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 FillCoarsePatch(lev, time, cons_new[lev], cons_new[lev-1],BCVars::Temp_bc_comp,BdyVars::t);
89 FillCoarsePatch(lev, time, xvel_new[lev], xvel_new[lev-1], xvel_bc(), BdyVars::u);
90 FillCoarsePatch(lev, time, yvel_new[lev], yvel_new[lev-1], yvel_bc(), BdyVars::v);
91 FillCoarsePatch(lev, time, zvel_new[lev], zvel_new[lev-1], zvel_bc(), BdyVars::null);
92
93 if (lev > hires_grid_level) {
94 FillCoarsePatch(lev, time, vec_h[lev].get(), vec_h[lev-1].get(),
95 foextrap_periodic_bc(),BdyVars::null,0,false);
96 FillCoarsePatch(lev, time, vec_h[lev].get(), vec_h[lev-1].get(),
97 foextrap_periodic_bc(),BdyVars::null,1,false);
98 } else {
99 set_bathymetry_averaged_down(lev);
100 }
101
102 FillCoarsePatch(lev, time, vec_Zt_avg1[lev].get(), vec_Zt_avg1[lev-1].get(),BCVars::cons_bc);
103 for (int icomp=0; icomp<3; icomp++) {
104 FillCoarsePatch(lev, time, vec_ubar[lev].get(), vec_ubar[lev-1].get(), ubar_bc(),
105 bdy_ubar(),icomp,false);
106 FillCoarsePatch(lev, time, vec_vbar[lev].get(), vec_vbar[lev-1].get(), vbar_bc(),
107 bdy_vbar(),icomp,false);
108 }
109 for (int icomp=0; icomp<2; icomp++) {
110 FillCoarsePatch(lev, time, vec_ru[lev].get(), vec_ru[lev-1].get(), xvel_bc(),
111 BdyVars::null,icomp,false);
112 FillCoarsePatch(lev, time, vec_rv[lev].get(), vec_rv[lev-1].get(), yvel_bc(),
113 BdyVars::null,icomp,false);
114 FillCoarsePatch(lev, time, vec_ru2d[lev].get(), vec_ru2d[lev-1].get(), xvel_bc(),
115 BdyVars::null,icomp,false);
116 FillCoarsePatch(lev, time, vec_rv2d[lev].get(), vec_rv2d[lev-1].get(), yvel_bc(),
117 BdyVars::null,icomp,false);
118 }
119
120 // Not totally sure foextrap is right here
121 FillCoarsePatchPC(lev, time, vec_mskr[lev].get(), vec_mskr[lev-1].get(),
122 foextrap_bc());
123
124 calculate_nodal_masks(lev);
125
126
127 set_grid_scale(lev);
128 stretch_transform(lev);
129
130 init_set_vmix(lev);
131 set_hmixcoef(lev);
132 set_coriolis(lev);
133 bool apply_eminusp = false;
134 set_zeta_to_Ztavg(lev,apply_eminusp);
135 // Previously set smflux
136
137#ifdef REMORA_USE_NETCDF
138 if (solverChoice.do_rivers) {
139 init_riv_pos_from_netcdf(lev);
140 }
141#endif
142
143 // ********************************************************************************************
144 // If we are making a new level then the FillPatcher for this level hasn't been allocated yet
145 // ********************************************************************************************
146 if (cf_width >= 0) {
147 Construct_REMORAFillPatchers(lev);
148 Define_REMORAFillPatchers(lev);
149 }
150
151#ifdef REMORA_USE_PARTICLES
152 // particleData.Redistribute();
153#endif
154}
155
156/**
157 * Remake an existing level using provided BoxArray and DistributionMapping and
158 * fill with existing fine and coarse data.
