static Real hst_dPhi(const GridS *pG, const int i, const int j, const int k)
{
Real nJ,Q,cs,dPhi,Phi1;
Real kx,kxt,ky,k2,k20;
Real x1,x2,x3,zmax;
int nwx,nwy;
int ks = pG->ks, ke = pG->ke;
cc_pos(pG,i,j,k,&x1,&x2,&x3);
nJ = par_getd("problem","nJ");
Q = par_getd("problem","Q");
nwx = par_geti_def("problem","nwx",-6);
nwy = par_geti_def("problem","nwy",1);
zmax = par_getd("domain1","x3max");
kx = nwx*2*PI;
ky = nwy*2*PI;
kxt = kx+qshear*ky*pG->time;
k2 =kxt*kxt+ky*ky;
k20 =kx*kx+ky*ky;
cs = sqrt(4.0-2.0*qshear)/(PI*nJ*Q);
Phi1 = -4.0*PI*nJ*cs*cs/k20*(pG->U[k][j][i].d-1.0);
#ifdef SELF_GRAVITY_USING_FFT_DISK
Phi1 *= 1-0.5*(exp(-sqrt(k20)*(zmax-fabs(x3)))+exp(-sqrt(k20)*(zmax+fabs(x3))));
#endif
dPhi = (pG->Phi[k][j][i]-Phi1)/(pG->U[k][j][i].d-1)*k2;
dPhi /= 1-0.5*(exp(-sqrt(k2)*(zmax-fabs(x3)))+exp(-sqrt(k2)*(zmax+fabs(x3))));
return dPhi;
}
static Real hst_m2(const GridS *pG, const int i, const int j, const int k)
{
Real kx,kxt,ky;
Real x1,x2,x3;
int nwx,nwy;
Real nJ,Q,beta,cs,B0;
nJ = par_getd("problem","nJ");
Q = par_getd("problem","Q");
beta = par_getd("problem","beta");
cs = sqrt(4.0-2.0*qshear)/PI/nJ/Q;
B0 = cs/sqrt(beta);
cc_pos(pG,i,j,k,&x1,&x2,&x3);
nwx = par_geti_def("problem","nwx",-6);
nwy = par_geti_def("problem","nwy",1);
kx = nwx*2*PI;
ky = nwy*2*PI;
kxt = kx+qshear*ky*pG->time;
return -(pG->U[k][j][i].B2c-B0)/kxt/B0/cos(kxt*x1+ky*x2);
}
void problem_read_restart(MeshS *pM, FILE *fp)
{
int nl,nd,BCFlag_ix1,BCFlag_ox1;
/* Read Omega, and with viscosity and/or resistivity, read eta_Ohm and nu_V */
#ifdef SHEARING_BOX
Omega_0 = par_getd_def("problem","omega",1.0e-3);
qshear = par_getd_def("problem","qshear",1.5);
#endif
Mp = par_getd_def("problem","Mplanet",0.0);
Xplanet = par_getd_def("problem","Xplanet",0.0);
Yplanet = par_getd_def("problem","Yplanet",0.0);
Zplanet = par_getd_def("problem","Zplanet",0.0);
Rsoft = par_getd_def("problem","Rsoft",0.1);
ramp_time = 0.0;
insert_time = par_getd_def("problem","insert_time",0.0);
#ifdef VISCOSITY
nu_iso = par_getd_def("problem","nu_iso",0.0);
nu_aniso = par_getd_def("problem","nu_aniso",0.0);
#endif
/* enroll gravitational potential of planet & shearing-box potential fns */
StaticGravPot = PlanetPot;
ShearingBoxPot = UnstratifiedDisk;
/* enroll new history variables */
dump_history_enroll(hst_rho_Vx_dVy, "<rho Vx dVy>");
dump_history_enroll(hst_rho_dVy2, "<rho dVy^2>");
#ifdef ADIABATIC
dump_history_enroll(hst_E_total, "<E + rho Phi>");
#endif
BCFlag_ix1 = par_geti_def("domain1","bc_ix1",0);
BCFlag_ox1 = par_geti_def("domain1","bc_ox1",0);
for (nl=0; nl<(pM->NLevels); nl++){
for (nd=0; nd<(pM->DomainsPerLevel[nl]); nd++){
if (pM->Domain[nl][nd].Disp[0] == 0 && BCFlag_ix1 != 4)
bvals_mhd_fun(&(pM->Domain[nl][nd]), left_x1, constant_iib);
if (pM->Domain[nl][nd].MaxX[0] == pM->Domain[nl][nd].RootMaxX[0]
&& BCFlag_ox1 != 4)
bvals_mhd_fun(&(pM->Domain[nl][nd]), right_x1, constant_oib);
}
}
return;
}
static Real hst_uy(const GridS *pG, const int i, const int j, const int k)
{
Real kx,kxt,ky;
Real x1,x2,x3;
int nwx,nwy;
cc_pos(pG,i,j,k,&x1,&x2,&x3);
nwx = par_geti_def("problem","nwx",-6);
nwy = par_geti_def("problem","nwy",1);
kx = nwx*2*PI;
ky = nwy*2*PI;
kxt = kx+qshear*ky*pG->time;
return (pG->U[k][j][i].M2/pG->U[k][j][i].d-1)/sin(kxt*x1+ky*x2);
}
int commit_parameters(){
int out_level = par_geti_def("log","out_level",0);
int err_level = par_geti_def("log","err_level",0);
ath_log_set_level(out_level, err_level);
if(has_external_gravitational_potential) {
StaticGravPot = grav_pot;
}
CourNo = par_getd("time","cour_no");
#ifdef ISOTHERMAL
Iso_csound = par_getd("problem","iso_csound");
Iso_csound2 = Iso_csound*Iso_csound;
#else
Gamma = par_getd("problem","gamma");
Gamma_1 = Gamma - 1.0;
Gamma_2 = Gamma - 2.0;
#endif
init_domain(&level0_Grid, &level0_Domain);
init_grid(&level0_Grid, &level0_Domain);
if ((Potentials = (Real***)calloc_3d_array(
level0_Grid.Nx3 + 2 * nghost,
level0_Grid.Nx2 + 2 * nghost,
level0_Grid.Nx1 + 2 * nghost,
sizeof(Real))) == NULL)
{
return -1;
}
return 0;
}
void problem_read_restart(MeshS *pM, FILE *fp)
{
DomainS *pD = (DomainS*)&(pM->Domain[0][0]);
GridS *pG = pD->Grid;
ShearingBoxPot = StratifiedDisk;
Omega_0 = par_getd("problem","omega");
qshear = par_getd_def("problem","qshear",1.5);
ipert = par_geti_def("problem","ipert",1);
x1min = pG->MinX[0];
x1max = pG->MaxX[0];
Lx = x1max - x1min;
x2min = pG->MinX[1];
x2max = pG->MaxX[1];
Ly = x2max - x2min;
x3min = pM->RootMinX[2];
x3max = pM->RootMaxX[2];
Lz = x3max - x3min;
Lg = nghost*pG->dx3; /* size of the ghost zone */
vsc1 = par_getd_def("problem","vsc1",0.05); /* in unit of iso_sound (N.B.!) */
vsc2 = par_getd_def("problem","vsc2",0.0);
vsc1 = vsc1 * Iso_csound;
vsc2 = vsc2 * Iso_csound;
Npar = (int)(sqrt(par_geti("particle","parnumgrid")));
nlis = par_geti_def("problem","nlis",pG->Nx[0]*pG->Nx[1]*pG->Nx[2]);
ntrack = par_geti_def("problem","ntrack",2000);
dump_history_enroll(hst_rho_Vx_dVy, "<rho Vx dVy>");
return;
}
void problem(DomainS *pDomain)
{
GridS *pGrid = pDomain->Grid;
int is = pGrid->is, ie = pGrid->ie;
int js = pGrid->js, je = pGrid->je;
int ks = pGrid->ks, ke = pGrid->ke;
int i,j,k,BCFlag;
Real x1,x2,x3;
Real den = 1.0, pres = 1.0e-6;
static int frst=1; /* flag so new history variables enrolled only once */
#ifdef SHEARING_BOX
/* specify xy (r-phi) plane */
ShBoxCoord = xy;
#endif
/* Read problem parameters. Note Omega_0 set to 10^{-3} by default */
#ifdef SHEARING_BOX
Omega_0 = par_getd_def("problem","omega",1.0e-3);
qshear = par_getd_def("problem","qshear",1.5);
#endif
Mp = par_getd_def("problem","Mplanet",0.0);
Xplanet = par_getd_def("problem","Xplanet",0.0);
Yplanet = par_getd_def("problem","Yplanet",0.0);
Zplanet = par_getd_def("problem","Zplanet",0.0);
Rsoft = par_getd_def("problem","Rsoft",0.1);
ramp_time = 0.0;
insert_time = par_getd_def("problem","insert_time",0.0);
/* Compute field strength based on beta. */
#ifdef ISOTHERMAL
pres = Iso_csound2;
#endif
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
cc_pos(pGrid,i,j,k,&x1,&x2,&x3);
/* Initialize d, M, and P. With FARGO do not initialize the background shear */
