/*
* === FUNCTION ======================================================================
* Name: makeNewGrid
* Arguments: int gridDim - Dimensions dimXdim of new grid.
* Returns: Pointer to new grid object.
* Description: Makes new grid object and sets all data points to 0.
* =====================================================================================
*/
Grid * makeNewGrid(int gridDimX, int gridDimY) {
fftw_mpi_init() ;
Grid * newGrid = malloc(sizeof(Grid)) ;
ptrdiff_t localDimY, globalOffset, localDimX ;
newGrid->allocScheme = fftw_mpi_local_size_2d(gridDimY, gridDimX, MPI_COMM_WORLD, &localDimY, &globalOffset);
newGrid->localGridDimY = localDimY ;
newGrid->localGridDimX = gridDimX ;
newGrid->globalGridDimY = gridDimY ;
newGrid->globalGridDimX = gridDimX ;
newGrid->globalOffset = globalOffset ;
newGrid->gridPoints = fftw_alloc_real(newGrid->allocScheme) ;
return newGrid ;
} /* ----- end of function makeNewGrid ----- */
int main(int argc, char* argv[])
{
MPI_Init(&argc, &argv);
fftw_mpi_init();
example_2d();
example_3d();
hypre_example_2d();
hypre_example_3d();
MPI_Finalize();
}
int main(int argc,char **args)
{
PetscErrorCode ierr;
PetscMPIInt rank,size;
PetscInt N0=50,N1=20,N=N0*N1,DIM;
PetscRandom rdm;
PetscScalar a;
PetscReal enorm;
Vec x,y,z;
PetscBool view=PETSC_FALSE,use_interface=PETSC_TRUE;
ierr = PetscInitialize(&argc,&args,(char*)0,help);CHKERRQ(ierr);
#if !defined(PETSC_USE_COMPLEX)
SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP, "This example requires complex numbers");
#endif
ierr = PetscOptionsBegin(PETSC_COMM_WORLD, NULL, "FFTW Options", "ex143");CHKERRQ(ierr);
ierr = PetscOptionsBool("-vec_view draw", "View the vectors", "ex143", view, &view, NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-use_FFTW_interface", "Use PETSc-FFTW interface", "ex143",use_interface, &use_interface, NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-use_FFTW_interface",&use_interface,NULL);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD, &rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
if (!use_interface) {
/* Use mpi FFTW without PETSc-FFTW interface, 2D case only */
/*---------------------------------------------------------*/
fftw_plan fplan,bplan;
fftw_complex *data_in,*data_out,*data_out2;
ptrdiff_t alloc_local,local_n0,local_0_start;
DIM = 2;
if (!rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Use FFTW without PETSc-FFTW interface, DIM %D\n",DIM);CHKERRQ(ierr);
}
fftw_mpi_init();
N = N0*N1;
alloc_local = fftw_mpi_local_size_2d(N0,N1,PETSC_COMM_WORLD,&local_n0,&local_0_start);
data_in = (fftw_complex*)fftw_malloc(sizeof(fftw_complex)*alloc_local);
data_out = (fftw_complex*)fftw_malloc(sizeof(fftw_complex)*alloc_local);
data_out2 = (fftw_complex*)fftw_malloc(sizeof(fftw_complex)*alloc_local);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,(PetscInt)local_n0*N1,(PetscInt)N,(const PetscScalar*)data_in,&x);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) x, "Real Space vector");CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,(PetscInt)local_n0*N1,(PetscInt)N,(const PetscScalar*)data_out,&y);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) y, "Frequency space vector");CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,(PetscInt)local_n0*N1,(PetscInt)N,(const PetscScalar*)data_out2,&z);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) z, "Reconstructed vector");CHKERRQ(ierr);
fplan = fftw_mpi_plan_dft_2d(N0,N1,data_in,data_out,PETSC_COMM_WORLD,FFTW_FORWARD,FFTW_ESTIMATE);
bplan = fftw_mpi_plan_dft_2d(N0,N1,data_out,data_out2,PETSC_COMM_WORLD,FFTW_BACKWARD,FFTW_ESTIMATE);
ierr = VecSetRandom(x, rdm);CHKERRQ(ierr);
if (view) {ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
fftw_execute(fplan);
if (view) {ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
fftw_execute(bplan);
/* Compare x and z. FFTW computes an unnormalized DFT, thus z = N*x */
a = 1.0/(PetscReal)N;
ierr = VecScale(z,a);CHKERRQ(ierr);
if (view) {ierr = VecView(z, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
ierr = VecAXPY(z,-1.0,x);CHKERRQ(ierr);
ierr = VecNorm(z,NORM_1,&enorm);CHKERRQ(ierr);
if (enorm > 1.e-11 && !rank) {
ierr = PetscPrintf(PETSC_COMM_SELF," Error norm of |x - z| %g\n",(double)enorm);CHKERRQ(ierr);
}
/* Free spaces */
fftw_destroy_plan(fplan);
fftw_destroy_plan(bplan);
fftw_free(data_in); ierr = VecDestroy(&x);CHKERRQ(ierr);
fftw_free(data_out); ierr = VecDestroy(&y);CHKERRQ(ierr);
fftw_free(data_out2);ierr = VecDestroy(&z);CHKERRQ(ierr);
} else {
/* Use PETSc-FFTW interface */
/*-------------------------------------------*/
PetscInt i,*dim,k;
Mat A;
N=1;
for (i=1; i<5; i++) {
DIM = i;
ierr = PetscMalloc1(i,&dim);CHKERRQ(ierr);
for (k=0; k<i; k++) {
dim[k]=30;
}
N *= dim[i-1];
/* Create FFTW object */
if (!rank) printf("Use PETSc-FFTW interface...%d-DIM: %d\n",(int)DIM,(int)N);
ierr = MatCreateFFT(PETSC_COMM_WORLD,DIM,dim,MATFFTW,&A);CHKERRQ(ierr);
/* Create vectors that are compatible with parallel layout of A - must call MatCreateVecs()! */
ierr = MatCreateVecsFFTW(A,&x,&y,&z);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) x, "Real space vector");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) y, "Frequency space vector");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) z, "Reconstructed vector");CHKERRQ(ierr);
/* Set values of space vector x */
ierr = VecSetRandom(x,rdm);CHKERRQ(ierr);
if (view) {ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
/* Apply FFTW_FORWARD and FFTW_BACKWARD */
ierr = MatMult(A,x,y);CHKERRQ(ierr);
if (view) {ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
ierr = MatMultTranspose(A,y,z);CHKERRQ(ierr);
/* Compare x and z. FFTW computes an unnormalized DFT, thus z = N*x */
a = 1.0/(PetscReal)N;
ierr = VecScale(z,a);CHKERRQ(ierr);
if (view) {ierr = VecView(z,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
ierr = VecAXPY(z,-1.0,x);CHKERRQ(ierr);
ierr = VecNorm(z,NORM_1,&enorm);CHKERRQ(ierr);
if (enorm > 1.e-9 && !rank) {
ierr = PetscPrintf(PETSC_COMM_SELF," Error norm of |x - z| %e\n",enorm);CHKERRQ(ierr);
}
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&z);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFree(dim);CHKERRQ(ierr);
}
}
ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
void init_fft2d_(void )
{
int i,j,k;
double vm2,vm1,v,vp1,vp2,vb;
commx = MPI_Comm_f2c(topo_.commxc);
MPI_Comm_rank(commx, &irankx);
MPI_Comm_size(commx, &isizex);
commyz = MPI_Comm_f2c(topo_.commyzc);
MPI_Comm_rank(commyz, &irankyz);
MPI_Comm_size(commyz, &isizeyz);
fftw_mpi_init();
howmany = topo_.mxlc;
//***********
alloc_ly = fftw_mpi_local_size_2d(my, mz, commx, &ly, &lys);