159 * overrides the pure virtual function in AmrCore
160 * @param[in ] lev level to make
161 * @param[in ] time current time
162 * @param[in ] ba BoxArray for the level
163 * @param[in ] dm DistributionMapping for the level
164 */
165void
166REMORA::RemakeLevel (int lev, Real time, const BoxArray& ba, const DistributionMapping& dm)
167{
168 BoxArray ba_old(cons_new[lev]->boxArray());
169 DistributionMapping dm_old(cons_new[lev]->DistributionMap());
170
171 BoxList bl2d = ba.boxList();
172 for (auto& b : bl2d) {
173 b.setRange(2,0);
174 }
175 BoxArray ba2d(std::move(bl2d));
176
177 amrex::Print() << "Remaking level " << lev << std::endl;
178 amrex::Print() << "GRIDS AT LEVEL " << lev << " ARE " << ba << std::endl;
179
180#if (NGROW==2)
181 int ngrow_state = ComputeGhostCells(solverChoice.spatial_order)+1;
182 int ngrow_vels = ComputeGhostCells(solverChoice.spatial_order)+1;
183 int ngrow_zeta = ComputeGhostCells(solverChoice.spatial_order)+1;
184 int ngrow_h = ComputeGhostCells(solverChoice.spatial_order)+1;
185 int ngrow_velbar = ComputeGhostCells(solverChoice.spatial_order);
186#else
187 int ngrow_state = ComputeGhostCells(solverChoice.spatial_order)+2;
188 int ngrow_vels = ComputeGhostCells(solverChoice.spatial_order)+2;
189 int ngrow_zeta = ComputeGhostCells(solverChoice.spatial_order)+2;
190 int ngrow_h = ComputeGhostCells(solverChoice.spatial_order)+2;
191 int ngrow_velbar = ComputeGhostCells(solverChoice.spatial_order)+1;
192#endif
193
194 MultiFab tmp_cons_new(ba, dm, ncons, ngrow_state);
195 MultiFab tmp_cons_old(ba, dm, ncons, ngrow_state);
196
197 MultiFab tmp_xvel_new(convert(ba, IntVect(1,0,0)), dm, 1, ngrow_vels);
198 MultiFab tmp_xvel_old(convert(ba, IntVect(1,0,0)), dm, 1, ngrow_vels);
199
200 MultiFab tmp_yvel_new(convert(ba, IntVect(0,1,0)), dm, 1, ngrow_vels);
201 MultiFab tmp_yvel_old(convert(ba, IntVect(0,1,0)), dm, 1, ngrow_vels);
202
203 MultiFab tmp_zvel_new(convert(ba, IntVect(0,0,1)), dm, 1, IntVect(ngrow_vels,ngrow_vels,0));
204 MultiFab tmp_zvel_old(convert(ba, IntVect(0,0,1)), dm, 1, IntVect(ngrow_vels,ngrow_vels,0));
205
206 MultiFab tmp_Zt_avg1_new(ba2d, dm, 1, IntVect(ngrow_zeta,ngrow_zeta,0));
207 MultiFab tmp_h(ba2d, dm, 2, IntVect(ngrow_h,ngrow_h,0));
208
209 MultiFab tmp_ubar_new(convert(ba2d, IntVect(1,0,0)), dm, 3, IntVect(ngrow_velbar,ngrow_velbar,0));
210
211 MultiFab tmp_vbar_new(convert(ba2d, IntVect(0,1,0)), dm, 3, IntVect(ngrow_velbar,ngrow_velbar,0));
212
213 MultiFab tmp_ru_new(convert(ba, IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0));
214 MultiFab tmp_rv_new(convert(ba, IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0));
215
216 MultiFab tmp_ru2d_new(convert(ba2d, IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0));
217 MultiFab tmp_rv2d_new(convert(ba2d, IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0));
218
219 init_masks(lev, ba, dm);
220
221 tmp_cons_new.setVal(zero);
222 tmp_xvel_new.setVal(zero);
223 tmp_yvel_new.setVal(zero);
224 tmp_zvel_new.setVal(zero);
225
226 tmp_cons_old.setVal(zero);
227 tmp_xvel_old.setVal(zero);
228 tmp_yvel_old.setVal(zero);
229 tmp_zvel_old.setVal(zero);
230
231 tmp_ru_new.setVal(zero);
232 tmp_rv_new.setVal(zero);
233
234 tmp_ru2d_new.setVal(zero);
235 tmp_rv2d_new.setVal(zero);
236
237 tmp_ubar_new.setVal(zero);
