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 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, BCVars::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 // Place-holder for source array -- for now just set to 0
43 MultiFab source(ba,dm,nvars,1);
44 source.setVal(0.0_rt);
45
46 //-----------------------------------------------------------------------
47 // Time step momentum equation
48 //-----------------------------------------------------------------------
49
50 //Only used locally, probably should be rearranged into FArrayBox declaration
51 MultiFab mf_AK(ba,dm,1,IntVect(NGROW,NGROW,0)); //2d missing j coordinate
52 MultiFab mf_DC(ba,dm,1,IntVect(NGROW,NGROW,NGROW-1)); //2d missing j coordinate
53 MultiFab mf_Hzk(ba,dm,1,IntVect(NGROW,NGROW,NGROW-1)); //2d missing j coordinate
54 MultiFab mf_logdrg_tmp(ba,dm,1,IntVect(NGROW,NGROW,0));
55
56 MultiFab* mf_z_r = vec_z_r[lev].get();
57 MultiFab* mf_z_w = vec_z_w[lev].get();
58 MultiFab* mf_h = vec_hOfTheConfusingName[lev].get();
59 MultiFab* mf_pm = vec_pm[lev].get();
60 MultiFab* mf_pn = vec_pn[lev].get();
61 MultiFab* mf_fcor = vec_fcor[lev].get();
62
63 MultiFab* mf_gls = vec_gls[lev].get();
64 MultiFab* mf_tke = vec_tke[lev].get();
65
66 //Consider passing these into the advance function or renaming relevant things
67
68 MultiFab mf_rho(ba,dm,1,IntVect(NGROW,NGROW,0));
69 std::unique_ptr<MultiFab>& mf_rhoS = vec_rhoS[lev];
70 std::unique_ptr<MultiFab>& mf_rhoA = vec_rhoA[lev];
71 std::unique_ptr<MultiFab>& mf_bvf = vec_bvf[lev];
72 std::unique_ptr<MultiFab>& mf_ru = vec_ru[lev];
73 std::unique_ptr<MultiFab>& mf_rv = vec_rv[lev];
74 std::unique_ptr<MultiFab>& mf_rufrc = vec_rufrc[lev];
75 std::unique_ptr<MultiFab>& mf_rvfrc = vec_rvfrc[lev];
76 std::unique_ptr<MultiFab>& mf_sustr = vec_sustr[lev];
77 std::unique_ptr<MultiFab>& mf_svstr = vec_svstr[lev];
78 std::unique_ptr<MultiFab>& mf_rdrag = vec_rdrag[lev];
79 std::unique_ptr<MultiFab>& mf_rdrag2 = vec_rdrag2[lev];
80 std::unique_ptr<MultiFab>& mf_ZoBot = vec_ZoBot[lev];
81 std::unique_ptr<MultiFab>& mf_bustr = vec_bustr[lev];
82 std::unique_ptr<MultiFab>& mf_bvstr = vec_bvstr[lev];
83
84 std::unique_ptr<MultiFab>& mf_mskr = vec_mskr[lev];
85 std::unique_ptr<MultiFab>& mf_msku = vec_msku[lev];
86 std::unique_ptr<MultiFab>& mf_mskv = vec_mskv[lev];
87 std::unique_ptr<MultiFab>& mf_mskp = vec_mskp[lev];
88
89 MultiFab mf_rw(ba,dm,1,IntVect(NGROW,NGROW,0));
90
91 std::unique_ptr<MultiFab>& mf_visc2_p = vec_visc2_p[lev];
92 std::unique_ptr<MultiFab>& mf_visc2_r = vec_visc2_r[lev];
93
94 // We need to set these because otherwise in the first call to remora_advance we may
95 // read uninitialized data on ghost values in setting the bc's on the velocities
96 mf_rho.setVal(0.e34_rt,IntVect(AMREX_D_DECL(NGROW-1,NGROW-1,0)));
97 mf_rhoS->setVal(0.e34_rt,IntVect(AMREX_D_DECL(NGROW-1,NGROW-1,0)));
98 mf_rhoA->setVal(0.e34_rt,IntVect(AMREX_D_DECL(NGROW-1,NGROW-1,0)));
99
100 mf_DC.setVal(0);
101
102 FillPatchNoBC(lev, time, *cons_new[lev], cons_new, BdyVars::t);
103 FillPatchNoBC(lev, time, *xvel_new[lev], xvel_new, BdyVars::u);
104 FillPatchNoBC(lev, time, *yvel_new[lev], yvel_new, BdyVars::v);
105
106 mf_rw.setVal(0.0_rt);
107 mf_rufrc->setVal(0);
108 mf_rvfrc->setVal(0);
109
110 int iic = istep[lev];
111 int ntfirst = 0;
112 if(iic==ntfirst) {
113 MultiFab::Copy(S_new,S_old,0,0,S_new.nComp(),S_new.nGrowVect());
114 MultiFab::Copy(U_new,U_old,0,0,U_new.nComp(),U_new.nGrowVect());
115 MultiFab::Copy(V_new,V_old,0,0,V_new.nComp(),V_new.nGrowVect());
116 MultiFab::Copy(W_new,W_old,0,0,W_new.nComp(),W_new.nGrowVect());
117 }
118
119 // If we're not doing bulk fluxes, set surface momentum fluxes directly.
