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p3D_acoustic_O24.c
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p3D_acoustic_O24.c
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/*
3D acoustic wave propagation in homogeneous isotropic media, using PETSc
2017
PETSc - Portable, Extensible Toolkit for Scientific Computation
https://www.mcs.anl.gov/petsc/
# TECH DETAILS:
Finite-Differences in Time Domain (FDTD)
Implicit time stepping
O(2,4)
Schemes derived from Taylor series: in space [-1:16:-30:16:-1]/12dx2, in time [2:-5:4:-1]/dt2
# HOW TO USE: (PETSc has to be installed)
make all
./run_O24.sh
Author: Oleg Ovcharenko, PhD student at KAUST (ErSE, ECRC)
Email: [email protected]
*/
#include <stdio.h>
#include <petscdmda.h>
#include <petscksp.h>
#include <math.h>
#include <time.h>
#include <sys/types.h>
#include <sys/stat.h>
#include <unistd.h>
#define debprint(expr) PetscPrintf(PETSC_COMM_WORLD, #expr " = %f \n", expr);
// Constants
#define PI 3.1415926535
#define DEGREES_TO_RADIANS PI/180.f
//User-functions prototypes
PetscErrorCode compute_A_u(KSP, Mat, Mat, void *); // Build A, for Ax=b
PetscErrorCode update_b_u(KSP, Vec, void *); // Build b, for Ax=b
PetscErrorCode save_Vec_to_m_file(Vec, void *); // Save wavefield into MATLAB .m file
PetscErrorCode Save_seismograms_to_txt_files(KSP, void *); // Save seism. to .txt files
PetscErrorCode source_term(void *); // Compute source term for current time step
PetscErrorCode Write_seismograms(KSP, Vec, void *); // Append new value to the seismograms
PetscScalar ***f3tensor(PetscInt, PetscInt, PetscInt, PetscInt,PetscInt, PetscInt); // Create 3D array
/*
User-defined structures
*/
// Wavefield
typedef struct {
Vec u; // Pressure wavefield at T
Vec um1; // Pressure wavefield at T-1
Vec um2; // Pressure wavefield at T-2
Vec um3; // Pressure wavefield at T-3
} wfield;
// Model parameters
typedef struct {
PetscInt nx; // Number of grid points along X
PetscInt ny;
PetscInt nz;
PetscScalar dx; // Grid spacing [km]
PetscScalar dy;
PetscScalar dz;
PetscScalar xmax; // Limits along OX, xmin ... xmax [km]
PetscScalar xmin;
PetscScalar ymax;
PetscScalar ymin;
PetscScalar zmax;
PetscScalar zmin;
PetscScalar vel; // Wave propagation velocity [km/s]
} model_par;
typedef struct{
PetscScalar dt; // Time step [s]
PetscScalar t0;
PetscScalar tmax; // Total simulation time [s]
PetscScalar t; // Current simulation time [s]
PetscInt it; // Current simulation step
PetscInt nt; // Total simulation steps
} time_par;
typedef struct{
PetscInt isrc; // Source position, in grid points
PetscInt jsrc;
PetscInt ksrc;
PetscScalar factor; // Source ampliturde
PetscScalar angle_force;
PetscScalar f0; // Source frequency
PetscScalar fx; // Force x component
PetscScalar fy;
PetscScalar fz;
} source;
typedef struct
{
PetscInt nrec; // Number of receivers
PetscInt *irec; // Receiver positions, in grid points
PetscInt *jrec;
