add yaml format output for mode scalar

src/fix_ave_time.cpp

@@ -83,6 +83,8 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
   int expand = 0;
   char **earg;
   nvalues = utils::expand_args(FLERR,nvalues,&arg[6],mode,earg,lmp);
+  keyword.resize(nvalues);
+  key2col.clear();
 
   if (earg != &arg[6]) expand = 1;
   arg = earg;
@@ -98,6 +100,8 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
 
   for (int i = 0; i < nvalues; i++) {
     ArgInfo argi(arg[i]);
+    keyword[i] = arg[i];
+    key2col[arg[i]] = i;
 
     if ((argi.get_type() == ArgInfo::NONE)
         || (argi.get_type() == ArgInfo::UNKNOWN)
@@ -269,9 +273,8 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
       for (int i = 0; i < nvalues; i++) fprintf(fp," %s",earg[i]);
       fprintf(fp,"\n");
     }
-    if (ferror(fp))
+    if (yaml_flag) fputs("---\n",fp);
-      error->one(FLERR,"Error writing file header");
+    if (ferror(fp)) error->one(FLERR,"Error writing file header: {}", utils::getsyserror());
-
     filepos = platform::ftell(fp);
   }
 
@@ -456,8 +459,10 @@ FixAveTime::~FixAveTime()
 
   delete[] extlist;
 
-  if (fp && me == 0) fclose(fp);
+  if (fp && me == 0) {
-
+    if (yaml_flag) fputs("...\n", fp);
+    fclose(fp);
+  }
   memory->destroy(column);
 
   delete[] vector;
@@ -669,11 +674,22 @@ void FixAveTime::invoke_scalar(bigint ntimestep)
   if (fp && me == 0) {
     clearerr(fp);
     if (overwrite) platform::fseek(fp,filepos);
+    if (yaml_flag) {
+      if (!yaml_header || overwrite) {
+        yaml_header = true;
+        fputs("keywords: ['Step', ", fp);
+        for (auto k : keyword) fmt::print(fp, "'{}', ", k);
+        fputs("]\ndata:\n", fp);
+      }
+      fmt::print(fp, "  - [{}, ", ntimestep);
+      for (i = 0; i < nvalues; i++) fmt::print(fp,"{}, ",vector_total[i]/norm);
+      fputs("]\n", fp);
+    } else {
       fmt::print(fp,"{}",ntimestep);
       for (i = 0; i < nvalues; i++) fprintf(fp,format,vector_total[i]/norm);
       fprintf(fp,"\n");
       if (ferror(fp)) error->one(FLERR,"Error writing out time averaged data");
-
+    }
     fflush(fp);
 
     if (overwrite) {
@@ -994,6 +1010,34 @@ double FixAveTime::compute_array(int i, int j)
   return 0.0;
 }
 
+/* ----------------------------------------------------------------------
+   modify settings
+------------------------------------------------------------------------- */
+
+int FixAveTime::modify_param(int narg, char **arg)
+{
+  if (strcmp(arg[0], "colname") == 0) {
+    if (narg < 3) utils::missing_cmd_args(FLERR, "fix_modify colname", error);
+    int icol = -1;
+    if (utils::is_integer(arg[1])) {
+      icol = utils::inumeric(FLERR, arg[1], false, lmp);
+      if (icol < 0) icol = keyword.size() + icol + 1;
+      icol--;
+    } else {
+      try {
+        icol = key2col.at(arg[1]);
+      } catch (std::out_of_range &) {
+        icol = -1;
+      }
+    }
+    if ((icol < 0) || (icol >= (int) keyword.size()))
+      error->all(FLERR, "Thermo_modify colname column {} invalid", arg[1]);
+    keyword[icol] = arg[2];
+    return 3;
+  }
+  return 0;
+}
+
 /* ----------------------------------------------------------------------
    parse optional args
 ------------------------------------------------------------------------- */
@@ -1009,7 +1053,7 @@ void FixAveTime::options(int iarg, int narg, char **arg)
   noff = 0;
   offlist = nullptr;
   overwrite = 0;
-  yaml_flag = false;
+  yaml_flag = yaml_header = false;
   format_user = nullptr;
   format = (char *) " %g";
   title1 = nullptr;

src/fix_ave_time.h

@@ -22,6 +22,8 @@ FixStyle(ave/time,FixAveTime);
 
 #include "fix.h"
 
+#include <map>
+
 namespace LAMMPS_NS {
 
 class FixAveTime : public Fix {
@@ -32,6 +34,7 @@ class FixAveTime : public Fix {
   void init() override;
   void setup(int) override;
   void end_of_step() override;
+  int modify_param(int, char **) override;
   double compute_scalar() override;
   double compute_vector(int) override;
   double compute_array(int, int) override;
@@ -48,7 +51,7 @@ class FixAveTime : public Fix {
   int any_variable_length;
   int all_variable_length;
   int lockforever;
-  bool yaml_flag;
+  bool yaml_flag, yaml_header;
 
   int ave, nwindow, startstep, mode;
   int noff, overwrite;
@@ -57,6 +60,9 @@ class FixAveTime : public Fix {
   char *title1, *title2, *title3;
   bigint filepos;
 
+  std::map<std::string, int> key2col;
+  std::vector<std::string> keyword;
+
   int norm, iwindow, window_limit;
   double *vector;
   double *vector_total;