REMORA
Regional Modeling of Oceans Refined Adaptively
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REMORA_setup_step.cpp
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1#include <REMORA.H>
2
3using namespace amrex;
4
5/**
6 * @param[in ] lev level to operate on
7 * @param[in ] time time at start of step
8 * @param[in ] dt_lev time step at level
9 */
10void
11REMORA::setup_step (int lev, Real time, Real dt_lev)
12{
13 BL_PROFILE("REMORA::setup_step()");
14
15 MultiFab& S_old = *cons_old[lev];
16 MultiFab& S_new = *cons_new[lev];
17
18 MultiFab& U_old = *xvel_old[lev];
19 MultiFab& V_old = *yvel_old[lev];
20 MultiFab& W_old = *zvel_old[lev];
21
22 MultiFab& U_new = *xvel_new[lev];
23 MultiFab& V_new = *yvel_new[lev];
24 MultiFab& W_new = *zvel_new[lev];
25
26 [[maybe_unused]] int nvars = S_old.nComp();
27
28 // Fill ghost cells/faces at old time
29 FillPatchNoBC(lev, time, *cons_old[lev], cons_old, BdyVars::t);
30 FillPatchNoBC(lev, time, *xvel_old[lev], xvel_old, BdyVars::u);
31 FillPatchNoBC(lev, time, *yvel_old[lev], yvel_old, BdyVars::v);
32 FillPatch(lev, time, *zvel_old[lev], zvel_old, zvel_bc(), BdyVars::null);
33
34 ////////// //pre_step3d corrections to boundaries
35
36 const BoxArray& ba = S_old.boxArray();
37 const DistributionMapping& dm = S_old.DistributionMap();
38
39 const int nrhs = 0;
40 int nstp = 0;
41
42 //-----------------------------------------------------------------------
43 // Time step momentum equation
44 //-----------------------------------------------------------------------
45
46 //Only used locally, probably should be rearranged into FArrayBox declaration
47
48 MultiFab mf_DC(ba,dm,1,IntVect(NGROW,NGROW,NGROW-1)); //2d missing j coordinate
49 MultiFab mf_logdrg_tmp(ba,dm,1,IntVect(NGROW,NGROW,0));
50 MultiFab mf_rho(ba,dm,1,IntVect(NGROW,NGROW,0));
51
52 MultiFab* mf_z_r = vec_z_r[lev].get();
53 MultiFab* mf_z_w = vec_z_w[lev].get();
54 MultiFab* mf_h = vec_h[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();
58
59 MultiFab* mf_gls = vec_gls[lev].get();
60 MultiFab* mf_tke = vec_tke[lev].get();
61
62 //Consider passing these into the advance function or renaming relevant things
63
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];
78
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];
83
84 std::unique_ptr<MultiFab>& mf_visc2_p = vec_visc2_p[lev];
85 std::unique_ptr<MultiFab>& mf_visc2_r = vec_visc2_r[lev];
86
87 // We need to set these because otherwise in the first call to remora_advance we may
88 // read uninitialized data on ghost values in setting the bc's on the velocities
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)));
92 mf_DC.setVal(0);
93
94 FillPatchNoBC(lev, time, *cons_new[lev], cons_new, BdyVars::t);
95 FillPatchNoBC(lev, time, *xvel_new[lev], xvel_new, BdyVars::u);
96 FillPatchNoBC(lev, time, *yvel_new[lev], yvel_new, BdyVars::v);
97
98 mf_rufrc->setVal(0);
99 mf_rvfrc->setVal(0);
100
101 int iic = istep[lev];
102 int ntfirst = 0;
103 if(iic==ntfirst) {
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());
108 }
109
110 // If we're not doing bulk fluxes, set surface momentum fluxes directly.
111 // Otherwise, calculate them from winds, so those need to be set
112 if (solverChoice.atm2ocn_flux_mode) {
113 // Surface stress and heat/moisture fluxes were already populated from the driver.
114 } else if (!solverChoice.bulk_fluxes) {
115 set_smflux(lev);
116 } else {
117 set_wind(lev);
118 }
119
120 auto N = Geom(lev).Domain().size()[2]-1; // Number of vertical "levs" aka, NZ
121
122 const auto dlo = amrex::lbound(Geom(lev).Domain());
123 const auto dhi = amrex::ubound(Geom(lev).Domain());
124
125 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
126 {
127 Array4<Real const> const& h = vec_h[lev]->const_array(mfi);
128 Array4<Real const> const& Hz = vec_Hz[lev]->const_array(mfi);
129 Array4<Real > const& Huon = vec_Huon[lev]->array(mfi);
130 Array4<Real > const& Hvom = vec_Hvom[lev]->array(mfi);
131
132 Array4<Real const> const& z_w = mf_z_w->const_array(mfi);
133 Array4<Real const> const& z_r = mf_z_r->const_array(mfi);
134 Array4<Real const> const& uold = U_old.const_array(mfi);
135 Array4<Real const> const& vold = V_old.const_array(mfi);
136 Array4<Real > const& rho = mf_rho.array(mfi);
137 Array4<Real > const& rhoA = mf_rhoA->array(mfi);
138 Array4<Real > const& rhoS = mf_rhoS->array(mfi);
