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;
}
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 problem(DomainS *pDomain)
{
GridS *pGrid=(pDomain->Grid);
int i, is = pGrid->is, ie = pGrid->ie;
int j, js = pGrid->js, je = pGrid->je;
int k, ks = pGrid->ks, ke = pGrid->ke;
Real x1,x2,x3;
Real rho, p, prat, density, pressure, pi, vel, n, amp, lx, ly;
dt_line_integral_output = par_getd("problem", "dt_line_integral");
/* size of the domain (in physical coordinates) */
lx = pDomain->RootMaxX[0] - pDomain->RootMinX[0];
ly = pDomain->RootMaxX[1] - pDomain->RootMinX[1];
p = 1.0;
/* if prat=0.8, vx = -1.8965 (t&e find other vals)*/
pi=3.14159;
n = 2; /*Oscillations of perturbation*/
amp = 0.05 ; /* Size of perturbation ~ 0.05 */
/* setup uniform ambient medium with spherical over-pressured region */
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);
if (x1 > amp*sin(n*pi*x2/ly)) {
pressure = 0.1175;
} else {
pressure = 1;
}
if (x1 > amp*sin(n*pi*x2/ly)) {
vel= -1.96071;
} else {
vel= -0.7;
}
if (x1 > amp*sin(n*pi*x2/ly)) {
density= 0.357013;
} else {
density= 1;
}
pGrid->U[0][j][i].d = density;
pGrid->U[0][j][i].M1 = density*vel;
pGrid->U[0][j][i].M2 = 0.0;
#ifndef ISOTHERMAL
pGrid->U[0][j][i].E = pressure/Gamma_1 + (SQR(pGrid->U[0][j][i].M1) + SQR(pGrid->U[0][j][i].M2))/(2.0*(pGrid->U[0][j][i].d));
#endif
}
}
}
/* Adding history dumps*/
void dump_history_enroll(const ConsFun_t pfun, const char *label);
dump_history_enroll(pleft, "<pbvals>");
dump_history_enroll(vyintegral, "<vyintegral>");
/* enroll special functions */
bvals_mhd_fun(pDomain,left_x1, bc_ix1);
return;
}
static void initialize(Grid *pGrid, Domain *pD)
{
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 nbuf, mpierr, nx1gh, nx2gh, nx3gh;
float kwv, kpara, kperp;
char donedrive = 0;
/* -----------------------------------------------------------
* Variables within this block are stored globally, and used
* within preprocessor macros. Don't create variables with
* these names within your function if you are going to use
* OFST(), KCOMP(), or KWVM() within the function! */
/* Get local grid size */
nx1 = (ie-is+1);
nx2 = (je-js+1);
nx3 = (ke-ks+1);
/* Get global grid size */
gnx1 = pD->ide - pD->ids + 1;
gnx2 = pD->jde - pD->jds + 1;
gnx3 = pD->kde - pD->kds + 1;
/* Get extents of local FFT grid in global coordinates */
gis=is+pGrid->idisp; gie=ie+pGrid->idisp;
gjs=js+pGrid->jdisp; gje=je+pGrid->jdisp;
gks=ks+pGrid->kdisp; gke=ke+pGrid->kdisp;
/* ----------------------------------------------------------- */
/* Get size of arrays with ghost cells */
nx1gh = nx1 + 2*nghost;
nx2gh = nx2 + 2*nghost;
nx3gh = nx3 + 2*nghost;
/* Get input parameters */
/* interval for generating new driving spectrum; also interval for
* driving when IMPULSIVE_DRIVING is used */
dtdrive = par_getd("problem","dtdrive");
#ifdef MHD
/* magnetic field strength */
beta = par_getd("problem","beta");
/* beta = isothermal pressure/magnetic pressure */
B0 = sqrt(2.0*Iso_csound2*rhobar/beta);
#endif /* MHD */
/* energy injection rate */
dedt = par_getd("problem","dedt");
/* parameters for spectrum */
ispect = par_geti("problem","ispect");
if (ispect == 1) {
expo = par_getd("problem","expo");
} else if (ispect == 2) {
kpeak = par_getd("problem","kpeak")*2.0*PI;
} else {
ath_error("Invalid value for ispect\n");
}
/* Cutoff wavenumbers of spectrum */
klow = par_getd("problem","klow"); /* in integer units */
khigh = par_getd("problem","khigh"); /* in integer units */
dkx = 2.0*PI/(pGrid->dx1*gnx1); /* convert k from integer */