PetscInt *krec;
PetscScalar ***seis; // Array to store seismograms [nrec][nt][2]
} receivers;
typedef struct { // User context that gathers all the structures above
wfield wf;
model_par model;
time_par time;
source src;
receivers rec;
} ctx_t;
typedef int bool; // TRUE-FALSE definition
#define true 1
#define false 0
/*
Main function
*/
int
main(int argc, char * args[])
{
/*
VARIABLES
*/
bool FOUTPUT = true; // Print information each IT_DISPLAY steps
bool SAVE_WAVEFIELD_MATLAB = false; // Save the whole wavefield to .m file each IT_DISPLAY steps
int IT_DISPLAY = 50; // Number of time steps to give output
struct stat st = {0};
// Create folders for output if they are missing
if (stat("./seism/", &st) == -1)
{
mkdir("./seism/", 0700);
}
if (stat("./wavefields/", &st) == -1)
{
mkdir("./wavefields/", 0700);
}
PetscErrorCode ierr; // PETSc error code
DM da; // Mesh-object
// Initialize the PETSc database and MPI
ierr = PetscInitialize(&argc, &args, NULL, NULL); CHKERRQ(ierr);
MPI_Comm comm = PETSC_COMM_WORLD; // The global PETSc MPI communicator
Vec b, *pu;
Vec *pum1;
Vec *pum2;
Vec *pum3;
PetscScalar *pvel;
PetscScalar *pdx, *pdy, *pdz, *pxmax, *pymax, *pzmax;
PetscScalar *pt0, *pdt, *ptmax;
PetscScalar norm;
PetscInt *pnx, *pny, *pnz, *pnt;
PetscInt tmp;
ctx_t ctx, *pctx; // User context structure
clock_t total_time_begin, total_time_end;
total_time_begin = clock(); // Start total time counter
/*
LIST OF POINTERS
*/
pctx = &ctx;
pu = &ctx.wf.u;
pum1 = &ctx.wf.um1;
pum2 = &ctx.wf.um2;
pum3 = &ctx.wf.um3;
pnx = &ctx.model.nx;
pny = &ctx.model.ny;
pnz = &ctx.model.nz;
pdx = &ctx.model.dx;
pdy = &ctx.model.dy;
pdz = &ctx.model.dz;
pxmax = &ctx.model.xmax;
pymax = &ctx.model.ymax;
pzmax = &ctx.model.zmax;
pvel = &ctx.model.vel;
pnt = &ctx.time.nt;
pt0 = &ctx.time.t0;
pdt = &ctx.time.dt;
ptmax = &ctx.time.tmax;
/*
CREATE DMDA OBJECT. MESH
*/
ierr = DMDACreate3d(comm, DM_BOUNDARY_GHOSTED, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, // Create mesh
DMDA_STENCIL_STAR, -32, -32, -32, PETSC_DECIDE, PETSC_DECIDE,
PETSC_DECIDE, 1, 2, NULL, NULL, NULL, &da); CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,pnx, pny, pnz, 0,0,0,0,0,0,0,0,0); CHKERRQ(ierr); // Get NX, NY, NZ
/*
CREATE GLOBAL VEC OBJECTS
*/
ierr = DMCreateGlobalVector(da, pu); CHKERRQ(ierr); // Create a global u vector derived from the DM object
ierr = VecDuplicate(*pu, &b); CHKERRQ(ierr); // RHS of the system
ierr = VecDuplicate(*pu, pum1); CHKERRQ(ierr); // u at time n-1
ierr = VecDuplicate(*pu, pum2); CHKERRQ(ierr); // u at time n-2
ierr = VecDuplicate(*pu, pum3); CHKERRQ(ierr); // u at time n-3
/*
SET MODEL PATRAMETERS
*/
// Wave propagation VELOCITY
*pvel = 3.5f;
ierr = PetscOptionsGetReal(NULL, NULL, "-vel",&ctx.model.vel, NULL); CHKERRQ(ierr); //input on-the-fly
// MODEL SIZE Xmax Ymax Zmax in meters
*pxmax = 8.f; //[km]
*pymax = 8.f;
*pzmax = 8.f;
