REMORA
Regional Modeling of Oceans Refined Adaptively
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REMORA_make_new_level.cpp
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1/**
2 * \file REMORA_make_new_level.cpp
3 */
4
5#include <REMORA.H>
6#include <REMORA_prob_common.H>
7
8#include <AMReX_buildInfo.H>
9
10using namespace amrex;
11
12/**
13 * Make a new level using provided BoxArray and DistributionMapping and
14 * fill with interpolated coarse level data (overrides the pure virtual function in AmrCore)
15 * regrid --> RemakeLevel (if level already existed)
16 * regrid --> MakeNewLevelFromCoarse (if adding new level)
17 *
18 * @param[in ] lev level to make
19 * @param[in ] time current time
20 * @param[in ] ba BoxArray for the level
21 * @param[in ] dm DistributionMapping for the level
22 */
23void
24REMORA::MakeNewLevelFromCoarse (int lev, Real time, const BoxArray& ba,
25 const DistributionMapping& dm)
26{
27 BoxList bl2d = ba.boxList();
28 for (auto& b : bl2d) {
29 b.setRange(2,0);
30 }
31 BoxArray ba2d(std::move(bl2d));
32
33 amrex::Print() << "Making level " << lev << " from coarse" << std::endl;
34 amrex::Print() << "GRIDS AT LEVEL " << lev << " ARE " << ba << std::endl;
35
36 cons_new[lev] = new MultiFab(ba, dm, ncons, cons_new[lev-1]->nGrowVect());
37 cons_old[lev] = new MultiFab(ba, dm, ncons, cons_new[lev-1]->nGrowVect());
38
39 xvel_new[lev] = new MultiFab(convert(ba, IntVect(1,0,0)), dm, 1, xvel_new[lev-1]->nGrowVect());
40 xvel_old[lev] = new MultiFab(convert(ba, IntVect(1,0,0)), dm, 1, xvel_new[lev-1]->nGrowVect());
41
42 yvel_new[lev] = new MultiFab(convert(ba, IntVect(0,1,0)), dm, 1, yvel_new[lev-1]->nGrowVect());
43 yvel_old[lev] = new MultiFab(convert(ba, IntVect(0,1,0)), dm, 1, yvel_new[lev-1]->nGrowVect());
44
45 zvel_new[lev] = new MultiFab(convert(ba, IntVect(0,0,1)), dm, 1, zvel_new[lev-1]->nGrowVect());
46 zvel_old[lev] = new MultiFab(convert(ba, IntVect(0,0,1)), dm, 1, zvel_new[lev-1]->nGrowVect());
47
48 resize_stuff(lev);
49
50 vec_Zt_avg1[lev].reset(new MultiFab(ba2d ,dm,1,IntVect(NGROW+1,NGROW+1,0))); //2d, average of the free surface (zeta)
51 vec_h[lev].reset(new MultiFab(ba2d ,dm,2,IntVect(NGROW+1,NGROW+1,0))); //2d, average of the free surface (zeta)
52 vec_ubar[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,3,IntVect(NGROW,NGROW,0)));
53 vec_vbar[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,3,IntVect(NGROW,NGROW,0)));
54
55 vec_ru[lev].reset(new MultiFab(convert(ba,IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS u (incl horizontal and vertical advection)
56 vec_rv[lev].reset(new MultiFab(convert(ba,IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS v
57
58 vec_ru2d[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS u for 2d
59 vec_rv2d[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS v for 2d
60
61 t_new[lev] = time;
62 t_old[lev] = time - bogus_large_value;
63
64 init_masks(lev, ba, dm);
65
66 init_stuff(lev, ba, dm);
67
68 cons_new[lev]->setVal(zero);
69 xvel_new[lev]->setVal(zero);
70 yvel_new[lev]->setVal(zero);
71 zvel_new[lev]->setVal(zero);
72
73 cons_old[lev]->setVal(zero);
74 xvel_old[lev]->setVal(zero);
75 yvel_old[lev]->setVal(zero);
76 zvel_old[lev]->setVal(zero);
77
78 vec_ru[lev]->setVal(zero);
79 vec_rv[lev]->setVal(zero);
80
81 vec_ru2d[lev]->setVal(zero);
82 vec_rv2d[lev]->setVal(zero);
83
84 vec_ubar[lev]->setVal(zero);
85 vec_vbar[lev]->setVal(zero);
86
87
88 // Before the fills: FillPatch masks domain-boundary ghosts through physbcs, so these must
89 // hold the real coastline rather than init_masks' all-water placeholder. Order matters:
90 // init_stuff reallocates the coordinates set_grid_scale fills, which set_masks may read.
91 set_grid_scale(lev);
92 set_masks(lev);
93
94 FillCoarsePatch(lev, time, cons_new[lev], cons_new[lev-1],BCVars::Temp_bc_comp,BdyVars::t);
95 FillCoarsePatch(lev, time, xvel_new[lev], xvel_new[lev-1], xvel_bc(), BdyVars::u);
96 FillCoarsePatch(lev, time, yvel_new[lev], yvel_new[lev-1], yvel_bc(), BdyVars::v);
97 FillCoarsePatch(lev, time, zvel_new[lev], zvel_new[lev-1], zvel_bc(), BdyVars::null);
98
99 if (lev > hires_grid_level) {
100 FillCoarsePatch(lev, time, vec_h[lev].get(), vec_h[lev-1].get(),
101 foextrap_periodic_bc(),BdyVars::null,0,false);
102 FillCoarsePatch(lev, time, vec_h[lev].get(), vec_h[lev-1].get(),
103 foextrap_periodic_bc(),BdyVars::null,1,false);
104 } else {
105 set_bathymetry_averaged_down(lev);
106 }
107
108 FillCoarsePatch(lev, time, vec_Zt_avg1[lev].get(), vec_Zt_avg1[lev-1].get(),BCVars::cons_bc);
109 for (int icomp=0; icomp<3; icomp++) {
110 FillCoarsePatch(lev, time, vec_ubar[lev].get(), vec_ubar[lev-1].get(), ubar_bc(),
111 bdy_ubar(),icomp,false);
112 FillCoarsePatch(lev, time, vec_vbar[lev].get(), vec_vbar[lev-1].get(), vbar_bc(),
113 bdy_vbar(),icomp,false);
114 }
115 for (int icomp=0; icomp<2; icomp++) {
116 FillCoarsePatch(lev, time, vec_ru[lev].get(), vec_ru[lev-1].get(), xvel_bc(),
117 BdyVars::null,icomp,false);
118 FillCoarsePatch(lev, time, vec_rv[lev].get(), vec_rv[lev-1].get(), yvel_bc(),
119 BdyVars::null,icomp,false);
120 FillCoarsePatch(lev, time, vec_ru2d[lev].get(), vec_ru2d[lev-1].get(), xvel_bc(),
121 BdyVars::null,icomp,false);
122 FillCoarsePatch(lev, time, vec_rv2d[lev].get(), vec_rv2d[lev-1].get(), yvel_bc(),
123 BdyVars::null,icomp,false);
124 }
125
126 stretch_transform(lev);
127
128 init_set_vmix(lev);
129 set_hmixcoef(lev);
130 set_coriolis(lev);
131 bool apply_eminusp = false;
132 set_zeta_to_Ztavg(lev,apply_eminusp);
133 // Previously set smflux
134
135#ifdef REMORA_USE_NETCDF
136 if (solverChoice.do_rivers) {
137 init_riv_pos_from_netcdf(lev);
138 }
139#endif
140
141 // ********************************************************************************************
142 // If we are making a new level then the FillPatcher for this level hasn't been allocated yet
143 // ********************************************************************************************
144 if (cf_width >= 0) {
145 Construct_REMORAFillPatchers(lev);
146 Define_REMORAFillPatchers(lev);
147 }
148 define_flux_register(lev);
149
150#ifdef REMORA_USE_PARTICLES
151 // particleData.Redistribute();
152#endif
153}
154
155/**
156 * Remake an existing level using provided BoxArray and DistributionMapping and
157 * fill with existing fine and coarse data.