pGrid->U[k][j][i].d = den;
// pGrid->U[k][j][i].d = 1.0+.5*(1-.02)*(tanh((x1-10.0)/3.5)-tanh((x1+10.0)/3.5))-.5*1.1*(tanh((x1-10.0)/15.0)-tanh((x1+10.0)/15.0));
pGrid->U[k][j][i].M1 = 0.0;
pGrid->U[k][j][i].M2 = 0.0;
#ifdef SHEARING_BOX
#ifndef FARGO
pGrid->U[k][j][i].M2 -= den*(qshear*Omega_0*x1);
#endif
#endif
pGrid->U[k][j][i].M3 = 0.0;
#ifdef ADIABATIC
pGrid->U[k][j][i].E = pres/Gamma_1
+ 0.5*(SQR(pGrid->U[k][j][i].M1) + SQR(pGrid->U[k][j][i].M2)
+ SQR(pGrid->U[k][j][i].M3))/den;
#endif
}
}}
/* enroll gravitational potential of planet & shearing-box potential fns */
StaticGravPot = PlanetPot;
ShearingBoxPot = UnstratifiedDisk;
/* enroll new history variables, only once */
if (frst == 1) {
dump_history_enroll(hst_rho_Vx_dVy, "<rho Vx dVy>");
dump_history_enroll(hst_rho_dVy2, "<rho dVy^2>");
#ifdef ADIABATIC
dump_history_enroll(hst_E_total, "<E + rho Phi>");
#endif
frst = 0;
}
/* With viscosity and/or resistivity, read diffusion coeffs */
#ifdef VISCOSITY
nu_iso = par_getd_def("problem","nu_iso",0.0);
nu_aniso = par_getd_def("problem","nu_aniso",0.0);
#endif
/* Enroll outflow BCs if perdiodic BCs NOT selected. This assumes the root
* level grid is specified by the <domain1> block in the input file */
BCFlag = par_geti_def("domain1","bc_ix1",0);
if (BCFlag != 4) {
if (pDomain->Disp[0] == 0) bvals_mhd_fun(pDomain, left_x1, constant_iib);
}
BCFlag = par_geti_def("domain1","bc_ox1",0);
if (BCFlag != 4) {
if (pDomain->MaxX[0] == pDomain->RootMaxX[0])
bvals_mhd_fun(pDomain, right_x1, constant_oib);
}
return;
}
void init_mesh(MeshS *pM)
{
int nblock,num_domains,nd,nl,level,maxlevel=0,nd_this_level;
int nDim,nDim_test,dim;
int *next_domainid;
char block[80];
int ncd,ir,irefine,l,m,n,roffset;
int i,Nx[3],izones;
div_t xdiv[3]; /* divisor with quot and rem members */
Real root_xmin[3], root_xmax[3]; /* min/max of x in each dir on root grid */
int Nproc_Comm_world=1,nproc=0,next_procID;
SideS D1,D2;
DomainS *pD, *pCD;
#ifdef MPI_PARALLEL
int ierr,child_found,groupn,Nranks,Nranks0,max_rank,irank,*ranks;
MPI_Group world_group;
/* Get total # of processes, in MPI_COMM_WORLD */
ierr = MPI_Comm_size(MPI_COMM_WORLD, &Nproc_Comm_world);
#endif
/* Start by initializing some quantaties in Mesh structure */
pM->time = 0.0;
pM->nstep = 0;
pM->outfilename = par_gets("job","problem_id");
/*--- Step 1: Figure out how many levels and domains there are. --------------*/
/* read levels of each domain block in input file and calculate max level */
num_domains = par_geti("job","num_domains");
#ifndef STATIC_MESH_REFINEMENT
if (num_domains > 1)
ath_error("[init_mesh]: num_domains=%d; for num_domains > 1 configure with --enable-smr\n",num_domains);
#endif
for (nblock=1; nblock<=num_domains; nblock++){
sprintf(block,"domain%d",nblock);
if (par_exist(block,"level") == 0)
ath_error("[init_mesh]: level does not exist in block %s\n",block);
level = par_geti(block,"level");
maxlevel = MAX(maxlevel,level);
}
/* set number of levels in Mesh, and allocate DomainsPerLevel array */
pM->NLevels = maxlevel + 1; /* level counting starts at 0 */
pM->DomainsPerLevel = (int*)calloc_1d_array(pM->NLevels,sizeof(int));
if (pM->DomainsPerLevel == NULL)
ath_error("[init_mesh]: malloc returned a NULL pointer\n");
/* Now figure out how many domains there are at each level */
for (nl=0; nl<=maxlevel; nl++){
nd_this_level=0;
for (nblock=1; nblock<=num_domains; nblock++){
sprintf(block,"domain%d",nblock);
if (par_geti(block,"level") == nl) nd_this_level++;
}
/* Error if there are any levels with no domains. Else set DomainsPerLevel */
if (nd_this_level == 0) {
ath_error("[init_mesh]: Level %d has zero domains\n",nl);
} else {
pM->DomainsPerLevel[nl] = nd_this_level;
}
}
/*--- Step 2: Set up root level. --------------------------------------------*/
/* Find the <domain> block in the input file corresponding to the root level,
* and set root level properties in Mesh structure */
if (pM->DomainsPerLevel[0] != 1)
ath_error("[init_mesh]: Level 0 has %d domains\n",pM->DomainsPerLevel[0]);
for (nblock=1; nblock<=num_domains; nblock++){
sprintf(block,"domain%d",nblock);
level = par_geti(block,"level");
if (level == 0){
root_xmin[0] = par_getd(block,"x1min");
root_xmax[0] = par_getd(block,"x1max");
root_xmin[1] = par_getd(block,"x2min");
root_xmax[1] = par_getd(block,"x2max");
root_xmin[2] = par_getd(block,"x3min");
root_xmax[2] = par_getd(block,"x3max");
Nx[0] = par_geti(block,"Nx1");
Nx[1] = par_geti(block,"Nx2");
Nx[2] = par_geti(block,"Nx3");
/* number of dimensions of root level, to test against all other inputs */
nDim=0;
for (i=0; i<3; i++) if (Nx[i]>1) nDim++;
if (nDim==0) ath_error("[init_mesh] None of Nx1,Nx2,Nx3 > 1\n");
/* some error tests of root grid */
for (i=0; i<3; i++) {
if (Nx[i] < 1) {
ath_error("[init_mesh]: Nx%d in %s must be >= 1\n",(i+1),block);
}
if(root_xmax[i] < root_xmin[i]) {
ath_error("[init_mesh]: x%dmax < x%dmin in %s\n",(i+1),block);
}
}
if (nDim==1 && Nx[0]==1) {
ath_error("[init_mesh]:1D requires Nx1>1: in %s Nx1=1,Nx2=%d,Nx3=%d\n",
block,Nx[1],Nx[2]);
}
if (nDim==2 && Nx[2]>1) {ath_error(
"[init_mesh]:2D requires Nx1,Nx2>1: in %s Nx1=%d,Nx2=%d,Nx3=%d\n",
block,Nx[0],Nx[1],Nx[2]);
}
/* Now that everything is OK, set root grid properties in Mesh structure */
for (i=0; i<3; i++) {
pM->Nx[i] = Nx[i];
pM->RootMinX[i] = root_xmin[i];
pM->RootMaxX[i] = root_xmax[i];
pM->dx[i] = (root_xmax[i] - root_xmin[i])/(Real)(Nx[i]);
}
/* Set BC flags on root domain */
pM->BCFlag_ix1 = par_geti_def(block,"bc_ix1",0);
pM->BCFlag_ix2 = par_geti_def(block,"bc_ix2",0);
pM->BCFlag_ix3 = par_geti_def(block,"bc_ix3",0);
pM->BCFlag_ox1 = par_geti_def(block,"bc_ox1",0);
pM->BCFlag_ox2 = par_geti_def(block,"bc_ox2",0);
pM->BCFlag_ox3 = par_geti_def(block,"bc_ox3",0);
}
}
/*--- Step 3: Allocate and initialize domain array. --------------------------*/
/* Allocate memory and set pointers for Domain array in Mesh. Since the
* number of domains nd depends on the level nl, this is a strange array
* because it is not [nl]x[nd]. Rather it is nl pointers to nd[nl] Domains.
