Ensure(FFT, can_be_constructed_from_DMDA)
{
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,20,2,1,NULL,&da);
CHKERRV(ierr);
ierr = scFftCreate(da, &fft);
assert_that(ierr, is_equal_to(0));
scFftDestroy(&fft);
CHKERRV(ierr);
ierr = DMDestroy(&da);
CHKERRV(ierr);
}
RigidKinematicsSolver::~RigidKinematicsSolver()
{
PetscErrorCode ierr;
PetscBool finalized;
PetscFunctionBeginUser;
ierr = PetscFinalized(&finalized); CHKERRV(ierr);
if (finalized) return;
ierr = destroy(); CHKERRV(ierr);
} // ~RigidKinematicsSolver
// Destructor.
ProbeBase::~ProbeBase()
{
PetscErrorCode ierr;
PetscBool finalized;
PetscFunctionBeginUser;
ierr = PetscFinalized(&finalized); CHKERRV(ierr);
if (finalized) return;
ierr = destroy(); CHKERRV(ierr);
} // ProbeBase::~ProbeBase
void SFieldEndRuns(SField sfv) {
mySField sf = static_cast<mySField>(sfv);
assert(sf->running);
PetscErrorCode ierr;
ierr = KSPDestroy(&sf->ksp);CHKERRV(ierr);
ierr = MatDestroy(&sf->J);CHKERRV(ierr);
ierr = VecDestroy(&sf->F);CHKERRV(ierr);
ierr = VecDestroy(&sf->U);CHKERRV(ierr);
delete [] sf->N_multi_idx;
sf->running = 0;
sf->N_multi_idx = 0;
}
SingleBodyBase::~SingleBodyBase()
{
PetscErrorCode ierr;
PetscBool finalized;
PetscFunctionBeginUser;
ierr = PetscFinalized(&finalized); CHKERRV(ierr);
if (finalized) return;
ierr = DMDestroy(&da); CHKERRV(ierr);
comm = MPI_COMM_NULL;
} // ~SingleBodyBase
// Destructor.
SolutionBase::~SolutionBase()
{
PetscErrorCode ierr;
PetscBool finalized;
PetscFunctionBeginUser;
ierr = PetscFinalized(&finalized); CHKERRV(ierr);
if (finalized) return;
ierr = VecDestroy(&UGlobal); CHKERRV(ierr);
ierr = VecDestroy(&pGlobal); CHKERRV(ierr);
comm = MPI_COMM_NULL;
} // ~SolutionBase
Ensure(FFT, registers_the_right_DM)
{
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,20,2,1,NULL,&da);
CHKERRV(ierr);
ierr = scFftCreate(da, &fft);
CHKERRV(ierr);
DM da1;
ierr = scFftGetDM(fft, &da1);
CHKERRV(ierr);
assert_that(da1, is_equal_to(da));
ierr = scFftDestroy(&fft);
CHKERRV(ierr);
ierr = DMDestroy(&da);
CHKERRV(ierr);
}
static void CholmodErrorHandler(int status,const char *file,int line,const char *message)
{
PetscErrorCode ierr;
PetscFunctionBegin;
if (status > CHOLMOD_OK) {
ierr = PetscInfo4(static_F,"CHOLMOD warning %d at %s:%d: %s\n",status,file,line,message);CHKERRV(ierr);
} else if (status == CHOLMOD_OK) { /* Documentation says this can happen, but why? */
ierr = PetscInfo3(static_F,"CHOLMOD OK at %s:%d: %s\n",file,line,message);CHKERRV(ierr);
} else {
ierr = PetscErrorPrintf("CHOLMOD error %d at %s:%d: %s\n",status,file,line,message);CHKERRV(ierr);
}
PetscFunctionReturnVoid();
}
void destroyArrays(simInfo *data)
{
PetscErrorCode ierr;
//ierr = MatDestroy(&C); CHKERRV(ierr);
//ierr = MatDestroy(&G); CHKERRV(ierr);
//ierr = ISDestroy(&is[0]); CHKERRV(ierr);
//ierr = ISDestroy(&is[1]); CHKERRV(ierr);
//ierr = PetscFree(is); CHKERRV(ierr);
ierr = VecDestroy(&(data->bc2)); CHKERRV(ierr);
ierr = VecDestroy(&(data->uPacked)); CHKERRV(ierr);
ierr = VecDestroy(&(data->pGlobal)); CHKERRV(ierr);
ierr = VecDestroy(&(data->bc2)); CHKERRV(ierr);
ierr = DMDestroy(&(data->vda)); CHKERRV(ierr);
ierr = DMDestroy(&(data->uda)); CHKERRV(ierr);
ierr = DMDestroy(&(data->pda)); CHKERRV(ierr);