/* alloc_ly=fftw_mpi_local_size_many(rnk, myz, howmany,
FFTW_MPI_DEFAULT_BLOCK, commx, &ly, &lys);
*/
//***********
if(((ly-topo_.mylc)!=0) || topo_.npzc>1) {
printf("Error,npz should equal to 1, or %d\t%d\n",irankx,ly-topo_.mylc);
MPI_Abort(commx,1);
}
minp = fftw_alloc_complex(alloc_ly);
mout = fftw_alloc_complex(alloc_ly);
if( !(freq = r3tensor(topo_.mxlc, topo_.mylc*topo_.mzlc, 2)) )
printf("Malloc error!\n");
if( !(data = r3tensor(topo_.mxlc, topo_.mylc*topo_.mzlc, 2)) )
printf("Malloc error!\n");
/* if( !(dar = r3tensor(topo_.mxlc, topo_.mylc, topo_.mzlc)) )
printf("Malloc error!\n");
if( !(dai = r3tensor(topo_.mxlc, topo_.mylc, topo_.mzlc)) )
printf("Malloc error!\n");
*/
//***********
mplanF = fftw_mpi_plan_dft_2d(my, mz, minp, mout, commx, FFTW_FORWARD, FFTW_MEASURE);
mplanR = fftw_mpi_plan_dft_2d(my, mz, minp, mout, commx, FFTW_BACKWARD, FFTW_MEASURE);
/* mplanF = fftw_mpi_plan_many_dft(rnk, myz, howmany,
FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK,
minp, mout, commx, FFTW_FORWARD, FFTW_MEASURE);
mplanR = fftw_mpi_plan_many_dft(rnk, myz, howmany,
FFTW_MPI_DEFAULT_BLOCK,FFTW_MPI_DEFAULT_BLOCK,
minp, mout, commx, FFTW_BACKWARD, FFTW_MEASURE);
*/
//***********
//***** Solver part ******
dxs = topo_.dx0*topo_.dx0;
dys = topo_.dy0*topo_.dy0;
dzs = topo_.dz0*topo_.dz0;
vm2=-1.0/12.0;
vm1=16.0/12.0;
v =-30.0/12.0;
vp1=16.0/12.0;
vp2=-1.0/12.0;
MatCreateMPIAIJ(commyz, PETSC_DECIDE, PETSC_DECIDE, mx, mx, 5, PETSC_NULL, 5, PETSC_NULL, &A);
ierr = MatGetOwnershipRange(A,&Istart,&Iend);
for (Ii=Istart; Ii<Iend; Ii++) {
i = Ii; j = Ii;
if ((i>1)&&(i<mx-2)) {
J = Ii - 2; MatSetValues(A,1,&Ii,1,&J,&vm2,INSERT_VALUES);
J = Ii - 1; ierr = MatSetValues(A,1,&Ii,1,&J,&vm1,INSERT_VALUES);CHKERRQ(ierr);
J = Ii; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
J = Ii + 1; ierr = MatSetValues(A,1,&Ii,1,&J,&vp1,INSERT_VALUES);CHKERRQ(ierr);
J = Ii + 2; ierr = MatSetValues(A,1,&Ii,1,&J,&vp2,INSERT_VALUES);CHKERRQ(ierr);
}
if (i==0) {
J = Ii; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (i==1) {
J = Ii - 1; vb = 11.0/12.0; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);CHKERRQ(ierr);
J = Ii ; vb = -5.0/3.0; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);
J = Ii + 1; vb = 0.5; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);
J = Ii + 2; vb = 1.0/3.0; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);
J = Ii + 3; vb = -1.0/12.0; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);
}
if (i==mx-2) {
J = Ii + 1; vb = 11.0/12.0; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);CHKERRQ(ierr);
J = Ii ; vb = -5.0/3.0; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);
J = Ii - 1; vb = 0.5; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);
J = Ii - 2; vb = 1.0/3.0; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);
J = Ii - 3; vb = -1.0/12.0; ierr = MatSetValues(A,1,&Ii,1,&J,&vb,INSERT_VALUES);
}
if (i==mx-1) {J = Ii; ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecCreate(commyz,&br);CHKERRQ(ierr);
ierr = VecSetSizes(br,PETSC_DECIDE,mx);CHKERRQ(ierr);
ierr = VecSetFromOptions(br);CHKERRQ(ierr);
ierr = VecDuplicate(br,&xr);CHKERRQ(ierr);
ierr = VecDuplicate(br,&bi);CHKERRQ(ierr);
ierr = VecDuplicate(br,&xi);CHKERRQ(ierr);
ierr = KSPCreate(commyz,&ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A,SAME_PRECONDITIONER);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);
PCSetType(pc,PCJACOBI);
ierr = KSPSetTolerances(ksp,1.e-7,1.e-50,PETSC_DEFAULT,
PETSC_DEFAULT);CHKERRQ(ierr);
//******* End *******
}
void init_field(int n_d, int *n, double *L, field_info *FFT) {
ptrdiff_t n_x_local;
ptrdiff_t i_x_start_local;
ptrdiff_t n_y_transpose_local;
ptrdiff_t i_y_start_transpose_local;
ptrdiff_t *n_x_rank;
int flag_active;
int n_active;
int min_size, max_size;
SID_log("Initializing ", SID_LOG_OPEN);
for(ptrdiff_t i_d = 0; i_d < n_d; i_d++) {
if(i_d < (n_d - 1))
SID_log("%dx", SID_LOG_CONTINUE, n[i_d]);
else
SID_log("%d element %d-d FFT ", SID_LOG_CONTINUE, n[i_d], n_d);
}
SID_log("(%d byte precision)...", SID_LOG_CONTINUE, (int)sizeof(GBPREAL));
// Initialize FFT sizes
FFT->n_d = n_d;
FFT->n = (ptrdiff_t *)SID_calloc(sizeof(ptrdiff_t) * FFT->n_d);
FFT->L = (double *)SID_calloc(sizeof(double) * FFT->n_d);
FFT->n_k_local = (ptrdiff_t *)SID_calloc(sizeof(ptrdiff_t) * FFT->n_d);
FFT->n_R_local = (ptrdiff_t *)SID_calloc(sizeof(ptrdiff_t) * FFT->n_d);
FFT->i_R_start_local = (ptrdiff_t *)SID_calloc(sizeof(ptrdiff_t) * FFT->n_d);
FFT->i_k_start_local = (ptrdiff_t *)SID_calloc(sizeof(ptrdiff_t) * FFT->n_d);
FFT->i_R_stop_local = (ptrdiff_t *)SID_calloc(sizeof(ptrdiff_t) * FFT->n_d);
FFT->i_k_stop_local = (ptrdiff_t *)SID_calloc(sizeof(ptrdiff_t) * FFT->n_d);
for(ptrdiff_t i_d = 0; i_d < FFT->n_d; i_d++) {
FFT->n[i_d] = n[i_d];
FFT->L[i_d] = L[i_d];
FFT->i_R_start_local[i_d] = 0;
FFT->i_k_start_local[i_d] = 0;
FFT->n_R_local[i_d] = FFT->n[i_d];
FFT->n_k_local[i_d] = FFT->n[i_d];
}
FFT->n_k_local[FFT->n_d - 1] = FFT->n[FFT->n_d - 1] / 2 + 1;
// Initialize FFTW
// Create an integer version of FFT->n[] to pass to ..._create_plan
int *n_int=(int *)SID_malloc(sizeof(int)*FFT->n_d);
for(int i_d=0;i_d<FFT->n_d;i_d++)
n_int[i_d]=(int)FFT->n[i_d];
#if FFTW_V2
#if USE_MPI
int total_local_size_int;
int n_x_local_int;
int i_x_start_local_int;
int n_y_transpose_local_int;
int i_y_start_transpose_local_int;
FFT->plan = rfftwnd_mpi_create_plan(SID.COMM_WORLD->comm, FFT->n_d, n_int, FFTW_REAL_TO_COMPLEX, FFTW_ESTIMATE);
FFT->iplan = rfftwnd_mpi_create_plan(SID.COMM_WORLD->comm, FFT->n_d, n_int, FFTW_COMPLEX_TO_REAL, FFTW_ESTIMATE);
rfftwnd_mpi_local_sizes(FFT->plan,
&(n_x_local_int),
&(i_x_start_local_int),
&(n_y_transpose_local_int),
&(i_y_start_transpose_local_int),
&total_local_size_int);
n_x_local = (ptrdiff_t)n_x_local_int;
i_x_start_local = (ptrdiff_t)i_x_start_local_int;
n_y_transpose_local = (ptrdiff_t)n_y_transpose_local_int;
i_y_start_transpose_local = (ptrdiff_t)i_y_start_transpose_local_int;
FFT->total_local_size = (size_t)total_local_size_int;
#else
FFT->total_local_size = 1;
for(ptrdiff_t i_d = 0; i_d < FFT->n_d; i_d++) {
if(i_d < FFT->n_d - 1)
FFT->total_local_size *= FFT->n[i_d];
else
FFT->total_local_size *= 2 * (FFT->n[i_d] / 2 + 1);
}
#if USE_DOUBLE
FFT->plan = fftwnd_create_plan(FFT->n_d, n_int, FFTW_REAL_TO_COMPLEX, FFTW_ESTIMATE | FFTW_IN_PLACE);
FFT->iplan = fftwnd_create_plan(FFT->n_d, n_int, FFTW_COMPLEX_TO_REAL, FFTW_ESTIMATE | FFTW_IN_PLACE);
#else
FFT->plan = rfftwnd_create_plan(FFT->n_d, n_int, FFTW_REAL_TO_COMPLEX, FFTW_ESTIMATE | FFTW_IN_PLACE);
FFT->iplan = rfftwnd_create_plan(FFT->n_d, n_int, FFTW_COMPLEX_TO_REAL, FFTW_ESTIMATE | FFTW_IN_PLACE);
#endif
#endif