* Compare to the calloc_2d_array() function in ath_array.c
*/
if((pM->Domain = (DomainS**)calloc((maxlevel+1),sizeof(DomainS*))) == NULL){
ath_error("[init_mesh] failed to allocate memory for %d Domain pointers\n",
(maxlevel+1));
}
if((pM->Domain[0]=(DomainS*)calloc(num_domains,sizeof(DomainS))) == NULL){
ath_error("[init_mesh] failed to allocate memory for Domains\n");
}
for(nl=1; nl<=maxlevel; nl++)
pM->Domain[nl] = (DomainS*)((unsigned char *)pM->Domain[nl-1] +
pM->DomainsPerLevel[nl-1]*sizeof(DomainS));
/* Loop over every <domain> block in the input file, and initialize each Domain
* in the mesh hierarchy (the Domain array), including the root level Domain */
next_domainid = (int*)calloc_1d_array(pM->NLevels,sizeof(int));
for(nl=0; nl<=maxlevel; nl++) next_domainid[nl] = 0;
for (nblock=1; nblock<=num_domains; nblock++){
sprintf(block,"domain%d",nblock);
/* choose nd coordinate in Domain array for this <domain> block according
* to the order it appears in input */
nl = par_geti(block,"level");
if (next_domainid[nl] > (pM->DomainsPerLevel[nl])-1)
ath_error("[init_mesh]: Exceeded available domain ids on level %d\n",nl);
nd = next_domainid[nl];
next_domainid[nl]++;
irefine = 1;
for (ir=1;ir<=nl;ir++) irefine *= 2; /* C pow fn only takes doubles !! */
/* Initialize level, number, input <domain> block number, and total number of
* cells in this Domain */
pM->Domain[nl][nd].Level = nl;
pM->Domain[nl][nd].DomNumber = nd;
pM->Domain[nl][nd].InputBlock = nblock;
pM->Domain[nl][nd].Nx[0] = par_geti(block,"Nx1");
pM->Domain[nl][nd].Nx[1] = par_geti(block,"Nx2");
pM->Domain[nl][nd].Nx[2] = par_geti(block,"Nx3");
/* error tests: dimensions of domain */
nDim_test=0;
for (i=0; i<3; i++) if (pM->Domain[nl][nd].Nx[i]>1) nDim_test++;
if (nDim_test != nDim) {
ath_error("[init_mesh]: in %s grid is %dD, but in root level it is %dD\n",
block,nDim_test,nDim);
}
for (i=0; i<3; i++) {
if (pM->Domain[nl][nd].Nx[i] < 1) {
ath_error("[init_mesh]: %s/Nx%d = %d must be >= 1\n",
block,(i+1),pM->Domain[nl][nd].Nx[i]);
}
}
if (nDim==1 && pM->Domain[nl][nd].Nx[0]==1) {ath_error(
"[init_mesh]: 1D requires Nx1>1 but in %s Nx1=1,Nx2=%d,Nx3=%d\n",
block,pM->Domain[nl][nd].Nx[1],pM->Domain[nl][nd].Nx[2]);
}
if (nDim==2 && pM->Domain[nl][nd].Nx[2]>1) {ath_error(
"[init_mesh]:2D requires Nx1,Nx2 > 1 but in %s Nx1=%d,Nx2=%d,Nx3=%d\n",
block,pM->Domain[nl][nd].Nx[0],pM->Domain[nl][nd].Nx[1],
pM->Domain[nl][nd].Nx[2]);
}
for (i=0; i<nDim; i++) {
xdiv[i] = div(pM->Domain[nl][nd].Nx[i], irefine);
if (xdiv[i].rem != 0){
ath_error("[init_mesh]: %s/Nx%d = %d must be divisible by %d\n",
block,(i+1),pM->Domain[nl][nd].Nx[i],irefine);
}
}
/* Set cell size based on level of domain, but only if Ncell > 1 */
for (i=0; i<3; i++) {
if (pM->Domain[nl][nd].Nx[i] > 1) {
pM->Domain[nl][nd].dx[i] = pM->dx[i]/(Real)(irefine);
} else {
pM->Domain[nl][nd].dx[i] = pM->dx[i];
}
}
/* Set displacement of Domain from origin. By definition, root level has 0
* displacement, so only read for levels other than root */
for (i=0; i<3; i++) pM->Domain[nl][nd].Disp[i] = 0;
if (nl != 0) {
if (par_exist(block,"iDisp") == 0)
ath_error("[init_mesh]: iDisp does not exist in block %s\n",block);
pM->Domain[nl][nd].Disp[0] = par_geti(block,"iDisp");
/* jDisp=0 if problem is only 1D */
if (pM->Nx[1] > 1) {
if (par_exist(block,"jDisp") == 0)
ath_error("[init_mesh]: jDisp does not exist in block %s\n",block);
pM->Domain[nl][nd].Disp[1] = par_geti(block,"jDisp");
}
/* kDisp=0 if problem is only 2D */
if (pM->Nx[2] > 1) {
if (par_exist(block,"kDisp") == 0)
ath_error("[init_mesh]: kDisp does not exist in block %s\n",block);
pM->Domain[nl][nd].Disp[2] = par_geti(block,"kDisp");
}
}
for (i=0; i<nDim; i++) {
xdiv[i] = div(pM->Domain[nl][nd].Disp[i], irefine);
if (xdiv[i].rem != 0){
ath_error("[init_mesh]: %s/Disp%d = %d must be divisible by %d\n",
block,(i+1),pM->Domain[nl][nd].Disp[i],irefine);
}
}
/* Use cell size and displacement from origin to compute min/max of x1/x2/x3 on
* this domain. Ensure that if Domain touches root grid boundary, the min/max
* of this Domain are set IDENTICAL to values in root grid */
for (i=0; i<3; i++){
if (pM->Domain[nl][nd].Disp[i] == 0) {
pM->Domain[nl][nd].MinX[i] = root_xmin[i];
} else {
pM->Domain[nl][nd].MinX[i] = root_xmin[i]
+ ((Real)(pM->Domain[nl][nd].Disp[i]))*pM->Domain[nl][nd].dx[i];
}
izones= (pM->Domain[nl][nd].Disp[i] + pM->Domain[nl][nd].Nx[i])/irefine;
if(izones == pM->Nx[i]){
pM->Domain[nl][nd].MaxX[i] = root_xmax[i];
} else {
pM->Domain[nl][nd].MaxX[i] = pM->Domain[nl][nd].MinX[i]
+ ((Real)(pM->Domain[nl][nd].Nx[i]))*pM->Domain[nl][nd].dx[i];
}
pM->Domain[nl][nd].RootMinX[i] = root_xmin[i];
pM->Domain[nl][nd].RootMaxX[i] = root_xmax[i];
}
} /*---------- end loop over domain blocks in input file ------------------*/
/*--- Step 4: Check that domains on the same level are non-overlapping. ------*/
/* Compare the integer coordinates of the sides of Domains at the same level.
* Print error if Domains overlap or touch. */
for (nl=maxlevel; nl>0; nl--){ /* start at highest level, and skip root */
for (nd=0; nd<(pM->DomainsPerLevel[nl])-1; nd++){
for (i=0; i<3; i++) {
D1.ijkl[i] = pM->Domain[nl][nd].Disp[i];
D1.ijkr[i] = pM->Domain[nl][nd].Disp[i] + pM->Domain[nl][nd].Nx[i];
}
for (ncd=nd+1; ncd<(pM->DomainsPerLevel[nl]); ncd++) {
for (i=0; i<3; i++) {
D2.ijkl[i] = pM->Domain[nl][ncd].Disp[i];
D2.ijkr[i] = pM->Domain[nl][ncd].Disp[i] + pM->Domain[nl][ncd].Nx[i];
}
if (D1.ijkl[0] <= D2.ijkr[0] && D1.ijkr[0] >= D2.ijkl[0] &&
D1.ijkl[1] <= D2.ijkr[1] && D1.ijkr[1] >= D2.ijkl[1] &&
D1.ijkl[2] <= D2.ijkr[2] && D1.ijkr[2] >= D2.ijkl[2]){
ath_error("Domains %d and %d at same level overlap or touch\n",
pM->Domain[nl][nd].InputBlock,pM->Domain[nl][ncd].InputBlock);
}
}
}}
/*--- Step 5: Check for illegal geometry of child/parent Domains -------------*/
for (nl=0; nl<maxlevel; nl++){
for (nd=0; nd<pM->DomainsPerLevel[nl]; nd++){
pD = (DomainS*)&(pM->Domain[nl][nd]); /* set ptr to this Domain */
for (i=0; i<3; i++) {
D1.ijkl[i] = pD->Disp[i];
D1.ijkr[i] = pD->Disp[i] + pD->Nx[i];
}
for (ncd=0; ncd<pM->DomainsPerLevel[nl+1]; ncd++){
pCD = (DomainS*)&(pM->Domain[nl+1][ncd]); /* set ptr to potential child*/
for (i=0; i<3; i++) {
D2.ijkl[i] = pCD->Disp[i]/2;
D2.ijkr[i] = 1;