139 Array4<Real > const& bvf = mf_bvf->array(mfi);
140 Array4<Real > const& alpha = (solverChoice.bulk_fluxes && !solverChoice.atm2ocn_flux_mode)
141 ? vec_alpha[lev]->array(mfi) : Array4<Real>();
142 Array4<Real > const& beta = (solverChoice.bulk_fluxes && !solverChoice.atm2ocn_flux_mode)
143 ? vec_beta[lev]->array(mfi) : Array4<Real>();
144
145 Array4<Real const> const& pm = mf_pm->const_array(mfi);
146 Array4<Real const> const& pn = mf_pn->const_array(mfi);
147
148 Array4<Real const> const& mskr = mf_mskr->const_array(mfi);
149
150 Box bx = mfi.tilebox();
151 Box gbx1 = mfi.growntilebox(IntVect(NGROW-1,NGROW-1,0));
152 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
153 Box ugbx2 = mfi.grownnodaltilebox(0,IntVect(NGROW,NGROW,0));
154 Box vgbx2 = mfi.grownnodaltilebox(1,IntVect(NGROW,NGROW,0));
155
156 Box bxD = bx;
157 bxD.makeSlab(2,0);
158 Box gbx1D = gbx1;
159 gbx1D.makeSlab(2,0);
160 Box gbx2D = gbx2;
161 gbx2D.makeSlab(2,0);
162
163 //
164 //-----------------------------------------------------------------------
165 // Compute horizontal mass fluxes, Hz*u/n and Hz*v/m (set_massflux_3d)
166 //-----------------------------------------------------------------------
167 //
168 ParallelFor(ugbx2, [=] AMREX_GPU_DEVICE (int i, int j, int k)
169 {
170 Real on_u = 2.0_rt / (pn(i-1,j,0)+pn(i,j,0));
171 Huon(i,j,k)=0.5_rt*(Hz(i,j,k)+Hz(i-1,j,k))*uold(i,j,k)* on_u;
172 });
173
174 ParallelFor(vgbx2, [=] AMREX_GPU_DEVICE (int i, int j, int k)
175 {
176 Real om_v= 2.0_rt / (pm(i,j-1,0)+pm(i,j,0));
177 Hvom(i,j,k)=0.5_rt*(Hz(i,j,k)+Hz(i,j-1,k))*vold(i,j,k)* om_v;
178 });
179
180 Array4<Real const> const& state_old = S_old.const_array(mfi);
181 rho_eos(gbx2,state_old,rho,rhoA,rhoS,bvf,alpha,beta,Hz,z_w,z_r,h,mskr,N);
182 }
183
184 const Real Cdb_min = solverChoice.Cdb_min;
185 const Real Cdb_max = solverChoice.Cdb_max;
186
187 if (solverChoice.longwave_netcdf_is_net && !solverChoice.longwave_down_from_netcdf) {
188 amrex::Abort("remora.longwave_netcdf_is_net=true requires remora.longwave_down_from_netcdf=true");
189 }
190
191 if (solverChoice.longwave_down && !solverChoice.longwave_down_from_netcdf) {
192 amrex::Abort("remora.longwave_down=true currently requires remora.longwave_down_from_netcdf=true");
193 }
194
195 MultiFab* lw_ptr = nullptr;
196
197 if (solverChoice.longwave_down_from_netcdf)
198 lw_ptr = vec_longwave_down[lev].get();
199 if (solverChoice.bulk_fluxes && !solverChoice.atm2ocn_flux_mode) {
200 bulk_fluxes(lev, cons_old[lev],vec_uwind[lev].get(),vec_vwind[lev].get(),
201 vec_Tair[lev].get(),vec_qair[lev].get(),vec_Pair[lev].get(),
202 vec_srflx[lev].get(),
203 lw_ptr,
204 vec_evap[lev].get(),
205 vec_sustr[lev].get(),vec_svstr[lev].get(),vec_stflux[lev].get(),
206 vec_lrflx[lev].get(),vec_lhflx[lev].get(),vec_shflx[lev].get(),N);
207 vec_evap[lev]->FillBoundary(geom[lev].periodicity());
208 }
209
210 if (solverChoice.do_temp_flux) {
211 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
212 {
213 Array4<Real > const& stflx = vec_stflx[lev]->array(mfi);
214 Array4<Real > const& btflx = vec_btflx[lev]->array(mfi);
215 Array4<Real const> const& stflux = vec_stflux[lev]->array(mfi);
216 Array4<Real const> const& btflux = vec_btflux[lev]->array(mfi);
217 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
218 Box gbx2D = gbx2;
219 gbx2D.makeSlab(2,0);
220 ParallelFor(gbx2D, [=] AMREX_GPU_DEVICE (int i, int j, int ) {
221 stflx(i,j,0,Temp_comp) = stflux(i,j,0,Temp_comp);
222 btflx(i,j,0,Temp_comp) = btflux(i,j,0,Temp_comp);
223 });
224 }
225 }
226 if (solverChoice.do_salt_flux) {
227 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
228 {
229 Array4<Real > const& stflx = vec_stflx[lev]->array(mfi);
230 Array4<Real > const& btflx = vec_btflx[lev]->array(mfi);
231 Array4<Real const> const& stflux = vec_stflux[lev]->const_array(mfi);
232 Array4<Real const> const& salt_old = S_old.const_array(mfi,Salt_comp);
233 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
234 Box gbx2D = gbx2;
235 gbx2D.makeSlab(2,0);
236 ParallelFor(gbx2D, [=] AMREX_GPU_DEVICE (int i, int j, int ) {
237 stflx(i,j,0,Salt_comp) = stflux(i,j,0,Salt_comp) * salt_old(i,j,N);
238 // The fact that this is btflx on the RHS matches what's in ROMS even though
239 // it's weird -- if it's non-zero, does that mean that it will run away since
240 // it's always getting multiplied by salt?
