moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Separate local and ghost cluster edges on VTK output

Browse Source 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti 2022-02-08 16:12:22 +01:00
parent 6a35a7a482
commit 769bab0faa
3 changed files with 61 additions and 14 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
gromacs/includes/vtk.h
View File

@ -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

8
gromacs/main.c
View File

@ -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_ghost_atoms_to_vtk_file(param.vtk_file, &atom, 0);
write_cluster_edges_to_vtk_file(param.vtk_file, &atom, 0);
write_data_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_ghost_atoms_to_vtk_file(param.vtk_file, &atom, n + 1);
write_cluster_edges_to_vtk_file(param.vtk_file, &atom, n + 1);
write_data_to_vtk_file(param.vtk_file, &atom, n + 1);
}
}

63
gromacs/vtk.c
View File

@ -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);
for(int ci = 0; ci < Nclusters_all; ++ci) {
fprintf(fp, "POINTS %d double\n", atom->Nlocal);
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);
for(int ci = 0; ci < Nclusters_all; ++ci) {
fprintf(fp, "LINES %d %d\n", N, N + tot_lines);
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++);