ierr = DMDestroy(&(data->pack)); CHKERRV(ierr);
}
void createArrays(simInfo *data)
{
PetscErrorCode ierr;
PetscInt *lx, *ly, m, n;
const PetscInt *lxu, *lyu;
// Create distributed array and get vectors
ierr = PetscPrintf(PETSC_COMM_WORLD, "\nCreate staggered U, V and P vectors [DMDACreate2d, DMDAGetInfo, DMDAGetOwnershipRanges, DMCreateGlobalVector]"); CHKERRV(ierr); hline();
ierr = DMCompositeCreate(PETSC_COMM_WORLD, &(data->pack)); CHKERRV(ierr);
// create u DA
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_BOX, data->nx-1, data->ny, PETSC_DECIDE, PETSC_DECIDE, 1, 1, NULL, NULL, &(data->uda)); CHKERRV(ierr);
ierr = DMCompositeAddDM(data->pack, data->uda); CHKERRV(ierr);
// determine process distribution of v
ierr = DMDAGetInfo(data->uda, NULL, NULL, NULL, NULL, &m, &n, NULL, NULL, NULL, NULL, NULL, NULL, NULL); CHKERRV(ierr);
ierr = DMDAGetOwnershipRanges(data->uda, &lxu, &lyu, NULL); CHKERRV(ierr);
ierr = PetscMalloc(m*sizeof(*lx), &lx); CHKERRV(ierr);
ierr = PetscMalloc(n*sizeof(*ly), &ly); CHKERRV(ierr);
ierr = PetscMemcpy(lx ,lxu, m*sizeof(*lx)); CHKERRV(ierr);
ierr = PetscMemcpy(ly ,lyu, n*sizeof(*ly)); CHKERRV(ierr);
lx[m-1]++;
// create v DA
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_STAR, data->nx, data->ny, m, n, 1, 1, lx, ly, &(data->pda)); CHKERRV(ierr);
// create vectors p and bc2
ierr = DMCreateGlobalVector(data->pda, &(data->pGlobal)); CHKERRV(ierr);
ierr = VecDuplicate(data->pGlobal, &(data->bc2)); CHKERRV(ierr);
ly[n-1]--;
// create p DA
ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_GHOSTED, DMDA_BOUNDARY_GHOSTED, DMDA_STENCIL_BOX, data->nx, data->ny-1, m, n, 1, 1, lx, ly, &(data->vda)); CHKERRV(ierr);
ierr = DMCompositeAddDM(data->pack, data->vda); CHKERRV(ierr);
PetscFree(lx);
PetscFree(ly);
// create vector uPacked
ierr = DMCreateGlobalVector(data->pack, &(data->uPacked)); CHKERRV(ierr);
}
void hline()
{
PetscErrorCode ierr;
ierr = PetscPrintf(PETSC_COMM_WORLD, "\n------------------------------------------------------------------------------------------------------------------------\n"); CHKERRV(ierr);
}
Ensure(FourthOrderJacobian, is_consistent_for_gaussian) {
ierr = checkJacobianPreConsistency(&fixture, waveAtRest, gaussian, 0.0, 0.0, PETSC_TRUE, 5.0e-3, PETSC_FALSE);CHKERRV(ierr);
}
Ensure(FourthOrderJacobian, is_consistent_for_sine_waves) {
ierr = checkJacobianPreConsistency(&fixture, waveAtRest, sine_wave, 0.0, 0.0, PETSC_TRUE, 1.0e-5, PETSC_FALSE);CHKERRV(ierr);
}
Ensure(FourthOrderJacobian, is_consistent_for_constant_fields) {
ierr = checkJacobianPreConsistency(&fixture, waveAtRest, constant_func, 0.0, 0.0, PETSC_TRUE, 1.0e-6, PETSC_FALSE);CHKERRV(ierr);
}
Ensure(FourthOrderJacobian, can_be_built) {
ierr = scJacobianBuildLinearPart(fixture.matFixture.da, fixture.matFixture.m, PETSC_TRUE);CHKERRV(ierr);
assert_that(ierr, is_equal_to(0));
}
void coulomb_trick(PetscErrorCode ierr, params *params)
{
size_t neval;
PetscReal a,b,abserr,coul_result;
PetscReal mf2,mu2,th2;
PetscInt start,end;
PetscInt rank;
PetscReal *_mu;
PetscReal *_th;
Vec MU_SEQ;
Vec TH_SEQ;
VecScatter ctm;
VecScatter ctt;
int_params int_params;
ierr = PetscPrintf(PETSC_COMM_WORLD,"---Beginning Coulomb Trick---\n");CHKERRV(ierr);