241 btflx(i,j,0,Salt_comp) = btflx(i,j,0,Salt_comp) * salt_old(i,j,0);
242 });
243 }
244 }
245
246 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
247 {
248 Array4<Real > const& bustr = mf_bustr->array(mfi);
249 Array4<Real > const& bvstr = mf_bvstr->array(mfi);
250 Array4<Real const> const& uold = U_old.const_array(mfi);
251 Array4<Real const> const& vold = V_old.const_array(mfi);
252 Array4<Real > const& logdrg_tmp = mf_logdrg_tmp.array(mfi);
253 Array4<Real const> const& z_r = mf_z_r->const_array(mfi);
254 Array4<Real const> const& z_w = mf_z_w->const_array(mfi);
255
256 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
257 Box gbx2D = gbx2;
258 gbx2D.makeSlab(2,0);
259 Box ubx1 = mfi.grownnodaltilebox(0,IntVect(NGROW-1,NGROW-1,0));
260 Box ubx1D = ubx1;
261 ubx1D.makeSlab(2,0);
262 Box vbx1 = mfi.grownnodaltilebox(1,IntVect(NGROW-1,NGROW-1,0));
263 Box vbx1D = vbx1;
264 vbx1D.makeSlab(2,0);
265 // Set bottom stress as defined in set_vbx.F
266 if (solverChoice.bottom_stress_type == BottomStressType::linear) {
267 Array4<Real const> const& rdrag = mf_rdrag->const_array(mfi);
268 ParallelFor(ubx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
269 {
270 bustr(i,j,0) = 0.5_rt * (rdrag(i-1,j,0)+rdrag(i,j,0))*(uold(i,j,0));
271 });
272 ParallelFor(vbx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
273 {
274 bvstr(i,j,0) = 0.5_rt * (rdrag(i,j-1,0)+rdrag(i,j,0))*(vold(i,j,0));
275 });
276 } else if (solverChoice.bottom_stress_type == BottomStressType::quadratic) {
277 Array4<Real const> const& rdrag2 = mf_rdrag2->const_array(mfi);
278 ParallelFor(ubx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
279 {
280 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));
281 Real vel_mag = std::sqrt(uold(i,j,0)*uold(i,j,0) + avg_v * avg_v);
282 bustr(i,j,0) = 0.5_rt * (rdrag2(i-1,j,0) + rdrag2(i,j,0)) * uold(i,j,0) * vel_mag;
283 });
284 ParallelFor(vbx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
285 {
286 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));
287 Real vel_mag = std::sqrt(avg_u * avg_u + vold(i,j,0) * vold(i,j,0));
288 bvstr(i,j,0) = 0.5_rt * (rdrag2(i,j-1,0) + rdrag2(i,j,0)) * vold(i,j,0) * vel_mag;
289 });
290 } else if (solverChoice.bottom_stress_type == BottomStressType::logarithmic) {
291 Array4<Real const> const& ZoBot = mf_ZoBot->const_array(mfi);
292 ParallelFor(gbx2D, [=] AMREX_GPU_DEVICE (int i, int j, int )
293 {
294 Real logz = 1.0_rt / (std::log((z_r(i,j,0) - z_w(i,j,0)) / ZoBot(i,j,0)));
295 Real cff = vonKar * vonKar * logz * logz;
296 logdrg_tmp(i,j,0) = std::min(Cdb_max,std::max(Cdb_min,cff));
297 });
298 ParallelFor(ubx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
299 {
300 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));
301 Real vel_mag = std::sqrt(uold(i,j,0)*uold(i,j,0) + avg_v * avg_v);
302 bustr(i,j,0) = 0.5_rt * (logdrg_tmp(i-1,j,0)+logdrg_tmp(i,j,0)) * uold(i,j,0) * vel_mag;
303 });
304 ParallelFor(vbx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
305 {
306 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));
307 Real vel_mag = std::sqrt(avg_u * avg_u + vold(i,j,0) * vold(i,j,0));
308 bvstr(i,j,0) = 0.5_rt * (logdrg_tmp(i,j-1,0) + logdrg_tmp(i,j,0)) * vold(i,j,0) * vel_mag;
309 });
310 }
311 }
312 FillPatch(lev, time, *vec_bustr[lev].get(), GetVecOfPtrs(vec_bustr), u2d_simple_bc(), BdyVars::null,0,true,false);
313 FillPatch(lev, time, *vec_bvstr[lev].get(), GetVecOfPtrs(vec_bvstr), v2d_simple_bc(), BdyVars::null,0,true,false);
314
315 if (solverChoice.vert_mixing_type == VertMixingType::analytic) {
316 // Update Akv if using analytic mixing
317 set_analytic_vmix(lev);
318 }
319
320 set_zeta_to_Ztavg(lev);
321
322 MultiFab mf_W(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW+1,NGROW+1,0));
323 mf_W.setVal(0.0_rt);
324
325
326 if (solverChoice.use_prestep) {
327 const int nnew = 0;
328 prestep(lev, U_old, V_old, U_new, V_new,
329 mf_ru.get(), mf_rv.get(),
330 S_old, S_new, mf_W,
331 mf_DC, mf_z_r, mf_z_w, mf_h, mf_pm, mf_pn,
332 mf_sustr.get(), mf_svstr.get(), mf_bustr.get(), mf_bvstr.get(),
333 mf_msku.get(), mf_mskv.get(),
334 iic, ntfirst, nnew, nstp, nrhs, N, dt_lev);
335 }
336
