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(DomainS *pDomain)
{
GridS *pGrid=(pDomain->Grid);
int i,il,iu,j,jl,ju,k,kl,ku;
int is,ie,js,je,ks,ke,nx1,nx2,nx3;
int shk_dir; /* Shock direction: {1,2,3} -> {x1,x2,x3} */
Real ang_2, ang_3; /* Rotation angles about the y and z' axis */
Real sin_a2, cos_a2, sin_a3, cos_a3;
Real x1,x2,x3;
Prim1DS Wl, Wr;
Cons1DS U1d, Ul, Ur;
Real Bxl=0.0, Bxr=0.0, Bxb=0.0;
/* speeds of shock, contact, head and foot of rarefaction for Sod test */
/* speeds of slow/fast shocks, Alfven wave and contact in RJ2a test */
Real tlim;
int err_test;
Real r,xs,xc,xf,xh,vs,vc,vf,vh;
Real xfp,xrp,xsp,xsm,xrm,xfm,vfp,vrp,vsp,vsm,vrm,vfm;
Real d0,v0,Mx,My,Mz,E0,r0,Bx,By,Bz;
#if (NSCALARS > 0)
int n;
#endif
is = pGrid->is; ie = pGrid->ie;
js = pGrid->js; je = pGrid->je;
ks = pGrid->ks; ke = pGrid->ke;
nx1 = (ie-is)+1 + 2*nghost;
nx2 = (je-js)+1 + 2*nghost;
nx3 = (ke-ks)+1 + 2*nghost;
printf("here1\n");
if (pDomain->Level == 0){
if ((RootSoln = (ConsS***)calloc_3d_array(nx3,nx2,nx1,sizeof(ConsS)))
== NULL) ath_error("[problem]: Error alloc memory for RootSoln\n");
}
/* Parse left state read from input file: dl,pl,ul,vl,wl,bxl,byl,bzl */
Wl.d = par_getd("problem","dl");
#ifdef ADIABATIC
Wl.P = par_getd("problem","pl");
#endif
Wl.Vx = par_getd("problem","v1l");
Wl.Vy = par_getd("problem","v2l");
Wl.Vz = par_getd("problem","v3l");
#ifdef MHD
Bxl = par_getd("problem","b1l");
Wl.By = par_getd("problem","b2l");
Wl.Bz = par_getd("problem","b3l");
#endif
#if (NSCALARS > 0)
Wl.r[0] = par_getd("problem","r0l");
#endif
/* Parse right state read from input file: dr,pr,ur,vr,wr,bxr,byr,bzr */
Wr.d = par_getd("problem","dr");
#ifdef ADIABATIC
Wr.P = par_getd("problem","pr");
#endif
Wr.Vx = par_getd("problem","v1r");
Wr.Vy = par_getd("problem","v2r");
Wr.Vz = par_getd("problem","v3r");
#ifdef MHD
Bxr = par_getd("problem","b1r");
Wr.By = par_getd("problem","b2r");
Wr.Bz = par_getd("problem","b3r");
if (Bxr != Bxl) ath_error(0,"[shkset1d] L/R values of Bx not the same\n");
#endif
#if (NSCALARS > 0)
Wr.r[0] = par_getd("problem","r0r");
#endif
printf("here2\n");
#ifdef SAC_INTEGRATOR
Ul = Prim1D_to_Cons1D(&Wl, &Bxl,&Bxb);
Ur = Prim1D_to_Cons1D(&Wr, &Bxr,&Bxb);
#elif defined SMAUG_INTEGRATOR
Ul = Prim1D_to_Cons1D(&Wl, &Bxl,&Bxb);
Ur = Prim1D_to_Cons1D(&Wr, &Bxr,&Bxb);
#else
Ul = Prim1D_to_Cons1D(&Wl, &Bxl);
Ur = Prim1D_to_Cons1D(&Wr, &Bxr);
#endif
printf("here3\n");
/* Parse shock direction */
shk_dir = par_geti("problem","shk_dir");
if (shk_dir != 1 && shk_dir != 2 && shk_dir != 3) {
ath_error("[problem]: shk_dir = %d must be either 1,2 or 3\n",shk_dir);
}
/* Set up the index bounds for initializing the grid */
iu = pGrid->ie + nghost;
il = pGrid->is - nghost;
if (pGrid->Nx[1] > 1) {
ju = pGrid->je + nghost;
jl = pGrid->js - nghost;
}
else {
ju = pGrid->je;
jl = pGrid->js;
}
if (pGrid->Nx[2] > 1) {
ku = pGrid->ke + nghost;
kl = pGrid->ks - nghost;
}
else {
ku = pGrid->ke;
kl = pGrid->ks;
}
printf("here4\n");
/* Initialize the grid including the ghost cells. Discontinuity is always
* located at x=0, so xmin/xmax in input file must be set appropriately. */
switch(shk_dir) {
/*--- shock in 1-direction ---------------------------------------------------*/
case 1: /* shock in 1-direction */
ang_2 = 0.0;
ang_3 = 0.0;
for (k=kl; k<=ku; k++) {
for (j=jl; j<=ju; j++) {
for (i=il; i<=iu; i++) {
cc_pos(pGrid, i, j, k, &x1, &x2, &x3);
/* set primitive and conserved variables to be L or R state */
if (x1 <= 0.0) {
U1d = Ul;
} else {
U1d = Ur;
}
/* Initialize conserved (and with SR the primitive) variables in Grid */
pGrid->U[k][j][i].d = U1d.d;
pGrid->U[k][j][i].M1 = U1d.Mx;
pGrid->U[k][j][i].M2 = U1d.My;
pGrid->U[k][j][i].M3 = U1d.Mz;
#ifdef MHD
pGrid->B1i[k][j][i] = Bxl;
pGrid->B2i[k][j][i] = U1d.By;
pGrid->B3i[k][j][i] = U1d.Bz;
pGrid->U[k][j][i].B1c = Bxl;
pGrid->U[k][j][i].B2c = U1d.By;
pGrid->U[k][j][i].B3c = U1d.Bz;
#endif
#ifdef ADIABATIC
pGrid->U[k][j][i].E = U1d.E;
#endif
#if (NSCALARS > 0)
pGrid->U[k][j][i].s[0] = U1d.s[0];
#endif
}
}
}
break;
/*--- shock in 2-direction ---------------------------------------------------*/
case 2: /* shock in 2-direction */
ang_2 = 0.0;
ang_3 = PI/2.0;
for (k=kl; k<=ku; k++) {
for (j=jl; j<=ju; j++) {
for (i=il; i<=iu; i++) {
cc_pos(pGrid, i, j, k, &x1, &x2, &x3);
/* set primitive variables to be L or R state */
if (x2 <= 0.0) {
U1d = Ul;
} else {
U1d = Ur;
}
/* Initialize conserved (and with SR the primitive) variables in Grid */
pGrid->U[k][j][i].d = U1d.d;
pGrid->U[k][j][i].M1 = -U1d.My;
pGrid->U[k][j][i].M2 = U1d.Mx;
pGrid->U[k][j][i].M3 = U1d.Mz;
#ifdef MHD
pGrid->B1i[k][j][i] = -U1d.By;
pGrid->B2i[k][j][i] = Bxl;
pGrid->B3i[k][j][i] = U1d.Bz;
pGrid->U[k][j][i].B1c = -U1d.By;
pGrid->U[k][j][i].B2c = Bxl;
pGrid->U[k][j][i].B3c = U1d.Bz;
#endif
#ifdef ADIABATIC
pGrid->U[k][j][i].E = U1d.E;
#endif
#if (NSCALARS > 0)
pGrid->U[k][j][i].s[0] = U1d.s[0];
#endif
}
}
}
break;