158 * overrides the pure virtual function in AmrCore
159 * @param[in ] lev level to make
160 * @param[in ] time current time
161 * @param[in ] ba BoxArray for the level
162 * @param[in ] dm DistributionMapping for the level
163 */
164void
165REMORA::RemakeLevel (int lev, Real time, const BoxArray& ba, const DistributionMapping& dm)
166{
167
168 BoxList bl2d = ba.boxList();
169 for (auto& b : bl2d) {
170 b.setRange(2,0);
171 }
172 BoxArray ba2d(std::move(bl2d));
173
174 amrex::Print() << "Remaking level " << lev << std::endl;
175 amrex::Print() << "GRIDS AT LEVEL " << lev << " ARE " << ba << std::endl;
176
177#if (NGROW==2)
178 int ngrow_state = ComputeGhostCells(solverChoice.spatial_order)+1;
179 int ngrow_vels = ComputeGhostCells(solverChoice.spatial_order)+1;
180 int ngrow_zeta = ComputeGhostCells(solverChoice.spatial_order)+1;
181 int ngrow_h = ComputeGhostCells(solverChoice.spatial_order)+1;
182 int ngrow_velbar = ComputeGhostCells(solverChoice.spatial_order);
183#else
184 int ngrow_state = ComputeGhostCells(solverChoice.spatial_order)+2;
185 int ngrow_vels = ComputeGhostCells(solverChoice.spatial_order)+2;
186 int ngrow_zeta = ComputeGhostCells(solverChoice.spatial_order)+2;
187 int ngrow_h = ComputeGhostCells(solverChoice.spatial_order)+2;
188 int ngrow_velbar = ComputeGhostCells(solverChoice.spatial_order)+1;
189#endif
190
191 MultiFab tmp_cons_new(ba, dm, ncons, ngrow_state);
192 MultiFab tmp_cons_old(ba, dm, ncons, ngrow_state);
193
194 MultiFab tmp_xvel_new(convert(ba, IntVect(1,0,0)), dm, 1, ngrow_vels);
195 MultiFab tmp_xvel_old(convert(ba, IntVect(1,0,0)), dm, 1, ngrow_vels);
196
197 MultiFab tmp_yvel_new(convert(ba, IntVect(0,1,0)), dm, 1, ngrow_vels);
198 MultiFab tmp_yvel_old(convert(ba, IntVect(0,1,0)), dm, 1, ngrow_vels);
199
200 MultiFab tmp_zvel_new(convert(ba, IntVect(0,0,1)), dm, 1, IntVect(ngrow_vels,ngrow_vels,0));
201 MultiFab tmp_zvel_old(convert(ba, IntVect(0,0,1)), dm, 1, IntVect(ngrow_vels,ngrow_vels,0));
202
203 MultiFab tmp_Zt_avg1_new(ba2d, dm, 1, IntVect(ngrow_zeta,ngrow_zeta,0));
204 MultiFab tmp_h(ba2d, dm, 2, IntVect(ngrow_h,ngrow_h,0));
205
206 MultiFab tmp_ubar_new(convert(ba2d, IntVect(1,0,0)), dm, 3, IntVect(ngrow_velbar,ngrow_velbar,0));
207
208 MultiFab tmp_vbar_new(convert(ba2d, IntVect(0,1,0)), dm, 3, IntVect(ngrow_velbar,ngrow_velbar,0));
209
210 MultiFab tmp_ru_new(convert(ba, IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0));
211 MultiFab tmp_rv_new(convert(ba, IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0));
212
213 MultiFab tmp_ru2d_new(convert(ba2d, IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0));
214 MultiFab tmp_rv2d_new(convert(ba2d, IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0));
215
216 init_masks(lev, ba, dm);
217
218 tmp_cons_new.setVal(zero);
219 tmp_xvel_new.setVal(zero);
220 tmp_yvel_new.setVal(zero);
221 tmp_zvel_new.setVal(zero);
222
223 tmp_cons_old.setVal(zero);
224 tmp_xvel_old.setVal(zero);
225 tmp_yvel_old.setVal(zero);
226 tmp_zvel_old.setVal(zero);
227
228 tmp_ru_new.setVal(zero);
229 tmp_rv_new.setVal(zero);
230
231 tmp_ru2d_new.setVal(zero);
232 tmp_rv2d_new.setVal(zero);
233
234 tmp_ubar_new.setVal(zero);
235 tmp_vbar_new.setVal(zero);
236
237
238 // As in MakeNewLevelFromCoarse. init_stuff comes along because set_grid_scale follows it.
239 init_stuff(lev, ba, dm);
240 set_grid_scale(lev);
241 set_masks(lev);
242
243 // This will fill the temporary MultiFabs with data from previous fine data as well as coarse where needed
244 FillPatch(lev, time, tmp_cons_new, cons_new, BCVars::cons_bc, BdyVars::t,0,true,false);
245 FillPatch(lev, time, tmp_xvel_new, xvel_new, xvel_bc(), BdyVars::u,0,true,false,0,0,zero,tmp_xvel_new);
246 FillPatch(lev, time, tmp_yvel_new, yvel_new, yvel_bc(), BdyVars::v,0,true,false,0,0,zero,tmp_yvel_new);
247 FillPatch(lev, time, tmp_zvel_new, zvel_new, zvel_bc(), BdyVars::null,0,true,false);
248 FillPatch(lev, time, tmp_Zt_avg1_new, GetVecOfPtrs(vec_Zt_avg1), zeta_bc(), BdyVars::null,0,true,false);
249
250 for (int icomp=0; icomp<3; icomp++) {
251 FillPatch(lev, time, tmp_ubar_new, GetVecOfPtrs(vec_ubar), ubar_bc(), bdy_ubar(), icomp,false,false);
252 FillPatch(lev, time, tmp_vbar_new, GetVecOfPtrs(vec_vbar), vbar_bc(), bdy_vbar(), icomp,false,false);
253 }
254 for (int icomp=0; icomp<2; icomp++) {
255 FillPatch(lev, time, tmp_ru_new, GetVecOfPtrs(vec_ru), xvel_bc(), BdyVars::null, icomp,false,false);
256 FillPatch(lev, time, tmp_rv_new, GetVecOfPtrs(vec_rv), yvel_bc(), BdyVars::null, icomp,false,false);
257 // These might want to have BCVars::ubar_bc and vbar_bc
258 FillPatch(lev, time, tmp_ru2d_new, GetVecOfPtrs(vec_ru2d), xvel_bc(), BdyVars::null, icomp,false,false);
259 FillPatch(lev, time, tmp_rv2d_new, GetVecOfPtrs(vec_rv2d), yvel_bc(), BdyVars::null, icomp,false,false);
260 }
261
262 MultiFab::Copy(tmp_cons_old,tmp_cons_new,0,0,ncons,tmp_cons_new.nGrowVect());
263 MultiFab::Copy(tmp_xvel_old,tmp_xvel_new,0,0, 1,tmp_xvel_new.nGrowVect());
264 MultiFab::Copy(tmp_yvel_old,tmp_yvel_new,0,0, 1,tmp_yvel_new.nGrowVect());
265 MultiFab::Copy(tmp_zvel_old,tmp_zvel_new,0,0, 1,tmp_zvel_new.nGrowVect());
266
267 std::swap(tmp_cons_new, *cons_new[lev]);
268 std::swap(tmp_cons_old, *cons_old[lev]);
269 std::swap(tmp_xvel_new, *xvel_new[lev]);
270 std::swap(tmp_xvel_old, *xvel_old[lev]);
271 std::swap(tmp_yvel_new, *yvel_new[lev]);
272 std::swap(tmp_yvel_old, *yvel_old[lev]);
273 std::swap(tmp_zvel_new, *zvel_new[lev]);
274 std::swap(tmp_zvel_old, *zvel_old[lev]);
275 std::swap(tmp_Zt_avg1_new, *vec_Zt_avg1[lev]);
276 std::swap(tmp_ubar_new, *vec_ubar[lev]);
277 std::swap(tmp_vbar_new, *vec_vbar[lev]);
278 std::swap(tmp_ru_new, *vec_ru[lev]);
279 std::swap(tmp_rv_new, *vec_rv[lev]);
280 std::swap(tmp_ru2d_new, *vec_ru2d[lev]);
281 std::swap(tmp_rv2d_new, *vec_rv2d[lev]);
282
283 // Handle bathymetry separately
284 if (lev > hires_grid_level) {
285 FillPatch(lev, time, tmp_h, GetVecOfPtrs(vec_h), foextrap_periodic_bc(), BdyVars::null,0,false,false);
286 FillPatch(lev, time, tmp_h, GetVecOfPtrs(vec_h), foextrap_periodic_bc(), BdyVars::null,1,false,false);
287 std::swap(tmp_h, *vec_h[lev]);
288 } else {
289 // Swap first: vec_h[lev] is still on the pre-regrid BoxArray at this point, and the
290 // branch above is what moves it onto the new one. set_bathymetry_averaged_down takes
291 // its data from vec_h_full_domain rather than from the old grids, so the old contents
292 // are not needed -- but its FillPatch uses the land masks, which init_masks has
293 // already rebuilt on the new BoxArray, so leaving vec_h[lev] on the old one mixes two
294 // BoxArrays inside REMORAPhysBCFunct.
295 std::swap(tmp_h, *vec_h[lev]);
296 set_bathymetry_averaged_down(lev);
297 }
298
299 t_new[lev] = time;
300 t_old[lev] = time - bogus_large_value;
301
302 stretch_transform(lev);
303
304 init_set_vmix(lev);
305 set_hmixcoef(lev);
306 set_coriolis(lev);
307 bool apply_eminusp = false;
308 set_zeta_to_Ztavg(lev,apply_eminusp);
309 // Previously set smflux here
310
311#ifdef REMORA_USE_NETCDF
312 if (solverChoice.do_rivers) {
313 init_riv_pos_from_netcdf(lev);
314 }
315#endif
316
317 // Both of these hold this level's layout and the one below it, so both have to be rebuilt
318 // whenever either changes. Unconditionally: AmrCore::regrid calls RemakeLevel only when
319 // this level's BoxArray changed or the coarser one's did, and in the latter case it
320 // passes this level's own ba and dm unchanged -- so testing them here would skip exactly
321 // the case where only the coarse side moved.
322 if (lev > 0 && cf_width >= 0) {
323 Define_REMORAFillPatchers(lev);
324 define_flux_register(lev);
325 }
326
327#ifdef REMORA_USE_PARTICLES
328 particleData.Redistribute();
329#endif
330}
331
332/**
333 * Make a new level from scratch using provided BoxArray and DistributionMapping.
