13 BL_PROFILE(
"REMORA::setup_step()");
26 int nvars = S_old.nComp();
36 const BoxArray& ba = S_old.boxArray();
37 const DistributionMapping& dm = S_old.DistributionMap();
49 MultiFab mf_logdrg_tmp(ba,dm,1,IntVect(
NGROW,
NGROW,0));
50 MultiFab mf_rho(ba,dm,1,IntVect(
NGROW,
NGROW,0));
52 MultiFab* mf_z_r =
vec_z_r[lev].get();
53 MultiFab* mf_z_w =
vec_z_w[lev].get();
55 MultiFab* mf_pm =
vec_pm[lev].get();
56 MultiFab* mf_pn =
vec_pn[lev].get();
57 MultiFab* mf_fcor =
vec_fcor[lev].get();
59 MultiFab* mf_gls =
vec_gls[lev].get();
60 MultiFab* mf_tke =
vec_tke[lev].get();
64 std::unique_ptr<MultiFab>& mf_rhoS =
vec_rhoS[lev];
65 std::unique_ptr<MultiFab>& mf_rhoA =
vec_rhoA[lev];
66 std::unique_ptr<MultiFab>& mf_bvf =
vec_bvf[lev];
67 std::unique_ptr<MultiFab>& mf_ru =
vec_ru[lev];
68 std::unique_ptr<MultiFab>& mf_rv =
vec_rv[lev];
69 std::unique_ptr<MultiFab>& mf_rufrc =
vec_rufrc[lev];
70 std::unique_ptr<MultiFab>& mf_rvfrc =
vec_rvfrc[lev];
71 std::unique_ptr<MultiFab>& mf_sustr =
vec_sustr[lev];
72 std::unique_ptr<MultiFab>& mf_svstr =
vec_svstr[lev];
73 std::unique_ptr<MultiFab>& mf_rdrag =
vec_rdrag[lev];
74 std::unique_ptr<MultiFab>& mf_rdrag2 =
vec_rdrag2[lev];
75 std::unique_ptr<MultiFab>& mf_ZoBot =
vec_ZoBot[lev];
76 std::unique_ptr<MultiFab>& mf_bustr =
vec_bustr[lev];
77 std::unique_ptr<MultiFab>& mf_bvstr =
vec_bvstr[lev];
79 std::unique_ptr<MultiFab>& mf_mskr =
vec_mskr[lev];
80 std::unique_ptr<MultiFab>& mf_msku =
vec_msku[lev];
81 std::unique_ptr<MultiFab>& mf_mskv =
vec_mskv[lev];
82 std::unique_ptr<MultiFab>& mf_mskp =
vec_mskp[lev];
84 std::unique_ptr<MultiFab>& mf_visc2_p =
vec_visc2_p[lev];
85 std::unique_ptr<MultiFab>& mf_visc2_r =
vec_visc2_r[lev];
89 mf_rho.setVal(0.e34_rt,IntVect(AMREX_D_DECL(
NGROW-1,
NGROW-1,0)));
90 mf_rhoS->setVal(0.e34_rt,IntVect(AMREX_D_DECL(
NGROW-1,
NGROW-1,0)));
91 mf_rhoA->setVal(0.e34_rt,IntVect(AMREX_D_DECL(
NGROW-1,
NGROW-1,0)));
101 int iic =
istep[lev];
104 MultiFab::Copy(S_new,S_old,0,0,S_new.nComp(),S_new.nGrowVect());
105 MultiFab::Copy(U_new,U_old,0,0,U_new.nComp(),U_new.nGrowVect());
106 MultiFab::Copy(V_new,V_old,0,0,V_new.nComp(),V_new.nGrowVect());
107 MultiFab::Copy(W_new,W_old,0,0,W_new.nComp(),W_new.nGrowVect());
118 auto N = Geom(lev).Domain().size()[2]-1;
120 const auto dlo = amrex::lbound(Geom(lev).Domain());
121 const auto dhi = amrex::ubound(Geom(lev).Domain());
123 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
126 Array4<Real const>
const& Hz =
vec_Hz[lev]->const_array(mfi);
127 Array4<Real >
const& Huon =
vec_Huon[lev]->array(mfi);
128 Array4<Real >
const& Hvom =
vec_Hvom[lev]->array(mfi);
130 Array4<Real const>
const& z_w = mf_z_w->const_array(mfi);
131 Array4<Real const>
const& z_r = mf_z_r->const_array(mfi);
132 Array4<Real const>
const& uold = U_old.const_array(mfi);
133 Array4<Real const>
const& vold = V_old.const_array(mfi);
134 Array4<Real >
const& rho = mf_rho.array(mfi);
135 Array4<Real >
const& rhoA = mf_rhoA->array(mfi);
136 Array4<Real >
const& rhoS = mf_rhoS->array(mfi);
137 Array4<Real >
const& bvf = mf_bvf->array(mfi);
141 Array4<Real const>