/*--- shock in 3-direction ---------------------------------------------------*/
case 3: /* shock in 3-direction */
ang_2 = PI/2.0;
ang_3 = 0.0;
for (k=kl; k<=ku; k++) {
for (j=jl; j<=ju; j++) {
for (i=il; i<=iu; i++) {
cc_pos(pGrid, i, j, k, &x1, &x2, &x3);
/* set primitive variables to be L or R state */
if (x3 <= 0.0) {
U1d = Ul;
} else {
U1d = Ur;
}
/* Initialize conserved (and with SR the primitive) variables in Grid */
pGrid->U[k][j][i].d = U1d.d;
pGrid->U[k][j][i].M1 = -U1d.Mz;
pGrid->U[k][j][i].M2 = U1d.My;
pGrid->U[k][j][i].M3 = U1d.Mx;
#ifdef MHD
pGrid->B1i[k][j][i] = -U1d.Bz;
pGrid->B2i[k][j][i] = U1d.By;
pGrid->B3i[k][j][i] = Bxl;
pGrid->U[k][j][i].B1c = -U1d.Bz;
pGrid->U[k][j][i].B2c = U1d.By;
pGrid->U[k][j][i].B3c = Bxl;
#endif
#ifdef ADIABATIC
pGrid->U[k][j][i].E = U1d.E;
#endif
#if (NSCALARS > 0)
pGrid->U[k][j][i].s[0] = U1d.s[0];
#endif
}
}
}
break;
default:
ath_error("[shkset1d]: invalid shk_dir = %i\n",shk_dir);
}
/* Compute Analytic solution for Sod and RJ4a tests, if required */
tlim = par_getd("time","tlim");
err_test = par_getd_def("problem","error_test",0);
if (err_test == 1) {
sin_a3 = sin(ang_3);
cos_a3 = cos(ang_3);
sin_a2 = sin(ang_2);
cos_a2 = cos(ang_2);
/* wave speeds for Sod test */
#ifdef HYDRO
vs = 1.7522; xs = vs*tlim;
vc = 0.92745; xc = vc*tlim;
vf = -0.07027; xf = vf*tlim;
vh = -1.1832; xh = vh*tlim;
#endif /* HYDRO */
/* wave speeds for RJ2a test */
#ifdef MHD
vfp = 2.2638; xfp = vfp*tlim;
vrp = (0.53432 + 1.0/sqrt(PI*1.309)); xrp = vrp*tlim;
vsp = (0.53432 + 0.48144/1.309); xsp = vsp*tlim;
vc = 0.57538; xc = vc*tlim;
vsm = (0.60588 - 0.51594/1.4903); xsm = vsm*tlim;
vrm = (0.60588 - 1.0/sqrt(PI*1.4903)); xrm = vrm*tlim;
vfm = (1.2 - 2.3305/1.08); xfm = vfm*tlim;
#endif /* MHD */
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);
r = cos_a2*(x1*cos_a3 + x2*sin_a3) + x3*sin_a2;
/* Sod solution */
#ifdef HYDRO
My = Mz = 0.0;
if (r > xs) {
d0 = 0.125;
Mx = 0.0;
E0 = 0.25;
r0 = 0.0;
} else if (r > xc) {
d0 = 0.26557;
Mx = 0.92745*d0;
E0 = 0.87204;
r0 = 0.0;
} else if (r > xf) {
d0 = 0.42632;
Mx = 0.92745*d0;
E0 = 0.94118;
r0 = 1.0;
} else if (r > xh) {
v0 = 0.92745*(r-xh)/(xf-xh);
d0 = 0.42632*pow((1.0+0.20046*(0.92745-v0)),5);
E0 = (0.30313*pow((1.0+0.20046*(0.92745-v0)),7))/0.4 + 0.5*d0*v0*v0;
r0 = 1.0;
Mx = v0*d0;
} else {
d0 = 1.0;
Mx = 0.0;
E0 = 2.5;
r0 = 1.0;
}
#endif /* HYDRO */
/* RJ2a solution (Dai & Woodward 1994 Tables Ia and Ib) */
#ifdef MHD
Bx = 2.0/sqrt(4.0*PI);
if (r > xfp) {
d0 = 1.0;
Mx = 0.0;
My = 0.0;
Mz = 0.0;
By = 4.0/sqrt(4.0*PI);
Bz = 2.0/sqrt(4.0*PI);
E0 = 1.0/Gamma_1 + 0.5*((Mx*Mx+My*My+Mz*Mz)/d0 + (Bx*Bx+By*By+Bz*Bz));
r0 = 0.0;
} else if (r > xrp) {
d0 = 1.3090;
Mx = 0.53432*d0;
My = -0.094572*d0;
Mz = -0.047286*d0;
By = 5.3452/sqrt(4.0*PI);
Bz = 2.6726/sqrt(4.0*PI);
E0 = 1.5844/Gamma_1 + 0.5*((Mx*Mx+My*My+Mz*Mz)/d0 + (Bx*Bx+By*By+Bz*Bz));
r0 = 0.0;
} else if (r > xsp) {
d0 = 1.3090;
Mx = 0.53432*d0;
My = -0.18411*d0;
Mz = 0.17554*d0;
By = 5.7083/sqrt(4.0*PI);
Bz = 1.7689/sqrt(4.0*PI);
E0 = 1.5844/Gamma_1 + 0.5*((Mx*Mx+My*My+Mz*Mz)/d0 + (Bx*Bx+By*By+Bz*Bz));
r0 = 0.0;
} else if (r > xc) {
d0 = 1.4735;
Mx = 0.57538*d0;
My = 0.047601*d0;
Mz = 0.24734*d0;
By = 5.0074/sqrt(4.0*PI);
Bz = 1.5517/sqrt(4.0*PI);
E0 = 1.9317/Gamma_1 + 0.5*((Mx*Mx+My*My+Mz*Mz)/d0 + (Bx*Bx+By*By+Bz*Bz));
r0 = 0.0;
} else if (r > xsm) {
d0 = 1.6343;
Mx = 0.57538*d0;
My = 0.047601*d0;
Mz = 0.24734*d0;
By = 5.0074/sqrt(4.0*PI);
Bz = 1.5517/sqrt(4.0*PI);
E0 = 1.9317/Gamma_1 + 0.5*((Mx*Mx+My*My+Mz*Mz)/d0 + (Bx*Bx+By*By+Bz*Bz));
r0 = 1.0;
} else if (r > xrm) {
d0 = 1.4903;
Mx = 0.60588*d0;
My = 0.22157*d0;
Mz = 0.30125*d0;
By = 5.5713/sqrt(4.0*PI);
Bz = 1.7264/sqrt(4.0*PI);
E0 = 1.6558/Gamma_1 + 0.5*((Mx*Mx+My*My+Mz*Mz)/d0 + (Bx*Bx+By*By+Bz*Bz));
r0 = 1.0;
} else if (r > xfm) {
d0 = 1.4903;
Mx = 0.60588*d0;
My = 0.11235*d0;
Mz = 0.55686*d0;
By = 5.0987/sqrt(4.0*PI);
Bz = 2.8326/sqrt(4.0*PI);
E0 = 1.6558/Gamma_1 + 0.5*((Mx*Mx+My*My+Mz*Mz)/d0 + (Bx*Bx+By*By+Bz*Bz));
r0 = 1.0;
} else {
d0 = 1.08;
Mx = 1.2*d0;
My = 0.01*d0;
Mz = 0.5*d0;
By = 3.6/sqrt(4.0*PI);
Bz = 2.0/sqrt(4.0*PI);
E0 = 0.95/Gamma_1 + 0.5*((Mx*Mx+My*My+Mz*Mz)/d0 + (Bx*Bx+By*By+Bz*Bz));
r0 = 1.0;
}
#endif /* MHD */
RootSoln[k][j][i].d = d0;
RootSoln[k][j][i].M1 = Mx*cos_a2*cos_a3 - My*sin_a3 - Mz*sin_a2*cos_a3;
RootSoln[k][j][i].M2 = Mx*cos_a2*sin_a3 + My*cos_a3 - Mz*sin_a2*sin_a3;
RootSoln[k][j][i].M3 = Mx*sin_a2 + Mz*cos_a2;
#ifdef MHD
RootSoln[k][j][i].B1c = Bx*cos_a2*cos_a3 - By*sin_a3 - Bz*sin_a2*cos_a3;
RootSoln[k][j][i].B2c = Bx*cos_a2*sin_a3 + By*cos_a3 - Bz*sin_a2*sin_a3;
RootSoln[k][j][i].B3c = Bx*sin_a2 + Bz*cos_a2;
#endif /* MHD */
#ifndef ISOTHERMAL
RootSoln[k][j][i].E = E0;
#endif /* ISOTHERMAL */
#if (NSCALARS > 0)
for (n=0; n<NSCALARS; n++) RootSoln[k][j][i].s[n] = r0*d0;
#endif
}
}}
} /* end calculation of analytic (root) solution */
return;
}
/* problem: */
void problem(DomainS *pDomain)
{
GridS *pG = pDomain->Grid;