#else
#if USE_MPI
#if USE_DOUBLE
fftw_mpi_init();
FFT->total_local_size = fftw_mpi_local_size_many_transposed(FFT->n_d,
FFT->n,
1,
FFTW_MPI_DEFAULT_BLOCK,
FFTW_MPI_DEFAULT_BLOCK,
SID_COMM_WORLD->comm,
&(n_x_local),
&(i_x_start_local),
&(n_y_transpose_local),
&(i_y_start_transpose_local));
FFT->plan = fftw_mpi_plan_dft_r2c(FFT->n_d, FFT->n, FFT->field_local, FFT->cfield_local, SID_COMM_WORLD->comm, FFTW_ESTIMATE);
FFT->iplan = fftw_mpi_plan_dft_c2r(FFT->n_d, FFT->n, FFT->cfield_local, FFT->field_local, SID_COMM_WORLD->comm, FFTW_ESTIMATE);
#else
fftwf_mpi_init();
FFT->total_local_size = fftwf_mpi_local_size_many_transposed(FFT->n_d,
FFT->n,
1,
FFTW_MPI_DEFAULT_BLOCK,
FFTW_MPI_DEFAULT_BLOCK,
SID_COMM_WORLD->comm,
&(n_x_local),
&(i_x_start_local),
&(n_y_transpose_local),
&(i_y_start_transpose_local));
FFT->plan = fftwf_mpi_plan_dft_r2c(FFT->n_d, FFT->n, FFT->field_local, FFT->cfield_local, SID_COMM_WORLD->comm, FFTW_ESTIMATE);
FFT->iplan = fftwf_mpi_plan_dft_c2r(FFT->n_d, FFT->n, FFT->cfield_local, FFT->field_local, SID_COMM_WORLD->comm, FFTW_ESTIMATE);
#endif
#else
FFT->total_local_size = 1;
for(ptrdiff_t i_d=0; i_d < FFT->n_d; i_d++) {
if(i_d < FFT->n_d - 1)
FFT->total_local_size *= FFT->n[i_d];
else
FFT->total_local_size *= 2 * (FFT->n[i_d] / 2 + 1);
}
#if USE_DOUBLE
FFT->plan = fftw_plan_dft_r2c(FFT->n_d, FFT->n, FFT->field_local, FFT->cfield_local, FFTW_ESTIMATE);
FFT->iplan = fftw_plan_dft_c2r(FFT->n_d, FFT->n, FFT->cfield_local, FFT->field_local, FFTW_ESTIMATE);
#else
FFT->plan = fftwf_plan_dft_r2c(FFT->n_d, FFT->n, FFT->field_local, FFT->cfield_local, FFTW_ESTIMATE);
FFT->iplan = fftwf_plan_dft_c2r(FFT->n_d, FFT->n, FFT->cfield_local, FFT->field_local, FFTW_ESTIMATE);
#endif
#endif
#endif
SID_free(SID_FARG n_int);
// Set empty slabs to start at 0 to make ignoring them simple.
if(n_x_local == 0)
i_x_start_local = 0;
if(n_y_transpose_local == 0)
i_y_start_transpose_local = 0;
// Modify the local slab dimensions according to what FFTW chose.
FFT->i_R_start_local[0] = i_x_start_local;
FFT->n_R_local[0] = n_x_local;
if(FFT->n_d > 1) {
FFT->i_k_start_local[1] = i_y_start_transpose_local;
FFT->n_k_local[1] = n_y_transpose_local;
}
// Allocate field
#if USE_FFTW3
FFT->field_local = (gbpFFT_real *)fftwf_alloc_real(FFT->total_local_size);
#else
FFT->field_local = (gbpFFT_real *)SID_malloc(sizeof(gbpFFT_real)*FFT->total_local_size);
#endif
FFT->cfield_local = (gbpFFT_complex *)FFT->field_local;
// Upper limits of slab decomposition
for(ptrdiff_t i_d = 0; i_d < FFT->n_d; i_d++) {
FFT->i_R_stop_local[i_d] = FFT->i_R_start_local[i_d] + FFT->n_R_local[i_d] - 1;
FFT->i_k_stop_local[i_d] = FFT->i_k_start_local[i_d] + FFT->n_k_local[i_d] - 1;
}
// FFTW padding sizes
if(FFT->n_d > 1) {
FFT->pad_size_R = 2 * (FFT->n_R_local[FFT->n_d - 1] / 2 + 1) - FFT->n_R_local[FFT->n_d - 1];
FFT->pad_size_k = 0;
} else {
FFT->pad_size_R = 0;
FFT->pad_size_k = 0;
}
// Number of elements (global and local) in the FFT
ptrdiff_t i_d = 0;
for(FFT->n_field = 1, FFT->n_field_R_local = 1, FFT->n_field_k_local = 1; i_d < FFT->n_d; i_d++) {
FFT->n_field *= (size_t)FFT->n[i_d];
FFT->n_field_R_local *= (size_t)FFT->n_R_local[i_d];
FFT->n_field_k_local *= (size_t)FFT->n_k_local[i_d];
}
// Clear the field
clear_field(FFT);
// Initialize the FFT's real-space grid
FFT->R_field = (double **)SID_malloc(sizeof(double *) * FFT->n_d);
FFT->dR = (double *)SID_malloc(sizeof(double *) * FFT->n_d);
for(ptrdiff_t i_d = 0; i_d < FFT->n_d; i_d++) {
FFT->R_field[i_d] = (double *)SID_malloc(sizeof(double) * (FFT->n[i_d] + 1));
FFT->dR[i_d] = FFT->L[i_d] / (double)(FFT->n[i_d]);
for(ptrdiff_t i_i = 0; i_i < FFT->n[i_d]; i_i++)
FFT->R_field[i_d][i_i] = FFT->L[i_d] * ((double)i_i / (double)(FFT->n[i_d]));
FFT->R_field[i_d][FFT->n[i_d]] = FFT->L[i_d];
}
// Initialize the FFT's k-space grid
FFT->k_field = (double **)SID_malloc(sizeof(double *) * FFT->n_d);
FFT->dk = (double *)SID_malloc(sizeof(double *) * FFT->n_d);
FFT->k_Nyquist = (double *)SID_malloc(sizeof(double *) * FFT->n_d);
for(ptrdiff_t i_d = 0; i_d < FFT->n_d; i_d++) {
FFT->k_field[i_d] = (double *)SID_malloc(sizeof(double) * FFT->n[i_d]);
FFT->dk[i_d] = TWO_PI / FFT->L[i_d];
FFT->k_Nyquist[i_d] = TWO_PI * (double)(FFT->n[i_d]) / FFT->L[i_d] / 2.;
for(ptrdiff_t i_i = 0; i_i < FFT->n[i_d]; i_i++) {
if(i_i >= FFT->n[i_d] / 2)
FFT->k_field[i_d][i_i] = TWO_PI * (double)(i_i - FFT->n[i_d]) / FFT->L[i_d];
else
FFT->k_field[i_d][i_i] = TWO_PI * (double)(i_i) / FFT->L[i_d];
}
}
// Flags
FFT->flag_padded = GBP_FALSE;
// Slab info
FFT->slab.n_x_local = FFT->n_R_local[0];
FFT->slab.i_x_start_local = FFT->i_R_start_local[0];
FFT->slab.i_x_stop_local = FFT->i_R_stop_local[0];
FFT->slab.x_min_local = FFT->R_field[0][FFT->i_R_start_local[0]];
if(FFT->slab.n_x_local > 0)
FFT->slab.x_max_local = FFT->R_field[0][FFT->i_R_stop_local[0] + 1];
else
FFT->slab.x_max_local = FFT->slab.x_min_local;
SID_Allreduce(&(FFT->slab.x_max_local), &(FFT->slab.x_max), 1, SID_DOUBLE, SID_MAX, SID_COMM_WORLD);
#if USE_MPI
// All ranks are not necessarily assigned any slices, so
// we need to figure out what ranks are to the right and the left for
// buffer exchanges
n_x_rank = (ptrdiff_t *)SID_malloc(sizeof(ptrdiff_t) * SID.n_proc);
n_x_rank[SID.My_rank] = (ptrdiff_t)FFT->slab.n_x_local;
if(n_x_rank[SID.My_rank] > 0)
flag_active = GBP_TRUE;
else
flag_active = GBP_FALSE;
SID_Allreduce(&flag_active, &n_active, 1, SID_INT, SID_SUM, SID_COMM_WORLD);
SID_Allreduce(&n_x_rank[SID.My_rank], &min_size, 1, SID_INT, SID_MIN, SID_COMM_WORLD);
SID_Allreduce(&n_x_rank[SID.My_rank], &max_size, 1, SID_INT, SID_MAX, SID_COMM_WORLD);
for(int i_rank = 0; i_rank < SID.n_proc; i_rank++)
SID_Bcast(&(n_x_rank[i_rank]), 1, SID_INT, i_rank, SID_COMM_WORLD);
FFT->slab.rank_to_right = -1;
for(int i_rank = SID.My_rank + 1; i_rank < SID.My_rank + SID.n_proc && FFT->slab.rank_to_right < 0; i_rank++) {
int j_rank = i_rank % SID.n_proc;
if(n_x_rank[j_rank] > 0)
FFT->slab.rank_to_right = j_rank;
}
if(FFT->slab.rank_to_right < 0)
FFT->slab.rank_to_right = SID.My_rank;
FFT->slab.rank_to_left = -1;
for(int i_rank = SID.My_rank - 1; i_rank > SID.My_rank - SID.n_proc && FFT->slab.rank_to_left < 0; i_rank--) {
int j_rank = i_rank;
if(i_rank < 0)
j_rank = i_rank + SID.n_proc;
if(n_x_rank[j_rank] > 0)
FFT->slab.rank_to_left = j_rank;
}
if(FFT->slab.rank_to_left < 0)
FFT->slab.rank_to_left = SID.My_rank;
free(n_x_rank);
SID_log("(%d cores unused, min/max slab size=%d/%d)...", SID_LOG_CONTINUE, SID.n_proc - n_active, min_size, max_size);
#else
FFT->slab.rank_to_right = SID.My_rank;
FFT->slab.rank_to_left = SID.My_rank;
if(FFT->slab.n_x_local > 0) {
flag_active = GBP_TRUE;
n_active = 1;