/* Driven or decaying */
idrive = par_geti("problem","idrive");
if ((idrive < 0) || (idrive > 1)) ath_error("Invalid value for idrive\n");
/* If restarting with decaying turbulence, no driving necessary. */
if ((idrive == 1) && (pGrid->nstep > 0)) {
donedrive = 1;
}
if (donedrive == 0) {
/* Allocate memory for components of velocity perturbation */
if ((dv1=(Real***)calloc_3d_array(nx3gh,nx2gh,nx1gh,sizeof(Real)))==NULL) {
ath_error("[problem]: Error allocating memory for vel pert\n");
}
if ((dv2=(Real***)calloc_3d_array(nx3gh,nx2gh,nx1gh,sizeof(Real)))==NULL) {
ath_error("[problem]: Error allocating memory for vel pert\n");
}
if ((dv3=(Real***)calloc_3d_array(nx3gh,nx2gh,nx1gh,sizeof(Real)))==NULL) {
ath_error("[problem]: Error allocating memory for vel pert\n");
}
}
/* Initialize the FFT plan */
plan = ath_3d_fft_quick_plan(pGrid, pD, NULL, ATH_FFT_BACKWARD);
/* Allocate memory for FFTs */
if (donedrive == 0) {
fv1 = ath_3d_fft_malloc(plan);
fv2 = ath_3d_fft_malloc(plan);
fv3 = ath_3d_fft_malloc(plan);
}
/* Enroll outputs */
dump_history_enroll(hst_dEk,"<dE_K>");
dump_history_enroll(hst_dEb,"<dE_B>");
return;
}
void problem_read_restart(MeshS *pM, FILE *fp)
{
R0 = par_getd_def("problem", "R0",2.0);
Hbc = par_getd_def("problem","Hbc",1);
Mbc = par_getd_def("problem","Mbc",1);
StaticGravPot = grav_pot;
x1GravAcc = grav_acc;
bvals_mhd_fun(&(pM->Domain[0][0]),left_x1,disk_ir);
bvals_mhd_fun(&(pM->Domain[0][0]),right_x1,disk_or);
#ifdef FARGO
OrbitalProfile = Omega;
ShearProfile = Shear;
#endif
// Enroll history functions
//
#ifdef MHD
dump_history_enroll(Br, "<Br>");
dump_history_enroll(Bp, "<Bp>");
dump_history_enroll(Bz, "<Bz>");
dump_history_enroll(Mrp, "<Mrp>");
dump_history_enroll(Trp, "<Trp>");
dump_history_enroll(MdotR1, "<MdotR1>");
dump_history_enroll(MdotR2, "<MdotR2>");
dump_history_enroll(MdotR3, "<MdotR3>");
dump_history_enroll(MdotR4, "<MdotR4>");
dump_history_enroll(Msub, "<Msub>");
dump_history_enroll(Mrpsub, "<Mrpsub>");
dump_history_enroll(Bpsub, "<Bpsub>");
dump_history_enroll(Bzsub, "<Bzsub>");
dump_history_enroll(Pbsub, "<Pbsub>");
#endif
return;
}
void problem(DomainS *pDomain)
{
int i,j,k;
int is,ie,il,iu,js,je,jl,ju,ks,ke,kl,ku;
int nx1,nx2,nx3,myid=0;
Real x1,x2,x3,y1, r;
GridS *pG = pDomain->Grid;
is = pG->is; ie = pG->ie; nx1 = ie-is+1;
js = pG->js; je = pG->je; nx2 = je-js+1;
ks = pG->ks; ke = pG->ke; nx3 = ke-ks+1;
il = is-nghost*(nx1>1); iu = ie+nghost*(nx1>1); nx1 = iu-il+1;
jl = js-nghost*(nx2>1); ju = je+nghost*(nx2>1); nx2 = ju-jl+1;
kl = ks-nghost*(nx3>1); ku = ke+nghost*(nx3>1); nx3 = ku-kl+1;
rho0 = par_getd_def("problem", "rho0", 100.0);
Amp = par_getd_def("problem", "Amp", 1.0e-2);
Beta = par_getd_def("problem", "Beta",100.0);
R0 = par_getd_def("problem", "R0",2.0);
rhomin = par_getd_def("problem","rhomin",1.0e-3);
Field = par_getd_def("problem","Field",0);
Hbc = par_getd_def("problem","Hbc",1);
Mbc = par_getd_def("problem","Mbc",1);
Mc = par_getd_def("problem","Mc",20.0);
srand(SEED + myID_Comm_world);
for (k=kl; k<=ku; k++) {
for (j=jl; j<=ju; j++) {
for (i=il; i<=iu; i++) {
cc_pos(pG,i,j,k,&x1,&x2,&x3);
x1 = x1vc(pG,i);
r = 2.0*rand()/((double)RAND_MAX) - 1.0;
pG->U[k][j][i].d = rho0;
#ifdef FARGO
pG->U[k][j][i].M2 = 0.0;
#else
pG->U[k][j][i].M2 = pG->U[k][j][i].d*avg1d(vphi,pG,i,j,k);
#endif
pG->U[k][j][i].M2 += pG->U[k][j][i].d*Amp*r*Iso_csound*ChiMag(x1);
r = 2.0*rand()/((double)RAND_MAX)-1.0;
pG->U[k][j][i].M1 = 0.0;
pG->U[k][j][i].M3 = pG->U[k][j][i].d*Amp*r*Iso_csound*ChiMag(x1);
#ifdef MHD
pG->U[k][j][i].B1c = 0.0;