337 // We use FillBoundary not FillPatch here since mf_W is single-level scratch space
338 mf_W.FillBoundary(geom[lev].periodicity());
339 (*physbcs[lev])(mf_W,*mf_mskr.get(),0,1,mf_W.nGrowVect(),t_new[lev],zvel_bc());
340
341#ifdef REMORA_USE_NETCDF
342 // Get u and v climatology if we're going to do nudging
343 if (solverChoice.do_m3_clim_nudg) {
344 u_clim_data_from_file->update_interpolated_to_time(t_new[lev], lev, xvel_new[lev], geom, ref_ratio);
345 v_clim_data_from_file->update_interpolated_to_time(t_new[lev], lev, yvel_new[lev], geom, ref_ratio);
346 }
347#endif
348
349 for ( MFIter mfi(S_old, TilingIfNotGPU()); mfi.isValid(); ++mfi )
350 {
351 Array4<Real const> const& Hz = vec_Hz[lev]->const_array(mfi);
352 Array4<Real> const& Huon = vec_Huon[lev]->array(mfi);
353 Array4<Real> const& Hvom = vec_Hvom[lev]->array(mfi);
354 Array4<Real> const& z_r = (mf_z_r)->array(mfi);
355 Array4<Real> const& z_w = (mf_z_w)->array(mfi);
356 Array4<Real const> const& uold = U_old.const_array(mfi);
357 Array4<Real const> const& vold = V_old.const_array(mfi);
358 Array4<Real> const& u = U_new.array(mfi);
359 Array4<Real> const& v = V_new.array(mfi);
360 Array4<Real> const& rho = (mf_rho).array(mfi);
361 Array4<Real> const& ru = (mf_ru)->array(mfi);
362 Array4<Real> const& rv = (mf_rv)->array(mfi);
363 Array4<Real> const& rufrc = (mf_rufrc)->array(mfi);
364 Array4<Real> const& rvfrc = (mf_rvfrc)->array(mfi);
365 Array4<Real> const& W = (mf_W).array(mfi);
366 Array4<Real> const& sustr = (mf_sustr)->array(mfi);
367 Array4<Real> const& svstr = (mf_svstr)->array(mfi);
368 Array4<Real> const& bustr = (mf_bustr)->array(mfi);
369 Array4<Real> const& bvstr = (mf_bvstr)->array(mfi);
370 Array4<Real> const& visc2_p = (mf_visc2_p)->array(mfi);
371 Array4<Real> const& visc2_r = (mf_visc2_r)->array(mfi);
372
373 Array4<Real const> const& pm = mf_pm->const_array(mfi);
374 Array4<Real const> const& pn = mf_pn->const_array(mfi);
375 Array4<Real const> const& fcor = mf_fcor->const_array(mfi);
376
377 Array4<Real const> const& msku = mf_msku->const_array(mfi);
378 Array4<Real const> const& mskv = mf_mskv->const_array(mfi);
379 Array4<Real const> const& mskp = mf_mskp->const_array(mfi);
380
381 Box bx = mfi.tilebox();
382
383 Box tbxp1 = bx;
384 Box tbxp2 = bx;
385 Box xbx = mfi.nodaltilebox(0);
386 Box ybx = mfi.nodaltilebox(1);
387 Box xbx_adj = mfi.nodaltilebox(0);
388 Box ybx_adj = mfi.nodaltilebox(1);
389
390 auto xbx_lo = lbound(xbx_adj);
391 auto xbx_hi = ubound(xbx_adj);
392 auto ybx_lo = lbound(ybx_adj);
393 auto ybx_hi = ubound(ybx_adj);
394
395 if (xbx_lo.x == dlo.x) {
396 xbx_adj.growLo(0,-1);
397 } else if (xbx_hi.x == dhi.x) {
398 xbx_adj.growHi(0,-1);
399 }
400
401 if (ybx_lo.y == dlo.y) {
402 ybx_adj.growLo(1,-1);
403 } else if (ybx_hi.y == dhi.y) {
404 ybx_adj.growHi(1,-1);
405 }
406
407 Box gbx1 = mfi.growntilebox(IntVect(NGROW-1,NGROW-1,0));
408 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
409
410 Box utbx = mfi.nodaltilebox(0);
411 Box vtbx = mfi.nodaltilebox(1);
412
413 tbxp1.grow(IntVect(NGROW-1,NGROW-1,0));
414 tbxp2.grow(IntVect(NGROW,NGROW,0));
415
416 Box bxD = bx;
417 bxD.makeSlab(2,0);
418 Box gbx1D = gbx1;
419 gbx1D.makeSlab(2,0);
420 Box gbx2D = gbx2;
421 gbx2D.makeSlab(2,0);
422
423 Box tbxp1D = tbxp1;
424 tbxp1D.makeSlab(2,0);
425 Box tbxp2D = tbxp2;
426 tbxp2D.makeSlab(2,0);
427
428 FArrayBox fab_FC(surroundingNodes(tbxp2,2),1,amrex::The_Async_Arena()); //3D
429 auto FC=fab_FC.array();
430
431 FArrayBox fab_fomn(tbxp2D,1,amrex::The_Async_Arena());
432 auto fomn=fab_fomn.array();
433
434 if (solverChoice.use_coriolis) {
435 ParallelFor(tbxp2D, [=] AMREX_GPU_DEVICE (int i, int j, int )
436 {
437 fomn(i,j,0) = fcor(i,j,0)*(1.0_rt/(pm(i,j,0)*pn(i,j,0)));
438 });
439 }
440
441 ParallelFor(gbx2, [=] AMREX_GPU_DEVICE (int i, int j, int k)
442 {
443 FC(i,j,k)=0.0_rt;
444 });
445
446 prsgrd(tbxp1,gbx1,utbx,vtbx,ru,rv,pn,pm,rho,FC,Hz,z_r,z_w,msku,mskv,nrhs,N);
447
448 // Apply mixing to temperature and, if use_salt, salt
449 int ncomp = solverChoice.use_salt ? 2 : 1;
450 Array4<Real> const& s_arr = S_new.array(mfi);
451 Array4<Real> const& s_arr_rhs = S_old.array(mfi);