min_size = FFT->slab.n_x_local;
max_size = FFT->slab.n_x_local;
} else {
flag_active = GBP_FALSE;
n_active = 0;
min_size = 0;
max_size = 0;
}
#endif
SID_log("Done.", SID_LOG_CLOSE);
}
void init_common(void) {
/* This routine will initialize everything */
int i,j,k;
DEBUG_START_FUNC;
#ifdef MPI_SUPPORT
#ifdef FFTW3_MPI_SUPPORT
fftw_mpi_init();
#endif
#endif
#ifdef _OPENMP
if( !(fftw_init_threads()) ) ERROR_HANDLER( ERROR_CRITICAL, "Threads initialisation failed");
#endif
/* We start with the coordinate system */
kx = (double *) fftw_malloc( sizeof(double) * NTOTAL_COMPLEX );
if (kx == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for kx allocation");
ky = (double *) fftw_malloc( sizeof(double) * NTOTAL_COMPLEX );
if (ky == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for ky allocation");
kz = (double *) fftw_malloc( sizeof(double) * NTOTAL_COMPLEX );
if (kz == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for kz allocation");
kxt = (double *) fftw_malloc( sizeof(double) * NTOTAL_COMPLEX );
if (kxt == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for kxt allocation");
kyt = (double *) fftw_malloc( sizeof(double) * NTOTAL_COMPLEX );
if (kyt == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for kyt allocation");
kzt = (double *) fftw_malloc( sizeof(double) * NTOTAL_COMPLEX );
if (kzt == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for kzt allocation");
k2t = (double *) fftw_malloc( sizeof(double) * NTOTAL_COMPLEX );
if (k2t == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for k2t allocation");
ik2t = (double *) fftw_malloc( sizeof(double) * NTOTAL_COMPLEX );
if (ik2t == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for ik2t allocation");
for( i = 0; i < NX_COMPLEX / NPROC; i++) {
for( j = 0; j < NY_COMPLEX; j++) {
for( k = 0; k < NZ_COMPLEX; k++) {
kx[ IDX3D ] = (2.0 * M_PI) / param.lx *
(fmod( NX_COMPLEX * rank / NPROC + i + (NX_COMPLEX / 2) , NX_COMPLEX ) - NX_COMPLEX / 2 );
#ifdef WITH_2D
ky[ IDX3D ] = (2.0 * M_PI) / param.ly * j;
kz[ IDX3D ] = 0.0;
#else
ky[ IDX3D ] = (2.0 * M_PI) / param.ly *
(fmod( j + (NY_COMPLEX / 2) , NY_COMPLEX ) - NY_COMPLEX / 2 );
kz[ IDX3D ] = (2.0 * M_PI) / param.lz * k;
#endif
kxt[ IDX3D ]= kx[IDX3D];
kyt[ IDX3D ]= ky[IDX3D];
kzt[ IDX3D ]= kz[IDX3D];
k2t[ IDX3D ] = kxt[IDX3D] * kxt[IDX3D] +
kyt[IDX3D] * kyt[IDX3D] +
kzt[IDX3D] * kzt[IDX3D];
if ( k2t[IDX3D] == 0.0 ) ik2t[IDX3D] = 1.0;
else ik2t[IDX3D] = 1.0 / k2t[IDX3D];
}
}
}
kxmax = 2.0 * M_PI/ param.lx * ( (NX / 2) - 1);
kymax = 2.0 * M_PI/ param.ly * ( (NY / 2) - 1);
kzmax = 2.0 * M_PI/ param.lz * ( (NZ / 2) - 1);
#ifdef WITH_2D
kzmax = 0.0;
#endif
kmax=pow(kxmax*kxmax+kymax*kymax+kzmax*kzmax,0.5);
/* Initialize the dealiazing mask Or the nyquist frequency mask (in case dealiasing is not required) */
mask = (double *) fftw_malloc( sizeof(double) * NTOTAL_COMPLEX );
if (mask == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for mask allocation");
for( i = 0; i < NX_COMPLEX/NPROC; i++) {
for( j = 0; j < NY_COMPLEX; j++) {
for( k = 0; k < NZ_COMPLEX; k++) {
mask[ IDX3D ] = 1.0;
if(param.antialiasing) {
if( fabs( kx[ IDX3D ] ) > 2.0/3.0 * kxmax)
mask[ IDX3D ] = 0.0;
if( fabs( ky[ IDX3D ] ) > 2.0/3.0 * kymax)
mask[ IDX3D ] = 0.0;
#ifndef WITH_2D
if( fabs( kz[ IDX3D ] ) > 2.0/3.0 * kzmax)
mask[ IDX3D ] = 0.0;
#endif
}
else {
if ( NX_COMPLEX / NPROC * rank + i == NX_COMPLEX / 2 )
mask[ IDX3D ] = 0.0;
if ( j == NY_COMPLEX / 2 )
mask[ IDX3D ] = 0.0;
#ifndef WITH_2D
if ( k == NZ_COMPLEX )
mask[ IDX3D ] = 0.0;
#endif
}
}
}
}
if(param.antialiasing) {
kxmax = kxmax * 2.0 / 3.0;
kymax = kymax * 2.0 / 3.0;
kzmax = kzmax * 2.0 / 3.0;
kmax = kmax * 2.0 / 3.0;
}
// Allocate fields
// Complex fields
w1 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w1 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w1 allocation");
w2 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w2 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w2 allocation");
w3 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w3 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w3 allocation");
w4 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w4 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w4 allocation");
w5 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w5 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w5 allocation");
w6 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w6 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w6 allocation");
w7 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w7 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w7 allocation");
w8 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w8 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w8 allocation");
w9 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w9 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w9 allocation");
w10 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w10 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w10 allocation");
w11 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w11 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w11 allocation");
w12 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w12 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w12 allocation");
w13 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w13 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w13 allocation");
w14 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w14 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w14 allocation");
w15 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w15 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w15 allocation");
w16 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w16 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w15 allocation");
w17 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w17 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w15 allocation");
w18 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (w18 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for w15 allocation");
wh1 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (wh1 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for wh1 allocation");
wh2 = (double complex *) fftw_malloc( sizeof(double complex) * NTOTAL_COMPLEX);
if (wh2 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for wh2 allocation");
wh3 = (double complex *) fftw_malloc( sizeof(double complex) * NX*(NY/2+1));
if (wh3 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for wh3 allocation");
wh4 = (double complex *) fftw_malloc( sizeof(double complex) * NX*(NY/2+1)*NZ);
if (wh4 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for wh4 allocation");