int i,j,k,n,converged;
int is,ie,il,iu,js,je,jl,ju,ks,ke,kl,ku;
int nx1, nx2, nx3;
Real x1, x2, x3;
Real a,b,c,d,xmin,xmax,ymin,ymax;
Real x,y,xslow,yslow,xfast,yfast;
Real R0,R1,R2,rho,Mdot,K,Omega,Pgas,beta,vR,BR,vphi,Bphi;
ConsS *Wind=NULL;
Real *pU=NULL,*pUl=NULL,*pUr=NULL;
Real lsf,rsf;
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;
#ifndef CYLINDRICAL
ath_error("[cylwindrotb]: This problem only works in cylindrical!\n");
#endif
#ifndef MHD
ath_error("[cylwindrotb]: This problem only works in MHD!\n");
#endif
if (nx1==1) {
ath_error("[cylwindrotb]: Only R can be used in 1D!\n");
}
else if (nx2==1 && nx3>1) {
ath_error("[cylwindrotb]: Only (R,phi) can be used in 2D!\n");
}
/* Allocate memory for wind solution */
if ((Wind = (ConsS*)calloc_1d_array(nx1+1,sizeof(ConsS))) == NULL)
ath_error("[cylwindrotb]: Error allocating memory\n");
/* Allocate memory for grid solution */
if ((RootSoln = (ConsS***)calloc_3d_array(nx3,nx2,nx1,sizeof(ConsS))) == NULL)
ath_error("[cylwindrotb]: Error allocating memory\n");
theta = par_getd("problem","theta");
omega = par_getd("problem","omega");
vz = par_getd("problem","vz");
/* This numerical solution was obtained from MATLAB.
* Ideally, we replace this with a nonlinear solver... */
xslow = 0.5243264128;
yslow = 2.4985859152;
xfast = 1.6383327831;
yfast = 0.5373957134;
E = 7.8744739104;
eta = 2.3608500383;
xmin = par_getd("domain1","x1min")/R_A;
xmax = par_getd("domain1","x1max")/R_A;
ymin = 0.45/rho_A;
ymax = 2.6/rho_A;
printf("theta = %f,\t omega = %f,\t eta = %f,\t E = %f\n", theta,omega,eta,E);
printf("xslow = %f,\t yslow = %f,\t xfast = %f,\t yfast = %f\n", xslow,yslow,xfast,yfast);
printf("xmin = %f,\t ymin = %f,\t xmax = %f,\t ymax = %f\n", xmin,ymin,xmax,ymax);
/* Calculate the 1D wind solution at cell-interfaces */
for (i=il; i<=iu+1; i++) {
memset(&(Wind[i]),0.0,sizeof(ConsS));
cc_pos(pG,i,js,ks,&x1,&x2,&x3);
/* Want the solution at R-interfaces */
R0 = x1 - 0.5*pG->dx1;
x = R0/R_A;
/* Look for a sign change interval */
if (x < xslow) {
sign_change(myfunc,yslow,10.0*ymax,x,&a,&b);
sign_change(myfunc,b,10.0*ymax,x,&a,&b);
} else if (x < 1.0) {
sign_change(myfunc,1.0+TINY_NUMBER,yslow,x,&a,&b);
} else if (x < xfast) {
sign_change(myfunc,yfast,1.0-TINY_NUMBER,x,&a,&b);
if (!sign_change(myfunc,b,1.0-TINY_NUMBER,x,&a,&b)) {
a = yfast;
b = 1.0-TINY_NUMBER;
}
} else {
sign_change(myfunc,0.5*ymin,yfast,x,&a,&b);
}
/* Use bisection to find the root */
converged = bisection(myfunc,a,b,x,&y);
if(!converged) {
ath_error("[cylwindrotb]: Bisection did not converge!\n");
}
/* Construct the solution */
rho = rho_A*y;
Mdot = sqrt(R_A*SQR(rho_A)*GM*eta);
Omega = sqrt((GM*omega)/pow(R_A,3));
K = (GM*theta)/(Gamma*pow(rho_A,Gamma_1)*R_A);
Pgas = K*pow(rho,Gamma);
vR = Mdot/(R0*rho);
beta = sqrt(1.0/rho_A);
BR = beta*rho*vR;
vphi = R0*Omega*(1.0/SQR(x)-y)/(1.0-y);
Bphi = beta*rho*(vphi-R0*Omega);
Wind[i].d = rho;
Wind[i].M1 = rho*vR;
Wind[i].M2 = rho*vphi;
Wind[i].M3 = rho*vz;
Wind[i].B1c = BR;
Wind[i].B2c = Bphi;
Wind[i].B3c = 0.0;
Wind[i].E = Pgas/Gamma_1
+ 0.5*(SQR(Wind[i].B1c) + SQR(Wind[i].B2c) + SQR(Wind[i].B3c))
+ 0.5*(SQR(Wind[i].M1 ) + SQR(Wind[i].M2 ) + SQR(Wind[i].M3 ))/Wind[i].d;
}
/* Average the wind solution across the zone for cc variables */
for (i=il; i<=iu; i++) {
memset(&(pG->U[ks][js][i]),0.0,sizeof(ConsS));
cc_pos(pG,i,js,ks,&x1,&x2,&x3);
lsf = (x1 - 0.5*pG->dx1)/x1;
rsf = (x1 + 0.5*pG->dx1)/x1;
pU = (Real*)&(pG->U[ks][js][i]);
pUl = (Real*)&(Wind[i]);
pUr = (Real*)&(Wind[i+1]);
for (n=0; n<NWAVE; n++) {
pU[n] = 0.5*(lsf*pUl[n] + rsf*pUr[n]);
}
pG->B1i[ks][js][i] = Wind[i].B1c;
pG->B2i[ks][js][i] = 0.5*(lsf*Wind[i].B2c + rsf*Wind[i+1].B2c);
pG->B3i[ks][js][i] = 0.5*(lsf*Wind[i].B3c + rsf*Wind[i+1].B3c);
}
/* Copy 1D solution across the grid and save */
for (k=kl; k<=ku; k++) {
for (j=jl; j<=ju; j++) {
for (i=il; i<=iu; i++) {
pG->U[k][j][i] = pG->U[ks][js][i];
pG->B1i[k][j][i] = pG->B1i[ks][js][i];
pG->B2i[k][j][i] = pG->B2i[ks][js][i];
pG->B3i[k][j][i] = pG->B3i[ks][js][i];
RootSoln[k][j][i] = pG->U[ks][js][i];
}
}
}
StaticGravPot = grav_pot;
bvals_mhd_fun(pDomain,left_x1,do_nothing_bc);
bvals_mhd_fun(pDomain,right_x1,do_nothing_bc);
free_1d_array((void *)Wind);
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 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 dump_binary(MeshS *pM, OutputS *pOut)
{
GridS *pGrid;
PrimS ***W;
FILE *p_binfile;
char *fname,*plev=NULL,*pdom=NULL;
char levstr[8],domstr[8];
int n,ndata[7];
/* Upper and Lower bounds on i,j,k for data dump */
int i,j,k,il,iu,jl,ju,kl,ku,nl,nd;
Real dat[2],*datax,*datay,*dataz;
Real *pData,x1,x2,x3;
int coordsys = -1;
/* Loop over all Domains in Mesh, and output Grid data */
for (nl=0; nl<(pM->NLevels); nl++){
for (nd=0; nd<(pM->DomainsPerLevel[nl]); nd++){
if (pM->Domain[nl][nd].Grid != NULL){
/* write files if domain and level match input, or are not specified (-1) */
if ((pOut->nlevel == -1 || pOut->nlevel == nl) &&