334 * This is called both for initialization and for restart
335 * (overrides the pure virtual function in AmrCore)
336 * main.cpp --> REMORA::InitData --> InitFromScratch --> MakeNewGrids --> MakeNewLevelFromScratch
337 * restart --> MakeNewGrids --> MakeNewLevelFromScratch
338 *
339 * @param[in ] lev level to make
340 * @param[in ] time current time
341 * @param[in ] ba BoxArray for the level
342 * @param[in ] dm DistributionMapping for the level
343 */
344void REMORA::MakeNewLevelFromScratch (int lev, Real time, const BoxArray& ba,
345 const DistributionMapping& dm)
346{
347 // Set BoxArray grids and DistributionMapping dmap in AMReX_AmrMesh.H class
348 SetBoxArray(lev, ba);
349 SetDistributionMap(lev, dm);
350
351 BoxList bl2d = ba.boxList();
352 for (auto& b : bl2d) {
353 b.setRange(2,0);
354 }
355 BoxArray ba2d(std::move(bl2d));
356
357 amrex::Print() << "Making level " << lev << " from scratch" << std::endl;
358 amrex::Print() << "GRIDS AT LEVEL " << lev << " ARE " << ba << std::endl;
359
360 // The number of ghost cells for density must be 1 greater than that for velocity
361 // so that we can go back in forth between velocity and momentum on all faces
362#if NGROW==2
363 int ngrow_state = ComputeGhostCells(solverChoice.spatial_order)+1;
364 int ngrow_vels = ComputeGhostCells(solverChoice.spatial_order)+1;
365#else
366 int ngrow_state = ComputeGhostCells(solverChoice.spatial_order)+2;
367 int ngrow_vels = ComputeGhostCells(solverChoice.spatial_order)+2;
368#endif
369
370 cons_old[lev] = new MultiFab(ba, dm, ncons, ngrow_state);
371 cons_new[lev] = new MultiFab(ba, dm, ncons, ngrow_state);
372
373 xvel_new[lev] = new MultiFab(convert(ba, IntVect(1,0,0)), dm, 1, ngrow_vels);
374 xvel_old[lev] = new MultiFab(convert(ba, IntVect(1,0,0)), dm, 1, ngrow_vels);
375
376 yvel_new[lev] = new MultiFab(convert(ba, IntVect(0,1,0)), dm, 1, ngrow_vels);
377 yvel_old[lev] = new MultiFab(convert(ba, IntVect(0,1,0)), dm, 1, ngrow_vels);
378
379 zvel_new[lev] = new MultiFab(convert(ba, IntVect(0,0,1)), dm, 1, IntVect(ngrow_vels,ngrow_vels,0));
380 zvel_old[lev] = new MultiFab(convert(ba, IntVect(0,0,1)), dm, 1, IntVect(ngrow_vels,ngrow_vels,0));
381
382 resize_stuff(lev);
383
384 vec_Zt_avg1[lev].reset(new MultiFab(ba2d ,dm,1,IntVect(NGROW+1,NGROW+1,0))); //2d, average of the free surface (zeta)
385 vec_h[lev].reset(new MultiFab(ba2d ,dm,2,IntVect(NGROW+1,NGROW+1,0))); //2d, bathymetry
386 vec_ubar[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,3,IntVect(NGROW,NGROW,0)));
387 vec_vbar[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,3,IntVect(NGROW,NGROW,0)));
388
389 vec_ru[lev].reset(new MultiFab(convert(ba,IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS u (incl horizontal and vertical advection)
390 vec_rv[lev].reset(new MultiFab(convert(ba,IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS v
391
392 vec_ru2d[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS u (incl horizontal and vertical advection)
393 vec_rv2d[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS v
394
395 init_masks(lev, ba, dm);
396 init_stuff(lev, ba, dm);
397
398 init_only(lev, time);
399
400#ifdef REMORA_USE_PARTICLES
401 if (restart_chkfile.empty()) {
402 if (lev == 0) {
403 initializeTracers((ParGDBBase*)GetParGDB(),vec_z_phys_nd);
404 } else {
405 particleData.Redistribute();
406 }
407 }
408#endif
409}
410
411/**
412 * @param[in ] lev level do operate on
413 */
414void REMORA::resize_stuff(int lev)
415{
416 vec_z_phys_nd.resize(lev+1);
417
418 vec_h_full_domain.resize(hires_grid_level+1);
419 // Sized for both hires knobs: the initial-state cascade needs a mask at
420 // hires_init_level, which may sit above hires_grid_level.
421 vec_mskr_full_domain.resize(std::max(hires_grid_level, hires_init_level)+1);
422
423 vec_h.resize(lev+1);
424 vec_Zt_avg1.resize(lev+1);
425 vec_z_w.resize(lev+1);
426 vec_z_r.resize(lev+1);
427 vec_Hz.resize(lev+1);
428 vec_Huon.resize(lev+1);
429 vec_Hvom.resize(lev+1);
430 vec_Akv.resize(lev+1);
431 vec_Akt.resize(lev+1);
432 vec_visc2_p.resize(lev+1);
433 vec_visc2_r.resize(lev+1);
434 vec_diff2.resize(lev+1);
435 vec_ru.resize(lev+1);
436 vec_rv.resize(lev+1);
437 vec_ru2d.resize(lev+1);
438 vec_rv2d.resize(lev+1);
439 vec_rufrc.resize(lev+1);
440 vec_rvfrc.resize(lev+1);
441 vec_sustr.resize(lev+1);
442 vec_svstr.resize(lev+1);
443 vec_btflx.resize(lev+1);
444 vec_stflx.resize(lev+1);
445 vec_btflux.resize(lev+1);
446 vec_stflux.resize(lev+1);
447 vec_lrflx.resize(lev+1);
448 vec_longwave_down.resize(lev+1);
449 vec_lhflx.resize(lev+1);
450 vec_shflx.resize(lev+1);
451 vec_rain.resize(lev+1);
452 vec_evap.resize(lev+1);
453 vec_rdrag.resize(lev+1);
454 vec_rdrag2.resize(lev+1);
455 vec_ZoBot.resize(lev+1);
456 vec_bustr.resize(lev+1);
457 vec_bvstr.resize(lev+1);
458 vec_uwind.resize(lev+1);
459 vec_vwind.resize(lev+1);
460 vec_Tair.resize(lev+1);
461 vec_qair.resize(lev+1);
462 vec_Pair.resize(lev+1);
463 vec_srflx.resize(lev+1);
464 vec_cloud.resize(lev+1);
465 vec_EminusP.resize(lev+1);
466 vec_alpha.resize(lev+1);
467 vec_beta.resize(lev+1);
468
469 vec_DU_avg1.resize(lev+1);
470 vec_DU_avg2.resize(lev+1);
471 vec_DV_avg1.resize(lev+1);
472 vec_DV_avg2.resize(lev+1);
473 vec_Dubar_old.resize(lev+1);
474 vec_Dubar_new.resize(lev+1);
475 vec_Dvbar_old.resize(lev+1);
476 vec_Dvbar_new.resize(lev+1);
477 vec_rubar.resize(lev+1);
478 vec_rvbar.resize(lev+1);
479 vec_rzeta.resize(lev+1);
480 vec_ubar.resize(lev+1);
481 vec_vbar.resize(lev+1);
482 vec_zeta.resize(lev+1);
483 vec_zeta_full_domain.resize(hires_init_level+1);
484 vec_mskr.resize(lev+1);
485 vec_msku.resize(lev+1);
486 vec_mskv.resize(lev+1);
487 vec_mskp.resize(lev+1);
488 vec_mskr3d.resize(lev+1);
489 // Indexed by the coarse level of a pair, so lev entries would do; sized like the rest to
490 // keep the indexing uniform.
491 vec_mskr_crse_on_fine.resize(lev+1);
492 vec_msku_crse_on_fine.resize(lev+1);
493 vec_mskv_crse_on_fine.resize(lev+1);
494 vec_sstore.resize(lev+1);
495
496 vec_cons_full_domain.resize(hires_init_level+1);
497 vec_xvel_full_domain.resize(hires_init_level+1);
498 vec_yvel_full_domain.resize(hires_init_level+1);
499
500 vec_pm.resize(lev+1);
501 vec_pn.resize(lev+1);
502 vec_fcor.resize(lev+1);
503 vec_pm_full_domain.resize(hires_grid_level+1);
504 vec_pn_full_domain.resize(hires_grid_level+1);
505
506 vec_xr.resize(lev+1);
507 vec_yr.resize(lev+1);
508 vec_xu.resize(lev+1);
509 vec_yu.resize(lev+1);
510 vec_xv.resize(lev+1);
511 vec_yv.resize(lev+1);
512 vec_xp.resize(lev+1);
513 vec_yp.resize(lev+1);
514 vec_lonp.resize(lev+1);
515 vec_latp.resize(lev+1);
516
517 vec_dndx.resize(lev+1);
518 vec_dmde.resize(lev+1);
519
520 vec_rhoS.resize(lev+1);
521 vec_rhoA.resize(lev+1);
522 vec_bvf.resize(lev+1);
523
524 vec_tke.resize(lev+1);
525 vec_gls.resize(lev+1);
526 vec_Lscale.resize(lev+1);
527 vec_Akk.resize(lev+1);
528 vec_Akp.resize(lev+1);
529
530 vec_river_position.resize(lev+1);
531
532 if (lev==0) vec_nudg_coeff.resize(num_bdy_vars());
533
534 vec_nudg_coeff[BdyVars::u].resize(lev+1);
535 vec_nudg_coeff[BdyVars::v].resize(lev+1);
536 for (int icomp = 0; icomp < ncons; ++icomp) {
537 vec_nudg_coeff[BdyVars::cons(icomp)].resize(lev+1);
538 }
539 vec_nudg_coeff[bdy_ubar()].resize(lev+1);
540 vec_nudg_coeff[bdy_vbar()].resize(lev+1);
541 vec_nudg_coeff[bdy_zeta()].resize(lev+1);
542}
543
544/**
545 * @param[in ] lev level to operate on
546 * @param[in ] ba BoxArray for the level
547 * @param[in ] dm DistributionMapping for the level
548 */
549void REMORA::init_masks (int lev, const BoxArray& ba, const DistributionMapping& dm)
550{
551 BoxList bl2d = ba.boxList();
552 for (auto& b : bl2d) {
553 b.setRange(2,0);
554 }
555
556 BoxArray ba2d(std::move(bl2d));
557 vec_mskr[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
558 vec_msku[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW+1,NGROW+1,0)));
559 vec_mskv[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW+1,NGROW+1,0)));
560 vec_mskp[lev].reset(new MultiFab(convert(ba2d,IntVect(1,1,0)),dm,1,IntVect(NGROW+1,NGROW+1,0)));
561
562 vec_mskr3d[lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0)));
563
564 vec_mskr[lev]->setVal(one);
565 vec_msku[lev]->setVal(one);
566 vec_mskv[lev]->setVal(one);
567 vec_mskp[lev]->setVal(one);
568
569 vec_mskr3d[lev]->setVal(one);
570}
571
572/**
573 * @param[in ] lev level to operate on
574 * @param[in ] ba BoxArray for the level
575 * @param[in ] dm DistributionMapping for the level
576 */
577void REMORA::init_stuff (int lev, const BoxArray& ba, const DistributionMapping& dm)
578{
579 // ********************************************************************************************
580 // Initialize the boundary conditions
581 // ********************************************************************************************
582 physbcs[lev] = std::make_unique<REMORAPhysBCFunct> (lev, geom[lev], domain_bcs_type, domain_bcs_type_d,
583 m_bc_extdir_vals, ncons);
584
585 BoxList bl2d = ba.boxList();
586 for (auto& b : bl2d) {
587 b.setRange(2,0);
588 }
589 BoxArray ba2d(std::move(bl2d));
590
591 BoxList bl1d = ba.boxList();
592 for (auto& b : bl1d) {
593 b.setRange(0,0);
594 b.setRange(1,0);
595 }
596 BoxArray ba1d(std::move(bl1d));
597
598 BoxArray ba_nd(ba);
599 ba_nd.surroundingNodes();
600 BoxArray ba_w(ba);
601 ba_w.surroundingNodes(2);
602
603 vec_z_phys_nd[lev].reset (new MultiFab(ba_nd,dm,1,IntVect(NGROW,NGROW,1))); // z at psi points (nodes) MIGHT NEED NGROW+1
604 vec_z_w[lev].reset (new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW+1,NGROW+1,0))); // z at w points (cell faces)
605 vec_z_r[lev].reset (new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0))); // z at r points (cell center)
606 vec_Hz[lev].reset (new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,NGROW+1))); // like in ROMS, thickness of cell in z
607
608 vec_Huon[lev].reset (new MultiFab(convert(ba,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0))); // mass flux for u component
609 vec_Hvom[lev].reset (new MultiFab(convert(ba,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0))); // mass flux for v component
610
611 vec_Akv[lev].reset (new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0))); // vertical mixing coefficient (.in)
612 // NAT components, not ncons: vertical mixing coefficients exist for the active tracers
613 // alone, and passive tracers mix with the salinity one. See akt_comp().