120 // Otherwise, calculate them from winds, so those need to be set
121 if (!solverChoice.bulk_fluxes) {
122 set_smflux(lev);
123 } else {
124 set_wind(lev);
125 }
126
127 auto N = Geom(lev).Domain().size()[2]-1; // Number of vertical "levs" aka, NZ
128
129 const auto dlo = amrex::lbound(Geom(lev).Domain());
130 const auto dhi = amrex::ubound(Geom(lev).Domain());
131
132 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
133 {
134 Array4<Real const> const& h = vec_hOfTheConfusingName[lev]->const_array(mfi);
135 Array4<Real const> const& Hz = vec_Hz[lev]->const_array(mfi);
136 Array4<Real > const& Huon = vec_Huon[lev]->array(mfi);
137 Array4<Real > const& Hvom = vec_Hvom[lev]->array(mfi);
138
139 Array4<Real const> const& z_w = mf_z_w->const_array(mfi);
140 Array4<Real const> const& z_r = mf_z_r->const_array(mfi);
141 Array4<Real const> const& uold = U_old.const_array(mfi);
142 Array4<Real const> const& vold = V_old.const_array(mfi);
143 Array4<Real > const& rho = mf_rho.array(mfi);
144 Array4<Real > const& rhoA = mf_rhoA->array(mfi);
145 Array4<Real > const& rhoS = mf_rhoS->array(mfi);
146 Array4<Real > const& bvf = mf_bvf->array(mfi);
147 Array4<Real > const& alpha = (solverChoice.bulk_fluxes) ? vec_alpha[lev]->array(mfi) : Array4<Real>();
148 Array4<Real > const& beta = (solverChoice.bulk_fluxes) ? vec_beta[lev]->array(mfi) : Array4<Real>();
149
150 Array4<Real const> const& pm = mf_pm->const_array(mfi);
151 Array4<Real const> const& pn = mf_pn->const_array(mfi);
152
153 Array4<Real const> const& mskr = mf_mskr->const_array(mfi);
154
155 Box bx = mfi.tilebox();
156 Box gbx1 = mfi.growntilebox(IntVect(NGROW-1,NGROW-1,0));
157 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
158
159 Box bxD = bx;
160 bxD.makeSlab(2,0);
161 Box gbx1D = gbx1;
162 gbx1D.makeSlab(2,0);
163 Box gbx2D = gbx2;
164 gbx2D.makeSlab(2,0);
165
166 FArrayBox fab_FC(gbx2,1,amrex::The_Async_Arena()); //3D
167 FArrayBox fab_FX(gbx2,1,amrex::The_Async_Arena()); //3D
168 FArrayBox fab_FE(gbx2,1,amrex::The_Async_Arena()); //3D
169 FArrayBox fab_BC(gbx2,1,amrex::The_Async_Arena());
170 FArrayBox fab_CF(gbx2,1,amrex::The_Async_Arena());
171
172 //
173 //-----------------------------------------------------------------------
174 // Compute horizontal mass fluxes, Hz*u/n and Hz*v/m (set_massflux_3d)
175 //-----------------------------------------------------------------------
176 //
177 ParallelFor(Box(Huon), [=] AMREX_GPU_DEVICE (int i, int j, int k)