(pOut->ndomain == -1 || pOut->ndomain == nd)){
pGrid = pM->Domain[nl][nd].Grid;
il = pGrid->is, iu = pGrid->ie;
jl = pGrid->js, ju = pGrid->je;
kl = pGrid->ks, ku = pGrid->ke;
#ifdef WRITE_GHOST_CELLS
il = pGrid->is - nghost;
iu = pGrid->ie + nghost;
if(pGrid->Nx[1] > 1){
jl = pGrid->js - nghost;
ju = pGrid->je + nghost;
}
if(pGrid->Nx[2] > 1){
kl = pGrid->ks - nghost;
ku = pGrid->ke + nghost;
}
#endif /* WRITE_GHOST_CELLS */
ndata[0] = iu-il+1;
ndata[1] = ju-jl+1;
ndata[2] = ku-kl+1;
/* calculate primitive variables, if needed */
if(strcmp(pOut->out,"prim") == 0) {
if((W = (PrimS***)
calloc_3d_array(ndata[2],ndata[1],ndata[0],sizeof(PrimS))) == NULL)
ath_error("[dump_bin]: failed to allocate Prim array\n");
for (k=kl; k<=ku; k++) {
for (j=jl; j<=ju; j++) {
for (i=il; i<=iu; i++) {
W[k-kl][j-jl][i-il] = Cons_to_Prim(&(pGrid->U[k][j][i]));
}}}
}
/* construct filename, open file */
if (nl>0) {
plev = &levstr[0];
sprintf(plev,"lev%d",nl);
}
if (nd>0) {
pdom = &domstr[0];
sprintf(pdom,"dom%d",nd);
}
if((fname = ath_fname(plev,pM->outfilename,plev,pdom,num_digit,
pOut->num,NULL,"bin")) == NULL){
ath_error("[dump_binary]: Error constructing filename\n");
}
if((p_binfile = fopen(fname,"wb")) == NULL){
ath_error("[dump_binary]: Unable to open binary dump file\n");
return;
}
free(fname);
/* Write the coordinate system information */
#if defined CARTESIAN
coordsys = -1;
#elif defined CYLINDRICAL
coordsys = -2;
#elif defined SPHERICAL
coordsys = -3;
#endif
fwrite(&coordsys,sizeof(int),1,p_binfile);
/* Write number of zones and variables */
ndata[3] = NVAR;
ndata[4] = NSCALARS;
#ifdef SELF_GRAVITY
ndata[5] = 1;
#else
ndata[5] = 0;
#endif
#ifdef PARTICLES
ndata[6] = 1;
#else
ndata[6] = 0;
#endif
fwrite(ndata,sizeof(int),7,p_binfile);
/* Write (gamma-1) and isothermal sound speed */
#ifdef ISOTHERMAL
dat[0] = (Real)0.0;
dat[1] = (Real)Iso_csound;
#elif defined ADIABATIC
dat[0] = (Real)Gamma_1 ;
dat[1] = (Real)0.0;
#else
dat[0] = dat[1] = 0.0; /* Anything better to put here? */
#endif
fwrite(dat,sizeof(Real),2,p_binfile);
/* Write time, dt */
dat[0] = (Real)pGrid->time;
dat[1] = (Real)pGrid->dt;
fwrite(dat,sizeof(Real),2,p_binfile);
/* Allocate Memory */
if((datax = (Real *)malloc(ndata[0]*sizeof(Real))) == NULL){
ath_error("[dump_binary]: malloc failed for temporary array\n");
return;
}
if((datay = (Real *)malloc(ndata[1]*sizeof(Real))) == NULL){
ath_error("[dump_binary]: malloc failed for temporary array\n");
return;
}
if((dataz = (Real *)malloc(ndata[2]*sizeof(Real))) == NULL){
ath_error("[dump_binary]: malloc failed for temporary array\n");
return;
}
/* compute x,y,z coordinates of cell centers, and write out */
for (i=il; i<=iu; i++) {
cc_pos(pGrid,i,jl,kl,&x1,&x2,&x3);
pData = ((Real *) &(x1));
datax[i-il] = (Real)(*pData);
}
fwrite(datax,sizeof(Real),(size_t)ndata[0],p_binfile);
for (j=jl; j<=ju; j++) {
cc_pos(pGrid,il,j,kl,&x1,&x2,&x3);
pData = ((Real *) &(x2));
datay[j-jl] = (Real)(*pData);
}
fwrite(datay,sizeof(Real),(size_t)ndata[1],p_binfile);
for (k=kl; k<=ku; k++) {
cc_pos(pGrid,il,jl,k,&x1,&x2,&x3);
pData = ((Real *) &(x3));
dataz[k-kl] = (Real)(*pData);
}
fwrite(dataz,sizeof(Real),(size_t)ndata[2],p_binfile);
/* Write cell-centered data (either conserved or primitives) */
for (n=0;n<NVAR; n++) {
for (k=0; k<ndata[2]; k++) {
for (j=0; j<ndata[1]; j++) {
for (i=0; i<ndata[0]; i++) {
if (strcmp(pOut->out,"cons") == 0){
pData = ((Real*)&(pGrid->U[k+kl][j+jl][i+il])) + n;
} else if(strcmp(pOut->out,"prim") == 0) {
pData = ((Real*)&(W[k][j][i])) + n;
}
datax[i] = (Real)(*pData);
}
fwrite(datax,sizeof(Real),(size_t)ndata[0],p_binfile);
}}
}
#ifdef SELF_GRAVITY
for (k=0; k<ndata[2]; k++) {
for (j=0; j<ndata[1]; j++) {
for (i=0; i<ndata[0]; i++) {
pData = &(pGrid->Phi[k+kl][j+jl][i+il]);
datax[i] = (Real)(*pData);
}
fwrite(datax,sizeof(Real),(size_t)ndata[0],p_binfile);
}}
#endif
#ifdef PARTICLES
if (pOut->out_pargrid) {
for (k=0; k<ndata[2]; k++) {
for (j=0; j<ndata[1]; j++) {
for (i=0; i<ndata[0]; i++) {
datax[i] = pGrid->Coup[k+kl][j+jl][i+il].grid_d;
}
fwrite(datax,sizeof(Real),(size_t)ndata[0],p_binfile);
}}
for (k=0; k<ndata[2]; k++) {
for (j=0; j<ndata[1]; j++) {
for (i=0; i<ndata[0]; i++) {
datax[i] = pGrid->Coup[k+kl][j+jl][i+il].grid_v1;
}
fwrite(datax,sizeof(Real),(size_t)ndata[0],p_binfile);
}}
for (k=0; k<ndata[2]; k++) {
for (j=0; j<ndata[1]; j++) {
for (i=0; i<ndata[0]; i++) {
datax[i] = pGrid->Coup[k+kl][j+jl][i+il].grid_v2;
}
fwrite(datax,sizeof(Real),(size_t)ndata[0],p_binfile);
}}
for (k=0; k<ndata[2]; k++) {
for (j=0; j<ndata[1]; j++) {
for (i=0; i<ndata[0]; i++) {
datax[i] = pGrid->Coup[k+kl][j+jl][i+il].grid_v3;
}
fwrite(datax,sizeof(Real),(size_t)ndata[0],p_binfile);
}}
}
#endif
/* close file and free memory */
fclose(p_binfile);
free(datax);
free(datay);
free(dataz);
if(strcmp(pOut->out,"prim") == 0) free_3d_array(W);
}}
}
}
}
void problem(DomainS *pDomain)
{
GridS *pGrid = pDomain->Grid;