wh5 = (double complex *) fftw_malloc( sizeof(double complex) * NX*(NY/2+1)*NZ);
if (wh5 == NULL) ERROR_HANDLER( ERROR_CRITICAL, "No memory for wh5 allocation");
// Initialize wh1,wh2,wh3;
for(i=0;i<NX*(NY/2+1);i++) {wh1[i]=0; wh2[i]=0; wh3[i]=0;}
/* Will use the same memory space for real and complex fields */
wr1 = (double *) w1;
wr2 = (double *) w2;
wr3 = (double *) w3;
wr4 = (double *) w4;
wr5 = (double *) w5;
wr6 = (double *) w6;
wr7 = (double *) w7;
wr8 = (double *) w8;
wr9 = (double *) w9;
wr10 = (double *) w10;
wr11 = (double *) w11;
wr12 = (double *) w12;
wr13 = (double *) w13;
wr14 = (double *) w14;
wr15 = (double *) w15;
wr16 = (double *) w16;
wr17 = (double *) w17;
wr18 = (double *) w18;
wrh1 = (double *) wh1;
wrh2 = (double *) wh2;
wrh3 = (double *) wh3;
wrh4 = (double *) wh4;
wrh5 = (double *) wh5;
// Physic initialisation
// init_real_mask();
//set Reynolds numbers using input powers AJB 08/03/12
param.reynolds = pow(10.0,param.reynolds);
nu = 1.0 / param.reynolds;
#ifdef BOUSSINESQ
param.reynolds_th = pow(10.0,param.reynolds_th);
nu_th = 1.0 / param.reynolds_th;
#endif
#ifdef MHD
param.reynolds_m = pow(10.0,param.reynolds_m);
eta = 1.0 / param.reynolds_m;
#endif
DEBUG_END_FUNC;
return;
}
int main(int narg, char **args)
{
MPI_Init(&narg, &args);
#ifdef _USE_FFTW_FILTER
fftw_mpi_init();
#endif
Json::Value root;
jsonParser::parseJsonInputFile(root, narg, args);
int dim = jsonParser::getDimensionality(root, DEFAULT_DIMENSIONALITY);
GRID grid(dim);
EM_FIELD myfield;
CURRENT current;
std::vector<SPECIE*> species;
std::vector<SPECIE*>::const_iterator spec_iterator;
my_rng_generator rng;
//*******************************************BEGIN GRID DEFINITION*******************************************************
jsonParser::setXrange(root, &grid);
jsonParser::setYrange(root, &grid);
jsonParser::setZrange(root, &grid);
jsonParser::setNCells(root, &grid);
jsonParser::setNprocs(root, &grid);
jsonParser::setStretchedGrid(root, &grid);
jsonParser::setBoundaryConditions(root, &grid);
jsonParser::setRadiationFriction(root, &grid);
jsonParser::setMasterProc(root, &grid);
grid.mpi_grid_initialize(&narg, args);
jsonParser::setCourantFactor(root, &grid);
jsonParser::setSimulationTime(root, &grid);
jsonParser::setMovingWindow(root, &grid);
srand(time(NULL));
grid.initRNG(rng, RANDOM_NUMBER_GENERATOR_SEED);
grid.finalize();
jsonParser::setDumpControl(root, &grid);
grid.visualDiag();
//********************************************END GRID DEFINITION********************************************************
//*******************************************BEGIN FIELD DEFINITION*********************************************************
myfield.allocate(&grid);
myfield.setAllValuesToZero();
jsonParser::setLaserPulses(root, &myfield);
myfield.boundary_conditions();
current.allocate(&grid);
current.setAllValuesToZero();
//*******************************************END FIELD DEFINITION***********************************************************
//******************** BEGIN TO READ OF user defined INPUT - PARAMETERS ****************************************
bool isThereSpecial = false;
bool areThereSpheres = false;
std::string fileSpheresName;
Json::Value special;
SPHERES myspheres;
if (isThereSpecial = jsonParser::setValue(special, root, "special")) {
if (areThereSpheres = jsonParser::setString(&fileSpheresName, special, "spheresFile")) {
readAndAllocateSpheres(myspheres, fileSpheresName, grid);
selectSpheres(myspheres, grid);
}
}
std::map<std::string, PLASMA*>::iterator pIterator;
//******************** END READ OF "SPECIAL" (user defined) INPUT - PARAMETERS ****************************************
//*******************************************BEGIN SPECIES DEFINITION*********************************************************
std::map<std::string, PLASMA*> plasmas;
jsonParser::setPlasmas(root, plasmas);
if (areThereSpheres) {
for (pIterator = plasmas.begin(); pIterator != plasmas.end(); pIterator++) {
(pIterator)->second->params.spheres = &myspheres;
}
}
jsonParser::setSpecies(root, species, plasmas, &grid, rng);
uint64_t totPartNum = 0;
for (spec_iterator = species.begin(); spec_iterator != species.end(); spec_iterator++) {
totPartNum += (*spec_iterator)->printParticleNumber();
}
if (grid.myid == grid.master_proc) {
std::cout << "Total particle number: " << totPartNum << std::endl;
}
if (areThereSpheres) {
delete[] myspheres.coords;
}
//*******************************************END SPECIES DEFINITION***********************************************************
//*******************************************BEGIN DIAG DEFINITION**************************************************
std::map<std::string, outDomain*> outDomains;
OUTPUT_MANAGER manager(&grid, &myfield, ¤t, species);
jsonParser::setDomains(root, outDomains);
jsonParser::setOutputRequests(root, manager, outDomains, species);
jsonParser::setOutputDirPath(root, manager);
manager.initialize();
//*******************************************END DIAG DEFINITION**************************************************
grid.setDumpPath(DIRECTORY_DUMP);
//@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ MAIN CYCLE (DO NOT MODIFY) @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
if (grid.myid == grid.master_proc) {
printf("----- START temporal cicle -----\n");
fflush(stdout);
}
int dumpID = 1;
grid.istep = 0;
if (grid.dumpControl.doRestart) {
dumpID = grid.dumpControl.restartFromDump;
restartFromDump(&dumpID, &grid, &myfield, species);
}
while (grid.istep <= grid.getTotalNumberOfTimesteps())
{
#ifdef NO_ALLOCATION
manager.close();
MPI_Finalize();
exit(0);
#endif
grid.printTStepEvery(FREQUENCY_STDOUT_STATUS);
manager.callDiags(grid.istep);
myfield.openBoundariesE_1();
myfield.new_halfadvance_B();
myfield.boundary_conditions();
current.setAllValuesToZero();
for (spec_iterator = species.begin(); spec_iterator != species.end(); spec_iterator++) {
(*spec_iterator)->current_deposition_standard(¤t);
}
current.pbc();
for (spec_iterator = species.begin(); spec_iterator != species.end(); spec_iterator++) {
(*spec_iterator)->position_parallel_pbc();
}
myfield.openBoundariesB();
myfield.new_advance_E(¤t);
myfield.boundary_conditions();
#ifdef _USE_FFTW_FILTER
myfield.fftw_filter_Efield();
myfield.boundary_conditions();
#endif
myfield.openBoundariesE_2();
if (!(grid.istep % 20)) {
//myfield.applyFilter(fltr_Ex|fltr_Ey, dir_x|dir_y);
}
myfield.new_halfadvance_B();
myfield.boundary_conditions();
for (spec_iterator = species.begin(); spec_iterator != species.end(); spec_iterator++) {
if (grid.isRadiationFrictionEnabled()) {
(*spec_iterator)->momenta_advance_with_friction(&myfield, grid.getLambda0());