178 {
179 Real on_u = 2.0_rt / (pn(i-1,j,0)+pn(i,j,0));
180 Huon(i,j,k)=0.5_rt*(Hz(i,j,k)+Hz(i-1,j,k))*uold(i,j,k)* on_u;
181 });
182
183 ParallelFor(Box(Hvom), [=] AMREX_GPU_DEVICE (int i, int j, int k)
184 {
185 Real om_v= 2.0_rt / (pm(i,j-1,0)+pm(i,j,0));
186 Hvom(i,j,k)=0.5_rt*(Hz(i,j,k)+Hz(i,j-1,k))*vold(i,j,k)* om_v;
187 });
188
189 Array4<Real const> const& state_old = S_old.const_array(mfi);
190 rho_eos(gbx2,state_old,rho,rhoA,rhoS,bvf,alpha,beta,Hz,z_w,z_r,h,mskr,N);
191 }
192
193 const Real Cdb_min = solverChoice.Cdb_min;
194 const Real Cdb_max = solverChoice.Cdb_max;
195
196 if (solverChoice.bulk_fluxes) {
197 bulk_fluxes(lev, cons_old[lev],vec_uwind[lev].get(),vec_vwind[lev].get(),
198 vec_evap[lev].get(),
199 vec_sustr[lev].get(),vec_svstr[lev].get(),vec_stflux[lev].get(),
200 vec_lrflx[lev].get(),vec_lhflx[lev].get(),vec_shflx[lev].get(),N);
201 vec_evap[lev]->FillBoundary(geom[lev].periodicity());
202 }
203
204 if (solverChoice.do_temp_flux) {
205 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
206 {
207 Array4<Real > const& stflx = vec_stflx[lev]->array(mfi);
208 Array4<Real > const& btflx = vec_btflx[lev]->array(mfi);
209 Array4<Real const> const& stflux = vec_stflux[lev]->array(mfi);
210 Array4<Real const> const& btflux = vec_btflux[lev]->array(mfi);
211 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
212 Box gbx2D = gbx2;
213 gbx2D.makeSlab(2,0);
214 ParallelFor(gbx2D, [=] AMREX_GPU_DEVICE (int i, int j, int ) {
215 stflx(i,j,0,Temp_comp) = stflux(i,j,0,Temp_comp);
216 btflx(i,j,0,Temp_comp) = btflux(i,j,0,Temp_comp);
217 });
218 }
219 }
220 if (solverChoice.do_salt_flux) {
221 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
222 {
223 Array4<Real > const& stflx = vec_stflx[lev]->array(mfi);
224 Array4<Real > const& btflx = vec_btflx[lev]->array(mfi);
225 Array4<Real const> const& stflux = vec_stflux[lev]->const_array(mfi);
226 Array4<Real const> const& salt_old = S_old.const_array(mfi,Salt_comp);
227 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
228 Box gbx2D = gbx2;
229 gbx2D.makeSlab(2,0);
230 ParallelFor(gbx2D, [=] AMREX_GPU_DEVICE (int i, int j, int ) {
231 stflx(i,j,0,Salt_comp) = stflux(i,j,0,Salt_comp) * salt_old(i,j,N);
232 // The fact that this is btflx on the RHS matches what's in ROMS even though
233 // it's weird -- if it's non-zero, does that mean that it will run away since
234 // it's always getting multiplied by salt?