print_progress_header(ierr);
int_params.epsabs=1e-4;
int_params.epsrel=1e-8;
int_params.N_work=4000;
int_params.flag_asy=params->flag_asy;
MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
for(PetscInt i=0;i<params->nf;i++)
{
int_params.p_bohr.push_back(params->p_bohr[i]);
}
gsl_function F;
F.function = &ct_integrand;
F.params=&int_params;
ierr = VecScatterCreateToAll(params->mu,&ctm,&MU_SEQ);CHKERRV(ierr);
ierr = VecScatterBegin(ctm,params->mu,MU_SEQ,INSERT_VALUES,SCATTER_FORWARD);CHKERRV(ierr);
ierr = VecScatterEnd(ctm,params->mu,MU_SEQ,INSERT_VALUES,SCATTER_FORWARD);CHKERRV(ierr);
ierr = VecGetArray(MU_SEQ,&_mu);CHKERRV(ierr);
ierr = VecScatterCreateToAll(params->theta,&ctt,&TH_SEQ);CHKERRV(ierr);
ierr = VecScatterBegin(ctt,params->theta,TH_SEQ,INSERT_VALUES,SCATTER_FORWARD);CHKERRV(ierr);
ierr = VecScatterEnd(ctt,params->theta,TH_SEQ,INSERT_VALUES,SCATTER_FORWARD);CHKERRV(ierr);
ierr = VecGetArray(TH_SEQ,&_th);CHKERRV(ierr);
ierr = VecGetOwnershipRange(params->CT,&start,&end);CHKERRV(ierr);
PetscInt step;
step=1;
if(params->Jz==0){step=2;start=start+(start%2);}
gsl_integration_cquad_workspace *work = gsl_integration_cquad_workspace_alloc(int_params.N_work);
for (PetscInt i=start; i<end; i+=step)
{
//if((i-start)%((end-start)/10)==0){ierr = PetscPrintf(PETSC_COMM_SELF,"----Cc: r%d -> %d\\%d\n",rank,(i-start),(end-start));CHKERRV(ierr);}
// if(params->Jz !=0 || i%2==0){
get_index(i,&int_params,params);
int_params.mu2 = _mu[params->nm_tot[int_params.index_f]+int_params.index_m];
int_params.th2 = _th[params->nt_tot[int_params.index_f]+int_params.index_t];
// ierr = PetscPrintf(PETSC_COMM_SELF,"Pts: %d %d %f %f\n",int_params.index_m,int_params.index_t,int_params.mu2,int_params.th2);CHKERRV(ierr);
if(int_params.index_s<2){int_params.Jzc = params->Jz;}
else{int_params.Jzc= -params->Jz;}
// if (int_params.Jzc !=0 || int_params.index_s%2==0)
// {
int_params.mf = params->m[int_params.index_f];
mf2=int_params.mf*int_params.mf;
mu2=int_params.mu2;
th2=int_params.th2;
int_params.x2 = (1.0+mu2*th2/sqrt(mf2+mu2*mu2))/2.0;
int_params.k2 = mu2*sqrt(1.0-th2*th2);
a = 0.0;
b = params->lambda[int_params.index_f]/2.0;
// if (int_params.Jzc !=0 || int_params.index_s%2==0)
// {
// gsl_integration_cquad_workspace *work = gsl_integration_cquad_workspace_alloc(int_params.N_work);
gsl_integration_cquad(&F,a,b,int_params.epsabs,int_params.epsrel,work,&coul_result,&abserr,&neval);
// gsl_integration_cquad_workspace_free(work);
ierr = VecSetValues(params->CT,1,&i,&coul_result,ADD_VALUES);CHKERRV(ierr);
if (params->Jz==0)
{
PetscInt ishift;
ishift=i+(3-2*int_params.index_s);
ierr = VecSetValues(params->CT,1,&ishift,&coul_result,ADD_VALUES);CHKERRV(ierr);
}
// }
// ierr = PetscPrintf(PETSC_COMM_SELF,"Pts: %d %d %f %f %f\n",int_params.index_m,int_params.index_t,int_params.mu2,int_params.th2,coul_result);CHKERRV(ierr);
if((i-start)%((end-start)/4)==0){ierr = PetscPrintf(PETSC_COMM_SELF,"|");CHKERRV(ierr);}
}
gsl_integration_cquad_workspace_free(work);
ierr = VecRestoreArray(MU_SEQ,&_mu);CHKERRV(ierr);
ierr = VecScatterDestroy(&ctm);CHKERRV(ierr);
ierr = VecDestroy(&MU_SEQ);CHKERRV(ierr);
ierr = VecRestoreArray(TH_SEQ,&_th);CHKERRV(ierr);