238 tmp_vbar_new.setVal(zero);
239
240
241 // This will fill the temporary MultiFabs with data from previous fine data as well as coarse where needed
242 FillPatch(lev, time, tmp_cons_new, cons_new, BCVars::cons_bc, BdyVars::t,0,true,false);
243 FillPatch(lev, time, tmp_xvel_new, xvel_new, xvel_bc(), BdyVars::u,0,true,false,0,0,zero,tmp_xvel_new);
244 FillPatch(lev, time, tmp_yvel_new, yvel_new, yvel_bc(), BdyVars::v,0,true,false,0,0,zero,tmp_yvel_new);
245 FillPatch(lev, time, tmp_zvel_new, zvel_new, zvel_bc(), BdyVars::null,0,true,false);
246 FillPatch(lev, time, tmp_Zt_avg1_new, GetVecOfPtrs(vec_Zt_avg1), zeta_bc(), BdyVars::null,0,true,false);
247
248 for (int icomp=0; icomp<3; icomp++) {
249 FillPatch(lev, time, tmp_ubar_new, GetVecOfPtrs(vec_ubar), ubar_bc(), bdy_ubar(), icomp,false,false);
250 FillPatch(lev, time, tmp_vbar_new, GetVecOfPtrs(vec_vbar), vbar_bc(), bdy_vbar(), icomp,false,false);
251 }
252 for (int icomp=0; icomp<2; icomp++) {
253 FillPatch(lev, time, tmp_ru_new, GetVecOfPtrs(vec_ru), xvel_bc(), BdyVars::null, icomp,false,false);
254 FillPatch(lev, time, tmp_rv_new, GetVecOfPtrs(vec_rv), yvel_bc(), BdyVars::null, icomp,false,false);
255 // These might want to have BCVars::ubar_bc and vbar_bc
256 FillPatch(lev, time, tmp_ru2d_new, GetVecOfPtrs(vec_ru2d), xvel_bc(), BdyVars::null, icomp,false,false);
257 FillPatch(lev, time, tmp_rv2d_new, GetVecOfPtrs(vec_rv2d), yvel_bc(), BdyVars::null, icomp,false,false);
258 }
259
260 MultiFab::Copy(tmp_cons_old,tmp_cons_new,0,0,ncons,tmp_cons_new.nGrowVect());
261 MultiFab::Copy(tmp_xvel_old,tmp_xvel_new,0,0, 1,tmp_xvel_new.nGrowVect());
262 MultiFab::Copy(tmp_yvel_old,tmp_yvel_new,0,0, 1,tmp_yvel_new.nGrowVect());
263 MultiFab::Copy(tmp_zvel_old,tmp_zvel_new,0,0, 1,tmp_zvel_new.nGrowVect());
264
265 std::swap(tmp_cons_new, *cons_new[lev]);
266 std::swap(tmp_cons_old, *cons_old[lev]);
267 std::swap(tmp_xvel_new, *xvel_new[lev]);
268 std::swap(tmp_xvel_old, *xvel_old[lev]);
269 std::swap(tmp_yvel_new, *yvel_new[lev]);
270 std::swap(tmp_yvel_old, *yvel_old[lev]);
271 std::swap(tmp_zvel_new, *zvel_new[lev]);
272 std::swap(tmp_zvel_old, *zvel_old[lev]);
273 std::swap(tmp_Zt_avg1_new, *vec_Zt_avg1[lev]);
274 std::swap(tmp_ubar_new, *vec_ubar[lev]);
275 std::swap(tmp_vbar_new, *vec_vbar[lev]);
276 std::swap(tmp_ru_new, *vec_ru[lev]);
277 std::swap(tmp_rv_new, *vec_rv[lev]);
278 std::swap(tmp_ru2d_new, *vec_ru2d[lev]);
279 std::swap(tmp_rv2d_new, *vec_rv2d[lev]);
280
281 // Handle bathymetry separately
282 if (lev > hires_grid_level) {
283 FillPatch(lev, time, tmp_h, GetVecOfPtrs(vec_h), foextrap_periodic_bc(), BdyVars::null,0,false,false);
284 FillPatch(lev, time, tmp_h, GetVecOfPtrs(vec_h), foextrap_periodic_bc(), BdyVars::null,1,false,false);
285 std::swap(tmp_h, *vec_h[lev]);
286 } else {
287 // Swap first: vec_h[lev] is still on the pre-regrid BoxArray at this point, and the
288 // branch above is what moves it onto the new one. set_bathymetry_averaged_down takes
289 // its data from vec_h_full_domain rather than from the old grids, so the old contents
290 // are not needed -- but its FillPatch uses the land masks, which init_masks has
291 // already rebuilt on the new BoxArray, so leaving vec_h[lev] on the old one mixes two
292 // BoxArrays inside REMORAPhysBCFunct.