if (pCD->Nx[i] > 1) D2.ijkr[i] = (pCD->Disp[i] + pCD->Nx[i])/2;
}
if (D1.ijkl[0] <= D2.ijkr[0] && D1.ijkr[0] >= D2.ijkl[0] &&
D1.ijkl[1] <= D2.ijkr[1] && D1.ijkr[1] >= D2.ijkl[1] &&
D1.ijkl[2] <= D2.ijkr[2] && D1.ijkr[2] >= D2.ijkl[2]){
/* check for child Domains that touch edge of parent (and are not at edges of
* root), extends past edge of parent, or are < nghost/2 from edge of parent */
for (dim=0; dim<nDim; dim++){
irefine = 1;
for (i=1;i<=nl;i++) irefine *= 2; /* parent refinement lev */
roffset = (pCD->Disp[dim] + pCD->Nx[dim])/(2*irefine) - pM->Nx[dim];
if (((D2.ijkl[dim] == D1.ijkl[dim]) && (pD->Disp[dim] != 0)) ||
((D2.ijkr[dim] == D1.ijkr[dim]) && (roffset != 0))) {
for (i=0; i<nDim; i++) {
D1.ijkl[i] /= irefine; /* report indices scaled to root */
D1.ijkr[i] /= irefine;
D2.ijkl[i] /= irefine;
D2.ijkr[i] /= irefine;
}
ath_error("[init_mesh] child Domain D%d[is,ie,js,je,ks,ke]=[%d %d %d %d %d %d] touches parent D%d[is,ie,js,je,ks,ke]=[%d %d %d %d %d %d]\n",
pCD->InputBlock,D2.ijkl[0],D2.ijkr[0],D2.ijkl[1],D2.ijkr[1],
D2.ijkl[2],D2.ijkr[2],pD->InputBlock,D1.ijkl[0],D1.ijkr[0],
D1.ijkl[1],D1.ijkr[1],D1.ijkl[2],D1.ijkr[2]);
}
if ((D2.ijkl[dim] < D1.ijkl[dim]) ||
(D2.ijkr[dim] > D1.ijkr[dim])) {
for (i=0; i<nDim; i++) {
D1.ijkl[i] /= irefine; /* report indices scaled to root */
D1.ijkr[i] /= irefine;
D2.ijkl[i] /= irefine;
D2.ijkr[i] /= irefine;
}
ath_error("[init_mesh] child Domain D%d[is,ie,js,je,ks,ke]=[%d %d %d %d %d %d] extends past parent D%d[is,ie,js,je,ks,ke]=[%d %d %d %d %d %d]\n",
pCD->InputBlock,D2.ijkl[0],D2.ijkr[0],D2.ijkl[1],D2.ijkr[1],
D2.ijkl[2],D2.ijkr[2],pD->InputBlock,D1.ijkl[0],D1.ijkr[0],
D1.ijkl[1],D1.ijkr[1],D1.ijkl[2],D1.ijkr[2]);
}
if (((2*(D2.ijkl[dim]-D1.ijkl[dim]) < nghost) &&
(2*(D2.ijkl[dim]-D1.ijkl[dim]) > 0 )) ||
((2*(D1.ijkr[dim]-D2.ijkr[dim]) < nghost) &&
(2*(D1.ijkr[dim]-D2.ijkr[dim]) > 0 ))) {
for (i=0; i<nDim; i++) {
D1.ijkl[i] /= irefine; /* report indices scaled to root */
D1.ijkr[i] /= irefine;
D2.ijkl[i] /= irefine;
D2.ijkr[i] /= irefine;
}
ath_error("[init_mesh] child Domain D%d[is,ie,js,je,ks,ke]=[%d %d %d %d %d %d] closer than nghost/2 to parent D%d[is,ie,js,je,ks,ke]=[%d %d %d %d %d %d]\n",
pCD->InputBlock,D2.ijkl[0],D2.ijkr[0],D2.ijkl[1],D2.ijkr[1],
D2.ijkl[2],D2.ijkr[2],pD->InputBlock,D1.ijkl[0],D1.ijkr[0],
D1.ijkl[1],D1.ijkr[1],D1.ijkl[2],D1.ijkr[2]);
}
}
}
}
}}
/*--- Step 6: Divide each Domain into Grids, and allocate to processor(s) ---*/
/* Get the number of Grids in each direction. These are given either in the
* <domain?> block in the input file, or by automatic decomposition given the
* number of processor desired for this domain. */
next_procID = 0; /* start assigning processors to Grids at ID=0 */
for (nl=0; nl<=maxlevel; nl++){
for (nd=0; nd<(pM->DomainsPerLevel[nl]); nd++){
pD = (DomainS*)&(pM->Domain[nl][nd]); /* set ptr to this Domain */
sprintf(block,"domain%d",pD->InputBlock);
#ifndef MPI_PARALLEL
for (i=0; i<3; i++) pD->NGrid[i] = 1;
#else
nproc = par_geti_def(block,"AutoWithNProc",0);
/* Read layout of Grids from input file */
if (nproc == 0){
pD->NGrid[0] = par_geti_def(block,"NGrid_x1",1);
pD->NGrid[1] = par_geti_def(block,"NGrid_x2",1);
pD->NGrid[2] = par_geti_def(block,"NGrid_x3",1);
if (pD->NGrid[0] == 0)
ath_error("[init_mesh] Cannot enter NGrid_x1=0 in %s\n",block);
if (pD->NGrid[1] == 0)
ath_error("[init_mesh] Cannot enter NGrid_x2=0 in %s\n",block);
if (pD->NGrid[2] == 0)
ath_error("[init_mesh] Cannot enter NGrid_x3=0 in %s\n",block);
}
/* Auto decompose Domain into Grids. To use this option, set "AutoWithNProc"
* to number of processors desired for this Domain */
else if (nproc > 0){
if(dom_decomp(pD->Nx[0],pD->Nx[1],pD->Nx[2],nproc,
&(pD->NGrid[0]),&(pD->NGrid[1]),&(pD->NGrid[2])))
ath_error("[init_mesh]: Error in automatic Domain decomposition\n");
/* Store the domain decomposition in the par database */
par_seti(block,"NGrid_x1","%d",pD->NGrid[0],"x1 decomp");
par_seti(block,"NGrid_x2","%d",pD->NGrid[1],"x2 decomp");
par_seti(block,"NGrid_x3","%d",pD->NGrid[2],"x3 decomp");
} else {
ath_error("[init_mesh] invalid AutoWithNProc=%d in %s\n",nproc,block);
}
#endif /* MPI_PARALLEL */
/* test for conflicts between number of grids and dimensionality */
for (i=0; i<3; i++){
if(pD->NGrid[i] > 1 && pD->Nx[i] <= 1)
ath_error("[init_mesh]: %s/NGrid_x%d = %d and Nx%d = %d\n",block,
(i+1),pD->NGrid[i],(i+1),pD->Nx[i]);
}
/* check there are more processors than Grids needed by this Domain. */
nproc = (pD->NGrid[0])*(pD->NGrid[1])*(pD->NGrid[2]);
if(nproc > Nproc_Comm_world) ath_error(
"[init_mesh]: %d Grids requested by block %s and only %d procs\n"
,nproc,block,Nproc_Comm_world);
/* Build 3D array to store data on Grids in this Domain */
if ((pD->GData = (GridsDataS***)calloc_3d_array(pD->NGrid[2],pD->NGrid[1],
pD->NGrid[0],sizeof(GridsDataS))) == NULL) ath_error(
"[init_mesh]: GData calloc returned a NULL pointer\n");
/* Divide the domain into blocks */
for (i=0; i<3; i++) {
xdiv[i] = div(pD->Nx[i], pD->NGrid[i]);
}
/* Distribute cells in Domain to Grids. Assign each Grid to a processor ID in
* the MPI_COMM_WORLD communicator. For single-processor jobs, there is only
* one ID=0, and the GData array will have only one element. */
for(n=0; n<(pD->NGrid[2]); n++){
for(m=0; m<(pD->NGrid[1]); m++){
for(l=0; l<(pD->NGrid[0]); l++){
for (i=0; i<3; i++) pD->GData[n][m][l].Nx[i] = xdiv[i].quot;
pD->GData[n][m][l].ID_Comm_world = next_procID++;
if (next_procID > ((Nproc_Comm_world)-1)) next_procID=0;
}}}
/* If the Domain is not evenly divisible put the extra cells on the first
* Grids in each direction, maintaining the load balance as much as possible */
for(n=0; n<(pD->NGrid[2]); n++){
for(m=0; m<(pD->NGrid[1]); m++){
for(l=0; l<xdiv[0].rem; l++){
pD->GData[n][m][l].Nx[0]++;
}
}
}
xdiv[0].rem=0;
for(n=0; n<(pD->NGrid[2]); n++){
for(m=0; m<xdiv[1].rem; m++) {
for(l=0; l<(pD->NGrid[0]); l++){
pD->GData[n][m][l].Nx[1]++;
}
}
}
xdiv[1].rem=0;
for(n=0; n<xdiv[2].rem; n++){
for(m=0; m<(pD->NGrid[1]); m++){
for(l=0; l<(pD->NGrid[0]); l++){
pD->GData[n][m][l].Nx[2]++;
}
}
}
xdiv[2].rem=0;
/* Initialize displacements from origin for each Grid */
for(n=0; n<(pD->NGrid[2]); n++){
for(m=0; m<(pD->NGrid[1]); m++){
pD->GData[n][m][0].Disp[0] = pD->Disp[0];
for(l=1; l<(pD->NGrid[0]); l++){