235 btflx(i,j,0,Salt_comp) = btflx(i,j,0,Salt_comp) * salt_old(i,j,0);
236 });
237 }
238 }
239
240 for ( MFIter mfi(S_new, TilingIfNotGPU()); mfi.isValid(); ++mfi )
241 {
242 Array4<Real > const& bustr = mf_bustr->array(mfi);
243 Array4<Real > const& bvstr = mf_bvstr->array(mfi);
244 Array4<Real const> const& uold = U_old.const_array(mfi);
245 Array4<Real const> const& vold = V_old.const_array(mfi);
246 Array4<Real > const& logdrg_tmp = mf_logdrg_tmp.array(mfi);
247 Array4<Real const> const& z_r = mf_z_r->const_array(mfi);
248 Array4<Real const> const& z_w = mf_z_w->const_array(mfi);
249
250 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
251 Box gbx2D = gbx2;
252 gbx2D.makeSlab(2,0);
253 Box ubx1 = mfi.grownnodaltilebox(0,IntVect(NGROW-1,NGROW-1,0));
254 Box ubx1D = ubx1;
255 ubx1D.makeSlab(2,0);
256 Box vbx1 = mfi.grownnodaltilebox(1,IntVect(NGROW-1,NGROW-1,0));
257 Box vbx1D = vbx1;
258 vbx1D.makeSlab(2,0);
259 // Set bottom stress as defined in set_vbx.F
260 if (solverChoice.bottom_stress_type == BottomStressType::linear) {
261 Array4<Real const> const& rdrag = mf_rdrag->const_array(mfi);
262 ParallelFor(ubx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
263 {
264 bustr(i,j,0) = 0.5_rt * (rdrag(i-1,j,0)+rdrag(i,j,0))*(uold(i,j,0));
265 });
266 ParallelFor(vbx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
267 {
268 bvstr(i,j,0) = 0.5_rt * (rdrag(i,j-1,0)+rdrag(i,j,0))*(vold(i,j,0));
269 });
270 } else if (solverChoice.bottom_stress_type == BottomStressType::quadratic) {
271 Array4<Real const> const& rdrag2 = mf_rdrag2->const_array(mfi);
272 ParallelFor(ubx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
273 {
274 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));
275 Real vel_mag = std::sqrt(uold(i,j,0)*uold(i,j,0) + avg_v * avg_v);
276 bustr(i,j,0) = 0.5_rt * (rdrag2(i-1,j,0) + rdrag2(i,j,0)) * uold(i,j,0) * vel_mag;
277 });
278 ParallelFor(vbx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
279 {
280 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));
281 Real vel_mag = std::sqrt(avg_u * avg_u + vold(i,j,0) * vold(i,j,0));
282 bvstr(i,j,0) = 0.5_rt * (rdrag2(i,j-1,0) + rdrag2(i,j,0)) * vold(i,j,0) * vel_mag;
283 });
284 } else if (solverChoice.bottom_stress_type == BottomStressType::logarithmic) {
285 Array4<Real const> const& ZoBot = mf_ZoBot->const_array(mfi);
286 ParallelFor(gbx2D, [=] AMREX_GPU_DEVICE (int i, int j, int )
287 {
288 Real logz = 1.0_rt / (std::log((z_r(i,j,0) - z_w(i,j,0)) / ZoBot(i,j,0)));
289 Real cff = vonKar * vonKar * logz * logz;
290 logdrg_tmp(i,j,0) = std::min(Cdb_max,std::max(Cdb_min,cff));
291 });
292 ParallelFor(ubx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
293 {
294 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));
295 Real vel_mag = std::sqrt(uold(i,j,0)*uold(i,j,0) + avg_v * avg_v);
296 bustr(i,j,0) = 0.5_rt * (logdrg_tmp(i-1,j,0)+logdrg_tmp(i,j,0)) * uold(i,j,0) * vel_mag;
297 });
298 ParallelFor(vbx1D, [=] AMREX_GPU_DEVICE (int i, int j, int )
299 {
300 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));
301 Real vel_mag = std::sqrt(avg_u * avg_u + vold(i,j,0) * vold(i,j,0));
302 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 });
304 }
305 }
306 FillPatch(lev, time, *vec_bustr[lev].get(), GetVecOfPtrs(vec_bustr), BCVars::u2d_simple_bc, BdyVars::null,0,true,false);
307 FillPatch(lev, time, *vec_bvstr[lev].get(), GetVecOfPtrs(vec_bvstr), BCVars::v2d_simple_bc, BdyVars::null,0,true,false);
308
309 if (solverChoice.vert_mixing_type == VertMixingType::analytic) {
310 // Update Akv if using analytic mixing
311 set_analytic_vmix(lev);
312 }
313
314 set_zeta_to_Ztavg(lev);
315