int i=0,j=0,k=0;
int is,ie,js,je,ks,ke,nx1,nx2,nx3,iprob;
Real x1c,x2c,x3c,x1f,x2f,x3f; /* cell- and face-centered coordinates */
Real x1size,x2size,x3size,lambda=0.0,ang_2=0.0,sin_a2=0.0,cos_a2=1.0,x,y;
Real rad,amp,vflow,drat,diag;
Real ***az,***ay,***ax;
#ifdef MHD
int ku;
#endif
#if (NSCALARS > 0)
int n;
#endif
is = pGrid->is; ie = pGrid->ie;
js = pGrid->js; je = pGrid->je;
ks = pGrid->ks; ke = pGrid->ke;
nx1 = (ie-is)+1 + 2*nghost;
nx2 = (je-js)+1 + 2*nghost;
nx3 = (ke-ks)+1 + 2*nghost;
if (((je-js) == 0)) {
ath_error("[field_loop]: This problem can only be run in 2D or 3D\n");
}
if ((ay = (Real***)calloc_3d_array(nx3, nx2, nx1, sizeof(Real))) == NULL) {
ath_error("[field_loop]: Error allocating memory for vector pot\n");
}
if ((az = (Real***)calloc_3d_array(nx3, nx2, nx1, sizeof(Real))) == NULL) {
ath_error("[field_loop]: Error allocating memory for vector pot\n");
}
if ((ax = (Real***)calloc_3d_array(nx3, nx2, nx1, sizeof(Real))) == NULL) {
ath_error("[field_loop]: Error allocating memory for vector pot\n");
}
/* Read initial conditions, diffusion coefficients (if needed) */
rad = par_getd("problem","rad");
amp = par_getd("problem","amp");
vflow = par_getd("problem","vflow");
drat = par_getd_def("problem","drat",1.0);
iprob = par_getd("problem","iprob");
#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 THERMAL_CONDUCTION
kappa_iso = par_getd_def("problem","kappa_iso",0.0);
kappa_aniso = par_getd_def("problem","kappa_aniso",0.0);
#endif
/* For (iprob=4) -- rotated cylinder in 3D -- set up rotation angle and
* wavelength of cylinder */
if(iprob == 4){
x1size = pDomain->RootMaxX[0] - pDomain->RootMinX[0];
x3size = pDomain->RootMaxX[2] - pDomain->RootMinX[2];
/* We put 1 wavelength in each direction. Hence the wavelength
* lambda = x1size*cos_a;
* AND lambda = x3size*sin_a;
* are both satisfied. */
if(x1size == x3size){
ang_2 = PI/4.0;
cos_a2 = sin_a2 = sqrt(0.5);
}
else{
ang_2 = atan(x1size/x3size);
sin_a2 = sin(ang_2);
cos_a2 = cos(ang_2);
}
/* Use the larger angle to determine the wavelength */
if (cos_a2 >= sin_a2) {
lambda = x1size*cos_a2;
} else {
lambda = x3size*sin_a2;
}
}
/* Use vector potential to initialize field loop */
for (k=ks; k<=ke+1; k++) {
for (j=js; j<=je+1; j++) {
for (i=is; i<=ie+1; i++) {
cc_pos(pGrid,i,j,k,&x1c,&x2c,&x3c);
x1f = x1c - 0.5*pGrid->dx1;
x2f = x2c - 0.5*pGrid->dx2;
x3f = x3c - 0.5*pGrid->dx3;
/* (iprob=1): field loop in x1-x2 plane (cylinder in 3D) */
if(iprob==1) {
ax[k][j][i] = 0.0;
ay[k][j][i] = 0.0;
if ((x1f*x1f + x2f*x2f) < rad*rad) {
az[k][j][i] = amp*(rad - sqrt(x1f*x1f + x2f*x2f));
} else {
az[k][j][i] = 0.0;
}
}
/* (iprob=2): field loop in x2-x3 plane (cylinder in 3D) */
if(iprob==2) {
if ((x2f*x2f + x3f*x3f) < rad*rad) {
ax[k][j][i] = amp*(rad - sqrt(x2f*x2f + x3f*x3f));
} else {
ax[k][j][i] = 0.0;
}
ay[k][j][i] = 0.0;
az[k][j][i] = 0.0;
}
/* (iprob=3): field loop in x3-x1 plane (cylinder in 3D) */
if(iprob==3) {
if ((x1f*x1f + x3f*x3f) < rad*rad) {
ay[k][j][i] = amp*(rad - sqrt(x1f*x1f + x3f*x3f));
} else {
ay[k][j][i] = 0.0;
}
ax[k][j][i] = 0.0;
az[k][j][i] = 0.0;
}
/* (iprob=4): rotated cylindrical field loop in 3D. Similar to iprob=1
* with a rotation about the x2-axis. Define coordinate systems (x1,x2,x3)
* and (x,y,z) with the following transformation rules:
* x = x1*cos(ang_2) + x3*sin(ang_2)
* y = x2
* z = -x1*sin(ang_2) + x3*cos(ang_2)
* This inverts to:
* x1 = x*cos(ang_2) - z*sin(ang_2)
* x2 = y
* x3 = x*sin(ang_2) + z*cos(ang_2)
*/
if(iprob==4) {
x = x1c*cos_a2 + x3f*sin_a2;
y = x2f;
/* shift x back to the domain -0.5*lambda <= x <= 0.5*lambda */
while(x > 0.5*lambda) x -= lambda;
while(x < -0.5*lambda) x += lambda;
if ((x*x + y*y) < rad*rad) {
ax[k][j][i] = amp*(rad - sqrt(x*x + y*y))*(-sin_a2);
} else {
ax[k][j][i] = 0.0;
}
ay[k][j][i] = 0.0;
x = x1f*cos_a2 + x3c*sin_a2;
y = x2f;
/* shift x back to the domain -0.5*lambda <= x <= 0.5*lambda */
while(x > 0.5*lambda) x -= lambda;
while(x < -0.5*lambda) x += lambda;
if ((x*x + y*y) < rad*rad) {
az[k][j][i] = amp*(rad - sqrt(x*x + y*y))*(cos_a2);
} else {
az[k][j][i] = 0.0;
}
}
/* (iprob=5): spherical field loop in rotated plane */
if(iprob==5) {
ax[k][j][i] = 0.0;
if ((x1f*x1f + x2c*x2c + x3f*x3f) < rad*rad) {
ay[k][j][i] = amp*(rad - sqrt(x1f*x1f + x2c*x2c + x3f*x3f));
} else {
ay[k][j][i] = 0.0;
}
if ((x1f*x1f + x2f*x2f + x3c*x3c) < rad*rad) {
az[k][j][i] = amp*(rad - sqrt(x1f*x1f + x2f*x2f + x3c*x3c));
} else {
az[k][j][i] = 0.0;
}
}
}}}
/* Initialize density and momenta. If drat != 1, then density and temperature
* will be different inside loop than background values
*/
x1size = pDomain->RootMaxX[0] - pDomain->RootMinX[0];
x2size = pDomain->RootMaxX[1] - pDomain->RootMinX[1];
x3size = pDomain->RootMaxX[2] - pDomain->RootMinX[2];
diag = sqrt(x1size*x1size + x2size*x2size + x3size*x3size);
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
pGrid->U[k][j][i].d = 1.0;
pGrid->U[k][j][i].M1 = pGrid->U[k][j][i].d*vflow*x1size/diag;
