sandbox/haouche/extract.c

How to use output_vtu.h with MPI (Brun.sh)

Here, I show you how to extract your data when using MPI.
We start by creating an extract_file.c and including the necessary libraries:

#include "navier-stokes/centered.h"
#include "two-phase.h"
#include "output_vtu.h"

In this example, our main_file.c uses:

• #include "navier-stokes/centered.h"
• #include "two-phase.h"

More generally, you should include in extract_file.c the same headers you used in your main_file.c.

Then, simply copy the code below. Here, we create a folder named vtufile to store the output:

int pt = 0;
int main(int argc, char *argv[]){	
	if (argc > 1) pt = atoi(argv[1]);
	system("mkdir -p vtufile");
	run();	
}

We now use output_vtu.h, and specifically the function output_vtu_bin_foreach, to save our data (e.g., the volume fraction f, the velocity field \mathbf{u} and the pressure field p).

event init (t = 0.0){
	char filename[80];
	while(1){
		sprintf(filename, "snap-%d",pt);
		printf("extracting %s\n",filename);
		fflush(stdout);
		if(!restore (file = filename)){
			printf("files ended");
			exit(0);
		}
	
		scalar *list;		
		bool linear;
		char name[80];
		sprintf(name, "vtufile/snap-%d.vtu",pt);
		FILE *ptr = fopen(name,"w");
		output_vtu_bin_foreach((scalar *) {f, p}, (vector *) {u}, ptr, false);
		fclose(ptr);
	
		pt = pt + 1;
	}
}

This is how you can extract your simulation data when using Brun.sh.

To summerize:

• in your main_file.c remove #include output_vtu.h
• in your extract_file.c include all the same headers as in your main file.c, plus #include output_vtu.h
• In the output_vtu_bin_foreach call, choose the variables you want to save: volume fraction, velocity field, pressure, etc.

Special thanks to Yashika and Anil for sharing this method!