Add separated parameter for dump_exyz

doc/gpumd/input_parameters/dump_exyz.rst

@@ -15,12 +15,14 @@ Syntax
    dump_exyz <interval> <has_velocity>
    dump_exyz <interval> <has_velocity> <has_force>
    dump_exyz <interval> <has_velocity> <has_force> <has_potential>
+   dump_exyz <interval> <has_velocity> <has_force> <has_potential> <separated>
 
 Here, the :attr:`interval` parameter is the output interval (number of steps) of the data.
 :attr:`has_velocity` can be 1 or 0, which means the velocities will or will not be included in the output.
 :attr:`has_force` can be 1 or 0, which means the forces will or will not be included in the output.
 :attr:`has_potential` can be 1 or 0, which means the atomic potential energies will or will not be included in the output.
 The atomic positions will always be included in the output.
+:attr:`separated` can be 1 or 0, which means the output will or will not be separated into individual frames.
 
 Examples
 --------
@@ -32,6 +34,7 @@ Examples
     dump_exyz 1000 1 1    # dump positions, velocities, and forces
     dump_exyz 1000 1 1 1  # dump positions, velocities, forces, and potentials
     dump_exyz 1000 0 1 1  # dump positions, forces and potentials
+    dump_exyz 100 0 1 1 1 # dump positions, forces and potentials into dump.100.xyz, dump.200.xyz and so on
 
 Caveats
 -------

src/measure/dump_exyz.cu

@@ -69,6 +69,7 @@ void Dump_EXYZ::parse(const char** param, int num_param)
   has_velocity_ = 0;
   has_force_ = 0;
   has_potential_ = 0;
+  separated_ = 0;
 
   if (num_param >= 3) {
     if (!is_valid_int(param[2], &has_velocity_)) {
@@ -102,12 +103,26 @@ void Dump_EXYZ::parse(const char** param, int num_param)
       printf("    with potential data.\n");
     }
   }
+
+  if (num_param >= 6) {
+     if (!is_valid_int(param[5], &separated_)) {
+      PRINT_INPUT_ERROR("separated should be an integer.");
+     }
+     if (separated_ == 0) {
+      printf("    dump_exyz into dump.xyz.\n");
+     } else {
+      printf("    dump_exyz into separated dump.*.xyz.\n");
+     }
+  }
 }
 
 void Dump_EXYZ::preprocess(const int number_of_atoms)
 {
   if (dump_) {
-    fid_ = my_fopen("dump.xyz", "a");
+    if (separated_ == 0) {
+      fid_ = my_fopen("dump.xyz", "a");
+    }
+
     gpu_total_virial_.resize(6);
     cpu_total_virial_.resize(6);
     if (has_force_) {
@@ -235,6 +250,11 @@ void Dump_EXYZ::process(
   if (has_potential_) {
     atom.potential_per_atom.copy_to_host(cpu_potential_per_atom_.data());
   }
+
+  if (separated_) {
+    std::string filename = "dump."+std::to_string(step+1)+".xyz";
+    fid_ = my_fopen(filename.data(), "w");
+  }
 
   // line 1
   fprintf(fid_, "%d\n", num_atoms_total);
@@ -265,14 +285,20 @@ void Dump_EXYZ::process(
     }
     fprintf(fid_, "\n");
   }
-
-  fflush(fid_);
+  if (separated_ == 0) {
+    fflush(fid_);
+  } else {
+    fclose(fid_);
+  }
+
 }
 
 void Dump_EXYZ::postprocess()
 {
   if (dump_) {
-    fclose(fid_);
+    if (separated_ == 0) {
+      fclose(fid_);
+    }
     dump_ = false;
   }
 }

src/measure/dump_exyz.cuh

@@ -40,6 +40,7 @@ private:
   int has_velocity_ = 0;
   int has_force_ = 0;
   int has_potential_ = 0;
+  int separated_ = 0;
   FILE* fid_;
   char filename_[200];
   void output_line2(