ierr = PetscOptionsGetReal(NULL, NULL, "-xmax",&ctx.model.xmax, NULL); CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL, NULL, "-ymax",&ctx.model.ymax, NULL); CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL, NULL, "-zmax",&ctx.model.zmax, NULL); CHKERRQ(ierr);
// GRID STEP DX DY and DZ
*pdx = *pxmax / *pnx; //[km]
*pdy = *pymax / *pny;
*pdz = *pzmax / *pnz;
PetscScalar cmax, cmin, lambda_min;
cmin = *pvel;
cmax = *pvel;
// TIME STEPPING PARAMETERS
*pdt = (*pdx) / cmax; //[sec], to have CFL = 1, could be set from runtime
ierr = PetscOptionsGetReal(NULL, NULL, "-dt",&ctx.time.dt, NULL); CHKERRQ(ierr);
*ptmax = 1.f; //[sec]
ierr = PetscOptionsGetReal(NULL, NULL, "-tmax",&ctx.time.tmax, NULL); CHKERRQ(ierr);
*pnt = *ptmax / *pdt;
// SOURCE PARAMETERS
ctx.src.isrc = (PetscInt) *pnx / 2;
ctx.src.jsrc = (PetscInt) *pny / 2;
ctx.src.ksrc = (PetscInt) *pnz / 2;
ierr = PetscOptionsGetInt(NULL, NULL, "-isrc",&ctx.src.isrc, NULL); CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL, NULL, "-jsrc",&ctx.src.jsrc, NULL); CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL, NULL, "-ksrc",&ctx.src.ksrc, NULL); CHKERRQ(ierr);
ctx.src.f0 = 20.f; //[Hz]
ierr = PetscOptionsGetReal(NULL, NULL, "-f0",&ctx.src.f0, NULL); CHKERRQ(ierr);
ctx.src.factor = pow(10.f,7); //amplitude
ctx.src.angle_force = 90; // degrees
lambda_min = cmin / ctx.src.f0; // Min wavelength in model
// RECEIVERS
ctx.rec.nrec = 20; // Number of receivers
ierr = PetscOptionsGetInt(NULL, NULL, "-nrec",&ctx.rec.nrec, NULL); CHKERRQ(ierr);
PetscInt irec[ctx.rec.nrec], *pirec; // Arrays for rec positions
PetscInt jrec[ctx.rec.nrec], *pjrec;
PetscInt krec[ctx.rec.nrec], *pkrec;
pirec = &irec[0];
pjrec = &jrec[0];
pkrec = &krec[0];
// Place receivers on diogonal
int i;
for (i = 0; i < ctx.rec.nrec; i++)
{
*(pirec + i) = (PetscInt) (ctx.rec.nrec - i) * (ctx.model.nx) / ctx.rec.nrec;
*(pjrec + i) = (PetscInt) (ctx.rec.nrec - i) * (ctx.model.ny) / ctx.rec.nrec;
*(pkrec + i) = (PetscInt) (ctx.rec.nrec - i) * (ctx.model.nz) / ctx.rec.nrec;
}
ctx.rec.irec = irec;
ctx.rec.jrec = jrec;
ctx.rec.krec = krec;
//Array with seismograms [NREC][NT][2], 2 is for time and displacement colums
PetscScalar ***seis;
seis = f3tensor(0,ctx.rec.nrec,0,*pnt,0,2);
ctx.rec.seis = seis;
// OUTPUT
PetscPrintf(PETSC_COMM_WORLD,"MODEL:\n");
PetscPrintf(PETSC_COMM_WORLD,"\t XMAX %f \t DX %f km \t NX %i\n", *pxmax, *pdx, *pnx);
PetscPrintf(PETSC_COMM_WORLD,"\t YMAX %f \t DY %f km \t NY %i\n", *pymax, *pdy, *pny);
PetscPrintf(PETSC_COMM_WORLD,"\t ZMAX %f \t DZ %f km \t NZ %i\n", *pzmax, *pdz, *pnz);
PetscPrintf(PETSC_COMM_WORLD,"\t MAX C \t %f km/s \n", cmax);
PetscPrintf(PETSC_COMM_WORLD,"\t MIN C \t %f km/s \n", cmin);
PetscPrintf(PETSC_COMM_WORLD,"\n");
PetscPrintf(PETSC_COMM_WORLD,"SOURCE:\n");
PetscPrintf(PETSC_COMM_WORLD,"\t ISRC %i \t JSRC %i \t KSRC %i\n", ctx.src.isrc, ctx.src.jsrc, ctx.src.ksrc);
PetscPrintf(PETSC_COMM_WORLD,"\t F0 \t %f Hz \n", ctx.src.f0);