}
else {
(*spec_iterator)->momenta_advance(&myfield);
}
}
grid.time += grid.dt;
moveWindow(&grid, &myfield, species);
grid.istep++;
if (grid.dumpControl.doDump) {
if (grid.istep != 0 && !(grid.istep % ((int)(grid.dumpControl.dumpEvery / grid.dt)))) {
dumpFilesForRestart(&dumpID, &grid, &myfield, species);
}
}
}
manager.close();
MPI_Finalize();
exit(0);
}
int main(int argc, char **argv) {
// Set up MPI
// ==========
ierr = MPI_Init(&argc, &argv);
ierr = MPI_Comm_rank(MPI_COMM_WORLD, &ThisTask);
ierr = MPI_Comm_size(MPI_COMM_WORLD, &NTask);
#ifdef SINGLE_PRECISION
fftwf_mpi_init();
#else
fftw_mpi_init();
#endif
if(argc < 2) {
if(ThisTask == 0) {
fprintf(stdout, "Input parameters not found\n");
fprintf(stdout, "Call with <ParameterFile>\n");
}
ierr = MPI_Finalize();
exit(0);
}
// Read the run parameters and setup code
// ======================================
int stepDistr;
int subtractLPT;
double da=0;
read_parameterfile(argv[1]);
if (UseCOLA == 1){
subtractLPT = 1;
stepDistr = 0;
StdDA = 0;
} else{
subtractLPT = 0;
stepDistr = 1;
StdDA = 2;
}
if (StdDA == 0){
fullT = 1;
nLPT = -2.5;
}
filter = 0; // Whether or not to smooth the forces
Scale = 2.*M_PI/Box; // The force smoothing scale
if(ThisTask == 0) {
printf("Run Parameters\n");
printf("==============\n");
printf("Cosmology:\n");
printf(" Omega Matter(z=0) = %lf\n",Omega);
printf(" Omega Baryon(z=0) = %lf\n",OmegaBaryon);
printf(" Hubble Parameter(z=0) = %lf\n",HubbleParam);
printf(" Sigma8(z=0) = %lf\n",Sigma8);
#ifndef GAUSSIAN
printf(" F_nl = %lf\n",Fnl);
#endif
printf(" Primordial Index = %lf\n",PrimordialIndex);
printf(" Initial Redshift = %lf\n",Init_Redshift);
printf(" Final Redshift = %lf\n",Final_Redshift);
#ifndef GAUSSIAN
printf(" F_nl Redshift = %lf\n",Fnl_Redshift);
#endif
printf("Simulation:\n");
printf(" Nmesh = %d\n", Nmesh);
printf(" Nsample = %d\n", Nsample);
printf(" Boxsize = %lf\n", Box);
printf(" Buffer Size = %lf\n", Buffer);
switch(WhichSpectrum) {
case 0:
switch (WhichTransfer) {
case 1:
printf(" Using Eisenstein & Hu Transfer Function\n");
break;
case 2:
printf(" Using Tabulated Transfer Function\n");
break;
default:
printf(" Using Efstathiou Transfer Function\n");
break;
}
break;
case 1:
printf(" Using Eisenstein & Hu Power Spectrum\n");
break;
case 2:
printf(" Using Tabulated Power Spectrum\n");
break;
default:
printf(" Using Efstathiou Power Spectrum\n");
break;
}
printf(" Number of Timesteps = %d\n",nsteps);
if (UseCOLA) {
printf(" Using COLA method\n\n");
} else {
printf(" Using Standard PM method\n\n");
}
fflush(stdout);
}
// Initial and final scale factors:
double ai=1.0/(1.0+Init_Redshift);
double af=1.0/(1.0+Final_Redshift);
if (stepDistr == 0) da=(af-ai)/((double)nsteps);
if (stepDistr == 1) da=(log(af)-log(ai))/((double)nsteps);
if (stepDistr == 2) da=(CosmoTime(af)-CosmoTime(ai))/((double)nsteps);
set_units();
if (ThisTask == 0) {
printf("Initialising Transfer Function/Power Spectrum\n");
printf("=============================================\n");
}
initialize_transferfunction();
initialize_powerspectrum();
initialize_ffts();
initialize_parts();
if(ThisTask == 0) {
printf("Creating initial conditions\n");
printf("===========================\n");
fflush(stdout);
}
// Create the calculate the Zeldovich and 2LPT displacements and create the initial conditions
// ===========================================================================================
int i, j, k, m;
unsigned int n, coord;
double A=ai; // This is the scale factor which we'll be advancing below.
double Di=growthD(1.0, A); // initial growth factor
double Di2=growthD2(A); // initial 2nd order growth factor
double Dv=DprimeQ(A,1.0); // T[D_{za}]=dD_{za}/dy
double Dv2=growthD2v(A); // T[D_{2lpt}]=dD_{2lpt}/dy
displacement_fields();
P = (struct part_data *) malloc((int)(ceil(NumPart*Buffer))*sizeof(struct part_data));
// Generate the initial particle positions and velocities
// If subtractLPT = 0 (non-COLA), then velocity is ds/dy, which is simply the 2LPT IC.
// Else set vel = 0 if we subtract LPT. This is the same as the action of the operator L_- from TZE, as initial velocities are in 2LPT.
for(i=0; i<Local_np; i++) {
for (j=0; j<Nsample; j++) {
for (k=0; k<Nsample; k++) {
coord = (i * Nsample + j) * Nsample + k;
P[coord].ID = ((i + Local_p_start) * Nsample + j) * Nsample + k;
for (m=0; m<3; m++) {
P[coord].Dz[m] = ZA[m][coord];
P[coord].D2[m] = LPT[m][coord];
if (subtractLPT == 0) {
P[coord].Vel[m]=P[coord].Dz[m]*Dv+P[coord].D2[m]*Dv2;
} else {
P[coord].Vel[m] = 0.0;
}
}
P[coord].Pos[0] = periodic_wrap((i+Local_p_start)*(Box/Nsample)+P[coord].Dz[0]*Di+P[coord].D2[0]*Di2);
P[coord].Pos[1] = periodic_wrap(j*(Box/Nsample)+P[coord].Dz[1]*Di+P[coord].D2[1]*Di2);
P[coord].Pos[2] = periodic_wrap(k*(Box/Nsample)+P[coord].Dz[2]*Di+P[coord].D2[2]*Di2);
}
}
}
for (i=0; i<3; i++) {
free(ZA[i]);
free(LPT[i]);
}
// Now, we get to the N-Body part where we evolve with time via the Kick-Drift-Kick Method
// =======================================================================================
int timeStep;
double AF=0,AI,AC,AFF=0;
double growth1 = Di;
double growth1L2 = Di2;
// The density grid and force grids and associated fftw plans
#ifndef MEMORY_MODE
density = (float_kind *)calloc(2*Total_size,sizeof(float_kind));
N11 = (float_kind *)calloc(2*Total_size,sizeof(float_kind));
N12 = (float_kind *)calloc(2*Total_size,sizeof(float_kind));
N13 = (float_kind *)calloc(2*Total_size,sizeof(float_kind));
P3D = (complex_kind*)density;
FN11 = (complex_kind*)N11;
FN12 = (complex_kind*)N12;
FN13 = (complex_kind*)N13;
#ifdef SINGLE_PRECISION
plan = fftwf_mpi_plan_dft_r2c_3d(Nmesh,Nmesh,Nmesh,density,P3D,MPI_COMM_WORLD,FFTW_ESTIMATE);
p11 = fftwf_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN11,N11,MPI_COMM_WORLD,FFTW_ESTIMATE);
p12 = fftwf_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN12,N12,MPI_COMM_WORLD,FFTW_ESTIMATE);
p13 = fftwf_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN13,N13,MPI_COMM_WORLD,FFTW_ESTIMATE);
#else
plan = fftw_mpi_plan_dft_r2c_3d(Nmesh,Nmesh,Nmesh,density,P3D,MPI_COMM_WORLD,FFTW_ESTIMATE);
p11 = fftw_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN11,N11,MPI_COMM_WORLD,FFTW_ESTIMATE);
p12 = fftw_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN12,N12,MPI_COMM_WORLD,FFTW_ESTIMATE);
p13 = fftw_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN13,N13,MPI_COMM_WORLD,FFTW_ESTIMATE);
#endif
#endif
if(ThisTask == 0) {
printf("Beginning timestepping\n");
printf("======================\n");
fflush(stdout);
}
// AI stores the scale factor to which the velocities have been kicked to. Initially it's just A.