ierr = VecScatterDestroy(&ctt);CHKERRV(ierr);
ierr = VecDestroy(&TH_SEQ);CHKERRV(ierr);
ierr = VecAssemblyBegin(params->CT);CHKERRV(ierr);
ierr = VecAssemblyEnd(params->CT);CHKERRV(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n---Finishing Coulomb Trick---\n");CHKERRV(ierr);
}
void read_input(PetscErrorCode ierr, char **argv, params *params)
//void read_input(char **argv,char *ofile_n, PetscInt *nf, PetscInt *Jz, PetscReal *alpha,std::vector<PetscReal> &m,std::vector<PetscInt> &nm,std::vector<PetscInt> &nt,std::vector<PetscReal> &lambda)
{
std::ifstream ifile;
std::string ifile_n;
std::string null;
PetscReal datar;
PetscReal datat;
PetscInt datai;
PetscInt N_mu_tot;
PetscInt N_theta_tot;
ifile_n = argv[1];
ifile.open(ifile_n.c_str());
if(!ifile.is_open())
{
ierr = PetscPrintf(PETSC_COMM_WORLD,"---Error:: Initialization File Doesn't Exist---\n");CHKERRV(ierr);
}
ifile >> params->ofile_n >> null;
ifile >> params->nf >> null;
ifile >> params->Jz >> null;
ifile >> params->alpha >> null;
ifile >> params->flag_nm_dis >> null;
ifile >> params->flag_nt_dis >> null;
ifile >> params->flag_anni >> null;
ifile >> params->flag_mix >> null;
ifile >> params->flag_asy >> null;
ifile >> params->flag_mumps >> null;
for(int i=0; i<params->nf; i++)
{
ifile >> null;
ifile >> datar >> null;
params->m.push_back(datar);
params->p_bohr.push_back(datar*params->alpha/2.0);
ifile >> datai >> null;
params->nm.push_back(datai);
ifile >> datai >> null;
params->nt.push_back(datai);
ifile >> datar >> null;
params->lambda.push_back(datar);
}
set_sflags(params);
ifile.close();
N_mu_tot=0;
N_theta_tot=0;
params->N_tot=0;
datat=0.0;
datar=0.0;
for( PetscInt i=0;i<params->nf;i++)
{
params->nm_tot.push_back(datar);
params->nt_tot.push_back(datat);
N_mu_tot+=params->nm[i];
N_theta_tot+=params->nt[i];
params->N_tot+=params->nm[i]*params->nt[i];
params->N_tot_f.push_back(params->N_tot);
datar+=params->nm[i];
datat+=params->nt[i];
}
get_outfile_name(params);
params->hfile.append(params->ofile_n);
params->hfile.append("_H");
ierr = VecCreate(PETSC_COMM_WORLD,¶ms->mu);CHKERRV(ierr);
ierr = VecSetSizes(params->mu,PETSC_DECIDE,N_mu_tot);CHKERRV(ierr);
ierr = VecSetFromOptions(params->mu);CHKERRV(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,¶ms->wmu);CHKERRV(ierr);
ierr = VecSetSizes(params->wmu,PETSC_DECIDE,N_mu_tot);CHKERRV(ierr);
ierr = VecSetFromOptions(params->wmu);CHKERRV(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,¶ms->theta);CHKERRV(ierr);
ierr = VecSetSizes(params->theta,PETSC_DECIDE,N_theta_tot);CHKERRV(ierr);
ierr = VecSetFromOptions(params->theta);CHKERRV(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,¶ms->wtheta);CHKERRV(ierr);
ierr = VecSetSizes(params->wtheta,PETSC_DECIDE,N_theta_tot);CHKERRV(ierr);
ierr = VecSetFromOptions(params->wtheta);CHKERRV(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,¶ms->CT);CHKERRV(ierr);
ierr = VecSetSizes(params->CT,PETSC_DECIDE,4*params->N_tot);CHKERRV(ierr);
ierr = VecSetFromOptions(params->CT);CHKERRV(ierr);
}
Ensure(FourthOrderJacobian, is_consistent_for_gaussian_right_moving) {
ierr = checkJacobianPreConsistency(&fixture, rightMovingWave, gaussian, 0.0, 0.0, PETSC_TRUE, 1.0e0, PETSC_FALSE);CHKERRV(ierr);
}