PetscPrintf(PETSC_COMM_WORLD,"\t MIN Lambda \t %f km \n", lambda_min);
PetscPrintf(PETSC_COMM_WORLD,"\t POINTS PER WAvelENGTH \t %f \n", lambda_min/(*pdx));
PetscPrintf(PETSC_COMM_WORLD,"\n");
PetscPrintf(PETSC_COMM_WORLD,"RECEIVERS:\n");
PetscPrintf(PETSC_COMM_WORLD,"\t NREC \t %i\n", ctx.rec.nrec);
PetscPrintf(PETSC_COMM_WORLD,"\t IREC \t JREC \t KSREC \n");
// PRINT RECEIVER POSITIONS'
int rr;
for (rr = 0; rr < ctx.rec.nrec; rr++)
{
PetscPrintf(PETSC_COMM_WORLD,"\t %i \t %i \t %i \n", ctx.rec.irec[rr], ctx.rec.jrec[rr], ctx.rec.krec[rr]);
}
PetscPrintf(PETSC_COMM_WORLD,"\n");
PetscPrintf(PETSC_COMM_WORLD,"TIME STEPPING: \n");
PetscPrintf(PETSC_COMM_WORLD,"\t TMAX %f \t DT %f \t NT %i\n", *ptmax, *pdt, *pnt);
PetscPrintf(PETSC_COMM_WORLD,"\n");
PetscPrintf(PETSC_COMM_WORLD,"CFL CONDITION: \t %f \n", cmax * (*pdt)/(*pdx));
PetscPrintf(PETSC_COMM_WORLD,"\n");
VecGetSize(*pu, &tmp);
PetscPrintf(PETSC_COMM_WORLD,"MATRICES AND VECTORS: \n");
PetscPrintf(PETSC_COMM_WORLD,"\t Vec elements \t %i\n", tmp);
PetscPrintf(PETSC_COMM_WORLD,"\t Mat \t %i x %i x %i \n", *pnx, *pny, *pnz);
PetscPrintf(PETSC_COMM_WORLD,"\n");
/*
CREATE KSP, KRYLOV SUBSPACE OBJECTS
*/
KSP ksp_u;
// Create Krylov solver for u component
ierr = KSPCreate(comm, &ksp_u); CHKERRQ(ierr); // Create the KPS object
ierr = KSPSetDM(ksp_u, (DM) da); CHKERRQ(ierr); // Set the DM to be used as preconditioner
ierr = KSPSetComputeOperators(ksp_u, compute_A_u, &ctx); CHKERRQ(ierr); // Compute and assemble the coefficient matrix A
ierr = KSPSetFromOptions(ksp_u); CHKERRQ(ierr); // KSP options can be changed during the runtime
/*
TIME LOOP
*/
clock_t begin=clock();
clock_t end;
int it;
int shoot_time;
for (it = 1; it <= *pnt; it ++)
{
ctx.time.it = it;
ctx.time.t = (PetscScalar) (it-1) * ctx.time.dt;
ierr = KSPSetComputeRHS(ksp_u, update_b_u, &ctx); CHKERRQ(ierr); // new rhs for next iteration
ierr = KSPSolve(ksp_u, b, *pu); CHKERRQ(ierr); // Solve the linear system using KSP
ierr = Write_seismograms(ksp_u, *pu, &ctx); CHKERRQ(ierr); // Append value to the seismograms
ierr = VecCopy(*pum2, *pum3); CHKERRQ(ierr); // copy vector um2 to um3
ierr = VecCopy(*pum1, *pum2); CHKERRQ(ierr); // copy vector um1 to um2
ierr = VecCopy(*pu, *pum1); CHKERRQ(ierr); // copy vector u to um1
shoot_time = (int) it%IT_DISPLAY;
if (FOUTPUT && shoot_time == 0)
{
end = clock();
ierr = PetscPrintf(PETSC_COMM_WORLD, "Time step: \t %i of %i\n", ctx.time.it, ctx.time.nt); CHKERRQ(ierr);
ierr = VecMax(*pu, NULL, &cmax); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "u max: \t %g \n", cmax); CHKERRQ(ierr);
ierr = VecMin(*pu, NULL, &cmin); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "u min: \t %g \n", cmin); CHKERRQ(ierr);
ierr = VecNorm(*pu,NORM_2,&norm); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "NORM: \t %g \n", norm); CHKERRQ(ierr);
double time_spent = (double)(end - begin) / CLOCKS_PER_SEC;
