // integer value to print

tools/lammps-gui/lammps-gui.appdata.xml

@@ -61,6 +61,8 @@
         Highlight warnings and error messages in Output window
         Make Tutorial wizards more compact
         Include download and compilation of WHAM software from Alan Grossfield
+        Add dialog to run WHAM directly from LAMMPS-GUI
+        Use mutex to avoid corruption of thermo data
       </description>
     </release>
     <release version="1.6.11" timestamp="1725080055">

tools/lammps-gui/lammpsgui.cpp

@@ -1015,6 +1015,7 @@ void LammpsGui::logupdate()
         void *ptr = lammps.last_thermo("setup", 0);
         if (ptr && *(int *)ptr) return;
 
+        lammps.last_thermo("lock", 0);
         ptr = lammps.last_thermo("num", 0);
         if (ptr) {
             int ncols = *(int *)ptr;
@@ -1066,6 +1067,7 @@ void LammpsGui::logupdate()
                 chartwindow->add_data(step, data, i);
             }
         }
+        lammps.last_thermo("unlock", 0);
     }
 
     // update list of available image file names