pD->GData[n][m][l].Disp[0] = pD->GData[n][m][l-1].Disp[0] +
pD->GData[n][m][l-1].Nx[0];
}
}
}
for(n=0; n<(pD->NGrid[2]); n++){
for(l=0; l<(pD->NGrid[0]); l++){
pD->GData[n][0][l].Disp[1] = pD->Disp[1];
for(m=1; m<(pD->NGrid[1]); m++){
pD->GData[n][m][l].Disp[1] = pD->GData[n][m-1][l].Disp[1] +
pD->GData[n][m-1][l].Nx[1];
}
}
}
for(m=0; m<(pD->NGrid[1]); m++){
for(l=0; l<(pD->NGrid[0]); l++){
pD->GData[0][m][l].Disp[2] = pD->Disp[2];
for(n=1; n<(pD->NGrid[2]); n++){
pD->GData[n][m][l].Disp[2] = pD->GData[n-1][m][l].Disp[2] +
pD->GData[n-1][m][l].Nx[2];
}
}
}
} /* end loop over ndomains */
} /* end loop over nlevels */
/* check that total number of Grids was partitioned evenly over total number of
* MPI processes available (equal to one for single processor jobs) */
if (next_procID != 0)
ath_error("[init_mesh]:total # of Grids != total # of MPI procs\n");
/*--- Step 7: Allocate a Grid for each Domain on this processor --------------*/
for (nl=0; nl<=maxlevel; nl++){
for (nd=0; nd<(pM->DomainsPerLevel[nl]); nd++){
pD = (DomainS*)&(pM->Domain[nl][nd]); /* set ptr to this Domain */
sprintf(block,"domain%d",pD->InputBlock);
pD->Grid = NULL;
/* Loop over GData array, and if there is a Grid assigned to this proc,
* allocate it */
for(n=0; n<(pD->NGrid[2]); n++){
for(m=0; m<(pD->NGrid[1]); m++){
for(l=0; l<(pD->NGrid[0]); l++){
if (pD->GData[n][m][l].ID_Comm_world == myID_Comm_world) {
if ((pD->Grid = (GridS*)malloc(sizeof(GridS))) == NULL)
ath_error("[init_mesh]: Failed to malloc a Grid for %s\n",block);
}
}}}
}
}
/*--- Step 8: Create an MPI Communicator for each Domain ---------------------*/
#ifdef MPI_PARALLEL
/* Allocate memory for ranks[] array */
max_rank = 0;
for (nl=0; nl<=maxlevel; nl++){
for (nd=0; nd<(pM->DomainsPerLevel[nl]); nd++){
pD = (DomainS*)&(pM->Domain[nl][nd]); /* set ptr to this Domain */
Nranks = (pD->NGrid[0])*(pD->NGrid[1])*(pD->NGrid[2]);
max_rank = MAX(max_rank, Nranks);
}}
ranks = (int*)calloc_1d_array(max_rank,sizeof(int));
/* Extract handle of group defined by MPI_COMM_WORLD communicator */
ierr = MPI_Comm_group(MPI_COMM_WORLD, &world_group);
for (nl=0; nl<=maxlevel; nl++){
for (nd=0; nd<(pM->DomainsPerLevel[nl]); nd++){
pD = (DomainS*)&(pM->Domain[nl][nd]); /* set ptr to this Domain */
/* Load integer array with ranks of processes in MPI_COMM_WORLD updating Grids
* on this Domain. The ranks of these processes in the new Comm_Domain
* communicator created below are equal to the indices of this array */
Nranks = (pD->NGrid[0])*(pD->NGrid[1])*(pD->NGrid[2]);
groupn = 0;
for(n=0; n<(pD->NGrid[2]); n++){
for(m=0; m<(pD->NGrid[1]); m++){
for(l=0; l<(pD->NGrid[0]); l++){
ranks[groupn] = pD->GData[n][m][l].ID_Comm_world;
pD->GData[n][m][l].ID_Comm_Domain = groupn;
groupn++;
}}}
/* Create a new group for this Domain; use it to create a new communicator */
ierr = MPI_Group_incl(world_group,Nranks,ranks,&(pD->Group_Domain));
ierr = MPI_Comm_create(MPI_COMM_WORLD,pD->Group_Domain,&(pD->Comm_Domain));
}}
free_1d_array(ranks);
#endif /* MPI_PARALLEL */
/*--- Step 9: Create MPI Communicators for Child and Parent Domains ----------*/
#if defined(MPI_PARALLEL) && defined(STATIC_MESH_REFINEMENT)
/* Initialize communicators to NULL, since not all Domains use them, and
* allocate memory for ranks[] array */
for (nl=0; nl<=maxlevel; nl++){
for (nd=0; nd<(pM->DomainsPerLevel[nl]); nd++){
pM->Domain[nl][nd].Comm_Parent = MPI_COMM_NULL;
pM->Domain[nl][nd].Comm_Children = MPI_COMM_NULL;
}
}
if (maxlevel > 0) {
ranks = (int*)calloc_1d_array(Nproc_Comm_world,sizeof(int));
}
/* For each Domain up to (maxlevel-1), initialize communicator with children */
for (nl=0; nl<maxlevel; nl++){
for (nd=0; nd<pM->DomainsPerLevel[nl]; nd++){
pD = (DomainS*)&(pM->Domain[nl][nd]); /* set ptr to this Domain */
child_found = 0;
/* Load integer array with ranks of processes in MPI_COMM_WORLD updating Grids
* on this Domain, in case a child Domain is found. Set IDs in Comm_Children
* communicator based on index in rank array, in case child found. If no
* child is found these ranks will never be used. */
Nranks = (pD->NGrid[0])*(pD->NGrid[1])*(pD->NGrid[2]);
groupn = 0;
for(n=0; n<(pD->NGrid[2]); n++){
for(m=0; m<(pD->NGrid[1]); m++){
for(l=0; l<(pD->NGrid[0]); l++){
ranks[groupn] = pD->GData[n][m][l].ID_Comm_world;
pD->GData[n][m][l].ID_Comm_Children = groupn;
groupn++;
}}}
/* edges of this Domain */
for (i=0; i<3; i++) {
D1.ijkl[i] = pD->Disp[i];
D1.ijkr[i] = pD->Disp[i] + pD->Nx[i];
}
/* Loop over all Domains at next level, looking for children of this Domain */
for (ncd=0; ncd<pM->DomainsPerLevel[nl+1]; ncd++){
pCD = (DomainS*)&(pM->Domain[nl+1][ncd]); /* set ptr to potential child*/
/* edges of potential child Domain */
for (i=0; i<3; i++) {
D2.ijkl[i] = pCD->Disp[i]/2;
D2.ijkr[i] = 1;
if (pCD->Nx[i] > 1) D2.ijkr[i] = (pCD->Disp[i] + pCD->Nx[i])/2;
}
if (D1.ijkl[0] < D2.ijkr[0] && D1.ijkr[0] > D2.ijkl[0] &&
D1.ijkl[1] < D2.ijkr[1] && D1.ijkr[1] > D2.ijkl[1] &&
D1.ijkl[2] < D2.ijkr[2] && D1.ijkr[2] > D2.ijkl[2]){
child_found = 1;
/* Child found. Add child processors to ranks array, but only if they are
* different from processes currently there (including parent and any previously
* found children). Set IDs associated with Comm_Parent communicator, since on
* the child Domain this is the same as the Comm_Children communicator on the
* parent Domain */
for(n=0; n<(pCD->NGrid[2]); n++){
for(m=0; m<(pCD->NGrid[1]); m++){
for(l=0; l<(pCD->NGrid[0]); l++){
irank = -1;
for (i=0; i<Nranks; i++) {
if(pCD->GData[n][m][l].ID_Comm_world == ranks[i]) irank = i;
}
if (irank == -1) {
ranks[groupn] = pCD->GData[n][m][l].ID_Comm_world;
pCD->GData[n][m][l].ID_Comm_Parent = groupn;
groupn++;
Nranks++;
} else {
pCD->GData[n][m][l].ID_Comm_Parent = ranks[irank];
}
}}}
}
}
/* After looping over all potential child Domains, create a new communicator if
* a child was found */
if (child_found == 1) {
ierr = MPI_Group_incl(world_group, Nranks, ranks, &(pD->Group_Children));
ierr = MPI_Comm_create(MPI_COMM_WORLD,pD->Group_Children,
&pD->Comm_Children);
/* Loop over children to set Comm_Parent communicators */
for (ncd=0; ncd<pM->DomainsPerLevel[nl+1]; ncd++){
pCD = (DomainS*)&(pM->Domain[nl+1][ncd]);
for (i=0; i<3; i++) {
D2.ijkl[i] = pCD->Disp[i]/2;
D2.ijkr[i] = 1;