316 MultiFab mf_W(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW+1,NGROW+1,0));
317 mf_W.setVal(0.0_rt);
318
319
320 if (solverChoice.use_prestep) {
321 const int nnew = 0;
322 prestep(lev, U_old, V_old, U_new, V_new,
323 mf_ru.get(), mf_rv.get(),
324 S_old, S_new, mf_W,
325 mf_DC, mf_z_r, mf_z_w, mf_h, mf_pm, mf_pn,
326 mf_sustr.get(), mf_svstr.get(), mf_bustr.get(), mf_bvstr.get(),
327 mf_msku.get(), mf_mskv.get(),
328 iic, ntfirst, nnew, nstp, nrhs, N, dt_lev);
329 }
330
331 // We use FillBoundary not FillPatch here since mf_W is single-level scratch space
332 mf_W.FillBoundary(geom[lev].periodicity());
333 (*physbcs[lev])(mf_W,*mf_mskr.get(),0,1,mf_W.nGrowVect(),t_new[lev],BCVars::zvel_bc);
334
335#ifdef REMORA_USE_NETCDF
336 // Get u and v climatology if we're going to do nudging
337 if (solverChoice.do_m3_clim_nudg) {
338 u_clim_data_from_file->update_interpolated_to_time(t_new[lev]);
339 v_clim_data_from_file->update_interpolated_to_time(t_new[lev]);
340 }
341#endif
342
343 for ( MFIter mfi(S_old, TilingIfNotGPU()); mfi.isValid(); ++mfi )
344 {
345 Array4<Real const> const& Hz = vec_Hz[lev]->const_array(mfi);
346 Array4<Real> const& Huon = vec_Huon[lev]->array(mfi);
347 Array4<Real> const& Hvom = vec_Hvom[lev]->array(mfi);
348 Array4<Real> const& z_r = (mf_z_r)->array(mfi);
349 Array4<Real> const& z_w = (mf_z_w)->array(mfi);
350 Array4<Real const> const& uold = U_old.const_array(mfi);
351 Array4<Real const> const& vold = V_old.const_array(mfi);
352 Array4<Real> const& u = U_new.array(mfi);
353 Array4<Real> const& v = V_new.array(mfi);
354 Array4<Real> const& rho = (mf_rho).array(mfi);
355 Array4<Real> const& ru = (mf_ru)->array(mfi);
356 Array4<Real> const& rv = (mf_rv)->array(mfi);
357 Array4<Real> const& rufrc = (mf_rufrc)->array(mfi);
358 Array4<Real> const& rvfrc = (mf_rvfrc)->array(mfi);
359 Array4<Real> const& W = (mf_W).array(mfi);
360 Array4<Real> const& sustr = (mf_sustr)->array(mfi);
361 Array4<Real> const& svstr = (mf_svstr)->array(mfi);
362 Array4<Real> const& bustr = (mf_bustr)->array(mfi);
363 Array4<Real> const& bvstr = (mf_bvstr)->array(mfi);
364 Array4<Real> const& visc2_p = (mf_visc2_p)->array(mfi);
365 Array4<Real> const& visc2_r = (mf_visc2_r)->array(mfi);
366
367 Array4<Real const> const& pm = mf_pm->const_array(mfi);
368 Array4<Real const> const& pn = mf_pn->const_array(mfi);
369 Array4<Real const> const& fcor = mf_fcor->const_array(mfi);
370
371 Array4<Real const> const& msku = mf_msku->const_array(mfi);
372 Array4<Real const> const& mskv = mf_mskv->const_array(mfi);
373 Array4<Real const> const& mskp = mf_mskp->const_array(mfi);
374
375 Box bx = mfi.tilebox();
376
377 Box tbxp1 = bx;
378 Box tbxp2 = bx;
379 Box xbx = mfi.nodaltilebox(0);
380 Box ybx = mfi.nodaltilebox(1);
381 Box xbx_adj = mfi.nodaltilebox(0);
382 Box ybx_adj = mfi.nodaltilebox(1);
383
384 auto xbx_lo = lbound(xbx_adj);
385 auto xbx_hi = ubound(xbx_adj);
386 auto ybx_lo = lbound(ybx_adj);
387 auto ybx_hi = ubound(ybx_adj);
388
389 if (xbx_lo.x == dlo.x) {
390 xbx_adj.growLo(0,-1);
391 } else if (xbx_hi.x == dhi.x) {
392 xbx_adj.growHi(0,-1);
393 }
394
395 if (ybx_lo.y == dlo.y) {
396 ybx_adj.growLo(1,-1);
397 } else if (ybx_hi.y == dhi.y) {
398 ybx_adj.growHi(1,-1);
399 }
400
401 Box gbx1 = mfi.growntilebox(IntVect(NGROW-1,NGROW-1,0));
402 Box gbx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));
403
404 Box utbx = mfi.nodaltilebox(0);
405 Box vtbx = mfi.nodaltilebox(1);
406
407 tbxp1.grow(IntVect(NGROW-1,NGROW-1,0));
408 tbxp2.grow(IntVect(NGROW,NGROW,0));
409
410 Box bxD = bx;
411 bxD.makeSlab(2,0);
412 Box gbx1D = gbx1;
413 gbx1D.makeSlab(2,0);
414 Box gbx2D = gbx2;
415 gbx2D.makeSlab(2,0);
416
417 Box tbxp1D = tbxp1;