pGrid->U[k][j][i].M2 = pGrid->U[k][j][i].d*vflow*x2size/diag;
pGrid->U[k][j][i].M3 = pGrid->U[k][j][i].d*vflow*x3size/diag;
cc_pos(pGrid,i,j,k,&x1c,&x2c,&x3c);
if ((x1c*x1c + x2c*x2c + x3c*x3c) < rad*rad) {
pGrid->U[k][j][i].d = drat;
pGrid->U[k][j][i].M1 = pGrid->U[k][j][i].d*vflow*x1size/diag;
pGrid->U[k][j][i].M2 = pGrid->U[k][j][i].d*vflow*x2size/diag;
pGrid->U[k][j][i].M3 = pGrid->U[k][j][i].d*vflow*x3size/diag;
}
#if (NSCALARS > 0)
for (n=0; n<NSCALARS; n++) pGrid->U[k][j][i].s[n] = 0.0;
if ((x1c*x1c + x2c*x2c + x3c*x3c) < rad*rad) {
for (n=0; n<NSCALARS; n++) pGrid->U[k][j][i].s[n] = 1.0;
}
#endif
}}}
/* boundary conditions on interface B */
#ifdef MHD
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie+1; i++) {
pGrid->B1i[k][j][i] = (az[k][j+1][i] - az[k][j][i])/pGrid->dx2 -
(ay[k+1][j][i] - ay[k][j][i])/pGrid->dx3;
}}}
for (k=ks; k<=ke; k++) {
for (j=js; j<=je+1; j++) {
for (i=is; i<=ie; i++) {
pGrid->B2i[k][j][i] = (ax[k+1][j][i] - ax[k][j][i])/pGrid->dx3 -
(az[k][j][i+1] - az[k][j][i])/pGrid->dx1;
}}}
if (ke > ks) {
ku = ke+1;
} else {
ku = ke;
}
for (k=ks; k<=ku; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
pGrid->B3i[k][j][i] = (ay[k][j][i+1] - ay[k][j][i])/pGrid->dx1 -
(ax[k][j+1][i] - ax[k][j][i])/pGrid->dx2;
}}}
#endif
/* initialize total energy and cell-centered B */
#if defined MHD || !defined ISOTHERMAL
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
#ifdef MHD
pGrid->U[k][j][i].B1c = 0.5*(pGrid->B1i[k][j][i ] +
pGrid->B1i[k][j][i+1]);
pGrid->U[k][j][i].B2c = 0.5*(pGrid->B2i[k][j ][i] +
pGrid->B2i[k][j+1][i]);
if (ke > ks)
pGrid->U[k][j][i].B3c = 0.5*(pGrid->B3i[k ][j][i] +
pGrid->B3i[k+1][j][i]);
else
pGrid->U[k][j][i].B3c = pGrid->B3i[k][j][i];
#endif
#ifndef ISOTHERMAL
pGrid->U[k][j][i].E = 1.0/Gamma_1
#ifdef MHD
+ 0.5*(SQR(pGrid->U[k][j][i].B1c) + SQR(pGrid->U[k][j][i].B2c)
+ SQR(pGrid->U[k][j][i].B3c))
#endif
+ 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 /* ISOTHERMAL */
}
}
}
#endif
free_3d_array((void***)az);
free_3d_array((void***)ay);
free_3d_array((void***)ax);
}
void _fill_grid_linearwave_1d(Grid *pGrid, Domain *pDomain, int wave_flag, double amp, double vflow, int wave_dir){
int i=0,j=0,k=0;
int is,ie,js,je,ks,ke,n,m,nx1,nx2,nx3;
Real d0,p0,u0,v0,w0,h0;
Real x1,x2,x3,r,ev[NWAVE],rem[NWAVE][NWAVE],lem[NWAVE][NWAVE];
Real x1max,x2max,lambda;
#ifdef MHD
Real bx0,by0,bz0,xfact,yfact;
#endif /* MHD */
is = pGrid->is; ie = pGrid->ie;
js = pGrid->js; je = pGrid->je;
ks = pGrid->ks; ke = pGrid->ke;
nx1 = (ie-is)+1 + 2*nghost;
nx2 = (je-js)+1 + 2*nghost;
nx3 = (ke-ks)+1 + 2*nghost;
if ((Soln = (Gas***)calloc_3d_array(nx3,nx2,nx1,sizeof(Gas))) == NULL)
ath_error("[linear_wave1d]: Error allocating memory\n");
/* Get eigenmatrix, where the quantities u0 and bx0 are parallel to the
* wavevector, and v0,w0,by0,bz0 are perpendicular. Background state chosen
* carefully so wave speeds are well-separated: Va=1, Vf=2, Vs=0.5 */
d0 = 1.0;
#ifndef ISOTHERMAL
p0 = 1.0/Gamma;
u0 = vflow*sqrt(Gamma*p0/d0);
#else
u0 = vflow*Iso_csound;
#endif
v0 = 0.0;
w0 = 0.0;
#ifdef MHD
bx0 = 1.0;
by0 = sqrt(2.0);
bz0 = 0.5;
xfact = 0.0;
yfact = 1.0;
#endif
for (n=0; n<NWAVE; n++) {
for (m=0; m<NWAVE; m++) {
rem[n][m] = 0.0;
lem[n][m] = 0.0;
}
}
#ifdef HYDRO
#ifdef ISOTHERMAL
esys_roe_iso_hyd(u0,v0,w0, ev,rem,lem);
#else
h0 = ((p0/Gamma_1 + 0.5*d0*(u0*u0+v0*v0+w0*w0)) + p0)/d0;
esys_roe_adb_hyd(u0,v0,w0,h0,ev,rem,lem);
ath_pout(0,"Ux - Cs = %e, %e\n",ev[0],rem[0][wave_flag]);
ath_pout(0,"Ux = %e, %e\n",ev[1],rem[1][wave_flag]);
ath_pout(0,"Ux + Cs = %e, %e\n",ev[4],rem[4][wave_flag]);
#endif /* ISOTHERMAL */
#endif /* HYDRO */
#ifdef MHD
#if defined(ISOTHERMAL)
esys_roe_iso_mhd(d0,u0,v0,w0,bx0,by0,bz0,xfact,yfact,ev,rem,lem);
ath_pout(0,"Ux - Cf = %e, %e\n",ev[0],rem[0][wave_flag]);
ath_pout(0,"Ux - Ca = %e, %e\n",ev[1],rem[1][wave_flag]);
ath_pout(0,"Ux - Cs = %e, %e\n",ev[2],rem[2][wave_flag]);
ath_pout(0,"Ux + Cs = %e, %e\n",ev[3],rem[3][wave_flag]);
ath_pout(0,"Ux + Ca = %e, %e\n",ev[4],rem[4][wave_flag]);
ath_pout(0,"Ux + Cf = %e, %e\n",ev[5],rem[5][wave_flag]);
#else
h0 = ((p0/Gamma_1+0.5*(bx0*bx0+by0*by0+bz0*bz0)+0.5*d0*(u0*u0+v0*v0+w0*w0))
+ (p0+0.5*(bx0*bx0+by0*by0+bz0*bz0)))/d0;
esys_roe_adb_mhd(d0,u0,v0,w0,h0,bx0,by0,bz0,xfact,yfact,ev,rem,lem);
ath_pout(0,"Ux - Cf = %e, %e\n",ev[0],rem[0][wave_flag]);
ath_pout(0,"Ux - Ca = %e, %e\n",ev[1],rem[1][wave_flag]);
ath_pout(0,"Ux - Cs = %e, %e\n",ev[2],rem[2][wave_flag]);
ath_pout(0,"Ux = %e, %e\n",ev[3],rem[3][wave_flag]);
ath_pout(0,"Ux + Cs = %e, %e\n",ev[4],rem[4][wave_flag]);
ath_pout(0,"Ux + Ca = %e, %e\n",ev[5],rem[5][wave_flag]);
ath_pout(0,"Ux + Cf = %e, %e\n",ev[6],rem[6][wave_flag]);
#endif /* ISOTHERMAL */
#endif /* MHD */
/* Now initialize 1D solution vector */
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
/* Set background state */
cc_pos(pGrid,i,j,k,&x1,&x2,&x3);
Soln[k][j][i].d = d0;
#ifndef ISOTHERMAL