ierr = PetscPrintf(PETSC_COMM_WORLD, "Elapsed time: \t %f sec \n", time_spent); CHKERRQ(ierr);
if (SAVE_WAVEFIELD_MATLAB)
{
char buffer[64];
snprintf(buffer, sizeof(buffer), "./wavefields/tmp_Bvec_%i.m", it);
ierr = save_Vec_to_m_file(*pu, &buffer); CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHKERRQ(ierr);
begin = clock();
}
}
ierr = Save_seismograms_to_txt_files(ksp_u, pctx); CHKERRQ(ierr); // Write seismograms into .txt files
/*
CLEAN ALLOCATIONS AND EXIT
*/
ierr = VecDestroy(&b); CHKERRQ(ierr);
ierr = VecDestroy(pu); CHKERRQ(ierr);
ierr = VecDestroy(pum1); CHKERRQ(ierr);
ierr = VecDestroy(pum2); CHKERRQ(ierr);
ierr = VecDestroy(pum3); CHKERRQ(ierr);
ierr = KSPDestroy(&ksp_u); CHKERRQ(ierr);
ierr = DMDestroy(&da); CHKERRQ(ierr);
// Print out total elapsed time
total_time_end = clock();
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n Please check ./seism/ for seismograms\n"); CHKERRQ(ierr);
double time_spent = (double)(total_time_end - total_time_begin) / CLOCKS_PER_SEC;
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n"); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Total time: \t %f sec \n", time_spent); CHKERRQ(ierr);
ierr = PetscFinalize(); CHKERRQ(ierr);
return 0;
}
// APPEND VALUE TO A SEISMOGRAM
PetscErrorCode
Write_seismograms(KSP ksp, Vec u ,void *ctx)
{
PetscFunctionBegin;
PetscErrorCode ierr;
PetscScalar ***_u;
ctx_t *c = (ctx_t *) ctx;
DM da;
ierr = KSPGetDM(ksp, &da); CHKERRQ(ierr); //Get the DM oject of the KSP
DMDALocalInfo grid;
ierr = DMDAGetLocalInfo(da, &grid); CHKERRQ(ierr); //Get the global information of the DM grid
ierr = DMDAVecGetArray(da, u, &_u); CHKERRQ(ierr);
PetscScalar t = c->time.t;
PetscInt it = c->time.it;
PetscInt nrec = c->rec.nrec;
PetscInt *irec = c->rec.irec;
PetscInt *jrec = c->rec.jrec;
PetscInt *krec = c->rec.krec;
int xrec;
for (xrec = 0; xrec < nrec; xrec++)
{
if ((irec[xrec] > grid.xs) && (irec[xrec] < (grid.xs + grid.xm)) &&
(jrec[xrec] > grid.ys) && (jrec[xrec] < (grid.ys + grid.ym)) &&
(krec[xrec] > grid.zs) && (krec[xrec] < (grid.zs + grid.zm)))
{
c->rec.seis[xrec][it-1][0] = t;
c->rec.seis[xrec][it-1][1] = _u[krec[xrec]][jrec[xrec]][irec[xrec]];
}
}
ierr = DMDAVecRestoreArray(da, u, &_u); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
// SAVE VECTOR TO .m FILE
PetscErrorCode
save_Vec_to_m_file(Vec u, void * filename)
{
PetscFunctionBegin;
PetscErrorCode ierr;
char * filename2 = (char *) filename;
ierr = PetscPrintf(PETSC_COMM_WORLD, "File created: %s .m \n",filename2); CHKERRQ(ierr);
PetscViewer viewer;
PetscViewerASCIIOpen(PETSC_COMM_WORLD, filename2, &viewer);
PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_MATLAB);
VecView(u, viewer);
PetscViewerPopFormat(viewer);
PetscViewerDestroy(&viewer);
PetscFunctionReturn(0);
}
// SOURCE TERM
PetscErrorCode
source_term(void * ctx)
{
PetscFunctionBegin;
PetscScalar f0, t, t0, a, source_term, factor;