if (Field == 2) {
pG->U[k][j][i].B2c = BpNet(x1,x2,x3);
} else {
pG->U[k][j][i].B2c = 0.0;
}
if (Field == 0) {
pG->U[k][j][i].B3c = BzZero(x1,x2,x3);
} else if (Field == 1) {
pG->U[k][j][i].B3c = BzNet(x1,x2,x3);
} else {
pG->U[k][j][i].B3c = 0.0;
}
pG->B1i[k][j][i] = 0.0;
pG->B2i[k][j][i] = pG->U[k][j][i].B2c;
pG->B3i[k][j][i] = pG->U[k][j][i].B3c;
#endif
}
}
}
#ifdef MHD
if (Field != 2) {
ScaleToBeta(pG,Beta);
}
#endif /* MHD */
StaticGravPot = grav_pot;
x1GravAcc = grav_acc;
bvals_mhd_fun(pDomain,left_x1,disk_ir);
bvals_mhd_fun(pDomain,right_x1,disk_or);
#ifdef FARGO
OrbitalProfile = Omega;
ShearProfile = Shear;
#endif
// Enroll history functions
//
#ifdef MHD
dump_history_enroll(Br, "<Br>");
dump_history_enroll(Bp, "<Bp>");
dump_history_enroll(Bz, "<Bz>");
dump_history_enroll(Mrp, "<Mrp>");
dump_history_enroll(Trp, "<Trp>");
dump_history_enroll(MdotR1, "<MdotR1>");
dump_history_enroll(MdotR2, "<MdotR2>");
dump_history_enroll(MdotR3, "<MdotR3>");
dump_history_enroll(MdotR4, "<MdotR4>");
dump_history_enroll(Msub, "<Msub>");
dump_history_enroll(Mrpsub, "<Mrpsub>");
dump_history_enroll(Bpsub, "<Bpsub>");
dump_history_enroll(Bzsub, "<Bzsub>");
dump_history_enroll(Pbsub, "<Pbsub>");
#endif
return;
}
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_read_restart(MeshS *pM, FILE *fp)
{
Real beta, Q, nJ, cs, cs2, Gcons;
/* Read problem parameters. */
Omega_0 = par_getd("problem","omega");
qshear = par_getd("problem","qshear");
/* 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");
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(pM->Nx[2] >1) grav_mean_rho = 1.0;
#endif
/* Set gravity constant*/
four_pi_G = 4.0*PI*Gcons;
#endif /* SELF_GRAVITY */
/* enroll gravitational potential function */
ShearingBoxPot = UnstratifiedDisk;
/* 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
/* should be modified for SMR version */
dVol = 1.0;
if (pM->dx[0] > 0.0) dVol /= pM->dx[0];
if (pM->dx[1] > 0.0) dVol /= pM->dx[1];
if (pM->dx[2] > 0.0) dVol /= pM->dx[2];
return;
}
void problem(DomainS *pDomain)
{
GridS *pGrid = pDomain->Grid;
int i=0,j=0,k=0;
int is,ie,js,je,ks,ke,iprob;
Real amp,drat,vflow,b0,a,sigma,x1,x2,x3;
long int iseed = -1;
static int frst=1; /* flag so new history variables enrolled only once */
is = pGrid->is; ie = pGrid->ie;
js = pGrid->js; je = pGrid->je;
ks = pGrid->ks; ke = pGrid->ke;
/* Read problem parameters */
iprob = par_geti("problem","iprob");
vflow = par_getd("problem","vflow");
drat = par_getd("problem","drat");
amp = par_getd("problem","amp");
#ifdef MHD
b0 = par_getd("problem","b0");
#endif
/* iprob=1. Two uniform streams moving at +/- vflow, random perturbations */
if (iprob == 1) {
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);
pGrid->U[k][j][i].d = 1.0;
pGrid->U[k][j][i].M1 = vflow + amp*(ran2(&iseed) - 0.5);
pGrid->U[k][j][i].M2 = amp*(ran2(&iseed) - 0.5);
pGrid->U[k][j][i].M3 = 0.0;
if (fabs(x2) < 0.25) {
pGrid->U[k][j][i].d = drat;
pGrid->U[k][j][i].M1 = -drat*(vflow + amp*(ran2(&iseed) - 0.5));
pGrid->U[k][j][i].M2 = drat*amp*(ran2(&iseed) - 0.5);
}
/* Pressure scaled to give a sound speed of 1 with gamma=1.4 */
#ifndef BAROTROPIC
pGrid->U[k][j][i].E = 2.5/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))/pGrid->U[k][j][i].d;
#endif /* BAROTROPIC */
#ifdef MHD
pGrid->B1i[k][j][i] = b0;
pGrid->U[k][j][i].B1c = b0;
#ifndef BAROTROPIC
pGrid->U[k][j][i].E += 0.5*b0*b0;
#endif /* BAROTROPIC */
#endif /* MHD */
}
#ifdef MHD
pGrid->B1i[k][j][ie+1] = b0;
#endif
}
}
}
/* iprob=2. Test suggested by E. Zweibel, based on Ryu & Jones.