if (pCD->Nx[i] > 1) D2.ijkr[i] = (pCD->Disp[i] + pCD->Nx[i])/2;
}
if (D1.ijkl[0] < D2.ijkr[0] && D1.ijkr[0] > D2.ijkl[0] &&
D1.ijkl[1] < D2.ijkr[1] && D1.ijkr[1] > D2.ijkl[1] &&
D1.ijkl[2] < D2.ijkr[2] && D1.ijkr[2] > D2.ijkl[2]){
pCD->Comm_Parent = pD->Comm_Children;
}
}
}
}}
#endif /* MPI_PARALLEL & STATIC_MESH_REFINEMENT */
free(next_domainid);
return;
}
void problem(DomainS *pDomain)
{
GridS *pGrid = pDomain->Grid;
ConsS **Soln;
int i, is = pGrid->is, ie = pGrid->ie;
int j, js = pGrid->js, je = pGrid->je;
int k, ks = pGrid->ks, ke = pGrid->ke;
int nx1, nx2;
int dir;
Real angle; /* Angle the wave direction makes with the x1-direction */
Real x1size,x2size,x1,x2,x3,cs,sn;
Real v_par, v_perp, den, pres;
Real lambda; /* Wavelength */
#ifdef RESISTIVITY
Real v_A, kva, omega_h, omega_l, omega_r;
#endif
nx1 = (ie - is + 1) + 2*nghost;
nx2 = (je - js + 1) + 2*nghost;
if (pGrid->Nx[1] == 1) {
ath_error("[problem] Grid must be 2D");
}
if ((Soln = (ConsS**)calloc_2d_array(nx2,nx1,sizeof(ConsS))) == NULL)
ath_error("[problem]: Error allocating memory for Soln\n");
if (pDomain->Level == 0){
if ((RootSoln =(ConsS**)calloc_2d_array(nx2,nx1,sizeof(ConsS)))==NULL)
ath_error("[problem]: Error allocating memory for RootSoln\n");
}
/* An angle = 0.0 is a wave aligned with the x1-direction. */
/* An angle = 90.0 is a wave aligned with the x2-direction. */
angle = par_getd("problem","angle");
x1size = pDomain->RootMaxX[0] - pDomain->RootMinX[0];
x2size = pDomain->RootMaxX[1] - pDomain->RootMinX[1];
/* Compute the sin and cos of the angle and the wavelength. */
/* Put one wavelength in the grid */
if (angle == 0.0) {
sin_a = 0.0;
cos_a = 1.0;
lambda = x1size;
}
else if (angle == 90.0) {
sin_a = 1.0;
cos_a = 0.0;
lambda = x2size;
}
else {
/* We put 1 wavelength in each direction. Hence the wavelength
* lambda = (pDomain->RootMaxX[0] - pDomain->RootMinX[0])*cos_a
* AND lambda = (pDomain->RootMaxX[1] - pDomain->RootMinX[1])*sin_a;
* are both satisfied. */
if(x1size == x2size){
cos_a = sin_a = sqrt(0.5);
}
else{
angle = atan((double)(x1size/x2size));
sin_a = sin(angle);
cos_a = cos(angle);
}
/* Use the larger angle to determine the wavelength */
if (cos_a >= sin_a) {
lambda = x1size*cos_a;
} else {
lambda = x2size*sin_a;
}
}
/* Initialize k_parallel */
k_par = 2.0*PI/lambda;
b_par = par_getd("problem","b_par");
den = 1.0;
ath_pout(0,"va_parallel = %g\nlambda = %g\n",b_par/sqrt(den),lambda);
b_perp = par_getd("problem","b_perp");
v_perp = b_perp/sqrt((double)den);
dir = par_geti_def("problem","dir",1); /* right(1)/left(2) polarization */
if (dir == 1) /* right polarization */
fac = 1.0;
else /* left polarization */
fac = -1.0;
#ifdef RESISTIVITY
Q_Hall = par_getd("problem","Q_H");
d_ind = 0.0;
v_A = b_par/sqrt((double)den);
if (Q_Hall > 0.0)
{
kva = k_par*v_A;
omega_h = 1.0/Q_Hall;
omega_r = 0.5*SQR(kva)/omega_h*(sqrt(1.0+SQR(2.0*omega_h/kva)) + 1.0);
omega_l = 0.5*SQR(kva)/omega_h*(sqrt(1.0+SQR(2.0*omega_h/kva)) - 1.0);
if (dir == 1) /* right polarization (whistler wave) */
v_perp = v_perp * kva / omega_r;
else /* left polarization */
v_perp = v_perp * kva / omega_l;
}
#endif
/* The gas pressure and parallel velocity are free parameters. */
pres = par_getd("problem","pres");
v_par = par_getd("problem","v_par");
/* Use the vector potential to initialize the interface magnetic fields
* The iterface fields are located at the left grid cell face normal */
for (k=ks; k<=ke; k++) {
for (j=js; j<=je+1; j++) {
for (i=is; i<=ie+1; i++) {
cc_pos(pGrid,i,j,k,&x1,&x2,&x3);
cs = cos(k_par*(x1*cos_a + x2*sin_a));
x1 -= 0.5*pGrid->dx1;
x2 -= 0.5*pGrid->dx2;
pGrid->B1i[k][j][i] = -(A3(x1,(x2+pGrid->dx2)) - A3(x1,x2))/pGrid->dx2;
pGrid->B2i[k][j][i] = (A3((x1+pGrid->dx1),x2) - A3(x1,x2))/pGrid->dx1;
pGrid->B3i[k][j][i] = b_perp*cs;
}
}
}
if (pGrid->Nx[2] > 1) {
for (j=js; j<=je+1; j++) {
for (i=is; i<=ie+1; i++) {
cc_pos(pGrid,i,j,k,&x1,&x2,&x3);
cs = cos(k_par*(x1*cos_a + x2*sin_a));
pGrid->B3i[ke+1][j][i] = b_perp*cs;
}
}
}
/* Now initialize the cell centered quantities */
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
cc_pos(pGrid,i,j,k,&x1,&x2,&x3);
sn = sin(k_par*(x1*cos_a + x2*sin_a)) * fac;
cs = cos(k_par*(x1*cos_a + x2*sin_a));
Soln[j][i].d = den;
Soln[j][i].M1 = den*(v_par*cos_a + v_perp*sn*sin_a);
Soln[j][i].M2 = den*(v_par*sin_a - v_perp*sn*cos_a);
Soln[j][i].M3 = -den*v_perp*cs;
pGrid->U[k][j][i].d = Soln[j][i].d;
pGrid->U[k][j][i].M1 = Soln[j][i].M1;
pGrid->U[k][j][i].M2 = Soln[j][i].M2;
pGrid->U[k][j][i].M3 = Soln[j][i].M3;
Soln[j][i].B1c = 0.5*(pGrid->B1i[k][j][i] + pGrid->B1i[k][j][i+1]);
Soln[j][i].B2c = 0.5*(pGrid->B2i[k][j][i] + pGrid->B2i[k][j+1][i]);
Soln[j][i].B3c = b_perp*cs;
pGrid->U[k][j][i].B1c = Soln[j][i].B1c;
pGrid->U[k][j][i].B2c = Soln[j][i].B2c;
pGrid->U[k][j][i].B3c = Soln[j][i].B3c;
#ifndef ISOTHERMAL
Soln[j][i].E = pres/Gamma_1 + 0.5*(SQR(pGrid->U[k][j][i].B1c) +
SQR(pGrid->U[k][j][i].B2c) + SQR(pGrid->U[k][j][i].B3c) )
+ 0.5*(SQR(pGrid->U[k][j][i].M1) + SQR(pGrid->U[k][j][i].M2) +
SQR(pGrid->U[k][j][i].M3) )/den;
pGrid->U[k][j][i].E = Soln[j][i].E;
#endif
}
}
}
/* save solution on root grid */
if (pDomain->Level == 0) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
RootSoln[j][i].d = Soln[j][i].d ;
RootSoln[j][i].M1 = Soln[j][i].M1;
RootSoln[j][i].M2 = Soln[j][i].M2;
RootSoln[j][i].M3 = Soln[j][i].M3;
#ifndef ISOTHERMAL
RootSoln[j][i].E = Soln[j][i].E ;
#endif /* ISOTHERMAL */
#ifdef MHD
RootSoln[j][i].B1c = Soln[j][i].B1c;
RootSoln[j][i].B2c = Soln[j][i].B2c;
RootSoln[j][i].B3c = Soln[j][i].B3c;
#endif
#if (NSCALARS > 0)
for (n=0; n<NSCALARS; n++)
RootSoln[j][i].s[n] = Soln[j][i].s[n];
#endif
}}
}
return;
}
void init_output(MeshS *pM)
{
int i,j,outn,maxout;
char block[80], *fmt, defid[10];
OutputS new_out;
int usr_expr_flag;
maxout = par_geti_def("job","maxout",MAXOUT_DEFAULT);
/* allocate output array */
if((OutArray = (OutputS *)malloc(maxout*sizeof(OutputS))) == NULL){
ath_error("[init_output]: Error allocating output array\n");
}
/*--- loop over maxout output blocks, reading parameters into a temporary -----*
*--- OutputS called new_out --------------------------------------------------*/
for (outn=1; outn<=maxout; outn++) {
sprintf(block,"output%d",outn);
/* An output format or output name is required.