PetscScalar force_x, force_y, force_z, angle_force;
ctx_t *c = (ctx_t *) ctx;
f0 = c->src.f0;
t0 = 1.2f / f0;
t = c->time.t;
factor = c->src.factor;
angle_force = c->src.angle_force;
//add the source (force vector located at a given grid point)
a = PI*PI*f0*f0;
//Gaussian
// source_term = factor * exp(-a * pow((t-t0),2));
//first derivative of a Gaussian
// source_term = - factor * 2.d0*a*(t-t0)*exp(-a*(t-t0)**2)
//Ricker source time function (second derivative of a Gaussian)
source_term = factor * (1.f - 2.f * a * pow(t-t0,2)) * exp(-a*pow(t-t0,2));
force_x = sin(angle_force * DEGREES_TO_RADIANS) * source_term;
force_y = cos(angle_force * DEGREES_TO_RADIANS) * source_term;
force_z = sin(angle_force * DEGREES_TO_RADIANS) * source_term;
c->src.fx = force_x;
c->src.fy = force_y;
c->src.fz = force_z;
PetscFunctionReturn(0);
}
// UPDATE RHS AT NEW TIME STEP
PetscErrorCode
update_b_u(KSP ksp, Vec b, void * ctx)
{
PetscFunctionBegin;
PetscErrorCode ierr;
PetscScalar dt2;
ctx_t *c = (ctx_t *) ctx;
source_term(c);
dt2 = pow(c->time.dt,2);
DM da;
ierr = KSPGetDM(ksp, &da); CHKERRQ(ierr); //Get the DM oject of the KSP
DMDALocalInfo grid;
ierr = DMDAGetLocalInfo(da, &grid); CHKERRQ(ierr); //Get the global information of the DM grid
PetscScalar hx = c->model.dx;
PetscScalar hy = c->model.dy;
PetscScalar hz = c->model.dz;
double *** _b;
double *** _um1, ***_um2, ***_um3;
ierr = DMDAVecGetArray(da, b, &_b); CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, c->wf.um1, &_um1); CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, c->wf.um2, &_um2); CHKERRQ(ierr);
ierr = DMDAVecGetArray(da, c->wf.um3, &_um3); CHKERRQ(ierr);
// Fill b
double f, source_term;
unsigned int k;
for(k = grid.zs; k < (grid.zs + grid.zm); k++) // Depth
{
unsigned int j;
for(j = grid.ys; j < (grid.ys + grid.ym); j++) // Columns
{
unsigned int i;
for(i = grid.xs; i < (grid.xs + grid.xm); i++) // Rows
{
// Nodes on the boundary layers
if((i == 0) || (i == (grid.mx - 1)) ||
(j == 0) || (j == (grid.my - 1)) ||
(k == 0) || (k == (grid.mz - 1)))
{
_b[k][j][i] = 0.f;
}
//Interior nodes
else
{
if ((i==c->src.isrc) && (j==c->src.jsrc) && (k==c->src.ksrc))
{
source_term = c->src.fx;
}
else
{
source_term = 0.f;
}
f = hx * hy * hz *
(5.f * _um1[k][j][i] - 4.f * _um2[k][j][i] + 1.f * _um3[k][j][i] + dt2 * source_term);
_b[k][j][i] = f;
}
}
}
}
ierr = DMDAVecRestoreArray(da, b, &_b); CHKERRQ(ierr); // Release the resource
ierr = DMDAVecRestoreArray(da, c->wf.um1, &_um1); CHKERRQ(ierr); // Release the resource
ierr = DMDAVecRestoreArray(da, c->wf.um2, &_um2); CHKERRQ(ierr); // Release the resource
ierr = DMDAVecRestoreArray(da, c->wf.um3, &_um3); CHKERRQ(ierr); // Release the resource
// FIX NULLSPACE-CAUSED PROBLEMS
MatNullSpace nullspace;
MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,0,&nullspace);
MatNullSpaceRemove(nullspace,b);
MatNullSpaceDestroy(&nullspace);
