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MD-Bench/gromacs/vtk.c

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/*
* Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
* All rights reserved. This file is part of MD-Bench.
* Use of this source code is governed by a LGPL-3.0
* license that can be found in the LICENSE file.
*/
#include <stdio.h>
#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);
#ifdef USE_SUPER_CLUSTERS
write_super_clusters_to_vtk_file(filename, atom, timestep);
#endif //#ifdef USE_SUPER_CLUSTERS
}
#ifdef USE_SUPER_CLUSTERS
int write_super_clusters_to_vtk_file(const char* filename, Atom* atom, int timestep) {
char timestep_filename[128];
snprintf(timestep_filename, sizeof timestep_filename, "%s_sup_%d.vtk", filename, timestep);
FILE* fp = fopen(timestep_filename, "wb");
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 UNSTRUCTURED_GRID\n");
fprintf(fp, "POINTS %d double\n", atom->Nsclusters_local * SCLUSTER_M);
for(int ci = 0; ci < atom->Nsclusters_local; ++ci) {
int factor = (rand() % 1000) + 1;
//double factor = ci * 10;
int ci_vec_base = SCI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_x = &atom->scl_x[ci_vec_base];
for(int cii = 0; cii < SCLUSTER_M; ++cii) {
fprintf(fp, "%.4f %.4f %.4f\n", ci_x[SCL_X_OFFSET + cii] * factor, ci_x[SCL_Y_OFFSET + cii] * factor, ci_x[SCL_Z_OFFSET + cii] * factor);
}
}
fprintf(fp, "\n\n");
fprintf(fp, "CELLS %d %d\n", atom->Nlocal, atom->Nlocal * 2);
for(int i = 0; i < atom->Nlocal; ++i) {
fprintf(fp, "1 %d\n", i);
}
fprintf(fp, "\n\n");
fprintf(fp, "CELL_TYPES %d\n", atom->Nlocal);
for(int i = 0; i < atom->Nlocal; ++i) {
fprintf(fp, "1\n");
}
fprintf(fp, "\n\n");
fprintf(fp, "POINT_DATA %d\n", atom->Nlocal);
fprintf(fp, "SCALARS mass double\n");
fprintf(fp, "LOOKUP_TABLE default\n");
for(int i = 0; i < atom->Nlocal; i++) {
fprintf(fp, "1.0\n");
}
fprintf(fp, "\n\n");
fclose(fp);
return 0;
}
#endif //USE_SUPER_CLUSTERS
int write_local_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep) {
char timestep_filename[128];
snprintf(timestep_filename, sizeof timestep_filename, "%s_local_%d.vtk", filename, timestep);
FILE* fp = fopen(timestep_filename, "wb");
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 UNSTRUCTURED_GRID\n");
fprintf(fp, "POINTS %d double\n", atom->Nlocal);
for(int ci = 0; ci < atom->Nclusters_local; ++ci) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
for(int cii = 0; cii < atom->iclusters[ci].natoms; ++cii) {
fprintf(fp, "%.4f %.4f %.4f\n", ci_x[CL_X_OFFSET + cii], ci_x[CL_Y_OFFSET + cii], ci_x[CL_Z_OFFSET + cii]);
}
}
fprintf(fp, "\n\n");
fprintf(fp, "CELLS %d %d\n", atom->Nlocal, atom->Nlocal * 2);
for(int i = 0; i < atom->Nlocal; ++i) {
fprintf(fp, "1 %d\n", i);
}
fprintf(fp, "\n\n");
fprintf(fp, "CELL_TYPES %d\n", atom->Nlocal);
for(int i = 0; i < atom->Nlocal; ++i) {
fprintf(fp, "1\n");
}
fprintf(fp, "\n\n");
fprintf(fp, "POINT_DATA %d\n", atom->Nlocal);
fprintf(fp, "SCALARS mass double\n");
fprintf(fp, "LOOKUP_TABLE default\n");
for(int i = 0; i < atom->Nlocal; i++) {
fprintf(fp, "1.0\n");
}
fprintf(fp, "\n\n");
fclose(fp);
return 0;
}
int write_ghost_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep) {
char timestep_filename[128];
snprintf(timestep_filename, sizeof timestep_filename, "%s_ghost_%d.vtk", filename, timestep);
FILE* fp = fopen(timestep_filename, "wb");
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 UNSTRUCTURED_GRID\n");
fprintf(fp, "POINTS %d double\n", atom->Nghost);
for(int ci = atom->Nclusters_local; ci < atom->Nclusters_local + atom->Nclusters_ghost; ++ci) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
for(int cii = 0; cii < atom->iclusters[ci].natoms; ++cii) {
fprintf(fp, "%.4f %.4f %.4f\n", ci_x[CL_X_OFFSET + cii], ci_x[CL_Y_OFFSET + cii], ci_x[CL_Z_OFFSET + cii]);
}
}
fprintf(fp, "\n\n");
fprintf(fp, "CELLS %d %d\n", atom->Nghost, atom->Nghost * 2);
for(int i = 0; i < atom->Nghost; ++i) {
fprintf(fp, "1 %d\n", i);
}
fprintf(fp, "\n\n");
fprintf(fp, "CELL_TYPES %d\n", atom->Nghost);
for(int i = 0; i < atom->Nghost; ++i) {
fprintf(fp, "1\n");
}
fprintf(fp, "\n\n");
fprintf(fp, "POINT_DATA %d\n", atom->Nghost);
fprintf(fp, "SCALARS mass double\n");
fprintf(fp, "LOOKUP_TABLE default\n");
for(int i = 0; i < atom->Nghost; i++) {
fprintf(fp, "1.0\n");
}
fprintf(fp, "\n\n");
fclose(fp);
return 0;
}
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_local_edges_%d.vtk", filename, timestep);
FILE* fp = fopen(timestep_filename, "wb");
int N = atom->Nclusters_local;
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);
for(int ci = 0; ci < N; ++ci) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
for(int cii = 0; cii < atom->iclusters[ci].natoms; ++cii) {
fprintf(fp, "%.4f %.4f %.4f\n", ci_x[CL_X_OFFSET + cii], ci_x[CL_Y_OFFSET + cii], ci_x[CL_Z_OFFSET + cii]);
}
tot_lines += atom->iclusters[ci].natoms;
}
fprintf(fp, "\n\n");
fprintf(fp, "LINES %d %d\n", N, N + tot_lines);
for(int ci = 0; ci < N; ++ci) {
fprintf(fp, "%d ", atom->iclusters[ci].natoms);
for(int cii = 0; cii < atom->iclusters[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) {
int ci_vec_base = CI_VECTOR_BASE_INDEX(ci);
MD_FLOAT *ci_x = &atom->cl_x[ci_vec_base];
for(int cii = 0; cii < atom->iclusters[ci].natoms; ++cii) {
fprintf(fp, "%.4f %.4f %.4f\n", ci_x[CL_X_OFFSET + cii], ci_x[CL_Y_OFFSET + cii], ci_x[CL_Z_OFFSET + cii]);
}
tot_lines += atom->iclusters[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->iclusters[ci].natoms);
for(int cii = 0; cii < atom->iclusters[ci].natoms; ++cii) {
fprintf(fp, "%d ", i++);
}
fprintf(fp, "\n");
}
fprintf(fp, "\n\n");
fclose(fp);
return 0;
}
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