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Add cluster edges in VTK output

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Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-02-08 00:11:10 +01:00
parent cd15911a97
commit 8deee3d954
3 changed files with 44 additions and 0 deletions
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1
gromacs/includes/vtk.h
View File

@ -26,4 +26,5 @@
#define __VTK_H_ #define __VTK_H_
extern int write_local_atoms_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_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);
#endif #endif

2
gromacs/main.c
View File

@ -273,6 +273,7 @@ int main(int argc, char** argv) {
if(param.vtk_file != NULL) { if(param.vtk_file != NULL) {
write_local_atoms_to_vtk_file(param.vtk_file, &atom, 0); write_local_atoms_to_vtk_file(param.vtk_file, &atom, 0);
write_ghost_atoms_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++) { for(int n = 0; n < param.ntimes; n++) {
@ -303,6 +304,7 @@ int main(int argc, char** argv) {
if(param.vtk_file != NULL) { if(param.vtk_file != NULL) {
write_local_atoms_to_vtk_file(param.vtk_file, &atom, n + 1); write_local_atoms_to_vtk_file(param.vtk_file, &atom, n + 1);
write_ghost_atoms_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);
} }
} }

41
gromacs/vtk.c
View File

@ -88,3 +88,44 @@ int write_ghost_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep
fclose(fp); fclose(fp);
return 0; return 0;
} }
int write_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);
FILE* fp = fopen(timestep_filename, "wb");
int Nclusters_all = 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->Nlocal + atom->Nghost);
for(int ci = 0; ci < Nclusters_all; ++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", Nclusters_all, Nclusters_all + tot_lines);
for(int ci = 0; ci < Nclusters_all; ++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;
}