* If neither is present we write an error message and move on. */
if((par_exist(block,"out_fmt") == 0) && (par_exist(block,"name") == 0)){
ath_perr(-1,"[init_output]: neither %s/out_fmt, nor %s/name exist\n",
block, block);
continue;
}
/* Zero (NULL) all members of the temporary OutputS structure "new_out" */
memset(&new_out,0,sizeof(OutputS));
/* The next output time and number */
new_out.t = par_getd_def(block,"time",pM->time);
new_out.num = par_geti_def(block,"num",0);
new_out.dt = par_getd(block,"dt");
new_out.n = outn;
/* level and domain number can be specified with SMR */
new_out.nlevel = par_geti_def(block,"level",-1);
new_out.ndomain = par_geti_def(block,"domain",-1);
if (par_exist(block,"dat_fmt")) new_out.dat_fmt = par_gets(block,"dat_fmt");
/* set id in output filename to input string if present, otherwise use "outN"
* as default, where N is output number */
sprintf(defid,"out%d",outn);
new_out.id = par_gets_def(block,"id",defid);
if(par_exist(block,"out_fmt"))
fmt = new_out.out_fmt = par_gets(block,"out_fmt");
/* out: controls what variable can be output (all, prim, or any of expr_*)
* out_fmt: controls format of output (single variable) or dump (all cons/prim)
* if "out" doesn't exist, we assume 'cons' variables are meant to be dumped */
new_out.out = par_gets_def(block,"out","cons");
#ifdef PARTICLES
/* check input for particle binning (=1, default) or not (=0) */
new_out.out_pargrid = par_geti_def(block,"pargrid",
check_particle_binning(new_out.out));
if ((new_out.out_pargrid < 0) || (new_out.out_pargrid >1)) {
ath_perr(-1,"[init_output]: %s/pargrid must be 0 or 1\n", block);
continue;
}
/* set particle property selection function. By default, will select all the
* particles. Used only when particle output is called, otherwise useless. */
if(par_exist(block,"par_prop")) {
new_out.par_prop = get_usr_par_prop(par_gets(block,"par_prop"));
if (new_out.par_prop == NULL) {
ath_pout(0,"[init_output]: Particle selection function not found! \
Now use the default one.\n");
new_out.par_prop = property_all;
}
}
void problem(DomainS *pDomain)
{
GridS *pG = pDomain->Grid;
int is = pG->is, ie = pG->ie;
int js = pG->js, je = pG->je;
int ks = pG->ks, ke = pG->ke;
int ixs,jxs,kxs,i,j,k;
long int iseed = -1; /* Initialize on the first call to ran2 */
Real x1,x2,x3,xmin,xmax,Lx,Ly,Lz;
Real rd, rp, rvx, rvy, rvz, rbx, rby, rbz;
Real beta,B0,P0,kx,ky,kz,amp,press;
Real Q,nJ,cs,cs2;
Real time0,kxt;
#ifdef SELF_GRAVITY
Real Gcons;
#endif
int nwx,nwy,nwz; /* input number of waves per Lx,Ly,Lz [default=1] */
double rval;
if(pG->Nx[2] == 1) ShBoxCoord = xy; /* 2D xy-plane */
/* Read problem parameters. */
Omega_0 = par_getd("problem","omega");
qshear = par_getd("problem","qshear");
amp = par_getd("problem","amp");
/* Read parameters for magnetic field */
beta = par_getd("problem","beta");
/* Read parameters for self gravity */
Q=par_getd("problem","Q");
nJ= par_getd("problem","nJ");
time0=par_getd_def("problem","time0",0.0);
cs=sqrt(4.0-2.0*qshear)/PI/nJ/Q;
cs2=SQR(cs);
#ifdef SELF_GRAVITY
Gcons = nJ*cs2;
grav_mean_rho = 1.0;
#ifndef SELF_GRAVITY_USING_FFT_DISK
if(pG->Nx[2] >1) grav_mean_rho = 1.0;
#endif
/* Set gravity constant*/
four_pi_G = 4.0*PI*Gcons;
#endif /* SELF_GRAVITY */
B0 = cs/sqrt(beta);
#ifndef BAROTROPIC
P0 = cs2/Gamma;
#endif
/* Ensure a different initial random seed for each process in an MPI calc. */
ixs = pG->Disp[0];
jxs = pG->Disp[1];
kxs = pG->Disp[2];
iseed = -1 - (ixs + pDomain->Nx[0]*(jxs + pDomain->Nx[1]*kxs));
Lx = pDomain->RootMaxX[0] - pDomain->RootMinX[0];
/* initialize wavenumbers, given input number of waves per L */
nwx = par_geti_def("problem","nwx",-6);
nwy = par_geti_def("problem","nwy",1);
ky = nwy*2.0*PI;
kx = nwx*2.0*PI;
kxt = kx+qshear*Omega_0*ky*time0;
pG->time=time0;
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
cc_pos(pG,i,j,k,&x1,&x2,&x3);
if (((i-pG->Disp[0]) == 58) && ((j-pG->Disp[1]) == 16))
printf("i=%d j=%d k=%d x1=%e x2=%e\n",i,j,k,x1,x2);
rd = 1.0+amp*cos(kxt*x1+ky*x2);
rvx = amp*kx/ky*sin(kxt*x1+ky*x2);
rvy = amp*sin(kxt*x1+ky*x2);
rvz = 0.0;
rp = cs2*(rd-1.0);
rbx = amp*nwy*cos(kxt*(x1-0.5*pG->dx1)+ky*x2);
rby = -amp*nwx*cos(kxt*x1+ky*(x2-0.5*pG->dx2));
rbz = 0.0;
pG->U[k][j][i].d = rd;
pG->U[k][j][i].M1 = rd*rvx;
pG->U[k][j][i].M2 = rd*rvy;
#ifndef FARGO
pG->U[k][j][i].M2 -= rd*(qshear*Omega_0*x1);
#endif
pG->U[k][j][i].M3 = rd*rvz;
#ifdef ADIABATIC
pG->U[k][j][i].E = (P0+rp)/Gamma_1
+ 0.5*(SQR(pG->U[k][j][i].M1) + SQR(pG->U[k][j][i].M2)
+ SQR(pG->U[k][j][i].M3))/rd;
#endif
#ifdef MHD
pG->B1i[k][j][i] = rbx;
pG->B2i[k][j][i] = B0+rby;
pG->B3i[k][j][i] = 0.0;
if (i==ie) cc_pos(pG,ie+1,j,k,&x1,&x2,&x3);
rbx = amp*nwy*cos(kx*(x1-0.5*pG->dx1)+ky*x2);
if (j==je) cc_pos(pG,i,je+1,k,&x1,&x2,&x3);
rby = -amp*nwx*cos(kx*x1+ky*(x2-0.5*pG->dx2));
if (i==ie) pG->B1i[k][j][ie+1] = rbx;
if (j==je) pG->B2i[k][je+1][i] = B0+rby;
if (pG->Nx[2] > 1 && k==ke) pG->B3i[ke+1][j][i] = 0.0;
#endif /* MHD */
}
}
}
#ifdef MHD
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
pG->U[k][j][i].B1c = 0.5*(pG->B1i[k][j][i]+pG->B1i[k][j][i+1]);
pG->U[k][j][i].B2c = 0.5*(pG->B2i[k][j][i]+pG->B2i[k][j+1][i]);
if (pG->Nx[2] >1) pG->U[k][j][i].B3c = 0.5*(pG->B3i[k][j][i]+pG->B3i[k+1][j][i]);
else pG->U[k][j][i].B3c =pG->B3i[k][j][i];
#ifdef ADIABATIC
pG->U[k][j][i].E += 0.5*(SQR(pG->U[k][j][i].B1c)
+ SQR(pG->U[k][j][i].B2c) + SQR(pG->U[k][j][i].B3c));
#endif
}
}
}
#endif /* MHD */
/* enroll gravitational potential function */
ShearingBoxPot = UnstratifiedDisk;
/* enroll new history variables, only once with SMR */
dVol = pDomain->Nx[0]*pDomain->Nx[1]*pDomain->Nx[2];
/* history dump for linear perturbation amplitude. See Kim & Ostriker 2001 */
dump_history_enroll(hst_sigma, "<sigma>");
dump_history_enroll(hst_ux, "<ux>");
dump_history_enroll(hst_uy, "<uy>");
#ifdef MHD
dump_history_enroll(hst_m1, "<m1>");
dump_history_enroll(hst_m2, "<m2>");
#endif
/* history dump for peturbed quantities at a specific grid point */
dump_history_enroll(hst_dSigma, "<dSigma>");
dump_history_enroll(hst_Vx, "<Vx>");
dump_history_enroll(hst_dVy, "<dVy>");
#ifdef MHD
dump_history_enroll(hst_Bx, "<Bx>");
dump_history_enroll(hst_dBy, "<dBy>");
#endif /* MHD */
#ifdef SELF_GRAVITY
dump_history_enroll(hst_Phi, "<Phi>");
dump_history_enroll(hst_dPhi, "<dPhi>");
#endif
#ifdef ADIABATIC
dump_history_enroll(hst_dE, "<dE>");
#endif
printf("=== end of problem setting ===\n");
return;
}
void problem(DomainS *pDomain)
{
GridS *pGrid = pDomain->Grid;
int i,j,k,ks,pt,tsmode;