614 vec_Akt[lev].reset (new MultiFab(convert(ba,IntVect(0,0,1)),dm,NAT,IntVect(NGROW,NGROW,0))); // vertical mixing coefficient (.in)
615
616 // check dimensionality
617 vec_visc2_p[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); // harmonic viscosity at psi points -- difference to 3d?
618 vec_visc2_r[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); // harmonic viscosity at rho points
619 vec_diff2[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0))); // harmonic diffusivity temperature/salt
620
621 //2d, (incl advection terms and surface/bottom stresses, integral over the whole column, k=0)
622 vec_rufrc[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0)));
623 vec_rvfrc[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0))); //2d, same as above but v
624
625 vec_sustr[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0))); //2d, surface stress
626 vec_svstr[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0))); //2d
627
628 if (solverChoice.bottom_stress_type == BottomStressType::linear) {
629 //2d, linear drag coefficient [m/s], defined at rho, somehow related to rdrg
630 vec_rdrag[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
631 } else if (solverChoice.bottom_stress_type == BottomStressType::quadratic) {
632 vec_rdrag2[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
633 }
634
635 if (solverChoice.bottom_stress_type == BottomStressType::logarithmic ||
636 solverChoice.vert_mixing_type == VertMixingType::GLS) {
637 vec_ZoBot[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
638 }
639
640 vec_bustr[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0))); //2d, bottom stress
641 vec_bvstr[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
642
643 //all 2d -- all associated with the 2D advance
644 //2d DU: sum(height[incl free surface?] * u)
645 vec_DU_avg1[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
646
647 //2d like above, but correct(or)?
648 vec_DU_avg2[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
649
650 vec_DV_avg1[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
651 vec_DV_avg2[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
652
653 // D*ubar and D*vbar: DU_avg2/on_u and DV_avg2/om_v, at the two ends of this level's step
654 vec_Dubar_old[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
655 vec_Dubar_new[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
656 vec_Dvbar_old[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
657 vec_Dvbar_new[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
658
659 vec_rubar[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,4,IntVect(NGROW,NGROW,0))); // 2d RHS ubar
660 vec_rvbar[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,4,IntVect(NGROW,NGROW,0)));
661 vec_rzeta[lev].reset(new MultiFab(ba2d,dm,4,IntVect(NGROW,NGROW,0))); // 2d RHS zeta
662
663 // starts off kind of like a depth-averaged u, but exists at more points and more timesteps (b/c fast 2D update) than full u
664 vec_zeta[lev].reset(new MultiFab(ba2d,dm,3,IntVect(NGROW+1,NGROW+1,0))); // 2d free surface
665
666 vec_pm[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+2,0)));
667 vec_pn[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+2,NGROW+1,0)));
668 vec_fcor[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
669
670 vec_xr[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
671 vec_yr[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
672
673 vec_xu[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
674 vec_yu[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
675 vec_xv[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
676 vec_yv[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
677 vec_xp[lev].reset(new MultiFab(convert(ba2d,IntVect(1,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
678 vec_yp[lev].reset(new MultiFab(convert(ba2d,IntVect(1,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
679
680 if (solverChoice.use_curvilinear_grid) {
681 vec_dndx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
682 vec_dmde[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
683 }
684
685 // tempstore, saltstore, etc
686 vec_sstore[lev].reset(new MultiFab(ba,dm,ncons,IntVect(NGROW,NGROW,0)));
687
688 vec_rhoS[lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW,NGROW,0)));
689 vec_rhoA[lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW,NGROW,0)));
690 vec_bvf[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0)));
691
692 vec_tke[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,3,IntVect(NGROW,NGROW,0)));
693 vec_gls[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,3,IntVect(NGROW,NGROW,0)));
694 vec_Lscale[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0)));
695 vec_Akk[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0)));
696 vec_Akp[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0)));
697
698 // surface/bottom tracer fluxes for update
699 vec_stflx[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0)));
700 vec_btflx[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0)));
701 // surface/bottom tracer fluxes to be filled by inputs
702 vec_stflux[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0)));
703 vec_btflux[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0)));
704
705 if (solverChoice.bulk_fluxes || solverChoice.atm2ocn_flux_mode) {
706 vec_uwind[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, surface wind u
707 vec_vwind[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, surface wind v
708 vec_Tair[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, air temperature
709 vec_qair[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, specific humidity
710 vec_Pair[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, air pressure
711 vec_srflx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, shortwave radiation flux
712 vec_longwave_down[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, external longwave radiation flux
713 vec_cloud[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, cloud cover fraction
714 vec_EminusP[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, evaporation minus precipitation
715 vec_alpha[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
716 vec_beta[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
717 vec_lrflx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
718 vec_lhflx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
719 vec_shflx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
720 vec_rain[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
721 vec_evap[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
722
723 vec_uwind[lev]->setVal(solverChoice.Uwind);
724 vec_vwind[lev]->setVal(solverChoice.Vwind);
725 vec_Tair[lev]->setVal(solverChoice.Tair);
726 vec_qair[lev]->setVal(solverChoice.Hair); // Hair can be specific humidity or RH
727 vec_Pair[lev]->setVal(solverChoice.Pair);
728 vec_srflx[lev]->setVal(solverChoice.srflux);
729 vec_longwave_down[lev]->setVal(solverChoice.longwave_rad);
730 vec_cloud[lev]->setVal(solverChoice.cloud);
731 vec_EminusP[lev]->setVal(solverChoice.EminusP);
732 vec_rain[lev]->setVal(solverChoice.rain);
733
734 // Set flux vars that will be computed in bulk_fluxes to zero so initial plotting works
735 vec_stflx[lev]->setVal(zero);
736 vec_lhflx[lev]->setVal(zero);
737 vec_shflx[lev]->setVal(zero);
738 vec_lrflx[lev]->setVal(zero); // possibly this should be set to longwave_rad like longwave_down
739 vec_evap[lev]->setVal(zero);
740 }
741
742 if (solverChoice.do_rivers) {
743 vec_river_position[lev].reset(new iMultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
744 vec_river_position[lev]->setVal(-1);
745 }
746
747 vec_nudg_coeff[BdyVars::u][lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0)));
748 vec_nudg_coeff[BdyVars::v][lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0)));
749 for (int icomp = 0; icomp < ncons; ++icomp) {
750 vec_nudg_coeff[BdyVars::cons(icomp)][lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0)));
751 }
752 vec_nudg_coeff[bdy_ubar()][lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
753 vec_nudg_coeff[bdy_vbar()][lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
754 vec_nudg_coeff[bdy_zeta()][lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
755
756 set_weights(lev);
757
758 vec_DU_avg1[lev]->setVal(zero);
759 vec_DU_avg2[lev]->setVal(zero);
760 vec_DV_avg1[lev]->setVal(zero);
761 vec_DV_avg2[lev]->setVal(zero);
762 vec_Dubar_old[lev]->setVal(zero);
763 vec_Dubar_new[lev]->setVal(zero);
764 vec_Dvbar_old[lev]->setVal(zero);
765 vec_Dvbar_new[lev]->setVal(zero);
766 vec_rubar[lev]->setVal(zero);
767 vec_rvbar[lev]->setVal(zero);
768 vec_rzeta[lev]->setVal(zero);
769
770 // Initialize these vars even if we aren't using GLS to
771 // avoid issues on e.g. checkpoint
772 vec_tke[lev]->setVal(solverChoice.gls_Kmin);
773 vec_gls[lev]->setVal(solverChoice.gls_Pmin);