AI=A;
for (timeStep=0;timeStep<=nsteps;timeStep++){
// AFF is the scale factor to which we should drift the particle positions.
// AF is the scale factor to which we should kick the particle velocities.
if (stepDistr == 0) AFF=A+da;
if (stepDistr == 1) AFF=A*exp(da);
if (stepDistr == 2) AFF=AofTime(CosmoTime(A)+da);
// half time-step for final kick
if (timeStep == nsteps) {
AF=A;
} else {
// Set to mid-point of interval. In the infinitesimal timestep limit, these choices are identical.
// How one chooses the mid-point when not in that limit is really an extra degree of freedom in the code
// but Tassev et al. report negligible effects from the different choices below.
// Hence, this is not exported as an extra switch at this point.
if (stepDistr == 0) AF=A+da*0.5;
if (stepDistr == 1) AF=A*exp(da*0.5);
if (stepDistr == 2) AF=AofTime((CosmoTime(AFF)+CosmoTime(A))*0.5);
}
if (ThisTask == 0) {
printf("Iteration = %d\n------------------\n",timeStep+1);
printf("a = %lf\n",A);
printf("z = %lf\n",1.0/A-1.0);
fflush(stdout);
}
// First we check whether all the particles are on the correct processor after the last time step/
// original 2LPT displacement and move them if not
if (ThisTask == 0) printf("Moving particles across task boundaries...\n");
MoveParticles();
#ifdef MEMORY_MODE
density = (float_kind *)calloc(2*Total_size,sizeof(float_kind));
P3D = (complex_kind*)density;
#ifdef SINGLE_PRECISION
plan = fftwf_mpi_plan_dft_r2c_3d(Nmesh,Nmesh,Nmesh,density,P3D,MPI_COMM_WORLD,FFTW_ESTIMATE);
#else
plan = fftw_mpi_plan_dft_r2c_3d(Nmesh,Nmesh,Nmesh,density,P3D,MPI_COMM_WORLD,FFTW_ESTIMATE);
#endif
#endif
// Then we do the Cloud-in-Cell assignment to get the density grid and FFT it.
if (ThisTask == 0) printf("Calculating density using Cloud-in-Cell...\n");
PtoMesh();
#ifdef MEMORY_MODE
N11 = (float_kind *)calloc(2*Total_size,sizeof(float_kind));
N12 = (float_kind *)calloc(2*Total_size,sizeof(float_kind));
N13 = (float_kind *)calloc(2*Total_size,sizeof(float_kind));
FN11 = (complex_kind*)N11;
FN12 = (complex_kind*)N12;
FN13 = (complex_kind*)N13;
#ifdef SINGLE_PRECISION
p11 = fftwf_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN11,N11,MPI_COMM_WORLD,FFTW_ESTIMATE);
p12 = fftwf_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN12,N12,MPI_COMM_WORLD,FFTW_ESTIMATE);
p13 = fftwf_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN13,N13,MPI_COMM_WORLD,FFTW_ESTIMATE);
#else
p11 = fftw_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN11,N11,MPI_COMM_WORLD,FFTW_ESTIMATE);
p12 = fftw_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN12,N12,MPI_COMM_WORLD,FFTW_ESTIMATE);
p13 = fftw_mpi_plan_dft_c2r_3d(Nmesh,Nmesh,Nmesh,FN13,N13,MPI_COMM_WORLD,FFTW_ESTIMATE);
#endif
#endif
// This returns N11,N12,N13 which hold the components of
// the vector (grad grad^{-2} density) on a grid.
if (ThisTask == 0) printf("Calculating forces...\n");
Forces();
#ifdef MEMORY_MODE
free(density);
for (i=0; i<3; i++) Disp[i] = (float *)malloc(NumPart*sizeof(float));
#ifdef SINGLE_PRECISION
fftwf_destroy_plan(plan);
#else
fftw_destroy_plan(plan);
#endif
#else
for (i=0; i<3; i++) Disp[i] = (float_kind *)malloc(NumPart*sizeof(float_kind));
#endif
// Now find the accelerations at the particle positions using 3-linear interpolation.
if (ThisTask == 0) printf("Calculating accelerations...\n");
MtoParticles();
#ifdef MEMORY_MODE
free(N11);
free(N12);
free(N13);
#ifdef SINGLE_PRECISION
fftwf_destroy_plan(p11);
fftwf_destroy_plan(p12);
fftwf_destroy_plan(p13);
#else
fftw_destroy_plan(p11);
fftw_destroy_plan(p12);
fftw_destroy_plan(p13);
#endif
#endif
// Calculate the mean displacement and subtract later.
if (ThisTask == 0) printf("Calculating mean of displacements...\n");
double sumDx=0,sumDy=0,sumDz=0;
for(n=0; n<NumPart; n++) {
sumDx += Disp[0][n];
sumDy += Disp[1][n];
sumDz += Disp[2][n];
}
// Make sumDx, sumDy and sumDz global averages
ierr = MPI_Allreduce(MPI_IN_PLACE,&sumDx,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
ierr = MPI_Allreduce(MPI_IN_PLACE,&sumDy,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
ierr = MPI_Allreduce(MPI_IN_PLACE,&sumDz,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
sumDx /= (double)TotNumPart; // We will subtract these below to conserve momentum.
sumDy /= (double)TotNumPart;
sumDz /= (double)TotNumPart;
if (ThisTask == 0) {
printf("Kicking the particles...\n");
fflush(stdout);
}
// Kick
// ===============
double dda;
double q1,q2;
double ax,ay,az;
double sumx=0,sumy=0,sumz=0;
double Om143=pow(Omega/(Omega+(1-Omega)*A*A*A),1./143.);
if (StdDA == 0) {
dda=Sphi(AI,AF,A);
} else if (StdDA == 1) {
dda=(AF-AI)*A/Qfactor(A);
} else {
dda=SphiStd(AI,AF);
}
q2=1.5*Omega*growth1*growth1*(1.0+7./3.*Om143)*A; // T^2[D_{2lpt}]=d^2 D_{2lpt}/dy^2
q1=1.5*Omega*growth1*A; // T^2[D_{ZA}]=d^2 D_{ZA}/dy^2
for(n=0; n<NumPart; n++) {
Disp[0][n] -= sumDx;
Disp[1][n] -= sumDy;
Disp[2][n] -= sumDz;
ax=-1.5*Omega*Disp[0][n]-subtractLPT*(P[n].Dz[0]*q1+P[n].D2[0]*q2)/A;
ay=-1.5*Omega*Disp[1][n]-subtractLPT*(P[n].Dz[1]*q1+P[n].D2[1]*q2)/A;
az=-1.5*Omega*Disp[2][n]-subtractLPT*(P[n].Dz[2]*q1+P[n].D2[2]*q2)/A;
P[n].Vel[0] += ax*dda;
P[n].Vel[1] += ay*dda;
P[n].Vel[2] += az*dda;
sumx += P[n].Vel[0];
sumy += P[n].Vel[1];
sumz += P[n].Vel[2];
}
for (i=0; i<3; i++) free(Disp[i]);
// Make sumx, sumy and sumz global averages
ierr = MPI_Allreduce(MPI_IN_PLACE,&sumx,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
ierr = MPI_Allreduce(MPI_IN_PLACE,&sumy,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
ierr = MPI_Allreduce(MPI_IN_PLACE,&sumz,1,MPI_DOUBLE,MPI_SUM,MPI_COMM_WORLD);
sumx /= (double)TotNumPart; // We will subtract these below to conserve momentum.