* Two uniform density flows with single mode perturbation
*/
if (iprob == 2) {
a = 0.05;
sigma = 0.2;
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);
pGrid->U[k][j][i].d = 1.0;
pGrid->U[k][j][i].M1 = vflow*tanh(x2/a);
pGrid->U[k][j][i].M2 = amp*sin(2.0*PI*x1)*exp(-(x2*x2)/(sigma*sigma));
pGrid->U[k][j][i].M3 = 0.0;
#ifndef BAROTROPIC
pGrid->U[k][j][i].E = 1.0/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))/pGrid->U[k][j][i].d;
#endif /* BAROTROPIC */
#ifdef MHD
pGrid->B1i[k][j][i] = b0;
pGrid->U[k][j][i].B1c = b0;
#ifndef BAROTROPIC
pGrid->U[k][j][i].E += 0.5*b0*b0;
#endif /* BAROTROPIC */
#endif /* MHD */
/* Use passive scalar to keep track of the fluids, since densities are same */
#if (NSCALARS > 0)
pGrid->U[k][j][i].s[0] = 0.0;
if (x2 > 0) pGrid->U[k][j][i].s[0] = 1.0;
#endif
}
#ifdef MHD
pGrid->B1i[k][j][ie+1] = b0;
#endif
}
}
}
/* iprob=3. Test in SR paper, based on iprob=2
*/
if (iprob == 3) {
a = 0.01;
sigma = 0.1;
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);
pGrid->U[k][j][i].d = 0.505 + 0.495*tanh((fabs(x2)-0.5)/a);
pGrid->U[k][j][i].M1 = vflow*tanh((fabs(x2)-0.5)/a);
pGrid->U[k][j][i].M2 = amp*vflow*sin(2.0*PI*x1)
*exp(-((fabs(x2)-0.5)*(fabs(x2)-0.5))/(sigma*sigma));
if (x2 < 0.0) pGrid->U[k][j][i].M2 *= -1.0;
pGrid->U[k][j][i].M1 *= pGrid->U[k][j][i].d;
pGrid->U[k][j][i].M2 *= pGrid->U[k][j][i].d;
pGrid->U[k][j][i].M3 = 0.0;
#ifndef BAROTROPIC
pGrid->U[k][j][i].E = 1.0/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))/pGrid->U[k][j][i].d;
#endif /* BAROTROPIC */
#ifdef MHD
pGrid->B1i[k][j][i] = b0;
pGrid->U[k][j][i].B1c = b0;
#ifndef BAROTROPIC
pGrid->U[k][j][i].E += 0.5*b0*b0;
#endif /* BAROTROPIC */
#endif /* MHD */
}
#ifdef MHD
pGrid->B1i[k][j][ie+1] = b0;
#endif
}
}
}
/* With viscosity and/or resistivity, read diffusion coeffs */
#ifdef RESISTIVITY
eta_Ohm = par_getd_def("problem","eta_O",0.0);
Q_Hall = par_getd_def("problem","Q_H",0.0);
Q_AD = par_getd_def("problem","Q_AD",0.0);
#endif
#ifdef VISCOSITY
nu_iso = par_getd_def("problem","nu_iso",0.0);
nu_aniso = par_getd_def("problem","nu_aniso",0.0);
#endif
/* enroll new history variables, only once */
if (frst == 1) {
#ifdef MHD
dump_history_enroll(hst_Bx, "<Bx>");
dump_history_enroll(hst_By, "<By>");
dump_history_enroll(hst_Bz, "<Bz>");
#endif /* MHD */
frst = 0;
}
}
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;
}