774 vec_Lscale[lev]->setVal(zero);
775 vec_Akk[lev]->setVal(solverChoice.Akk_bak);
776 vec_Akp[lev]->setVal(solverChoice.Akp_bak);
777
778 vec_stflx[lev]->setVal(zero);
779 vec_btflx[lev]->setVal(zero);
780 vec_stflux[lev]->setVal(zero);
781 vec_btflux[lev]->setVal(zero);
782 vec_sustr[lev]->setVal(zero);
783 vec_svstr[lev]->setVal(zero);
784
785 // NOTE: Used to set vec_pm and vec_pn to 1e34 here to make foextrap work
786 // when init_type = real. However, this does not appear to be necessary so removing
787
788 // Set initial linear drag coefficient
789 if (solverChoice.bottom_stress_type == BottomStressType::linear) {
790 vec_rdrag[lev]->setVal(solverChoice.rdrag);
791 } else if (solverChoice.bottom_stress_type == BottomStressType::quadratic) {
792 vec_rdrag2[lev]->setVal(solverChoice.rdrag2);
793 }
794
795 if (solverChoice.bottom_stress_type == BottomStressType::logarithmic ||
796 solverChoice.vert_mixing_type == VertMixingType::GLS) {
797 vec_ZoBot[lev]->setVal(solverChoice.Zob);
798 }
799
800
801 // ********************************************************************************************
802 // Create the REMORAFillPatcher object
803 // ********************************************************************************************
804 if (lev > 0 && cf_width >= 0) {
805 Construct_REMORAFillPatchers(lev);
806 Define_REMORAFillPatchers(lev);
807 }
808}
809
810/**
811 * Delete level data. Overrides the pure virtual function in AmrCore
812 *
813 * @param[in ] lev level to operate on
814 */
815void
816REMORA::ClearLevel (int lev)
817{
818 delete cons_new[lev]; delete xvel_new[lev]; delete yvel_new[lev]; delete zvel_new[lev];
819 delete cons_old[lev]; delete xvel_old[lev]; delete yvel_old[lev]; delete zvel_old[lev];
820}
821
822/**
823 * @param[in ] lev level to operate on
824 */
825void
826REMORA::set_grid_scale (int lev)
827{
828 // Even if we're using high-resolution grid initialization, don't set it up with average-down
829 if (solverChoice.ic_type == IC_Type::analytic) {
830 if (solverChoice.grid_scale_type == GridScaleType::constant) {
831 const auto dxi = Geom(lev).InvCellSize();
832 vec_pm[lev]->setVal(dxi[0]); vec_pm[lev]->FillBoundary(geom[lev].periodicity());
833 vec_pn[lev]->setVal(dxi[1]); vec_pn[lev]->FillBoundary(geom[lev].periodicity());
834 } else if (solverChoice.grid_scale_type == GridScaleType::analytic) {
835 prob->init_analytic_grid_scale(lev, Geom(lev), solverChoice, *this, *vec_pm[lev].get(), *vec_pn[lev].get());
836 vec_pm[lev]->FillBoundary(geom[lev].periodicity());
837 vec_pn[lev]->FillBoundary(geom[lev].periodicity());
838 }
839 set_grid_coords_from_grid_scale(lev);
840#ifdef REMORA_USE_NETCDF
841 } else if (solverChoice.ic_type == IC_Type::netcdf) {
842 if (lev == 0 && hires_grid_level < 0) {
843 init_grid_vars_from_netcdf(lev);
844 } else if (lev > hires_grid_level) {
845 Real dummy_time = zero;
846 FillCoarsePatch(lev,dummy_time,vec_pm[lev].get(), vec_pm[lev-1].get(), foextrap_bc());
847 FillCoarsePatch(lev,dummy_time,vec_pn[lev].get(), vec_pn[lev-1].get(), foextrap_bc());
848
849 int rrx = ref_ratio[lev-1][0];
850 int rry = ref_ratio[lev-1][1];
851 // pm and pn need to be rescaled by the refinement ratio
852 for ( MFIter mfi(*vec_pm[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
853 {
854 Array4<Real> const& pm = vec_pm[lev]->array(mfi);
855 Array4<Real> const& pn = vec_pn[lev]->array(mfi);
856 Box ubx = mfi.growntilebox(IntVect(NGROW+1,NGROW+2,0));
857 Box vbx = mfi.growntilebox(IntVect(NGROW+2,NGROW+1,0));
858 ParallelFor(ubx, [=] AMREX_GPU_DEVICE (int i, int j, int ) {
859 pm(i,j,0) = pm(i,j,0) * (rrx);
860 });
861 ParallelFor(vbx, [=] AMREX_GPU_DEVICE (int i, int j, int ) {
862 pn(i,j,0) = pn(i,j,0) * (rry);
863 });
864 }
865 set_grid_coords_from_grid_scale(lev);
866 } else {
867 set_grid_vars_averaged_down(lev);
868 set_grid_coords_from_grid_scale(lev);
869 }
870#endif
871 }
872 if (solverChoice.use_curvilinear_grid) {
873 set_curvilinear_terms_from_grid_scale(lev);
874 }
875}
876
877/**
878 * @param[in ]lev level to operate on
879 */
880void
881REMORA::set_grid_coords_from_grid_scale (int lev) {
882 for ( MFIter mfi(*vec_xr[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
883 {
884 Array4<const Real> const& pm = vec_pm[lev]->const_array(mfi);
885 Array4<const Real> const& pn = vec_pn[lev]->const_array(mfi);
886 Array4<Real> const& xr = vec_xr[lev]->array(mfi);
887 Array4<Real> const& yr = vec_yr[lev]->array(mfi);
888 Array4<Real> const& xu = vec_xu[lev]->array(mfi);
889 Array4<Real> const& yu = vec_yu[lev]->array(mfi);
890 Array4<Real> const& xv = vec_xv[lev]->array(mfi);
891 Array4<Real> const& yv = vec_yv[lev]->array(mfi);
892 Array4<Real> const& xp = vec_xp[lev]->array(mfi);
893 Array4<Real> const& yp = vec_yp[lev]->array(mfi);
894
895 Box bx = mfi.growntilebox(IntVect(NGROW,NGROW,0));
896 ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int)
897 {
898 xr(i,j,0) = (i + Real(0.5)) / pm(i,j,0);
899 yr(i,j,0) = (j + Real(0.5)) / pn(i,j,0);
900 });
901
902 ParallelFor(mfi.tilebox(IntVect(1,0,0),IntVect(NGROW,NGROW,0)), [=] AMREX_GPU_DEVICE (int i, int j, int)
903 {
904 xu(i,j,0) = i / pm(i,j,0);
905 yu(i,j,0) = (j + Real(0.5)) / pn(i,j,0);
906 });
907
908 ParallelFor(mfi.tilebox(IntVect(0,1,0),IntVect(NGROW,NGROW,0)), [=] AMREX_GPU_DEVICE (int i, int j, int)
909 {
910 xv(i,j,0) = (i + Real(0.5)) / pm(i,j,0);
911 yv(i,j,0) = j / pn(i,j,0);
912 });
913
914 ParallelFor(mfi.tilebox(IntVect(1,1,0),IntVect(NGROW,NGROW,0)), [=] AMREX_GPU_DEVICE (int i, int j, int)
915 {
916 xp(i,j,0) = i / pm(i,j,0);
917 yp(i,j,0) = j / pn(i,j,0);
918 });
919 }
920}
921
922/**
923 * @param[in ]lev level to operate on
924 */
925void
926REMORA::set_curvilinear_terms_from_grid_scale (int lev) {
927 for ( MFIter mfi(*vec_dndx[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
928 {
929 Array4<const Real> const& pm = vec_pm[lev]->const_array(mfi);
930 Array4<const Real> const& pn = vec_pn[lev]->const_array(mfi);
931 Array4<Real> const& dndx = vec_dndx[lev]->array(mfi);
932 Array4<Real> const& dmde = vec_dmde[lev]->array(mfi);
933
934 Box bx = mfi.growntilebox(IntVect(NGROW,NGROW,0));
935 ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int)
936 {
937 dndx(i,j,0) = Real(0.5) * (one / pn(i+1,j ,0) - one / pn(i-1,j ,0));
938 dmde(i,j,0) = Real(0.5) * (one / pm(i ,j+1,0) - one / pm(i ,j-1,0));
939 });
940 }
941}
942
943/**
944 * @param[in ] lev level to operate on
945 * @param[in ] apply_eminusp whether to apply the evaporation-minus-precipitation correction to Zt_avg1
946 */
947void
948REMORA::set_zeta_to_Ztavg (int lev, bool apply_eminusp)
949{
950 BL_PROFILE("REMORA::set_zeta_to_Ztavg()");
951 std::unique_ptr<MultiFab>& mf_zeta = vec_zeta[lev];
952 std::unique_ptr<MultiFab>& mf_Zt_avg1 = vec_Zt_avg1[lev];
953 if (solverChoice.eminusp_correct_ssh && apply_eminusp) {
954 for ( MFIter mfi(*vec_zeta[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
955 {
956 Array4<Real> const& Zt_avg1 = (mf_Zt_avg1)->array(mfi);
957 Array4<const Real> const& evap = vec_evap[lev]->const_array(mfi);
958 Array4<const Real> const& rain = vec_rain[lev]->const_array(mfi);
959 Array4<const Real> const& EminusP = vec_EminusP[lev]->const_array(mfi);
960 bool use_EminusP_from_input = solverChoice.eminusp &&
961 solverChoice.bulk_flux_type[BulkFlux::EminusP] != BulkForcingType::computed;
962
963 Box bx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));// bx2.grow(IntVect(NGROW,NGROW,0));
964
965 Real cff = dt[lev] / rhow;
966 Real dt_lev = dt[lev];
967
968 ParallelFor(bx2, [=] AMREX_GPU_DEVICE (int i, int j, int )
969 {
970 if (use_EminusP_from_input) {
971 // EminusP is treated as a kinematic freshwater flux (m/s).
972 Zt_avg1(i,j,0) = Zt_avg1(i,j,0) - EminusP(i,j,0) * dt_lev;
973 } else {
974 Zt_avg1(i,j,0) = Zt_avg1(i,j,0) - (evap(i,j,0) - rain(i,j,0)) * cff;
975 }
976 });
977 }
978 }
979 Gpu::streamSynchronize();
980
981 vec_Zt_avg1[lev]->FillBoundary(geom[lev].periodicity());
982
983 for ( MFIter mfi(*vec_zeta[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
984 {
985 Box bx3 = mfi.tilebox(); bx3.grow(IntVect(NGROW+1,NGROW+1,0));
986 Array4<Real> const& zeta = mf_zeta->array(mfi);
987 Array4<Real> const& Zt_avg1 = (mf_Zt_avg1)->array(mfi);
988
989 ParallelFor(bx3, 3, [=] AMREX_GPU_DEVICE (int i, int j, int , int n)
990 {
991 zeta(i,j,0,n) = Zt_avg1(i,j,0);
992 });
993 }
994}
995
996
997/**
998 * @param[in ] lev level to operate on
999 */
1000void
1001REMORA::calculate_nodal_masks (int lev)
1002{
1003 for ( MFIter mfi(*vec_mskr[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
1004 {
1005 Array4<const Real> const& mskr = vec_mskr[lev]->const_array(mfi);
1006 Array4< Real> const& msku = vec_msku[lev]->array(mfi);
1007 Array4< Real> const& mskv = vec_mskv[lev]->array(mfi);
1008 Array4< Real> const& mskp = vec_mskp[lev]->array(mfi);
1009
1010 // NGROW rings, not one: the stencil reaches mskr(i-1,j-1), and mskr carries NGROW+1.