418 tbxp1D.makeSlab(2,0);
419 Box tbxp2D = tbxp2;
420 tbxp2D.makeSlab(2,0);
421
422 FArrayBox fab_FC(surroundingNodes(tbxp2,2),1,amrex::The_Async_Arena()); //3D
423 FArrayBox fab_FX(gbx2,1,amrex::The_Async_Arena()); //3D
424 FArrayBox fab_FE(gbx2,1,amrex::The_Async_Arena()); //3D
425 FArrayBox fab_BC(gbx2,1,amrex::The_Async_Arena());
426 FArrayBox fab_CF(gbx2,1,amrex::The_Async_Arena());
427
428 FArrayBox fab_fomn(tbxp2D,1,amrex::The_Async_Arena());
429
430 auto FC=fab_FC.array();
431
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 t3dmix(bx, s_arr, s_arr_rhs, diff2_arr, Hz, pm, pn, msku, mskv, dt_lev, ncomp);
455
456 Array4<Real> const& diff2_arr_scalar = vec_diff2[lev]->array(mfi,Scalar_comp);
457 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);
458
459 if (solverChoice.use_coriolis) {
460 //-----------------------------------------------------------------------
461 // coriolis
462 //-----------------------------------------------------------------------
463 //
464 // ru, rv updated
465 // In ROMS, coriolis is the first (un-ifdefed) thing to happen in rhs3d_tile, which gets called after t3dmix
466 coriolis(xbx, ybx, uold, vold, ru, rv, Hz, fomn, nrhs, nrhs);
467 }
468
469#ifdef REMORA_USE_NETCDF
470 if (solverChoice.do_m3_clim_nudg) {
471 Array4<const Real> const& uclim = u_clim_data_from_file->mf_interpolated->const_array(mfi);
472 Array4<const Real> const& vclim = v_clim_data_from_file->mf_interpolated->const_array(mfi);
473 Array4<const Real> const& u_nudg_coeff = vec_nudg_coeff[BdyVars::u][lev]->const_array(mfi);
474 Array4<const Real> const& v_nudg_coeff = vec_nudg_coeff[BdyVars::v][lev]->const_array(mfi);
475 // These boxes are set to match ROMS
476 apply_clim_nudg(xbx_adj, 1, 0, ru, uold, uclim, u_nudg_coeff, Hz, pm, pn);
477 apply_clim_nudg(ybx_adj, 0, 1, rv, vold, vclim, v_nudg_coeff, Hz, pm, pn);
478 }
479#endif
480
481 ////rufrc from 3d is set to ru, then the wind stress (and bottom stress) is added, then the mixing is added
482 //rufrc=ru+sustr*om_u*on_u
483
484 rhs_uv_3d(xbx, ybx, uold, vold, ru, rv, rufrc, rvfrc,
485 sustr, svstr, bustr, bvstr, Huon, Hvom,
486 pm, pn, W, FC, nrhs, N);
487
488 if(solverChoice.use_uv3dmix) {
489 const int nnew = 0;
490 uv3dmix(xbx, ybx, u, v, uold, vold, rufrc, rvfrc, visc2_p, visc2_r, Hz, pm, pn, mskp, nrhs, nnew, dt_lev);
491 }
492 } // MFIter
493
494 int nnew = (iic +1)% 2;
495 nstp = iic % 2;
496 if (solverChoice.vert_mixing_type == VertMixingType::GLS) {
497 gls_prestep(lev, mf_gls, mf_tke, mf_W, mf_msku.get(), mf_mskv.get(),
498 nstp, nnew, iic, ntfirst, N, dt_lev);
499 }
500 nstp = 0;
501
502 // Commenting out for now, but not sure it's necessary
503 //FillPatch(lev, time, *cons_old[lev], cons_old, BCVars::cons_bc, BdyVars::t);
504 //FillPatch(lev, time, *cons_new[lev], cons_new, BCVars::cons_bc, BdyVars::t);
505 FillPatch(lev, time, *vec_sstore[lev], GetVecOfPtrs(vec_sstore), BCVars::cons_bc, BdyVars::t,0,true,true,0,0,dt_lev,*cons_old[lev]);
506
507 // Don't actually want to apply boundary conditions here
508 vec_Huon[lev]->FillBoundary(geom[lev].periodicity());
509 vec_Hvom[lev]->FillBoundary(geom[lev].periodicity());
510}
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:13
Temp_comp
#define Temp_comp
Definition REMORA_IndexDefines.H:8
Scalar_comp
#define Scalar_comp
Definition REMORA_IndexDefines.H:10
Salt_comp
#define Salt_comp
Definition REMORA_IndexDefines.H:9
NCTimeSeries::mf_interpolated
amrex::MultiFab * mf_interpolated
Definition REMORA_NCTimeSeries.H:35
NCTimeSeries::update_interpolated_to_time
void update_interpolated_to_time(amrex::Real time)
Calculate interpolated values at time, reading in data as necessary.