452 Array4<Real> const& diff2_arr = vec_diff2[lev]->array(mfi);
453
454 t3dmix2(bx, s_arr, s_arr_rhs, diff2_arr, Hz, z_r, pm, pn, msku, mskv, dt_lev, ncomp, N);
455
456 for (int itrac = Tracer_comp; itrac < ncons; ++itrac) {
457 Array4<Real> const& diff2_arr_scalar = vec_diff2[lev]->array(mfi,itrac);
458 t3dmix2(bx, S_new.array(mfi,itrac), S_old.array(mfi,itrac), diff2_arr_scalar, Hz, z_r, pm, pn, msku, mskv, dt_lev, 1, N);
459 }
460
461 if (solverChoice.use_coriolis) {
462 //-----------------------------------------------------------------------
463 // coriolis
464 //-----------------------------------------------------------------------
465 //
466 // ru, rv updated
467 // In ROMS, coriolis is the first (un-ifdefed) thing to happen in rhs3d_tile, which gets called after t3dmix
468 coriolis(xbx, ybx, uold, vold, ru, rv, Hz, fomn, nrhs, nrhs);
469 }
470
471 if (solverChoice.use_curvilinear_grid) {
472 Array4<Real const> const& dndx = vec_dndx[lev]->const_array(mfi);
473 Array4<Real const> const& dmde = vec_dmde[lev]->const_array(mfi);
474 curvilinear(bx, xbx, ybx, uold, vold, ru, rv, Hz, dndx, dmde, nrhs, nrhs);
475 }
476
477#ifdef REMORA_USE_NETCDF
478 if (solverChoice.do_m3_clim_nudg) {
479 Array4<const Real> const& uclim = u_clim_data_from_file->get_interpolated_mf(lev)->const_array(mfi);
480 Array4<const Real> const& vclim = v_clim_data_from_file->get_interpolated_mf(lev)->const_array(mfi);
481 Array4<const Real> const& u_nudg_coeff = vec_nudg_coeff[BdyVars::u][lev]->const_array(mfi);
482 Array4<const Real> const& v_nudg_coeff = vec_nudg_coeff[BdyVars::v][lev]->const_array(mfi);
483 // These boxes are set to match ROMS
484 apply_clim_nudg(xbx_adj, 1, 0, ru, uold, uclim, u_nudg_coeff, Hz, pm, pn);
485 apply_clim_nudg(ybx_adj, 0, 1, rv, vold, vclim, v_nudg_coeff, Hz, pm, pn);
486 }
487#endif
488
489 ////rufrc from 3d is set to ru, then the wind stress (and bottom stress) is added, then the mixing is added
490 //rufrc=ru+sustr*om_u*on_u
491
492 rhs_uv_3d(lev, xbx, ybx, uold, vold, ru, rv, rufrc, rvfrc,
493 sustr, svstr, bustr, bvstr, Huon, Hvom,
494 pm, pn, W, FC, nrhs, N);
495
496 if(solverChoice.use_uv3dmix) {
497 const int nnew = 0;
498 uv3dmix(xbx, ybx, u, v, uold, vold, rufrc, rvfrc, visc2_p, visc2_r, Hz, pm, pn, mskp, nrhs, nnew, dt_lev);
499 }
500 } // MFIter
501
502 int nnew = (iic +1)% 2;
503 nstp = iic % 2;
504 if (solverChoice.vert_mixing_type == VertMixingType::GLS) {
505 gls_prestep(lev, mf_gls, mf_tke, mf_W, mf_msku.get(), mf_mskv.get(),
506 nstp, nnew, iic, ntfirst, N, dt_lev);
507 }
508 nstp = 0;
509
510 // Commenting out for now, but not sure it's necessary
511 //FillPatch(lev, time, *cons_old[lev], cons_old, BCVars::cons_bc, BdyVars::t);
512 //FillPatch(lev, time, *cons_new[lev], cons_new, BCVars::cons_bc, BdyVars::t);
513 FillPatch(lev, time, *vec_sstore[lev], GetVecOfPtrs(vec_sstore), BCVars::cons_bc, BdyVars::t,0,true,true,0,0,dt_lev,*cons_old[lev]);
514
515 // Don't actually want to apply boundary conditions here
516 vec_Huon[lev]->FillBoundary(geom[lev].periodicity());
517 vec_Hvom[lev]->FillBoundary(geom[lev].periodicity());
518}
vonKar
constexpr amrex::Real vonKar
Definition REMORA_Constants.H:17
BottomStressType::logarithmic
@ logarithmic
BottomStressType::linear
@ linear
BottomStressType::quadratic
@ quadratic
VertMixingType::GLS
@ GLS
VertMixingType::analytic
@ analytic
NGROW
#define NGROW
Definition REMORA_IndexDefines.H:12
Temp_comp
#define Temp_comp
Definition REMORA_IndexDefines.H:8
Tracer_comp
#define Tracer_comp
Definition REMORA_IndexDefines.H:10
Salt_comp
#define Salt_comp
Definition REMORA_IndexDefines.H:9
time
Real time
Definition REMORA_InitAnalyticSMFlux_ChannelTest.H:1
mf_fcor
Real mf_fcor
Definition REMORA_InitAnalyticSMFlux_ChannelTest.H:7
REMORA::ncons
int ncons
Number of conserved scalars in the state (temperature + salt + passive scalars)
Definition REMORA.H:1480
REMORA::prsgrd
void prsgrd(const amrex::Box &bx, const amrex::Box &gbx, const amrex::Box &utbx, const amrex::Box &vtbx, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &rho, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const int nrhs, const int N)
Calculate pressure gradient.