1011 Box bx = mfi.tilebox(); bx.grow(IntVect(NGROW,NGROW,0)); bx.makeSlab(2,0);
1012
1013 ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int)
1014 {
1015 msku(i,j,0) = mskr(i-1,j ,0) * mskr(i,j,0);
1016 mskv(i,j,0) = mskr(i ,j-1,0) * mskr(i,j,0);
1017 // mskp is 2 along a straight land-sea boundary
1018 if ((mskr(i-1,j,0) > Real(0.5)) and (mskr(i,j,0) > Real(0.5)) and (mskr(i-1,j-1,0) > Real(0.5)) and (mskr(i,j-1,0) > Real(0.5))) {
1019 mskp(i,j,0) = one;
1020 } else if ((mskr(i-1,j,0) < Real(0.5)) and (mskr(i,j,0) > Real(0.5)) and (mskr(i-1,j-1,0) > Real(0.5)) and (mskr(i,j-1,0) > Real(0.5))) {
1021 mskp(i,j,0) = one;
1022 } else if ((mskr(i-1,j,0) > Real(0.5)) and (mskr(i,j,0) < Real(0.5)) and (mskr(i-1,j-1,0) > Real(0.5)) and (mskr(i,j-1,0) > Real(0.5))) {
1023 mskp(i,j,0) = one;
1024 } else if ((mskr(i-1,j,0) > Real(0.5)) and (mskr(i,j,0) > Real(0.5)) and (mskr(i-1,j-1,0) < Real(0.5)) and (mskr(i,j-1,0) > Real(0.5))) {
1025 mskp(i,j,0) = one;
1026 } else if ((mskr(i-1,j,0) > Real(0.5)) and (mskr(i,j,0) > Real(0.5)) and (mskr(i-1,j-1,0) > Real(0.5)) and (mskr(i,j-1,0) < Real(0.5))) {
1027 mskp(i,j,0) = one;
1028 } else if ((mskr(i-1,j,0) > Real(0.5)) and (mskr(i,j,0) < Real(0.5)) and (mskr(i-1,j-1,0) > Real(0.5)) and (mskr(i,j-1,0) < Real(0.5))) {
1029 mskp(i,j,0) = two;
1030 } else if ((mskr(i-1,j,0) < Real(0.5)) and (mskr(i,j,0) > Real(0.5)) and (mskr(i-1,j-1,0) < Real(0.5)) and (mskr(i,j-1,0) > Real(0.5))) {
1031 mskp(i,j,0) = two;
1032 } else if ((mskr(i-1,j,0) > Real(0.5)) and (mskr(i,j,0) > Real(0.5)) and (mskr(i-1,j-1,0) < Real(0.5)) and (mskr(i,j-1,0) < Real(0.5))) {
1033 mskp(i,j,0) = two;
1034 } else if ((mskr(i-1,j,0) < Real(0.5)) and (mskr(i,j,0) < Real(0.5)) and (mskr(i-1,j-1,0) > Real(0.5)) and (mskr(i,j-1,0) > Real(0.5))) {
1035 mskp(i,j,0) = two;
1036 } else {
1037 mskp(i,j,0) = zero;
1038 }
1039 });
1040 }
1041}
1042
1043/**
1044 * Rebuild the u-, v- and psi-point masks from vec_mskr and fill their ghost cells.
1045 *
1046 * Every path goes through here, so the levels cannot end up with different definitions.
1047 *
1048 * @param[in ] lev level to operate on
1049 */
1050void
1051REMORA::update_nodal_masks (int lev)
1052{
1053 calculate_nodal_masks(lev);
1054
1055 vec_msku[lev]->FillBoundary(geom[lev].periodicity());
1056 vec_mskv[lev]->FillBoundary(geom[lev].periodicity());
1057 vec_mskp[lev]->FillBoundary(geom[lev].periodicity());
1058}
1059
1060/**
1061 * @param[in ] lev level to operate on
1062 */
1063void
1064REMORA::fill_3d_masks (int lev)
1065{
1066 for ( MFIter mfi(*vec_mskr3d[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
1067 {
1068 Array4<const Real> const& mskr = vec_mskr[lev]->const_array(mfi);
1069 Array4< Real> const& mskr3d = vec_mskr3d[lev]->array(mfi);
1070
1071 // No stencil, so this can fill every ring mskr has.
1072 Box bx = mfi.tilebox(); bx.grow(IntVect(NGROW+1,NGROW+1,0));
1073
1074 ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k)
1075 {
1076 mskr3d(i,j,k) = mskr(i,j,0);
1077 });
1078 }
1079}
two
constexpr amrex::Real two
Definition REMORA_Constants.H:8
bogus_large_value
constexpr amrex::Real bogus_large_value
Definition REMORA_Constants.H:29
one
constexpr amrex::Real one
Definition REMORA_Constants.H:7
zero
constexpr amrex::Real zero
Definition REMORA_Constants.H:6
rhow
constexpr amrex::Real rhow
Definition REMORA_Constants.H:37
BottomStressType::logarithmic
@ logarithmic
BottomStressType::linear
@ linear
BottomStressType::quadratic
@ quadratic
GridScaleType::analytic
@ analytic
GridScaleType::constant
@ constant
VertMixingType::GLS
@ GLS
IC_Type::analytic
@ analytic
IC_Type::netcdf
@ netcdf
NGROW
#define NGROW
Definition REMORA_IndexDefines.H:30
NAT
#define NAT
Definition REMORA_IndexDefines.H:17
BulkForcingType::computed
@ computed
setVal
mf_h setVal(geomdata.ProbHi(2))
rry
int rry
Definition REMORA_InitAnalyticBathymetry_Upwelling_ML.H:3
rrx
int rrx
Definition REMORA_InitAnalyticBathymetry_Upwelling_ML.H:2
dxi
const auto dxi
Definition REMORA_InitAnalyticGridScale_BoundaryLayer.H:16
time
Real time
Definition REMORA_InitAnalyticSMFlux_ChannelTest.H:1
REMORA_prob_common.H
REMORA::vec_mskr_full_domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskr_full_domain
Land/sea mask at cell centers on the whole domain at each potential level. Specified at hires_grid_le...
Definition REMORA.H:421
REMORA::vec_EminusP
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_EminusP
evaporation minus precipitation [kg/m^2/s], defined at rho-points
Definition REMORA.H:521
REMORA::set_grid_vars_averaged_down
void set_grid_vars_averaged_down(int lev)
Set pm/pn by averaging down from higher-resolution grid.
Definition REMORA.cpp:827
REMORA::foextrap_periodic_bc
int foextrap_periodic_bc() const noexcept
Definition REMORA.H:1455
REMORA::ncons
int ncons
Number of conserved scalars in the state (temperature + salt + passive scalars + biology tracers)
Definition REMORA.H:1797
REMORA::vec_mskr_crse_on_fine
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskr_crse_on_fine
the level's rho-, u- and v-masks copied onto the layout of the level above it coarsened,...
Definition REMORA.H:598
REMORA::vec_zeta_full_domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_zeta_full_domain
high resolution initial free surface height (2D)
Definition REMORA.H:581
REMORA::vec_rv2d
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rv2d
v velocity RHS (2D, includes horizontal and vertical advection)
Definition REMORA.H:436
REMORA::vec_evap
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_evap
evaporation rate [kg/m^2/s]
Definition REMORA.H:517
REMORA::zvel_bc
int zvel_bc() const noexcept
Definition REMORA.H:1450
REMORA::xvel_bc
int xvel_bc() const noexcept
Definition REMORA.H:1448
REMORA::domain_bcs_type
amrex::Vector< amrex::BCRec > domain_bcs_type
vector (over BCVars) of BCRecs
Definition REMORA.H:1728
REMORA::calculate_nodal_masks
void calculate_nodal_masks(int lev)
Calculate u-, v-, and psi-point masks based on rho-point masks after analytic initialization.
Definition REMORA_make_new_level.cpp:1001
REMORA::vec_fcor
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_fcor
coriolis factor (2D)
Definition REMORA.H:612
REMORA::vec_btflux
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_btflux
Bottom tracer flux; input arrays.
Definition REMORA.H:512
REMORA::vec_rubar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rubar
barotropic x velocity for the RHS (2D)
Definition REMORA.H:568
REMORA::vec_xvel_full_domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_xvel_full_domain
multilevel data container for high res initial x velocities (u in ROMS)
Definition REMORA.H:404
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:413
REMORA::vec_pm
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pm
horizontal scaling factor: 1 / dx (2D)
Definition REMORA.H:603
REMORA::vec_ZoBot
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ZoBot
Bottom roughness length [m], defined at rho points.
Definition REMORA.H:537
REMORA::vec_DU_avg2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_DU_avg2
correct time average of barotropic x velocity flux for coupling (2D)
Definition REMORA.H:547
REMORA::vec_lrflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_lrflx
longwave radiation
Definition REMORA.H:497
REMORA::vec_yv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_yv
y_grid on v-points (2D)
Definition REMORA.H:627
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:393
REMORA::MakeNewLevelFromCoarse
virtual void MakeNewLevelFromCoarse(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Make a new level using provided BoxArray and DistributionMapping and fill with interpolated coarse le...
Definition REMORA_make_new_level.cpp:24
REMORA::stretch_transform
void stretch_transform(int lev)
Calculate vertical stretched coordinates.
Definition REMORA_DepthStretchTransform.H:92
REMORA::define_flux_register
void define_flux_register(int lev)
build or rebuild the flux register between lev and lev-1
Definition REMORA.cpp:2699
REMORA::set_curvilinear_terms_from_grid_scale
void set_curvilinear_terms_from_grid_scale(int lev)
Set curvilinear derivative terms on level lev based on pm and pn.