sumy /= (double)TotNumPart; // Should be conserved, but just in case 3-linear interpolation makes a problem.
sumz /= (double)TotNumPart; // Never checked whether this makes a difference.
if (timeStep == nsteps) {
if (ThisTask == 0) {
printf("Iteration %d finished\n------------------\n\n", timeStep+1);
printf("Timestepping finished\n\n");
fflush(stdout);
}
// At final timestep, add back LPT velocities if we had subtracted them.
// This corresponds to L_+ operator in TZE.
Dv = DprimeQ(A,1.0); // dD_{za}/dy
Dv2 = growthD2v(A); // dD_{2lpt}/dy
for(n=0; n<NumPart; n++) {
P[n].Vel[0] += -sumx+(P[n].Dz[0]*Dv+P[n].D2[0]*Dv2)*subtractLPT;
P[n].Vel[1] += -sumy+(P[n].Dz[1]*Dv+P[n].D2[1]*Dv2)*subtractLPT;
P[n].Vel[2] += -sumz+(P[n].Dz[2]*Dv+P[n].D2[2]*Dv2)*subtractLPT;
}
goto finalize; // Sorry for "goto" :)
}
if (ThisTask == 0) {
printf("Drifting the particles...\n");
fflush(stdout);
}
// Drift
// =============
double dyyy;
double da1,da2;
AC = AF;
AF = AFF;
if (StdDA == 0) {
dyyy=Sq(A,AF,AC);
} else if (StdDA == 1) {
dyyy=(AF-A)/Qfactor(AC);
} else {
dyyy=SqStd(A,AF);
}
da1=growthD(1.0, AF)-growth1; // change in D
da2=growthD2(AF)-growth1L2; // change in D_{2lpt}
for(n=0; n<NumPart; n++) {
P[n].Pos[0] += (P[n].Vel[0]-sumx)*dyyy;
P[n].Pos[1] += (P[n].Vel[1]-sumy)*dyyy;
P[n].Pos[2] += (P[n].Vel[2]-sumz)*dyyy;
P[n].Pos[0] = periodic_wrap(P[n].Pos[0]+subtractLPT*(P[n].Dz[0]*da1+P[n].D2[0]*da2));
P[n].Pos[1] = periodic_wrap(P[n].Pos[1]+subtractLPT*(P[n].Dz[1]*da1+P[n].D2[1]*da2));
P[n].Pos[2] = periodic_wrap(P[n].Pos[2]+subtractLPT*(P[n].Dz[2]*da1+P[n].D2[2]*da2));
}
// Step in time
// ================
A = AF; // WRT to the above name change, A = AFF
AI = AC; // WRT to the above name change, AI = AF
growth1 = growthD(1.0, A);
growth1L2 = growthD2(A);
if (ThisTask == 0) {
printf("Iteration %d finished\n------------------\n\n", timeStep+1);
fflush(stdout);
}
ierr = MPI_Barrier(MPI_COMM_WORLD);
}
// Here is the last little bit
// ===========================
finalize:
if (ThisTask == 0) {
printf("Finishing up\n");
printf("============\n");
fflush(stdout);
}
// Now convert velocities to v_{rsd}\equiv (ds/d\eta)/(a H(a))
velRSD(A);
// Output a slice just for the sake of doing something with P.
if (ThisTask == 0) {
printf("Converting to RSD velocities...\n");
printf("Outputting particles...\n");
}
slice();
print_spec();
fflush(stdout);
free_powertable();
free_transfertable();
#ifdef GENERIC_FNL
free(KernelTable);
#endif
free(P);
free(Slab_to_task);
free(Part_to_task);
free(Local_nx_table);
free(Local_np_table);
#ifndef MEMORY_MODE
free(density);
free(N11);
free(N12);
free(N13);
#ifdef SINGLE_PRECISION
fftwf_destroy_plan(plan);
fftwf_destroy_plan(p11);
fftwf_destroy_plan(p12);
fftwf_destroy_plan(p13);
#else
fftw_destroy_plan(plan);
fftw_destroy_plan(p11);
fftw_destroy_plan(p12);
fftw_destroy_plan(p13);
#endif
#endif
#ifdef SINGLE_PRECISION
fftwf_mpi_cleanup();
#else
fftw_mpi_cleanup();
#endif
if (ThisTask == 0) printf("Done :)\n");
MPI_Finalize();
return 0;
}
/*! This routines generates the FFTW-plans to carry out the parallel FFTs
* later on. Some auxiliary variables are also initialized.
*/
void pm_init_periodic(void)
{
int i;
int slab_to_task_local[PMGRID];
All.Asmth[0] = ASMTH * All.BoxSize / PMGRID;
All.Rcut[0] = RCUT * All.Asmth[0];
/* Initialize FFTW MPI */
#ifdef FFTW3
fftw_mpi_init();
#endif
#ifdef FFTW3
/* If using FFTW3, don't create plans yet, just figure out the local array sizes */
fftsize_complex = fftw_mpi_local_size_3d_transposed(PMGRID, PMGRID, 0.5*PMGRID2, MPI_COMM_WORLD, &nslab_x, &slabstart_x, &nslab_y, &slabstart_y);
fftsize_real = 2.*fftsize_complex;
fftw_plan_exists = false;
#else
/* Set up the FFTW plan files. */
fft_forward_plan = rfftw3d_mpi_create_plan(MPI_COMM_WORLD, PMGRID, PMGRID, PMGRID,
FFTW_REAL_TO_COMPLEX, FFTW_ESTIMATE | FFTW_IN_PLACE);
fft_inverse_plan = rfftw3d_mpi_create_plan(MPI_COMM_WORLD, PMGRID, PMGRID, PMGRID,
FFTW_COMPLEX_TO_REAL, FFTW_ESTIMATE | FFTW_IN_PLACE);
/* Workspace out the ranges on each processor. */
rfftwnd_mpi_local_sizes(fft_forward_plan, &nslab_x, &slabstart_x, &nslab_y, &slabstart_y, &fftsize);
#endif
for(i = 0; i < PMGRID; i++)
slab_to_task_local[i] = 0;
for(i = 0; i < nslab_x; i++)
slab_to_task_local[slabstart_x + i] = ThisTask;
MPI_Allreduce(slab_to_task_local, slab_to_task, PMGRID, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
MPI_Allreduce(&nslab_x, &smallest_slab, 1, MPI_INT, MPI_MIN, MPI_COMM_WORLD);
slabs_per_task = malloc(NTask * sizeof(int));
MPI_Allgather(&nslab_x, 1, MPI_INT, slabs_per_task, 1, MPI_INT, MPI_COMM_WORLD);
if(ThisTask == 0)
{
for(i = 0; i < NTask; i++)
printf("Task=%d FFT-Slabs=%d\n", i, slabs_per_task[i]);
}
first_slab_of_task = malloc(NTask * sizeof(int));
MPI_Allgather(&slabstart_x, 1, MPI_INT, first_slab_of_task, 1, MPI_INT, MPI_COMM_WORLD);
meshmin_list = malloc(3 * NTask * sizeof(int));
meshmax_list = malloc(3 * NTask * sizeof(int));
to_slab_fac = PMGRID / All.BoxSize;
MPI_Allreduce(&fftsize, &maxfftsize, 1, MPI_INT, MPI_MAX, MPI_COMM_WORLD);
}