Definition REMORA_NCTimeSeries.cpp:96
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:310
REMORA::vec_fcor
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_fcor
coriolis factor (2D)
Definition REMORA.H:360
REMORA::vec_btflux
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_btflux
Bottom tracer flux; input arrays.
Definition REMORA.H:305
REMORA::vec_hOfTheConfusingName
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_hOfTheConfusingName
Bathymetry data (2D, positive valued, h in ROMS)
Definition REMORA.H:229
REMORA::vec_pm
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pm
horizontal scaling factor: 1 / dx (2D)
Definition REMORA.H:355
REMORA::vec_ZoBot
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ZoBot
Bottom roughness length [m], defined at rho points.
Definition REMORA.H:317
REMORA::vec_lrflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_lrflx
longwave radiation
Definition REMORA.H:292
REMORA::cons_new
amrex::Vector< amrex::MultiFab * > cons_new
multilevel data container for current step's scalar data: temperature, salinity, passive scalar
Definition REMORA.H:217
REMORA::vec_vwind
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_vwind
Wind in the v direction, defined at rho-points.
Definition REMORA.H:289
REMORA::vec_mskr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskr
land/sea mask at cell centers (2D)
Definition REMORA.H:346
REMORA::vec_tke
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_tke
Turbulent kinetic energy.
Definition REMORA.H:403
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:299
REMORA::vec_gls
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_gls
Turbulent generic length scale.
Definition REMORA.H:405
REMORA::vec_sustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sustr
Surface stress in the u direction.
Definition REMORA.H:282
REMORA::v_clim_data_from_file
NCTimeSeries * v_clim_data_from_file
Data container for v-velocity climatology data read from file.
Definition REMORA.H:1022
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:223
REMORA::vec_sstore
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sstore
additional scratch space for calculations on temp, salt, etc
Definition REMORA.H:383
REMORA::t3dmix
void t3dmix(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 > &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)
Harmonic diffusivity for tracers.
Definition REMORA_t3dmix.cpp:19
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:232
REMORA::vec_msku
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_msku
land/sea mask at x-faces (2D)
Definition REMORA.H:348
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:248
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:192
REMORA::u_clim_data_from_file
NCTimeSeries * u_clim_data_from_file
Data container for u-velocity climatology data read from file.
Definition REMORA.H:1020
REMORA::xvel_old
amrex::Vector< amrex::MultiFab * > xvel_old
multilevel data container for last step's x velocities (u in ROMS)
Definition REMORA.H:210
REMORA::yvel_new
amrex::Vector< amrex::MultiFab * > yvel_new
multilevel data container for current step's y velocities (v in ROMS)
Definition REMORA.H:221
REMORA::vec_uwind
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_uwind
Wind in the u direction, defined at rho-points.