Definition REMORA_prsgrd.cpp:25
REMORA::vec_evap
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_evap
evaporation rate [kg/m^2/s]
Definition REMORA.H:434
REMORA::zvel_bc
int zvel_bc() const noexcept
Definition REMORA.H:1183
REMORA::vec_fcor
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_fcor
coriolis factor (2D)
Definition REMORA.H:500
REMORA::vec_btflux
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_btflux
Bottom tracer flux; input arrays.
Definition REMORA.H:429
REMORA::vec_h
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_h
multilevel data container for current step's z velocities (largely unused; W stored separately)
Definition REMORA.H:335
REMORA::vec_pm
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pm
horizontal scaling factor: 1 / dx (2D)
Definition REMORA.H:491
REMORA::vec_ZoBot
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ZoBot
Bottom roughness length [m], defined at rho points.
Definition REMORA.H:448
REMORA::vec_lrflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_lrflx
longwave radiation
Definition REMORA.H:414
REMORA::cons_new
amrex::Vector< amrex::MultiFab * > cons_new
multilevel data container for current step's scalar data: temperature, salinity, passive tracer
Definition REMORA.H:315
REMORA::vec_vwind
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_vwind
Wind in the v direction, defined at rho-points.
Definition REMORA.H:403
REMORA::vec_mskr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskr
land/sea mask at cell centers (2D)
Definition REMORA.H:480
REMORA::vec_tke
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_tke
Turbulent kinetic energy.
Definition REMORA.H:548
REMORA::rho_eos
void rho_eos(const amrex::Box &bx, const amrex::Array4< amrex::Real const > &state, const amrex::Array4< amrex::Real > &rho, const amrex::Array4< amrex::Real > &rhoA, const amrex::Array4< amrex::Real > &rhoS, const amrex::Array4< amrex::Real > &bvf, const amrex::Array4< amrex::Real > &alpha, const amrex::Array4< amrex::Real > &beta, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &h, const amrex::Array4< amrex::Real const > &mskr, const int N)
Wrapper around equation of state calculation.
Definition REMORA_rho_eos.cpp:22
REMORA::vec_stflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_stflx
Surface tracer flux; working arrays.
Definition REMORA.H:423
REMORA::t3dmix2
void t3dmix2(const amrex::Box &bx, const amrex::Array4< amrex::Real > &state, const amrex::Array4< amrex::Real > &state_rhs, const amrex::Array4< amrex::Real const > &diff2, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const amrex::Real dt_lev, const int ncomp, const int N)
Wrapper for harmonic diffusivity for tracers.
Definition REMORA_t3dmix.cpp:21
REMORA::vec_gls
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_gls
Turbulent generic length scale.
Definition REMORA.H:550
REMORA::vec_sustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sustr
Surface stress in the u direction.
Definition REMORA.H:396
REMORA::zvel_new
amrex::Vector< amrex::MultiFab * > zvel_new
multilevel data container for current step's z velocities (largely unused; W stored separately)
Definition REMORA.H:321
REMORA::vec_sstore
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sstore
additional scratch space for calculations on temp, salt, etc
Definition REMORA.H:528
REMORA::v_clim_data_from_file
std::unique_ptr< NCTimeSeries > v_clim_data_from_file
Data container for v-velocity climatology data read from file.
Definition REMORA.H:1327
REMORA::rhs_uv_3d
void rhs_uv_3d(int lev, const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real > &rufrc, const amrex::Array4< amrex::Real > &rvfrc, const amrex::Array4< amrex::Real const > &sustr, const amrex::Array4< amrex::Real const > &svstr, const amrex::Array4< amrex::Real const > &bustr, const amrex::Array4< amrex::Real const > &bvstr, const amrex::Array4< amrex::Real const > &Huon, const amrex::Array4< amrex::Real const > &Hvom, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &W, const amrex::Array4< amrex::Real > &FC, int nrhs, int N)
RHS terms for 3D momentum.
Definition REMORA_rhs_uv_3d.cpp:29
REMORA::vec_Hz
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Hz
Width of cells in the vertical (z-) direction (3D, Hz in ROMS)
Definition REMORA.H:341
REMORA::vec_msku
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_msku
land/sea mask at x-faces (2D)
Definition REMORA.H:482
REMORA::vec_rvfrc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rvfrc
v velocity RHS, integrated, including advection and bottom/surface stresses (2D)
Definition REMORA.H:357
REMORA::v2d_simple_bc
int v2d_simple_bc() const noexcept
Definition REMORA.H:1191
REMORA::u_clim_data_from_file
std::unique_ptr< NCTimeSeries > u_clim_data_from_file
Data container for u-velocity climatology data read from file.
Definition REMORA.H:1325
REMORA::FillPatchNoBC
void FillPatchNoBC(int lev, amrex::Real time, amrex::MultiFab &mf_to_be_filled, amrex::Vector< amrex::MultiFab * > const &mfs, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const bool fill_set=true)
Fill a new MultiFab by copying in phi from valid region and filling ghost cells without applying boun...
Definition REMORA_FillPatch.cpp:199
REMORA::xvel_old
amrex::Vector< amrex::MultiFab * > xvel_old
multilevel data container for last step's x velocities (u in ROMS)
Definition REMORA.H:308
REMORA::yvel_new
amrex::Vector< amrex::MultiFab * > yvel_new
multilevel data container for current step's y velocities (v in ROMS)
Definition REMORA.H:319
REMORA::vec_uwind
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_uwind
Wind in the u direction, defined at rho-points.