Definition REMORA_make_new_level.cpp:926
REMORA::vec_vwind
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_vwind
Wind in the v direction, defined at rho-points.
Definition REMORA.H:486
REMORA::prob
std::unique_ptr< ProblemBase > prob
Pointer to container of analytical functions for problem definition.
Definition REMORA.H:1679
REMORA::vec_mskr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskr
land/sea mask at cell centers (2D)
Definition REMORA.H:584
REMORA::Construct_REMORAFillPatchers
void Construct_REMORAFillPatchers(int lev)
Construct FillPatchers.
Definition REMORA.cpp:583
REMORA::init_grid_vars_from_netcdf
void init_grid_vars_from_netcdf(int lev)
Grid variable initialization from NetCDF file.
Definition REMORA_init_from_netcdf.cpp:530
REMORA::vec_rain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rain
precipitation rate [kg/m^2/s]
Definition REMORA.H:515
REMORA::vec_tke
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_tke
Turbulent kinetic energy.
Definition REMORA.H:667
REMORA::vec_stflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_stflx
Surface tracer flux; working arrays.
Definition REMORA.H:506
REMORA::update_nodal_masks
void update_nodal_masks(int lev)
Rebuild the u-, v- and psi-point masks from vec_mskr and fill their ghosts.
Definition REMORA_make_new_level.cpp:1051
REMORA::vec_gls
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_gls
Turbulent generic length scale.
Definition REMORA.H:669
REMORA::vec_sustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sustr
Surface stress in the u direction.
Definition REMORA.H:479
REMORA::vec_yp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_yp
y_grid on psi-points (2D)
Definition REMORA.H:632
REMORA::vec_xr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_xr
x_grid on rho points (2D)
Definition REMORA.H:615
REMORA::yvel_bc
int yvel_bc() const noexcept
Definition REMORA.H:1449
REMORA::vec_Dvbar_new
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Dvbar_new
see vec_Dvbar_old (2D)
Definition REMORA.H:560
REMORA::vec_ru2d
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ru2d
u velocity RHS (2D, includes horizontal and vertical advection)
Definition REMORA.H:434
REMORA::ClearLevel
virtual void ClearLevel(int lev) override
Delete level data Overrides the pure virtual function in AmrCore.
Definition REMORA_make_new_level.cpp:816
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:399
REMORA::ComputeGhostCells
AMREX_FORCE_INLINE int ComputeGhostCells(const int &spatial_order)
Helper function to determine number of ghost cells.
Definition REMORA.H:2074
REMORA::vec_sstore
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sstore
additional scratch space for calculations on temp, salt, etc
Definition REMORA.H:647
REMORA::vec_xv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_xv
x_grid on v-points (2D)
Definition REMORA.H:625
REMORA::init_only
void init_only(int lev, amrex::Real time)
Init (NOT restart or regrid)
Definition REMORA.cpp:1751
REMORA::init_set_vmix
void init_set_vmix(int lev)
Initialize vertical mixing coefficients from file or analytic.
Definition REMORA.cpp:902
REMORA::set_grid_scale
void set_grid_scale(int lev)
Set pm and pn arrays and x/y coords on level lev.
Definition REMORA_make_new_level.cpp:826
REMORA::set_coriolis
void set_coriolis(int lev)
Initialize Coriolis factor from file or analytic.
Definition REMORA.cpp:873
REMORA::foextrap_bc
int foextrap_bc() const noexcept
Definition REMORA.H:1456
REMORA::vec_Lscale
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Lscale
Vertical mixing turbulent length scale.
Definition REMORA.H:671
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:424
REMORA::vec_Akt
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akt
Vertical diffusion coefficient (3D)
Definition REMORA.H:444
REMORA::vec_msku
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_msku
land/sea mask at x-faces (2D)
Definition REMORA.H:586
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:440
REMORA::vec_pm_full_domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pm_full_domain
horizontal scaling factor: 1 / dx (2D) on whole domain
Definition REMORA.H:607
REMORA::xvel_old
amrex::Vector< amrex::MultiFab * > xvel_old
multilevel data container for last step's x velocities (u in ROMS)
Definition REMORA.H:386
REMORA::vec_Dubar_old
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Dubar_old
DU_avg2 per unit cell edge length, at the start and end of this level's step. What a subcycled finer ...
Definition REMORA.H:554
REMORA::yvel_new
amrex::Vector< amrex::MultiFab * > yvel_new
multilevel data container for current step's y velocities (v in ROMS)
Definition REMORA.H:397
REMORA::vec_uwind
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_uwind
Wind in the u direction, defined at rho-points.
Definition REMORA.H:484
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:438
REMORA::zeta_bc
int zeta_bc() const noexcept
Definition REMORA.H:1453
REMORA::Define_REMORAFillPatchers
void Define_REMORAFillPatchers(int lev)
Define FillPatchers.
Definition REMORA.cpp:639
REMORA::num_bdy_vars
int num_bdy_vars() const noexcept
Definition REMORA.H:1467
REMORA::vec_shflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_shflx
sensible heat flux
Definition REMORA.H:503
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:446
REMORA::vec_dmde
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_dmde
d(1/m)/d(eta)
Definition REMORA.H:644
REMORA::vec_rvbar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rvbar
barotropic y velocity for the RHS (2D)
Definition REMORA.H:570
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:390
REMORA::vec_z_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_r
z coordinates at rho points (cell centers)
Definition REMORA.H:453
REMORA::xvel_new
amrex::Vector< amrex::MultiFab * > xvel_new
multilevel data container for current step's x velocities (u in ROMS)
Definition REMORA.H:395
REMORA::vec_lhflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_lhflx
latent heat flux
Definition REMORA.H:501
REMORA::vec_mskp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskp
land/sea mask at cell corners (2D)
Definition REMORA.H:590
REMORA::bdy_zeta
int bdy_zeta() const noexcept
Definition REMORA.H:1466
REMORA::vec_bvf
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bvf
Brunt-Vaisala frequency (3D)
Definition REMORA.H:654
REMORA::RemakeLevel
virtual void RemakeLevel(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Remake an existing level using provided BoxArray and DistributionMapping and fill with existing fine ...
Definition REMORA_make_new_level.cpp:165
REMORA::vec_lonp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_lonp
longitude on psi-points (2D, degrees east); only filled when the grid NetCDF file carries lon_psi
Definition REMORA.H:636
REMORA::vec_mskv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskv
land/sea mask at y-faces (2D)
Definition REMORA.H:588
REMORA::init_masks
void init_masks(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)
Allocate MultiFabs for masks.
Definition REMORA_make_new_level.cpp:549
REMORA::physbcs
amrex::Vector< std::unique_ptr< REMORAPhysBCFunct > > physbcs
Vector (over level) of functors to apply physical boundary conditions.
Definition REMORA.H:1710
REMORA::vec_msku_crse_on_fine
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_msku_crse_on_fine
Definition REMORA.H:599
REMORA::fill_3d_masks
void fill_3d_masks(int lev)
Copy maskr to all z levels.
Definition REMORA_make_new_level.cpp:1064
REMORA::FillCoarsePatch
void FillCoarsePatch(int lev, amrex::Real time, amrex::MultiFab *mf_fine, amrex::MultiFab *mf_crse, const int bccomp, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=zero, const amrex::MultiFab &mf_calc=amrex::MultiFab())
fill an entire multifab by interpolating from the coarser level
Definition REMORA_FillPatch.cpp:435
REMORA::vec_rhoS
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoS
density perturbation
Definition REMORA.H:650
REMORA::init_riv_pos_from_netcdf
void init_riv_pos_from_netcdf(int lev)
Definition REMORA_init_from_netcdf.cpp:1006
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:448
REMORA::vec_yvel_full_domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_yvel_full_domain
multilevel data container for high res initial y velocities (v in ROMS)
Definition REMORA.H:406
REMORA::vec_svstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_svstr
Surface stress in the v direction.
Definition REMORA.H:481
REMORA::vec_Huon
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Huon
u-volume flux (3D)
Definition REMORA.H:426
REMORA::vec_h_full_domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_h_full_domain
Bathymetry data on the whole domain at each potential level.
Definition REMORA.H:416
REMORA::yvel_old
amrex::Vector< amrex::MultiFab * > yvel_old
multilevel data container for last step's y velocities (v in ROMS)
Definition REMORA.H:388
REMORA::init_stuff
void init_stuff(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)
Allocate MultiFabs for state and evolution variables.
Definition REMORA_make_new_level.cpp:577
REMORA::vec_rhoA
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoA
vertically-averaged density
Definition REMORA.H:652
REMORA::vec_DV_avg1
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_DV_avg1
time average of barotropic y velocity flux
Definition REMORA.H:549
REMORA::hires_init_level
int hires_init_level
Which level the high resolution initialization data is at.
Definition REMORA.H:2019
REMORA::bdy_vbar
int bdy_vbar() const noexcept
Definition REMORA.H:1465
REMORA::t_new
amrex::Vector< amrex::Real > t_new
new time at each level, in seconds since start_time
Definition REMORA.H:1700
REMORA::solverChoice
static SolverChoice solverChoice
Container for algorithmic choices.
Definition REMORA.H:1949
REMORA::set_grid_coords_from_grid_scale
void set_grid_coords_from_grid_scale(int lev)
Set x/y coords on level lev based on pm and pn.
Definition REMORA_make_new_level.cpp:881
REMORA::resize_stuff
void resize_stuff(int lev)
Resize variable containers to accommodate data on levels 0 to max_lev.
Definition REMORA_make_new_level.cpp:414
REMORA::vec_river_position
amrex::Vector< std::unique_ptr< amrex::iMultiFab > > vec_river_position
iMultiFab for river positions; contents are indices of rivers
Definition REMORA.H:1627
REMORA::vec_Akk
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akk
Turbulent kinetic energy vertical diffusion coefficient.
Definition REMORA.H:673
REMORA::set_masks
void set_masks(int lev)
Initialize land-sea masks from file or analytic.