const& pm = mf_pm->const_array(mfi);
142 Array4<Real const>
const& pn = mf_pn->const_array(mfi);
144 Array4<Real const>
const& mskr = mf_mskr->const_array(mfi);
146 Box bx = mfi.tilebox();
147 Box gbx1 = mfi.growntilebox(IntVect(
NGROW-1,
NGROW-1,0));
148 Box gbx2 = mfi.growntilebox(IntVect(
NGROW,
NGROW,0));
149 Box ugbx2 = mfi.grownnodaltilebox(0,IntVect(
NGROW,
NGROW,0));
150 Box vgbx2 = mfi.grownnodaltilebox(1,IntVect(
NGROW,
NGROW,0));
164 ParallelFor(ugbx2, [=] AMREX_GPU_DEVICE (
int i,
int j,
int k)
166 Real on_u = 2.0_rt / (pn(i-1,j,0)+pn(i,j,0));
167 Huon(i,j,k)=0.5_rt*(Hz(i,j,k)+Hz(i-1,j,k))*uold(i,j,k)* on_u;
170 ParallelFor(vgbx2, [=] AMREX_GPU_DEVICE (
int i,
int j,
int k)
172 Real om_v= 2.0_rt / (pm(i,j-1,0)+pm(i,j,0));
173 Hvom(i,j,k)=0.5_rt*(Hz(i,j,k)+Hz(i,j-1,k))*vold(i,j,k)* om_v;
176 Array4<Real const>
const& state_old = S_old.const_array(mfi);
177 rho_eos(gbx2,state_old,rho,rhoA,rhoS,bvf,alpha,beta,Hz,z_w,z_r,h,mskr,N);
188 vec_evap[lev]->FillBoundary(geom[lev].periodicity());
192 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
194 Array4<Real >
const& stflx =
vec_stflx[lev]->array(mfi);
195 Array4<Real >
const& btflx =
vec_btflx[lev]->array(mfi);
196 Array4<Real const>
const& stflux =
vec_stflux[lev]->array(mfi);
197 Array4<Real const>
const& btflux =
vec_btflux[lev]->array(mfi);
198 Box gbx2 = mfi.growntilebox(IntVect(
NGROW,
NGROW,0));
201 ParallelFor(gbx2D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int ) {
208 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
210 Array4<Real >
const& stflx =
vec_stflx[lev]->array(mfi);
211 Array4<Real >
const& btflx =
vec_btflx[lev]->array(mfi);
212 Array4<Real const>
const& stflux =
vec_stflux[lev]->const_array(mfi);
213 Array4<Real const>
const& salt_old = S_old.const_array(mfi,
Salt_comp);
214 Box gbx2 = mfi.growntilebox(IntVect(
NGROW,
NGROW,0));
217 ParallelFor(gbx2D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int ) {
227 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
229 Array4<Real >
const& bustr = mf_bustr->array(mfi);
230 Array4<Real >
const& bvstr = mf_bvstr->array(mfi);
231 Array4<Real const>
const& uold = U_old.const_array(mfi);
232 Array4<Real const>
const& vold = V_old.const_array(mfi);
233 Array4<Real >
const& logdrg_tmp = mf_logdrg_tmp.array(mfi);
234 Array4<Real const>
const& z_r = mf_z_r->const_array(mfi);
235 Array4<Real const>
const& z_w = mf_z_w->const_array(mfi);
237 Box gbx2 = mfi.growntilebox(IntVect(
NGROW,
NGROW,0));
240 Box ubx1 = mfi.grownnodaltilebox(0,IntVect(
NGROW-1,
NGROW-1,0));
243 Box vbx1 = mfi.grownnodaltilebox(1,IntVect(
NGROW-1,
NGROW-1,0));
248 Array4<Real const>
const& rdrag = mf_rdrag->const_array(mfi);
249 ParallelFor(ubx1D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int )
251 bustr(i,j,0) = 0.5_rt * (rdrag(i-1,j,0)+rdrag(i,j,0))*(uold(i,j,0));
253 ParallelFor(vbx1D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int )
255 bvstr(i,j,0) = 0.5_rt * (rdrag(i,j-1,0)+rdrag(i,j,0))*(vold(i,j,0));
258 Array4<Real const>
const& rdrag2 = mf_rdrag2->const_array(mfi);