Definition REMORA.H:401
REMORA::vec_rufrc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rufrc
u velocity RHS, integrated, including advection and bottom/surface stresses (2D)
Definition REMORA.H:355
REMORA::gls_prestep
void gls_prestep(int lev, amrex::MultiFab *mf_gls, amrex::MultiFab *mf_tke, amrex::MultiFab &mf_W, amrex::MultiFab *mf_msku, amrex::MultiFab *mf_mskv, const int nstp, const int nnew, const int iic, const int ntfirst, const int N, const amrex::Real dt_lev)
Prestep for GLS calculation.
Definition REMORA_gls.cpp:20
REMORA::vec_shflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_shflx
sensible heat flux
Definition REMORA.H:420
REMORA::vec_visc2_p
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_visc2_p
Harmonic viscosity defined on the psi points (corners of horizontal grid cells)
Definition REMORA.H:363
REMORA::vec_dmde
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_dmde
d(1/m)/d(eta)
Definition REMORA.H:525
REMORA::zvel_old
amrex::Vector< amrex::MultiFab * > zvel_old
multilevel data container for last step's z velocities (largely unused; W stored separately)
Definition REMORA.H:312
REMORA::vec_z_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_r
z coordinates at rho points (cell centers)
Definition REMORA.H:370
REMORA::xvel_new
amrex::Vector< amrex::MultiFab * > xvel_new
multilevel data container for current step's x velocities (u in ROMS)
Definition REMORA.H:317
REMORA::vec_lhflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_lhflx
latent heat flux
Definition REMORA.H:418
REMORA::u2d_simple_bc
int u2d_simple_bc() const noexcept
Definition REMORA.H:1190
REMORA::vec_mskp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskp
land/sea mask at cell corners (2D)
Definition REMORA.H:486
REMORA::prestep
void prestep(int lev, amrex::MultiFab &mf_uold, amrex::MultiFab &mf_vold, amrex::MultiFab &mf_u, amrex::MultiFab &mf_v, amrex::MultiFab *mf_ru, amrex::MultiFab *mf_rv, amrex::MultiFab &S_old, amrex::MultiFab &S_new, amrex::MultiFab &mf_W, amrex::MultiFab &mf_DC, const amrex::MultiFab *mf_z_r, const amrex::MultiFab *mf_z_w, const amrex::MultiFab *mf_h, const amrex::MultiFab *mf_pm, const amrex::MultiFab *mf_pn, const amrex::MultiFab *mf_sustr, const amrex::MultiFab *mf_svstr, const amrex::MultiFab *mf_bustr, const amrex::MultiFab *mf_bvstr, const amrex::MultiFab *mf_msku, const amrex::MultiFab *mf_mskv, const int iic, const int nfirst, const int nnew, int nstp, int nrhs, int N, const amrex::Real dt_lev)
Wrapper function for prestep.
Definition REMORA_prestep.cpp:38
REMORA::vec_bvf
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bvf
Brunt-Vaisala frequency (3D)
Definition REMORA.H:535
REMORA::vec_mskv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskv
land/sea mask at y-faces (2D)
Definition REMORA.H:484
REMORA::physbcs
amrex::Vector< std::unique_ptr< REMORAPhysBCFunct > > physbcs
Vector (over level) of functors to apply physical boundary conditions.
Definition REMORA.H:1417
REMORA::FillPatch
void FillPatch(int lev, amrex::Real time, amrex::MultiFab &mf_to_be_filled, amrex::Vector< amrex::MultiFab * > const &mfs, const int bccomp, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const bool fill_set=true, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=amrex::Real(0.0), const amrex::MultiFab &mf_calc=amrex::MultiFab())
Fill a new MultiFab by copying in phi from valid region and filling ghost cells.
Definition REMORA_FillPatch.cpp:30
REMORA::istep
amrex::Vector< int > istep
which step?
Definition REMORA.H:1403
REMORA::apply_clim_nudg
void apply_clim_nudg(const amrex::Box &bx, int ioff, int joff, const amrex::Array4< amrex::Real > &var, const amrex::Array4< amrex::Real const > &var_old, const amrex::Array4< amrex::Real const > &var_clim, const amrex::Array4< amrex::Real const > &clim_coeff, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Real dt_lev=amrex::Real(0.0))
Apply climatology nudging.
Definition REMORA_apply_clim_nudg.cpp:19
REMORA::uv3dmix
void uv3dmix(const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real > &u, const amrex::Array4< amrex::Real > &v, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &rufrc, const amrex::Array4< amrex::Real > &rvfrc, const amrex::Array4< amrex::Real const > &visc2_p, const amrex::Array4< amrex::Real const > &visc2_r, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &mskp, int nrhs, int nnew, const amrex::Real dt_lev)
Harmonic viscosity.
Definition REMORA_uv3dmix.cpp:25
REMORA::set_analytic_vmix
void set_analytic_vmix(int lev)
Set vertical mixing coefficients from analytic.
Definition REMORA.cpp:791
REMORA::vec_rhoS
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoS
density perturbation
Definition REMORA.H:531
REMORA::vec_visc2_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_visc2_r
Harmonic viscosity defined on the rho points (centers)
Definition REMORA.H:365
REMORA::vec_svstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_svstr
Surface stress in the v direction.