Definition REMORA.H:287
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:246
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:296
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:254
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:214
REMORA::vec_z_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_r
z coordinates at rho points (cell centers)
Definition REMORA.H:261
REMORA::xvel_new
amrex::Vector< amrex::MultiFab * > xvel_new
multilevel data container for current step's x velocities (u in ROMS)
Definition REMORA.H:219
REMORA::vec_lhflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_lhflx
latent heat flux
Definition REMORA.H:294
REMORA::vec_mskp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskp
land/sea mask at cell corners (2D)
Definition REMORA.H:352
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::rhs_uv_3d
void rhs_uv_3d(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:28
REMORA::vec_bvf
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bvf
Brunt-Vaisala frequency (3D)
Definition REMORA.H:390
REMORA::vec_mskv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskv
land/sea mask at y-faces (2D)
Definition REMORA.H:350
REMORA::physbcs
amrex::Vector< std::unique_ptr< REMORAPhysBCFunct > > physbcs
Vector (over level) of functors to apply physical boundary conditions.
Definition REMORA.H:1108
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:1094
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:599
REMORA::vec_rhoS
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoS
density perturbation
Definition REMORA.H:386
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:256
REMORA::vec_svstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_svstr
Surface stress in the v direction.
Definition REMORA.H:284
REMORA::vec_Huon
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Huon
u-volume flux (3D)
Definition REMORA.H:234
REMORA::bulk_fluxes
void bulk_fluxes(int lev, amrex::MultiFab *mf_cons, amrex::MultiFab *mf_uwind, amrex::MultiFab *mf_vwind, 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:20
REMORA::yvel_old
amrex::Vector< amrex::MultiFab * > yvel_old
multilevel data container for last step's y velocities (v in ROMS)
Definition REMORA.H:212
REMORA::vec_rhoA
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoA
vertically-averaged density
Definition REMORA.H:388
REMORA::t_new
amrex::Vector< amrex::Real > t_new
new time at each level
Definition REMORA.H:1098
REMORA::solverChoice
static SolverChoice solverChoice
Container for algorithmic choices.
Definition REMORA.H:1221
REMORA::vec_rdrag2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rdrag2
Quadratic drag coefficient [unitless], defined at rho points.
Definition REMORA.H:315
REMORA::vec_ru
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ru
u velocity RHS (3D, includes horizontal and vertical advection)
Definition REMORA.H:238
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:724
REMORA::vec_alpha
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_alpha
Thermal expansion coefficient (3D)
Definition REMORA.H:392
REMORA::cons_old
amrex::Vector< amrex::MultiFab * > cons_old
multilevel data container for last step's scalar data: temperature, salinity, passive scalar
Definition REMORA.H:208
REMORA::vec_bustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bustr
Bottom stress in the u direction.
Definition REMORA.H:320
REMORA::set_wind
void set_wind(int lev)
Initialize or calculate wind speed from file or analytic.
Definition REMORA.cpp:655
REMORA::vec_bvstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bvstr
Bottom stress in the v direction.
Definition REMORA.H:322
REMORA::vec_nudg_coeff
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > vec_nudg_coeff
Climatology nudging coefficients.
Definition REMORA.H:414
REMORA::vec_pn
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pn
horizontal scaling factor: 1 / dy (2D)
Definition REMORA.H:357
REMORA::vec_stflux
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_stflux
Surface tracer flux; input arrays.
Definition REMORA.H:301
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:313
REMORA::set_smflux
void set_smflux(int lev)
Initialize or calculate surface momentum flux from file or analytic.
Definition REMORA.cpp:637
REMORA::vec_rv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rv
v velocity RHS (3D, includes horizontal and vertical advection)
Definition REMORA.H:240
REMORA::vec_btflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_btflx
Bottom tracer flux; working arrays.
Definition REMORA.H:303
REMORA::vec_beta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_beta
Saline contraction coefficient (3D)
Definition REMORA.H:394
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_z_w
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_w
z coordinates at w points (faces between z-cells)
Definition REMORA.H:264
REMORA::vec_Hvom
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Hvom
v-volume flux (3D)
Definition REMORA.H:236
REMORA::vec_diff2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_diff2
Harmonic diffusivity for temperature / salinity.
Definition REMORA.H:258
SolverChoice::Cdb_min
amrex::Real Cdb_min
Definition REMORA_DataStruct.H:592
SolverChoice::bottom_stress_type
BottomStressType bottom_stress_type
Definition REMORA_DataStruct.H:567
SolverChoice::vert_mixing_type
VertMixingType vert_mixing_type
Definition REMORA_DataStruct.H:570
SolverChoice::Cdb_max
amrex::Real Cdb_max
Definition REMORA_DataStruct.H:591