259 ParallelFor(ubx1D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int )
261 Real avg_v = 0.25_rt * (vold(i,j,0) + vold(i,j+1,0) + vold(i-1,j,0) + vold(i-1,j+1,0));
262 Real vel_mag = std::sqrt(uold(i,j,0)*uold(i,j,0) + avg_v * avg_v);
263 bustr(i,j,0) = 0.5_rt * (rdrag2(i-1,j,0) + rdrag2(i,j,0)) * uold(i,j,0) * vel_mag;
265 ParallelFor(vbx1D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int )
267 Real avg_u = 0.25_rt * (uold(i,j,0) + uold(i+1,j,0) + uold(i,j-1,0) + uold(i+1,j-1,0));
268 Real vel_mag = std::sqrt(avg_u * avg_u + vold(i,j,0) * vold(i,j,0));
269 bvstr(i,j,0) = 0.5_rt * (rdrag2(i,j-1,0) + rdrag2(i,j,0)) * vold(i,j,0) * vel_mag;
272 Array4<Real const>
const& ZoBot = mf_ZoBot->const_array(mfi);
273 ParallelFor(gbx2D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int )
275 Real logz = 1.0_rt / (std::log((z_r(i,j,0) - z_w(i,j,0)) / ZoBot(i,j,0)));
277 logdrg_tmp(i,j,0) = std::min(Cdb_max,std::max(Cdb_min,cff));
279 ParallelFor(ubx1D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int )
281 Real avg_v = 0.25_rt * (vold(i,j,0) + vold(i,j+1,0) + vold(i-1,j,0) + vold(i-1,j+1,0));
282 Real vel_mag = std::sqrt(uold(i,j,0)*uold(i,j,0) + avg_v * avg_v);
283 bustr(i,j,0) = 0.5_rt * (logdrg_tmp(i-1,j,0)+logdrg_tmp(i,j,0)) * uold(i,j,0) * vel_mag;
285 ParallelFor(vbx1D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int )
287 Real avg_u = 0.25_rt * (uold(i,j,0) + uold(i+1,j,0) + uold(i,j-1,0) + uold(i+1,j-1,0));
288 Real vel_mag = std::sqrt(avg_u * avg_u + vold(i,j,0) * vold(i,j,0));
289 bvstr(i,j,0) = 0.5_rt * (logdrg_tmp(i,j-1,0) + logdrg_tmp(i,j,0)) * vold(i,j,0) * vel_mag;
303 MultiFab mf_W(convert(ba,IntVect(0,0,1)),dm,1,IntVect(
NGROW+1,
NGROW+1,0));
309 prestep(lev, U_old, V_old, U_new, V_new,
310 mf_ru.get(), mf_rv.get(),
312 mf_DC, mf_z_r, mf_z_w, mf_h, mf_pm, mf_pn,
313 mf_sustr.get(), mf_svstr.get(), mf_bustr.get(), mf_bvstr.get(),
314 mf_msku.get(), mf_mskv.get(),
315 iic, ntfirst, nnew, nstp, nrhs, N, dt_lev);
319 mf_W.FillBoundary(geom[lev].periodicity());
322#ifdef REMORA_USE_NETCDF
330 for ( MFIter mfi(S_old, TilingIfNotGPU()); mfi.isValid(); ++mfi )
332 Array4<Real const>
const& Hz =
vec_Hz[lev]->const_array(mfi);
333 Array4<Real>
const& Huon =
vec_Huon[lev]->array(mfi);
334 Array4<Real>
const& Hvom =
vec_Hvom[lev]->array(mfi);
335 Array4<Real>
const& z_r = (mf_z_r)->array(mfi);
336 Array4<Real>
const& z_w = (mf_z_w)->array(mfi);
337 Array4<Real const>
const& uold = U_old.const_array(mfi);
338 Array4<Real const>
const& vold = V_old.const_array(mfi);
339 Array4<Real>
const& u = U_new.array(mfi);
340 Array4<Real>
const& v = V_new.array(mfi);
341 Array4<Real>
const& rho = (mf_rho).array(mfi);
342 Array4<Real>
const& ru = (mf_ru)->array(mfi);
343 Array4<Real>
const& rv = (mf_rv)->array(mfi);
344 Array4<Real>
const& rufrc = (mf_rufrc)->array(mfi);
345 Array4<Real>
const& rvfrc = (mf_rvfrc)->array(mfi);
346 Array4<Real>
const& W = (mf_W).array(mfi);
347 Array4<Real>
const& sustr = (mf_sustr)->array(mfi);
348 Array4<Real>
const& svstr = (mf_svstr)->array(mfi);
349 Array4<Real>
const& bustr = (mf_bustr)->array(mfi);
350 Array4<Real>