Definition REMORA.H:398
REMORA::vec_Huon
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Huon
u-volume flux (3D)
Definition REMORA.H:343
REMORA::yvel_old
amrex::Vector< amrex::MultiFab * > yvel_old
multilevel data container for last step's y velocities (v in ROMS)
Definition REMORA.H:310
REMORA::vec_rhoA
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoA
vertically-averaged density
Definition REMORA.H:533
REMORA::t_new
amrex::Vector< amrex::Real > t_new
new time at each level
Definition REMORA.H:1407
REMORA::solverChoice
static SolverChoice solverChoice
Container for algorithmic choices.
Definition REMORA.H:1537
REMORA::vec_rdrag2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rdrag2
Quadratic drag coefficient [unitless], defined at rho points.
Definition REMORA.H:446
REMORA::vec_ru
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ru
u velocity RHS (3D, includes horizontal and vertical advection)
Definition REMORA.H:347
REMORA::vec_longwave_down
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_longwave_down
Downward longwave radiation.
Definition REMORA.H:416
REMORA::set_zeta_to_Ztavg
void set_zeta_to_Ztavg(int lev)
Set zeta components to be equal to time-averaged Zt_avg1.
Definition REMORA_make_new_level.cpp:890
REMORA::vec_alpha
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_alpha
Thermal expansion coefficient (3D)
Definition REMORA.H:537
REMORA::cons_old
amrex::Vector< amrex::MultiFab * > cons_old
multilevel data container for last step's scalar data: temperature, salinity, passive tracer
Definition REMORA.H:306
REMORA::vec_bustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bustr
Bottom stress in the u direction.
Definition REMORA.H:451
REMORA::set_wind
void set_wind(int lev)
Initialize or calculate wind speed from file or analytic.
Definition REMORA.cpp:1147
REMORA::vec_dndx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_dndx
d(1/n)/d(xi)
Definition REMORA.H:523
REMORA::vec_bvstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bvstr
Bottom stress in the v direction.
Definition REMORA.H:453
REMORA::vec_nudg_coeff
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > vec_nudg_coeff
Climatology nudging coefficients.
Definition REMORA.H:559
REMORA::vec_pn
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pn
horizontal scaling factor: 1 / dy (2D)
Definition REMORA.H:493
REMORA::curvilinear
void curvilinear(const amrex::Box &bx, const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &dndx, const amrex::Array4< amrex::Real const > &dmde, int nrhs, int nr)
Calculate curvilinear advection terms.
Definition REMORA_curvilinear.cpp:21
REMORA::vec_stflux
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_stflux
Surface tracer flux; input arrays.
Definition REMORA.H:425
REMORA::setup_step
void setup_step(int lev, amrex::Real time, amrex::Real dt_lev)
Set everything up for a step on a level.
Definition REMORA_setup_step.cpp:11
REMORA::vec_rdrag
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rdrag
Linear drag coefficient [m/s], defined at rho points.
Definition REMORA.H:444
REMORA::set_smflux
void set_smflux(int lev)
Initialize or calculate surface momentum flux from file or analytic.
Definition REMORA.cpp:1128
REMORA::vec_rv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rv
v velocity RHS (3D, includes horizontal and vertical advection)
Definition REMORA.H:349
REMORA::vec_btflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_btflx
Bottom tracer flux; working arrays.
Definition REMORA.H:427
REMORA::vec_beta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_beta
Saline contraction coefficient (3D)
Definition REMORA.H:539
REMORA::bulk_fluxes
void bulk_fluxes(int lev, amrex::MultiFab *mf_cons, amrex::MultiFab *mf_uwind, amrex::MultiFab *mf_vwind, amrex::MultiFab *mf_Tair, amrex::MultiFab *mf_qair, amrex::MultiFab *mf_Pair, amrex::MultiFab *mf_srflx, amrex::MultiFab *mf_longwave_down, amrex::MultiFab *mf_evap, amrex::MultiFab *mf_sustr, amrex::MultiFab *mf_svstr, amrex::MultiFab *mf_stflux, amrex::MultiFab *mf_lrflx, amrex::MultiFab *mf_lhflx, amrex::MultiFab *mf_shflx, const int N)
Calculate bulk temperature, salinity, wind fluxes.
Definition REMORA_bulk_flux.cpp:25
REMORA::vec_srflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_srflx
Shortwave radiation flux [W/m²], defined at rho-points.
Definition REMORA.H:412
REMORA::vec_Pair
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Pair
Air pressure [mb], defined at rho-points.
Definition REMORA.H:409
REMORA::coriolis
void coriolis(const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &fomn, int nrhs, int nr)
Calculate Coriolis terms.
Definition REMORA_coriolis.cpp:19
REMORA::vec_qair
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_qair
Specific humidity [kg/kg], defined at rho-points.
Definition REMORA.H:407
REMORA::vec_z_w
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_w
z coordinates at w points (faces between z-cells)
Definition REMORA.H:373
REMORA::vec_Tair
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Tair
Air temperature [°C], defined at rho-points.
Definition REMORA.H:405
REMORA::vec_Hvom
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Hvom
v-volume flux (3D)
Definition REMORA.H:345
REMORA::vec_diff2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_diff2
Harmonic diffusivity for temperature / salinity.
Definition REMORA.H:367
BCVars::cons_bc
static constexpr int cons_bc
Definition REMORA_IndexDefines.H:24
SolverChoice::Cdb_min
amrex::Real Cdb_min
Definition REMORA_DataStruct.H:721
SolverChoice::bottom_stress_type
BottomStressType bottom_stress_type
Definition REMORA_DataStruct.H:691
SolverChoice::vert_mixing_type
VertMixingType vert_mixing_type
Definition REMORA_DataStruct.H:697
SolverChoice::Cdb_max
amrex::Real Cdb_max
Definition REMORA_DataStruct.H:720