Soln[k][j][i].E = p0/Gamma_1 + 0.5*d0*u0*u0;
#ifdef MHD
Soln[k][j][i].E += 0.5*(bx0*bx0 + by0*by0 + bz0*bz0);
#endif /* MHD */
#endif /* ISOTHERMAL */
/* Select appropriate solution based on direction of wavevector */
switch(wave_dir){
/* wave in x1-direction */
case 1:
Soln[k][j][i].d += amp*sin(2.0*PI*x1)*rem[0][wave_flag];
#ifndef ISOTHERMAL
Soln[k][j][i].E += amp*sin(2.0*PI*x1)*rem[4][wave_flag];
#endif /* ISOTHERMAL */
Soln[k][j][i].M1 = d0*vflow;
Soln[k][j][i].M2 = 0.0;
Soln[k][j][i].M3 = 0.0;
Soln[k][j][i].M1 += amp*sin(2.0*PI*x1)*rem[1][wave_flag];
Soln[k][j][i].M2 += amp*sin(2.0*PI*x1)*rem[2][wave_flag];
Soln[k][j][i].M3 += amp*sin(2.0*PI*x1)*rem[3][wave_flag];
#ifdef MHD
Soln[k][j][i].B1c = bx0;
Soln[k][j][i].B2c = by0 + amp*sin(2.0*PI*x1)*rem[NWAVE-2][wave_flag];
Soln[k][j][i].B3c = bz0 + amp*sin(2.0*PI*x1)*rem[NWAVE-1][wave_flag];
#endif /* MHD */
#if (NSCALARS > 0)
for (n=0; n<NSCALARS; n++)
Soln[k][j][i].s[n] = amp*(1.0 + sin(2.0*PI*x1));
#endif
break;
/* Wave in x2-direction */
case 2:
Soln[k][j][i].d += amp*sin(2.0*PI*x2)*rem[0][wave_flag];
#ifndef ISOTHERMAL
Soln[k][j][i].E += amp*sin(2.0*PI*x2)*rem[4][wave_flag];
#endif /* ISOTHERMAL */
Soln[k][j][i].M1 = 0.0;
Soln[k][j][i].M2 = d0*vflow;
Soln[k][j][i].M3 = 0.0;
Soln[k][j][i].M1 += amp*sin(2.0*PI*x2)*rem[3][wave_flag];
Soln[k][j][i].M2 += amp*sin(2.0*PI*x2)*rem[1][wave_flag];
Soln[k][j][i].M3 += amp*sin(2.0*PI*x2)*rem[2][wave_flag];
#ifdef MHD
Soln[k][j][i].B1c = bz0 + amp*sin(2.0*PI*x2)*rem[NWAVE-1][wave_flag];
Soln[k][j][i].B2c = bx0;
Soln[k][j][i].B3c = by0 + amp*sin(2.0*PI*x2)*rem[NWAVE-2][wave_flag];
#endif /* MHD */
#if (NSCALARS > 0)
for (n=0; n<NSCALARS; n++)
Soln[k][j][i].s[n] = amp*(1.0 + sin(2.0*PI*x2));
#endif
break;
/* Wave in x3-direction */
case 3:
Soln[k][j][i].d += amp*sin(2.0*PI*x3)*rem[0][wave_flag];
#ifndef ISOTHERMAL
Soln[k][j][i].E += amp*sin(2.0*PI*x3)*rem[4][wave_flag];
#endif /* ISOTHERMAL */
Soln[k][j][i].M1 = 0.0;
Soln[k][j][i].M2 = 0.0;
Soln[k][j][i].M3 = d0*vflow;
Soln[k][j][i].M1 += amp*sin(2.0*PI*x3)*rem[2][wave_flag];
Soln[k][j][i].M2 += amp*sin(2.0*PI*x3)*rem[3][wave_flag];
Soln[k][j][i].M3 += amp*sin(2.0*PI*x3)*rem[1][wave_flag];
#ifdef MHD
Soln[k][j][i].B1c = by0 + amp*sin(2.0*PI*x3)*rem[NWAVE-2][wave_flag];
Soln[k][j][i].B2c = bz0 + amp*sin(2.0*PI*x3)*rem[NWAVE-1][wave_flag];
Soln[k][j][i].B3c = bx0;
#endif /* MHD */
#if (NSCALARS > 0)
for (n=0; n<NSCALARS; n++)
Soln[k][j][i].s[n] = amp*(1.0 + sin(2.0*PI*x3));
#endif
break;
default:
ath_error("[linear_wave1d]: wave direction %d not allowed\n",wave_dir);
}
}}}
/* Now set initial conditions to wave solution */
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
pGrid->U[k][j][i].d = Soln[k][j][i].d;
#ifndef ISOTHERMAL
pGrid->U[k][j][i].E = Soln[k][j][i].E;
#endif /* ISOTHERMAL */
pGrid->U[k][j][i].M1 = Soln[k][j][i].M1;
pGrid->U[k][j][i].M2 = Soln[k][j][i].M2;
pGrid->U[k][j][i].M3 = Soln[k][j][i].M3;
#ifdef MHD
pGrid->U[k][j][i].B1c = Soln[k][j][i].B1c;
pGrid->U[k][j][i].B2c = Soln[k][j][i].B2c;
pGrid->U[k][j][i].B3c = Soln[k][j][i].B3c;
pGrid->B1i[k][j][i] = Soln[k][j][i].B1c;
pGrid->B2i[k][j][i] = Soln[k][j][i].B2c;
pGrid->B3i[k][j][i] = Soln[k][j][i].B3c;
#endif /* MHD */
#if (NSCALARS > 0)
for (n=0; n<NSCALARS; n++)
pGrid->U[k][j][i].s[n] = Soln[k][j][i].s[n];
#endif
}}}
#ifdef MHD
if (pGrid->Nx1 > 1) {
for (k=ks; k<=ke; k++) {
for (j=js; j<=je; j++) {
pGrid->B1i[k][j][ie+1] = pGrid->B1i[k][j][ie];
}
}
}
if (pGrid->Nx2 > 1) {
for (k=ks; k<=ke; k++) {
for (i=is; i<=ie; i++) {
pGrid->B2i[k][je+1][i] = pGrid->B2i[k][je][i];
}
}
}
if (pGrid->Nx3 > 1) {
for (j=js; j<=je; j++) {
for (i=is; i<=ie; i++) {
pGrid->B3i[ke+1][j][i] = pGrid->B3i[ke][j][i];
}
}
}
#endif /* MHD */
/* For self-gravitating problems, read 4\piG and compute mean density */
#ifdef SELF_GRAVITY
four_pi_G = par_getd("problem","four_pi_G");
grav_mean_rho = d0;
#endif /* SELF_GRAVITY */
return;
}
/* problem: */
void problem(DomainS *pDomain)
{
GridS *pG = pDomain->Grid;
int i,j,k;
int is,ie,il,iu,js,je,jl,ju,ks,ke,kl,ku;
int nx1,nx2,nx3;
Real x1,x2,x3;
Real xs,vs,v,pgas0,pgas,alpha,beta,a,b,converged;
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;
#ifdef MHD
ath_error("[cylwindrot]: This problem only works in hydro!\n");
#endif
#ifndef CYLINDRICAL
ath_error("[cylwindrot]: This problem only works in cylindrical!\n");
#endif
if (nx1==1) {
ath_error("[cylwindrot]: This problem can only be run in 2D or 3D!\n");
}
else if (nx2==1 && nx3>1) {
ath_error("[cylwindrot]: Only (R,phi) can be used in 2D!\n");
}
/* Allocate memory for solution */
if ((RootSoln = (ConsS***)calloc_3d_array(nx3,nx2,nx1,sizeof(ConsS))) == NULL)
ath_error("[cylwindrot]: Error allocating memory for solution\n");
ang_mom = par_getd("problem","ang_mom");
c_infty = par_getd("problem","c_infty");
vz0 = par_getd("problem","vz0");
iprob = par_geti("problem","iprob");
printf("gamma = %f,\t ang_mom = %f,\t c_infty = %f\n", Gamma, ang_mom, c_infty);