PetscFunctionReturn(0);
}
// BUILD MATRIX A
PetscErrorCode
compute_A_u(KSP ksp, Mat A, Mat J, void * ctx)
{
PetscFunctionBegin;
PetscErrorCode ierr;
PetscScalar v[13], hx, hy, hz, hyhzdhx, hxhzdhy, hxhydhz;
PetscScalar dt, dt2;
PetscScalar vel, vel2;
PetscInt n;
DM da;
DMDALocalInfo grid;
MatStencil idxm; //A PETSc data structure to store information about a single row or column in the stencil
MatStencil idxn[13];
ctx_t *c = (ctx_t *) ctx;
ierr = KSPGetDM(ksp, &da); CHKERRQ(ierr); // Get the DMDA object
ierr = DMDAGetLocalInfo(da, &grid); CHKERRQ(ierr); // Get the grid information
vel = c->model.vel;
vel2 = pow(vel, 2);
dt = c->time.dt;
dt2 = dt * dt;
hx = c->model.dx;
hy = c->model.dy;
hz = c->model.dz;
hyhzdhx = hy * hz / (12.f * hx);
hxhzdhy = hx * hz / (12.f * hy);
hxhydhz = hx * hy / (12.f * hz);
/* Loop over the grid points */
unsigned int k;
for(k = grid.zs; k < (grid.zs + grid.zm); k++) // Depth
{
unsigned int j;
for(j = grid.ys; j < (grid.ys + grid.ym); j++) // Columns
{
unsigned int i;
for(i = grid.xs; i < (grid.xs + grid.xm); i++) // Rows
{
n = 1;
idxm.k = k;
idxm.j = j;
idxm.i = i;
idxn[0].k = k;
idxn[0].j = j;
idxn[0].i = i;
// Nodes on the boundary layers
if((i == 0) || (i == (grid.mx - 1)) ||
(j == 0) || (j == (grid.my - 1)) ||
(k == 0) || (k == (grid.mz - 1)))
{
v[0]=1.f;
}
// Interior nodes
else
{
v[0] = 30.f * vel2 * dt2 * (hyhzdhx + hxhzdhy + hxhydhz);
// If neighbor is not a known boundary value
// then we put an entry
if((i - 2) > 0)
{
idxn[n].j = j; // Get the column indices
idxn[n].i = i - 2;
idxn[n].k = k;
v[n] = vel2 * dt2 * hyhzdhx; // Fill with the value
n++; // One column added
idxn[n].j = j;
idxn[n].i = i - 1;
idxn[n].k = k;
v[n] = - 16.f * vel2 * dt2 * hyhzdhx;
n++;
}
if((i + 2) < (grid.mx - 1))
{
idxn[n].j = j;
idxn[n].i = i + 2;
idxn[n].k = k;
v[n] = vel2 * dt2 * hyhzdhx;
n++;
idxn[n].j = j;
idxn[n].i = i + 1;
idxn[n].k = k;
v[n] = - 16.f * vel2 * dt2 * hyhzdhx;
n++;
}
if((j - 2) > 0)
{
idxn[n].j = j - 2;
idxn[n].i = i;
idxn[n].k = k;
v[n] = vel2 * dt2 * hxhzdhy;
n++;
idxn[n].j = j - 1;
idxn[n].i = i;
idxn[n].k = k;
v[n] = - 16.f * vel2 * dt2 * hxhzdhy;
n++;
}
if((j + 2) < (grid.my - 1))
{
idxn[n].j = j + 2;
idxn[n].i = i;
idxn[n].k = k;
v[n] = vel2 * dt2 * hxhzdhy;
n++;
idxn[n].j = j + 1;
idxn[n].i = i;
idxn[n].k = k;
v[n] = - 16.f * vel2 * dt2 * hxhzdhy;
n++;
}
if((k - 2) > 0)
{
idxn[n].j = j;
idxn[n].i = i;
idxn[n].k = k - 2;
v[n] = vel2 * dt2 * hxhydhz;
n++;
idxn[n].j = j;
idxn[n].i = i;
idxn[n].k = k - 1;
v[n] = - 16.f * vel2 * dt2 * hxhydhz;
n++;
}
if((k + 2) < (grid.mz - 1))
{
idxn[n].j = j;
idxn[n].i = i;
idxn[n].k = k + 2;
v[n] = vel2 * dt2 * hxhydhz;
n++;
idxn[n].j = j;
idxn[n].i = i;
idxn[n].k = k + 1;
v[n] = - 16.f * vel2 * dt2 * hxhydhz;
n++;
}
v[0]+= 2.f * hx * hy * hz;
}
// Insert one row of the matrix A
ierr = MatSetValuesStencil(A, 1, (const MatStencil *) &idxm,
(PetscInt) n, (const MatStencil *) &idxn,