long p,q;
Real ScaleHg,tsmin,tsmax,tscrit,amin,amax,Hparmin,Hparmax;
Real *ep,*ScaleHpar,epsum,mratio,pwind,rhoaconv,etavk;
Real *epsilon,*uxNSH,*uyNSH,**wxNSH,**wyNSH;
Real rhog,h,x1,x2,x3,t,x1p,x2p,x3p,zmin,zmax,dx3_1,b;
long int iseed = myID_Comm_world; /* Initialize on the first call to ran2 */
if (pDomain->Nx[2] == 1) {
ath_error("[par_strat3d]: par_strat3d only works for 3D problem.\n");
}
#ifdef MPI_PARALLEL
if (pDomain->NGrid[2] > 2) {
ath_error(
"[par_strat3d]: The z-domain can not be decomposed into more than 2 grids\n");
}
#endif
/* Initialize boxsize */
x1min = pGrid->MinX[0];
x1max = pGrid->MaxX[0];
Lx = x1max - x1min;
x2min = pGrid->MinX[1];
x2max = pGrid->MaxX[1];
Ly = x2max - x2min;
x3min = par_getd("domain1","x3min");
x3max = par_getd("domain1","x3max");
Lz = x3max - x3min;
Lg = nghost*pGrid->dx3; /* size of the ghost zone */
ks = pGrid->ks;
/* Read initial conditions */
Omega_0 = par_getd("problem","omega");
qshear = par_getd_def("problem","qshear",1.5);
ipert = par_geti_def("problem","ipert",1);
vsc1 = par_getd_def("problem","vsc1",0.05); /* in unit of iso_sound (N.B.!) */
vsc2 = par_getd_def("problem","vsc2",0.0);
vsc1 = vsc1 * Iso_csound;
vsc2 = vsc2 * Iso_csound;
ScaleHg = Iso_csound/Omega_0;
/* particle number */
Npar = (long)(par_geti("particle","parnumgrid"));
pGrid->nparticle = Npar*npartypes;
for (i=0; i<npartypes; i++)
grproperty[i].num = Npar;
if (pGrid->nparticle+2 > pGrid->arrsize)
particle_realloc(pGrid, pGrid->nparticle+2);
ep = (Real*)calloc_1d_array(npartypes, sizeof(Real));
ScaleHpar = (Real*)calloc_1d_array(npartypes, sizeof(Real));
epsilon = (Real*)calloc_1d_array(npartypes, sizeof(Real));
wxNSH = (Real**)calloc_2d_array(pGrid->Nx[2]+1, npartypes,sizeof(Real));
wyNSH = (Real**)calloc_2d_array(pGrid->Nx[2]+1, npartypes,sizeof(Real));
uxNSH = (Real*)calloc_1d_array(pGrid->Nx[2]+1, sizeof(Real));
uyNSH = (Real*)calloc_1d_array(pGrid->Nx[2]+1, sizeof(Real));
/* particle stopping time */
tsmode = par_geti("particle","tsmode");
if (tsmode == 3) {/* fixed stopping time */
tsmin = par_getd("problem","tsmin"); /* in code unit */
tsmax = par_getd("problem","tsmax");
tscrit= par_getd("problem","tscrit");
for (i=0; i<npartypes; i++) {
tstop0[i] = tsmin*exp(i*log(tsmax/tsmin)/MAX(npartypes-1,1.0));
grproperty[i].rad = tstop0[i];
/* use fully implicit integrator for well coupled particles */
if (tstop0[i] < tscrit) grproperty[i].integrator = 3;
}
}
else {
amin = par_getd("problem","amin");
amax = par_getd("problem","amax");
for (i=0; i<npartypes; i++)
grproperty[i].rad = amin*exp(i*log(amax/amin)/MAX(npartypes-1,1.0));
if (tsmode <= 2) {/* Epstein/General regime */
/* conversion factor for rhoa */
rhoaconv = par_getd_def("problem","rhoaconv",1.0);
for (i=0; i<npartypes; i++)
grrhoa[i]=grproperty[i].rad*rhoaconv;
}
if (tsmode == 1) /* General drag formula */
alamcoeff = par_getd("problem","alamcoeff");
}
/* particle scale height */
Hparmax = par_getd("problem","hparmax"); /* in unit of gas scale height */
Hparmin = par_getd("problem","hparmin");
for (i=0; i<npartypes; i++)
ScaleHpar[i] = Hparmax*
exp(-i*log(Hparmax/Hparmin)/MAX(npartypes-1,1.0));
#ifdef FEEDBACK
mratio = par_getd_def("problem","mratio",0.0); /* total mass fraction */
pwind = par_getd_def("problem","pwind",0.0); /* power law index */
if (mratio < 0.0)
ath_error("[par_strat2d]: mratio must be positive!\n");
epsum = 0.0;
for (i=0; i<npartypes; i++)
{
ep[i] = pow(grproperty[i].rad,pwind); epsum += ep[i];
}
for (i=0; i<npartypes; i++)
{
ep[i] = mratio*ep[i]/epsum;
grproperty[i].m = sqrt(2.0*PI)*ScaleHg/Lz*ep[i]*
pGrid->Nx[0]*pGrid->Nx[1]*pGrid->Nx[2]/Npar;
}
#else
mratio = 0.0;
for (i=0; i<npartypes; i++)
ep[i] = 0.0;
#endif
/* NSH equilibrium */
for (k=pGrid->ks; k<=pGrid->ke+1; k++) {
h = pGrid->MinX[2] + (k-pGrid->ks)*pGrid->dx3;
q = k - ks;
etavk = fabs(vsc1+vsc2*SQR(h));
for (i=0; i<npartypes; i++) {
epsilon[i] = ep[i]/ScaleHpar[i]*exp(-0.5*SQR(h/ScaleHg)
*(SQR(1.0/ScaleHpar[i])-1.0))/erf(Lz/(sqrt(8.0)*ScaleHpar[i]*ScaleHg));
if (tsmode != 3)
tstop0[i] = get_ts(pGrid,i,exp(-0.5*SQR(h/ScaleHg)),Iso_csound,etavk);
}
MultiNSH(npartypes, tstop0, epsilon, etavk,
&uxNSH[q], &uyNSH[q], wxNSH[q], wyNSH[q]);
}
/* Now set initial conditions for the gas */
for (k=pGrid->ks; k<=pGrid->ke; k++) {
for (j=pGrid->js; j<=pGrid->je; j++) {
for (i=pGrid->is; i<=pGrid->ie; i++) {
cc_pos(pGrid,i,j,k,&x1,&x2,&x3);
rhog = exp(-0.5*SQR(x3/ScaleHg));
pGrid->U[k][j][i].d = rhog;
if (ipert != 1) {/* NSH velocity */
pGrid->U[k][j][i].M1 = 0.5*rhog*(uxNSH[k-ks]+uxNSH[k-ks+1]);
pGrid->U[k][j][i].M2 = 0.5*rhog*(uyNSH[k-ks]+uyNSH[k-ks+1]);
} else {
pGrid->U[k][j][i].M1 = 0.0;
pGrid->U[k][j][i].M2 = 0.0;
}
pGrid->U[k][j][i].M3 = 0.0;
#ifndef FARGO
pGrid->U[k][j][i].M2 -= qshear*rhog*Omega_0*x1;
#endif
}}}
/* Now set initial conditions for the particles */
p = 0;
dx3_1 = 1.0/pGrid->dx3;
zmin = pGrid->MinX[2];
zmax = pGrid->MaxX[2];
for (q=0; q<Npar; q++) {
for (pt=0; pt<npartypes; pt++) {
x1p = x1min + Lx*ran2(&iseed);
x2p = x2min + Ly*ran2(&iseed);
x3p = ScaleHpar[pt]*ScaleHg*Normal(&iseed);
while ((x3p >= zmax) || (x3p < zmin))
x3p = ScaleHpar[pt]*ScaleHg*Normal(&iseed);
pGrid->particle[p].property = pt;
pGrid->particle[p].x1 = x1p;
pGrid->particle[p].x2 = x2p;
pGrid->particle[p].x3 = x3p;
if (ipert != 1) {/* NSH velocity */
cellk(pGrid, x3p, dx3_1, &k, &b);
k = k-pGrid->ks; b = b - pGrid->ks;
pGrid->particle[p].v1 = (k+1-b)*wxNSH[k][pt]+(b-k)*wxNSH[k+1][pt];
pGrid->particle[p].v2 = (k+1-b)*wyNSH[k][pt]+(b-k)*wyNSH[k+1][pt];
} else {
pGrid->particle[p].v1 = 0.0;
pGrid->particle[p].v2 = vsc1+vsc2*SQR(x2p);
}
pGrid->particle[p].v3 = 0.0;
#ifndef FARGO
pGrid->particle[p].v2 -= qshear*Omega_0*x1p;
#endif
pGrid->particle[p].pos = 1; /* grid particle */
pGrid->particle[p].my_id = p;
#ifdef MPI_PARALLEL
pGrid->particle[p].init_id = myID_Comm_world;
#endif
p++;
}}
/* enroll gravitational potential function, shearing sheet BC functions */
ShearingBoxPot = StratifiedDisk;
dump_history_enroll(hst_rho_Vx_dVy, "<rho Vx dVy>");
/* set the # of the particles in list output
* (by default, output 1 particle per cell)
*/
nlis = par_geti_def("problem","nlis",pGrid->Nx[0]*pGrid->Nx[1]*pGrid->Nx[2]);
/* set the number of particles to keep track of */
ntrack = par_geti_def("problem","ntrack",2000);
/* set the threshold particle density */
dpar_thresh = par_geti_def("problem","dpar_thresh",10.0);
/* finalize */
free(ep); free(ScaleHpar);
free(epsilon);
free_2d_array(wxNSH); free_2d_array(wyNSH);
free(uxNSH); free(uyNSH);
return;
}