beta = 2.0*Gamma_1/(Gamma+1.0);
xs = (3.0-Gamma+sqrt(SQR(Gamma-3.0)-16.0*SQR(ang_mom)))/4.0;
lambda_s = 1.0/Gamma_1*pow(xs,beta)+pow(xs,beta-1.0)-0.5*SQR(ang_mom)*pow(xs,beta-2.0);
lambda_s = pow(lambda_s/(0.5+1.0/Gamma_1),1.0/beta);
vs = c_infty*pow(lambda_s/xs,0.5*beta);
printf("xs = %13.10f,\t lambda_s = %13.10f,\t vs = %13.10f\n", xs, lambda_s, vs);
// Compute 1D wind/accretion solution
for (i=il; i<=iu; i++) {
cc_pos(pG,i,j,k,&x1,&x2,&x3);
memset(&(pG->U[ks][js][i]),0.0,sizeof(ConsS));
vs = pow(lambda_s/x1,0.5*beta);
switch(iprob) {
case 1: /* Wind */
if (x1 < xs) {
a = TINY_NUMBER; b = vs;
}
else {
a = vs; b = HUGE_NUMBER;
}
break;
case 2: /* Accretion */
if (x1 < xs) {
a = vs; b = HUGE_NUMBER;
}
else {
a = TINY_NUMBER; b = vs;
}
break;
default: ath_error("[cylwindrot]: Not an accepted problem number!\n");
}
converged = bisection(myfunc,a,b,x1,&v);
if (!converged) ath_error("[cylwindrot]: Bisection did not converge!\n");
pG->U[ks][js][i].d = lambda_s/(x1*v);
pG->U[ks][js][i].M1 = lambda_s/x1;
if (iprob==2)
pG->U[ks][js][i].M1 *= -1.0;
pG->U[ks][js][i].M2 = pG->U[ks][js][i].d*ang_mom/x1;
pG->U[ks][js][i].M3 = pG->U[ks][js][i].d*vz0;
/* Initialize total energy */
#ifndef ISOTHERMAL
pgas0 = 1.0/Gamma;
pgas = pgas0*pow(pG->U[ks][js][i].d,Gamma);
pG->U[ks][js][i].E = pgas/Gamma_1
+ 0.5*(SQR(pG->U[ks][js][i].M1) + SQR(pG->U[ks][js][i].M2) + SQR(pG->U[ks][js][i].M3))/pG->U[ks][js][i].d;
#endif /* ISOTHERMAL */
}
/* Copy 1D solution and save */
for (k=kl; k<=ku; k++) {
for (j=jl; j<=ju; j++) {
for (i=il; i<=iu; i++) {
pG->U[k][j][i] = pG->U[ks][js][i];
RootSoln[k][j][i] = pG->U[ks][js][i];
}
}
}
StaticGravPot = grav_pot;
bvals_mhd_fun(pDomain,left_x1,do_nothing_bc);
bvals_mhd_fun(pDomain,right_x1,do_nothing_bc);
return;
}
int main(int argc, char* argv[]){
int i, j, k, n;
char *out_name=NULL;
if(argc < 5)
join_error("Usage: %s -o <out_name.vtk> file1.vtk file2.vtk ...\n",argv[0]);
file_count = argc-3; /* Number of input vtk files */
/* Parse the command line for the output filename */
for(i=1; i<argc-1; i++){
if(strcmp(argv[i],"-o") == 0){
i++; /* increment to the filename */
if((out_name = my_strdup(argv[i])) == NULL)
join_error("out_name = my_strdup(\"%s\") failed\n",argv[i]);
break;
}
}
/* An output filename is required */
if(out_name == NULL)
join_error("Usage: %s -o <out_name.vtk> file1.vtk file2.vtk ...\n",argv[0]);
printf("Output filename is \"%s\"\n",out_name);
printf("Found %d files on the command line\n",file_count);
/* ====================================================================== */
domain_1d = (VTK_Domain*)calloc(file_count,sizeof(VTK_Domain));
if(domain_1d == NULL)
join_error("calloc returned a NULL pointer for domain_1d\n");
/* Populate the 1d domain array with the filenames */
for(n=0, i=1; i<argc; i++){
if(strcmp(argv[i],"-o") == 0){
i++; /* increment to the filename */
}
else{
if((domain_1d[n].fname = my_strdup(argv[i])) == NULL){
join_error("domain_1d[%d].fname = my_strdup(\"%s\") failed\n",
n,argv[i]);
}
/* printf("domain_1d[%d].fname = \"%s\"\n",n,domain_1d[n].fname); */
n++; /* increment the domain counter */
}
}
init_domain_1d(); /* Read in the header information */
sort_domain_1d(); /* Sort the VTK_Domain elements in [k][j][i] order */
/* Allocate the domain_3d[][][] array */
domain_3d = (VTK_Domain***)
calloc_3d_array(NGrid_z, NGrid_y, NGrid_x, sizeof(VTK_Domain));
if(domain_3d == NULL)
join_error("calloc_3d_array() returned a NULL pointer\n");
/* Copy the contents of the domain_1d[] array to the domain_3d[][][] array */
n=0;
for(k=0; k<NGrid_z; k++){
for(j=0; j<NGrid_y; j++){
for(i=0; i<NGrid_x; i++){
domain_3d[k][j][i] = domain_1d[n++];
}
}
}
/* For debugging purposes, write out the origin for all of the grid
domains in what should now be an ascending order for a [k][j][i] array. */
/* This mimics the output in sort_domain_1d() and a diff should show
that they are exactly the same. */
/* for(k=0; k<NGrid_z; k++){
for(j=0; j<NGrid_y; j++){
for(i=0; i<NGrid_x; i++){
printf("[%d]: ox=%e oy=%e oz=%e\n",i + NGrid_x*(j + k*NGrid_y),
domain_3d[k][j][i].ox, domain_3d[k][j][i].oy,
domain_3d[k][j][i].oz);
}
}
} */
/* TO MAKE THIS CODE MORE BULLETPROOF ADD A CALL TO SOME FUNCTION TO
CHECK THAT THIS DOMAIN ARRAY SATISFIES A SET OF CONSISTENCY
CONDITIONS LIKE Nx IS CONSTANT ALONG Y- AND Z-DIRECTIONS, ETC. */
/* ====================================================================== */
write_joined_vtk(out_name);
/* ====================================================================== */
/* Now we need to do some cleanup */
free_3d_array((void ***)domain_3d);
domain_3d = NULL;
/* Now close the input files and free the input file names */
for(i=0; i<file_count; i++){
fclose(domain_1d[i].fp);
free(domain_1d[i].fname);
domain_1d[i].fname = NULL;
free(domain_1d[i].comment);
domain_1d[i].comment = NULL;
}
free(domain_1d);
domain_1d = NULL;
free(out_name);
out_name = NULL;
return(0) ;
}