(PetscScalar *) v, INSERT_VALUES); CHKERRQ(ierr);
}
}
}
/* Assemble the matrix */
ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(A ,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
// This function allocates memory for a 3D array. The function is taken from SOFI3D_acoustic
//https://git.scc.kit.edu/GPIAG-Software/SOFI3D/tree/0ca72edf3ef977813372dd26ccfeaf4c19361a69
PetscScalar ***f3tensor(PetscInt nrl, PetscInt nrh, PetscInt ncl, PetscInt nch,PetscInt ndl, PetscInt ndh)
{
PetscFunctionBegin;
/* allocate a float 3tensor with subscript range m[nrl..nrh][ncl..nch][ndl..ndh]
and intializing the matrix, e.g. m[nrl..nrh][ncl..nch][ndl..ndh]=0.0 */
PetscInt i,j,d, nrow=nrh-nrl+1,ncol=nch-ncl+1,ndep=ndh-ndl+1, NR_END=1;
PetscScalar ***t;
/* allocate pointers to pointers to rows */
t=(PetscScalar ***) malloc((size_t) ((nrow+NR_END)*sizeof(PetscScalar**)));
// if (!t) err("allocation failure 1 in function f3tensor() ");
t += NR_END;
t -= nrl;
/* allocate pointers to rows and set pointers to them */
t[nrl]=(PetscScalar **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(PetscScalar*)));
// if (!t[nrl]) err("allocation failure 2 in function f3tensor() ");
t[nrl] += NR_END;
t[nrl] -= ncl;
/* allocate rows and set pointers to them */
t[nrl][ncl]=(PetscScalar *) malloc((size_t)((nrow*ncol*ndep+NR_END)*sizeof(PetscScalar)));
t[nrl][ncl] += NR_END;
t[nrl][ncl] -= ndl;
for (j=ncl+1;j<=nch;j++) t[nrl][j]=t[nrl][j-1]+ndep;
for (i=nrl+1;i<=nrh;i++){
t[i]=t[i-1]+ncol;
t[i][ncl]=t[i-1][ncl]+ncol*ndep;
for (j=ncl+1;j<=nch;j++) t[i][j]=t[i][j-1]+ndep;
}
/* initializing 3tensor */
for (i=nrl;i<=nrh;i++)
for (j=ncl;j<=nch;j++)
for (d=ndl;d<=ndh;d++) t[i][j][d]=0.0;
/* return pointer to array of pointer to rows */
PetscFunctionReturn(t);
}
// WRITE DOWN FILES WITH SEISMOGRAMS
PetscErrorCode
Save_seismograms_to_txt_files(KSP ksp, void *ctx)
{
PetscFunctionBegin;
PetscErrorCode ierr;
ctx_t *c = (ctx_t *) ctx;
PetscInt nrec = c->rec.nrec;
PetscInt nt = c->time.nt;
PetscInt *irec = c->rec.irec;
PetscInt *jrec = c->rec.jrec;
PetscInt *krec = c->rec.krec;
DM da;
ierr = KSPGetDM(ksp, &da); CHKERRQ(ierr); //Get the DM oject of the KSP
DMDALocalInfo grid;
ierr = DMDAGetLocalInfo(da, &grid); CHKERRQ(ierr); //Get the global information of the DM grid
int xrec;
for (xrec = 0; xrec < nrec; xrec++)
{
if ((irec[xrec] > grid.xs) && (irec[xrec] < (grid.xs + grid.xm)) &&
(jrec[xrec] > grid.ys) && (jrec[xrec] < (grid.ys + grid.ym)) &&
(krec[xrec] > grid.zs) && (krec[xrec] < (grid.zs + grid.zm)))
{
char buffer[64];
snprintf(buffer, sizeof(buffer), "./seism/seis_%i_%i_%i_%i_%i_%i.txt",
xrec, c->rec.irec[xrec], c->rec.jrec[xrec], c->rec.krec[xrec], (int) c->src.f0, (int) c-> model.xmax);
FILE *fout = fopen(buffer, "wb");
int i;
for (i = 0; i < nt ; i++)
{
fprintf(fout, "%f \t %f \n", c->rec.seis[xrec][i][0], c->rec.seis[xrec][i][1]);
}
fclose(fout);
}
}
PetscFunctionReturn(0);
}