MD-Bench/lammps/vtk.c
2024-04-15 16:53:25 +02:00

219 lines
7.1 KiB
C

/*
* 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 <string.h>
#include <vtk.h>
#include <mpi.h>
static MPI_File _fh;
static inline void flushBuffer(char*);
int write_atoms_to_vtk_file(const char* filename, Atom* atom, int timestep) {
char timestep_filename[128];
snprintf(timestep_filename, sizeof timestep_filename, "%s_%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 i = 0; i < atom->Nlocal; ++i) {
fprintf(fp, "%.4f %.4f %.4f\n", atom_x(i), atom_y(i), atom_z(i));
}
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 vtkOpen(const char* filename, Comm* comm, Atom* atom ,int timestep)
{
char msg[256];
char timestep_filename[128];
snprintf(timestep_filename, sizeof timestep_filename, "%s_%d.vtk", filename, timestep);
MPI_File_open(MPI_COMM_WORLD, timestep_filename, MPI_MODE_WRONLY | MPI_MODE_CREATE, MPI_INFO_NULL, &_fh);
if(_fh == MPI_FILE_NULL) {
if(comm->myproc == 0) fprintf(stderr, "Could not open VTK file for writing!\n");
return -1;
}
if (comm->myproc==0){
sprintf(msg, "# vtk DataFile Version 2.0\n");
sprintf(msg, "%sParticle data\n",msg);
sprintf(msg, "%sASCII\n",msg);
sprintf(msg, "%sDATASET UNSTRUCTURED_GRID\n",msg);
sprintf(msg, "%sPOINTS %d double\n",msg, atom->Natoms);
flushBuffer(msg);
}
}
int vtkVector(Comm* comm, Atom* atom, Parameter* param)
{
if (_fh == MPI_FILE_NULL) {
if(comm->myproc==0) printf("vtk not initialize! Call vtkOpen first!\n");
return -1;
}
int sizeline= 25; //#initial guess of characters in "%.4f %.4f %.4f\n"
int extrabuff = 100;
int sizebuff = sizeline*atom->Nlocal+extrabuff;
int mysize = 0;
char* msg = (char*) malloc(sizebuff);
sprintf(msg, "");
for(int i = 0; i < atom->Nlocal; i++){
if(mysize+extrabuff >= sizebuff){
sizebuff*= 1.5;
msg = (char*) realloc(msg, sizebuff);
}
//TODO: do not forget to add param->xlo, param->ylo, param->zlo
sprintf(msg, "%s%.4f %.4f %.4f\n",msg, atom_x(i), atom_y(i), atom_z(i));
mysize = strlen(msg);
}
int gatherSize[comm->numproc];
MPI_Allgather(&mysize, 1, MPI_INT, gatherSize, 1, MPI_INT, MPI_COMM_WORLD);
int offset=0;
int globalSize = 0;
for(int i = 0; i < comm->myproc; i++)
offset+= gatherSize[i];
for(int i = 0; i < comm->numproc; i++)
globalSize+= gatherSize[i];
MPI_Offset displ;
MPI_Datatype FileType;
int GlobalSize[] = {globalSize};
int LocalSize[] = {mysize};
int Start[] = {offset};
if(LocalSize[0]>0){
MPI_Type_create_subarray(1, GlobalSize, LocalSize, Start, MPI_ORDER_C, MPI_CHAR, &FileType);
} else {
MPI_Type_vector(0,0,0,MPI_CHAR,&FileType);
}
MPI_Type_commit(&FileType);
MPI_File_get_size(_fh, &displ);
MPI_File_set_view(_fh, displ, MPI_CHAR, FileType, "native", MPI_INFO_NULL);
MPI_File_write_all (_fh, msg, mysize , MPI_CHAR ,MPI_STATUS_IGNORE);
MPI_Barrier(MPI_COMM_WORLD);
MPI_File_set_view(_fh,0,MPI_CHAR, MPI_CHAR, "native", MPI_INFO_NULL);
if (comm->myproc==0){
sprintf(msg, "\n\n");
sprintf(msg, "%sCELLS %d %d\n", msg, atom->Natoms, atom->Natoms * 2);
for(int i = 0; i < atom->Natoms; i++)
sprintf(msg, "%s1 %d\n", msg, i);
flushBuffer(msg);
sprintf(msg, "\n\n");
sprintf(msg, "%sCELL_TYPES %d\n",msg, atom->Natoms);
for(int i = 0; i < atom->Natoms; i++)
sprintf(msg, "%s1\n",msg);
flushBuffer(msg);
sprintf(msg, "\n\n");
sprintf(msg, "%sPOINT_DATA %d\n",msg,atom->Natoms);
sprintf(msg, "%sSCALARS mass double\n",msg);
sprintf(msg, "%sLOOKUP_TABLE default\n",msg);
for(int i = 0; i < atom->Natoms; i++)
sprintf(msg, "%s1.0\n",msg);
sprintf(msg, "%s\n\n",msg);
flushBuffer(msg);
}
}
void vtkClose()
{
MPI_File_close(&_fh);
_fh=MPI_FILE_NULL;
}
int printGhost(const char* filename, Atom* atom, int timestep, int me) {
char timestep_filename[128];
snprintf(timestep_filename, sizeof timestep_filename, "%s_%d_ghost%i.vtk", filename, timestep,me);
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 i = atom->Nlocal; i < atom->Nlocal+atom->Nghost; ++i) {
fprintf(fp, "%.4f %.4f %.4f\n", atom_x(i), atom_y(i), atom_z(i));
}
fprintf(fp, "\n\n");
fprintf(fp, "CELLS %d %d\n", atom->Nlocal, atom->Nlocal * 2);
for(int i = atom->Nlocal; i < atom->Nlocal+atom->Nghost; ++i) {
fprintf(fp, "1 %d\n", i);
}
fprintf(fp, "\n\n");
fprintf(fp, "CELL_TYPES %d\n", atom->Nlocal);
for(int i = atom->Nlocal; i < atom->Nlocal+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 = atom->Nlocal; i < atom->Nlocal+atom->Nghost; i++) {
fprintf(fp, "1.0\n");
}
fprintf(fp, "\n\n");
fclose(fp);
return 0;
}
void printvtk(const char* filename, Comm* comm, Atom* atom ,Parameter* param, int timestep)
{
if(comm->numproc == 1)
{
write_atoms_to_vtk_file(filename, atom, timestep);
return;
}
vtkOpen(filename, comm, atom, timestep);
vtkVector(comm, atom, param);
vtkClose();
//printGhost(filename, atom, timestep, comm->myproc);
}
static inline void flushBuffer(char* msg){
MPI_Offset displ;
MPI_File_get_size(_fh, &displ);
MPI_File_write_at(_fh, displ, msg, strlen(msg), MPI_CHAR, MPI_STATUS_IGNORE);
}