Definition REMORA.cpp:942
REMORA::vec_rdrag2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rdrag2
Quadratic drag coefficient [unitless], defined at rho points.
Definition REMORA.H:535
REMORA::set_zeta_to_Ztavg
void set_zeta_to_Ztavg(int lev, bool apply_eminusp=true)
Set zeta components to be equal to time-averaged Zt_avg1.
Definition REMORA_make_new_level.cpp:948
REMORA::vec_ru
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ru
u velocity RHS (3D, includes horizontal and vertical advection)
Definition REMORA.H:430
REMORA::bdy_ubar
int bdy_ubar() const noexcept
Definition REMORA.H:1464
REMORA::vec_xp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_xp
x_grid on psi-points (2D)
Definition REMORA.H:630
REMORA::vec_longwave_down
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_longwave_down
Downward longwave radiation.
Definition REMORA.H:499
REMORA::vec_zeta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_zeta
free surface height (2D)
Definition REMORA.H:578
REMORA::ubar_bc
int ubar_bc() const noexcept
Definition REMORA.H:1451
REMORA::vec_vbar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_vbar
barotropic y velocity (2D)
Definition REMORA.H:576
REMORA::vec_DU_avg1
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_DU_avg1
time average of barotropic x velocity flux (2D)
Definition REMORA.H:545
REMORA::vec_alpha
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_alpha
Thermal expansion coefficient (3D)
Definition REMORA.H:656
REMORA::vec_ubar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ubar
barotropic x velocity (2D)
Definition REMORA.H:574
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=false, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=zero, const amrex::MultiFab &mf_calc=amrex::MultiFab(), amrex::Vector< amrex::MultiFab * > const &mfs_crse_old={}, amrex::Vector< amrex::MultiFab * > const &mfs_crse_new={})
Fill a new MultiFab by copying in phi from valid region and filling ghost cells.
Definition REMORA_FillPatch.cpp:30
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:384
REMORA::vec_bustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bustr
Bottom stress in the u direction.
Definition REMORA.H:540
REMORA::vec_cons_full_domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_cons_full_domain
multilevel data container for high res initial data: temperature, salinity, passive tracer
Definition REMORA.H:402
REMORA::vbar_bc
int vbar_bc() const noexcept
Definition REMORA.H:1452
REMORA::vec_DV_avg2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_DV_avg2
correct time average of barotropic y velocity flux for coupling (2D)
Definition REMORA.H:551
REMORA::set_hmixcoef
void set_hmixcoef(int lev)
Initialize horizontal mixing coefficients.
Definition REMORA.cpp:1317
REMORA::vec_yu
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_yu
y_grid on u-points (2D)
Definition REMORA.H:622
REMORA::vec_dndx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_dndx
d(1/n)/d(xi)
Definition REMORA.H:642
REMORA::vec_bvstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bvstr
Bottom stress in the v direction.
Definition REMORA.H:542
REMORA::vec_rzeta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rzeta
free surface height for the RHS (2D)
Definition REMORA.H:572
REMORA::vec_z_phys_nd
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_phys_nd
z coordinates at psi points (cell nodes)
Definition REMORA.H:473
REMORA::vec_Dvbar_old
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Dvbar_old
DV_avg2 per unit cell edge length, see vec_Dubar_old (2D)
Definition REMORA.H:558
REMORA::vec_xu
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_xu
x_grid on u-points (2D)
Definition REMORA.H:620
REMORA::vec_pn_full_domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pn_full_domain
horizontal scaling factor: 1 / dy (2D) on whole domain
Definition REMORA.H:609
REMORA::vec_nudg_coeff
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > vec_nudg_coeff
Climatology nudging coefficients.
Definition REMORA.H:678
REMORA::set_weights
void set_weights(int lev)
Set weights for averaging 3D variables to 2D.
Definition REMORA_set_weights.cpp:11
REMORA::vec_pn
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pn
horizontal scaling factor: 1 / dy (2D)
Definition REMORA.H:605
REMORA::vec_Akv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akv
Vertical viscosity coefficient (3D)
Definition REMORA.H:442
REMORA::MakeNewLevelFromScratch
virtual void MakeNewLevelFromScratch(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Make a new level from scratch using provided BoxArray and DistributionMapping. Only used during initi...
Definition REMORA_make_new_level.cpp:344
REMORA::vec_mskv_crse_on_fine
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskv_crse_on_fine
Definition REMORA.H:600
REMORA::vec_stflux
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_stflux
Surface tracer flux; input arrays.
Definition REMORA.H:508
REMORA::vec_Dubar_new
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Dubar_new
see vec_Dubar_old (2D)
Definition REMORA.H:556
REMORA::vec_rdrag
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rdrag
Linear drag coefficient [m/s], defined at rho points.
Definition REMORA.H:533
REMORA::vec_cloud
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_cloud
cloud cover fraction [0-1], defined at rho-points
Definition REMORA.H:519
REMORA::vec_Zt_avg1
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Zt_avg1
Average of the free surface, zeta (2D)
Definition REMORA.H:476
REMORA::restart_chkfile
std::string restart_chkfile
If set, restart from this checkpoint file.
Definition REMORA.H:1783
REMORA::vec_rv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rv
v velocity RHS (3D, includes horizontal and vertical advection)
Definition REMORA.H:432
REMORA::vec_btflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_btflx
Bottom tracer flux; working arrays.
Definition REMORA.H:510
REMORA::cf_width
int cf_width
Nudging width at coarse-fine interface.
Definition REMORA.H:1637
REMORA::vec_beta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_beta
Saline contraction coefficient (3D)
Definition REMORA.H:658
REMORA::t_old
amrex::Vector< amrex::Real > t_old
old time at each level, in seconds since start_time
Definition REMORA.H:1702
REMORA::vec_mskr3d
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskr3d
land/sea mask at cell centers, copied to all z levels (3D)
Definition REMORA.H:592
REMORA::m_bc_extdir_vals
amrex::Vector< amrex::GpuArray< amrex::Real, AMREX_SPACEDIM *2 > > m_bc_extdir_vals
Array holding the Dirichlet values at walls which need them.
Definition REMORA.H:1736
REMORA::vec_srflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_srflx
Shortwave radiation flux [W/m²], defined at rho-points.
Definition REMORA.H:495
REMORA::set_bathymetry_averaged_down
void set_bathymetry_averaged_down(int lev)
Copy over bathymetry data that has been averaged down from high resolution input netcdf file.
Definition REMORA.cpp:810
REMORA::dt
amrex::Vector< amrex::Real > dt
time step at each level
Definition REMORA.H:1704
REMORA::vec_Pair
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Pair
Air pressure [mb], defined at rho-points.
Definition REMORA.H:492
REMORA::domain_bcs_type_d
amrex::Gpu::DeviceVector< amrex::BCRec > domain_bcs_type_d
GPU vector (over BCVars) of BCRecs.
Definition REMORA.H:1730
REMORA::vec_qair
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_qair
Specific humidity [kg/kg], defined at rho-points.
Definition REMORA.H:490
REMORA::hires_grid_level
int hires_grid_level
Which level the high resolution bathymetry is at.
Definition REMORA.H:2012
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:456
REMORA::vec_Tair
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Tair
Air temperature [°C], defined at rho-points.
Definition REMORA.H:488
REMORA::vec_yr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_yr
y_grid on rho points (2D)
Definition REMORA.H:617
REMORA::vec_Hvom
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Hvom
v-volume flux (3D)
Definition REMORA.H:428
REMORA::vec_Akp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akp
Turbulent length scale vertical diffusion coefficient.
Definition REMORA.H:675
REMORA::vec_diff2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_diff2
Harmonic diffusivity for temperature / salinity.
Definition REMORA.H:450
REMORA::vec_latp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_latp
latitude on psi-points (2D, degrees north); only filled when the grid NetCDF file carries lat_psi
Definition REMORA.H:639
BCVars::cons_bc
static constexpr int cons_bc
Definition REMORA_IndexDefines.H:36
BCVars::Temp_bc_comp
static constexpr int Temp_bc_comp
Definition REMORA_IndexDefines.H:37
BdyVars::t
static constexpr int t
cons component Temp_comp
Definition REMORA_IndexDefines.H:73
BdyVars::u
static constexpr int u
Definition REMORA_IndexDefines.H:71
BdyVars::v
static constexpr int v
Definition REMORA_IndexDefines.H:72
BdyVars::cons
int cons(int icomp) noexcept
Definition REMORA_IndexDefines.H:76
BdyVars::null
static constexpr int null
Definition REMORA_IndexDefines.H:70
BulkFlux::EminusP
@ EminusP
evaporation minus precipitation [m/s]
Definition REMORA_IndexDefines.H:156
SolverChoice::rdrag2
amrex::Real rdrag2
Definition REMORA_DataStruct.H:973
SolverChoice::Akk_bak
amrex::Real Akk_bak
Definition REMORA_DataStruct.H:1053
SolverChoice::EminusP
amrex::Real EminusP
Definition REMORA_DataStruct.H:1028
SolverChoice::bottom_stress_type
BottomStressType bottom_stress_type
Definition REMORA_DataStruct.H:946
SolverChoice::longwave_rad
amrex::Real longwave_rad
Definition REMORA_DataStruct.H:1026
SolverChoice::gls_Kmin
amrex::Real gls_Kmin
Definition REMORA_DataStruct.H:1041
SolverChoice::rdrag
amrex::Real rdrag
Definition REMORA_DataStruct.H:971
SolverChoice::vert_mixing_type
VertMixingType vert_mixing_type
Definition REMORA_DataStruct.H:956
SolverChoice::bulk_flux_type
std::array< BulkForcingType, BulkFlux::NumTypes > bulk_flux_type
Definition REMORA_DataStruct.H:885
SolverChoice::grid_scale_type
GridScaleType grid_scale_type
Definition REMORA_DataStruct.H:963
SolverChoice::gls_Pmin
amrex::Real gls_Pmin
Definition REMORA_DataStruct.H:1042
SolverChoice::Akp_bak
amrex::Real Akp_bak
Definition REMORA_DataStruct.H:1054