Separate local and ghost cluster edges on VTK output

Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>

gromacs/includes/vtk.h

@@ -24,7 +24,9 @@
 
 #ifndef __VTK_H_
 #define __VTK_H_
+extern void write_data_to_vtk_file(const char *filename, Atom* atom, int timestep);
 extern int write_local_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
 extern int write_ghost_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep);
-extern int write_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep);
+extern int write_local_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep);
+extern int write_ghost_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep);
 #endif

gromacs/main.c

@@ -271,9 +271,7 @@ int main(int argc, char** argv) {
     timer[TOTAL] = getTimeStamp();
 
     if(param.vtk_file != NULL) {
-        write_local_atoms_to_vtk_file(param.vtk_file, &atom, 0);
+        write_data_to_vtk_file(param.vtk_file, &atom, 0);
-        write_ghost_atoms_to_vtk_file(param.vtk_file, &atom, 0);
-        write_cluster_edges_to_vtk_file(param.vtk_file, &atom, 0);
     }
 
     for(int n = 0; n < param.ntimes; n++) {
@@ -302,9 +300,7 @@ int main(int argc, char** argv) {
         }
 
         if(param.vtk_file != NULL) {
-            write_local_atoms_to_vtk_file(param.vtk_file, &atom, n + 1);
+            write_data_to_vtk_file(param.vtk_file, &atom, n + 1);
-            write_ghost_atoms_to_vtk_file(param.vtk_file, &atom, n + 1);
-            write_cluster_edges_to_vtk_file(param.vtk_file, &atom, n + 1);
         }
     }
 

gromacs/vtk.c

@@ -2,6 +2,14 @@
 #include <stdlib.h>
 
 #include <atom.h>
+#include <vtk.h>
+
+void write_data_to_vtk_file(const char *filename, Atom* atom, int timestep) {
+    write_local_atoms_to_vtk_file(filename, atom, timestep);
+    write_ghost_atoms_to_vtk_file(filename, atom, timestep);
+    write_local_cluster_edges_to_vtk_file(filename, atom, timestep);
+    write_ghost_cluster_edges_to_vtk_file(filename, atom, timestep);
+}
 
 int write_local_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep) {
     char timestep_filename[128];
@@ -89,11 +97,11 @@ int write_ghost_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep
     return 0;
 }
 
-int write_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep) {
+int write_local_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep) {
     char timestep_filename[128];
-    snprintf(timestep_filename, sizeof timestep_filename, "%s_edges_%d.vtk", filename, timestep);
+    snprintf(timestep_filename, sizeof timestep_filename, "%s_local_edges_%d.vtk", filename, timestep);
     FILE* fp = fopen(timestep_filename, "wb");
-    int Nclusters_all = atom->Nclusters_local + atom->Nclusters_ghost;
+    int N = atom->Nclusters_local;
     int tot_lines = 0;
     int i = 0;
 
@@ -106,8 +114,8 @@ int write_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timest
     fprintf(fp, "Particle data\n");
     fprintf(fp, "ASCII\n");
     fprintf(fp, "DATASET POLYDATA\n");
-    fprintf(fp, "POINTS %d double\n", atom->Nlocal + atom->Nghost);
+    fprintf(fp, "POINTS %d double\n", atom->Nlocal);
-    for(int ci = 0; ci < Nclusters_all; ++ci) {
+    for(int ci = 0; ci < N; ++ci) {
         MD_FLOAT *cptr = cluster_pos_ptr(ci);
         for(int cii = 0; cii < atom->clusters[ci].natoms; ++cii) {
             fprintf(fp, "%.4f %.4f %.4f\n", cluster_x(cptr, cii), cluster_y(cptr, cii), cluster_z(cptr, cii));
@@ -116,8 +124,49 @@ int write_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timest
         tot_lines += atom->clusters[ci].natoms;
     }
     fprintf(fp, "\n\n");
-    fprintf(fp, "LINES %d %d\n", Nclusters_all, Nclusters_all + tot_lines);
+    fprintf(fp, "LINES %d %d\n", N, N + tot_lines);
-    for(int ci = 0; ci < Nclusters_all; ++ci) {
+    for(int ci = 0; ci < N; ++ci) {
+        fprintf(fp, "%d ", atom->clusters[ci].natoms);
+        for(int cii = 0; cii < atom->clusters[ci].natoms; ++cii) {
+            fprintf(fp, "%d ", i++);
+        }
+
+        fprintf(fp, "\n");
+    }
+    fprintf(fp, "\n\n");
+    fclose(fp);
+    return 0;
+}
+
+int write_ghost_cluster_edges_to_vtk_file(const char* filename, Atom* atom, int timestep) {
+    char timestep_filename[128];
+    snprintf(timestep_filename, sizeof timestep_filename, "%s_ghost_edges_%d.vtk", filename, timestep);
+    FILE* fp = fopen(timestep_filename, "wb");
+    int N = atom->Nclusters_local + atom->Nclusters_ghost;
+    int tot_lines = 0;
+    int i = 0;
+
+    if(fp == NULL) {
+        fprintf(stderr, "Could not open VTK file for writing!\n");
+        return -1;
+    }
+
+    fprintf(fp, "# vtk DataFile Version 2.0\n");
+    fprintf(fp, "Particle data\n");
+    fprintf(fp, "ASCII\n");
+    fprintf(fp, "DATASET POLYDATA\n");
+    fprintf(fp, "POINTS %d double\n", atom->Nghost);
+    for(int ci = atom->Nclusters_local; ci < N; ++ci) {
+        MD_FLOAT *cptr = cluster_pos_ptr(ci);
+        for(int cii = 0; cii < atom->clusters[ci].natoms; ++cii) {
+            fprintf(fp, "%.4f %.4f %.4f\n", cluster_x(cptr, cii), cluster_y(cptr, cii), cluster_z(cptr, cii));
+        }
+
+        tot_lines += atom->clusters[ci].natoms;
+    }
+    fprintf(fp, "\n\n");
+    fprintf(fp, "LINES %d %d\n", atom->Nclusters_ghost, atom->Nclusters_ghost + tot_lines);
+    for(int ci = atom->Nclusters_local; ci < N; ++ci) {
         fprintf(fp, "%d ", atom->clusters[ci].natoms);
         for(int cii = 0; cii < atom->clusters[ci].natoms; ++cii) {
             fprintf(fp, "%d ", i++);