const& bvstr = (mf_bvstr)->array(mfi);
351 Array4<Real>
const& visc2_p = (mf_visc2_p)->array(mfi);
352 Array4<Real>
const& visc2_r = (mf_visc2_r)->array(mfi);
354 Array4<Real const>
const& pm = mf_pm->const_array(mfi);
355 Array4<Real const>
const& pn = mf_pn->const_array(mfi);
356 Array4<Real const>
const& fcor = mf_fcor->const_array(mfi);
358 Array4<Real const>
const& msku = mf_msku->const_array(mfi);
359 Array4<Real const>
const& mskv = mf_mskv->const_array(mfi);
360 Array4<Real const>
const& mskp = mf_mskp->const_array(mfi);
362 Box bx = mfi.tilebox();
366 Box xbx = mfi.nodaltilebox(0);
367 Box ybx = mfi.nodaltilebox(1);
368 Box xbx_adj = mfi.nodaltilebox(0);
369 Box ybx_adj = mfi.nodaltilebox(1);
371 auto xbx_lo = lbound(xbx_adj);
372 auto xbx_hi = ubound(xbx_adj);
373 auto ybx_lo = lbound(ybx_adj);
374 auto ybx_hi = ubound(ybx_adj);
376 if (xbx_lo.x == dlo.x) {
377 xbx_adj.growLo(0,-1);
378 }
else if (xbx_hi.x == dhi.x) {
379 xbx_adj.growHi(0,-1);
382 if (ybx_lo.y == dlo.y) {
383 ybx_adj.growLo(1,-1);
384 }
else if (ybx_hi.y == dhi.y) {
385 ybx_adj.growHi(1,-1);
388 Box gbx1 = mfi.growntilebox(IntVect(
NGROW-1,
NGROW-1,0));
389 Box gbx2 = mfi.growntilebox(IntVect(
NGROW,
NGROW,0));
391 Box utbx = mfi.nodaltilebox(0);
392 Box vtbx = mfi.nodaltilebox(1);
405 tbxp1D.makeSlab(2,0);
407 tbxp2D.makeSlab(2,0);
409 FArrayBox fab_FC(surroundingNodes(tbxp2,2),1,amrex::The_Async_Arena());
410 auto FC=fab_FC.array();
412 FArrayBox fab_fomn(tbxp2D,1,amrex::The_Async_Arena());
413 auto fomn=fab_fomn.array();
416 ParallelFor(tbxp2D, [=] AMREX_GPU_DEVICE (
int i,
int j,
int )
418 fomn(i,j,0) = fcor(i,j,0)*(1.0_rt/(pm(i,j,0)*pn(i,j,0)));
422 ParallelFor(gbx2, [=] AMREX_GPU_DEVICE (
int i,
int j,
int k)
427 prsgrd(tbxp1,gbx1,utbx,vtbx,ru,rv,pn,pm,rho,FC,Hz,z_r,z_w,msku,mskv,nrhs,N);
431 Array4<Real>
const& s_arr = S_new.array(mfi);
432 Array4<Real>
const& s_arr_rhs = S_old.array(mfi);
433 Array4<Real>
const& diff2_arr =
vec_diff2[lev]->array(mfi);
435 t3dmix(bx, s_arr, s_arr_rhs, diff2_arr, Hz, pm, pn, msku, mskv, dt_lev, ncomp);
438 t3dmix(bx, S_new.array(mfi,
Scalar_comp), S_old.array(mfi,
Scalar_comp), diff2_arr_scalar, Hz, pm, pn, msku, mskv, dt_lev, 1);
447 coriolis(xbx, ybx, uold, vold, ru, rv, Hz, fomn, nrhs, nrhs);
450#ifdef REMORA_USE_NETCDF
457 apply_clim_nudg(xbx_adj, 1, 0, ru, uold, uclim, u_nudg_coeff, Hz, pm, pn);
458 apply_clim_nudg(ybx_adj, 0, 1, rv, vold, vclim, v_nudg_coeff, Hz, pm, pn);
465 rhs_uv_3d(lev, xbx, ybx, uold, vold, ru, rv, rufrc, rvfrc,
466 sustr, svstr, bustr, bvstr, Huon, Hvom,
467 pm, pn, W, FC, nrhs, N);
471 uv3dmix(xbx, ybx, u, v, uold, vold, rufrc, rvfrc, visc2_p, visc2_r, Hz, pm, pn, mskp, nrhs, nnew, dt_lev);
475 int nnew = (iic +1)% 2;
478 gls_prestep(lev, mf_gls, mf_tke, mf_W, mf_msku.get(), mf_mskv.get(),
479 nstp, nnew, iic, ntfirst, N, dt_lev);
486 FillPatch(lev, time, *
vec_sstore[lev], GetVecOfPtrs(
vec_sstore),
BCVars::cons_bc,
BdyVars::t,0,
true,
true,0,0,dt_lev,*
cons_old[lev]);
489 vec_Huon[lev]->FillBoundary(geom[lev].periodicity());
490 vec_Hvom[lev]->FillBoundary(geom[lev].periodicity());