293 std::swap(tmp_h, *vec_h[lev]);
294 set_bathymetry_averaged_down(lev);
295 }
296
297 t_new[lev] = time;
298 t_old[lev] = time - bogus_large_value;
299
300 init_masks(lev, ba, dm);
301 FillCoarsePatchPC(lev, time, vec_mskr[lev].get(), vec_mskr[lev-1].get(),
302 foextrap_bc());
303 calculate_nodal_masks(lev);
304
305 init_stuff(lev, ba, dm);
306
307 set_grid_scale(lev);
308 stretch_transform(lev);
309
310 init_set_vmix(lev);
311 set_hmixcoef(lev);
312 set_coriolis(lev);
313 bool apply_eminusp = false;
314 set_zeta_to_Ztavg(lev,apply_eminusp);
315 // Previously set smflux here
316
317#ifdef REMORA_USE_NETCDF
318 if (solverChoice.do_rivers) {
319 init_riv_pos_from_netcdf(lev);
320 }
321#endif
322
323 // We need to re-define the FillPatcher if the grids have changed
324 if (lev > 0 && cf_width >= 0) {
325 bool ba_changed = (ba != ba_old);
326 bool dm_changed = (dm != dm_old);
327 if (ba_changed || dm_changed) {
328 Define_REMORAFillPatchers(lev);
329 }
330 }
331
332#ifdef REMORA_USE_PARTICLES
333 particleData.Redistribute();
334#endif
335}
336
337/**
338 * Make a new level from scratch using provided BoxArray and DistributionMapping.
339 * This is called both for initialization and for restart
340 * (overrides the pure virtual function in AmrCore)
341 * main.cpp --> REMORA::InitData --> InitFromScratch --> MakeNewGrids --> MakeNewLevelFromScratch
342 * restart --> MakeNewGrids --> MakeNewLevelFromScratch
343 *
344 * @param[in ] lev level to make
345 * @param[in ] time current time
346 * @param[in ] ba BoxArray for the level
347 * @param[in ] dm DistributionMapping for the level
348 */
349void REMORA::MakeNewLevelFromScratch (int lev, Real time, const BoxArray& ba,
350 const DistributionMapping& dm)
351{
352 // Set BoxArray grids and DistributionMapping dmap in AMReX_AmrMesh.H class
353 SetBoxArray(lev, ba);
354 SetDistributionMap(lev, dm);
355
356 BoxList bl2d = ba.boxList();
357 for (auto& b : bl2d) {
358 b.setRange(2,0);
359 }
360 BoxArray ba2d(std::move(bl2d));
361
362 amrex::Print() << "Making level " << lev << " from scratch" << std::endl;
363 amrex::Print() << "GRIDS AT LEVEL " << lev << " ARE " << ba << std::endl;
364
365 // The number of ghost cells for density must be 1 greater than that for velocity
366 // so that we can go back in forth between velocity and momentum on all faces
367#if NGROW==2
368 int ngrow_state = ComputeGhostCells(solverChoice.spatial_order)+1;
369 int ngrow_vels = ComputeGhostCells(solverChoice.spatial_order)+1;
370#else
371 int ngrow_state = ComputeGhostCells(solverChoice.spatial_order)+2;
372 int ngrow_vels = ComputeGhostCells(solverChoice.spatial_order)+2;
373#endif
374
375 cons_old[lev] = new MultiFab(ba, dm, ncons, ngrow_state);
376 cons_new[lev] = new MultiFab(ba, dm, ncons, ngrow_state);
377
378 xvel_new[lev] = new MultiFab(convert(ba, IntVect(1,0,0)), dm, 1, ngrow_vels);
379 xvel_old[lev] = new MultiFab(convert(ba, IntVect(1,0,0)), dm, 1, ngrow_vels);
380
381 yvel_new[lev] = new MultiFab(convert(ba, IntVect(0,1,0)), dm, 1, ngrow_vels);
382 yvel_old[lev] = new MultiFab(convert(ba, IntVect(0,1,0)), dm, 1, ngrow_vels);
383
384 zvel_new[lev] = new MultiFab(convert(ba, IntVect(0,0,1)), dm, 1, IntVect(ngrow_vels,ngrow_vels,0));
385 zvel_old[lev] = new MultiFab(convert(ba, IntVect(0,0,1)), dm, 1, IntVect(ngrow_vels,ngrow_vels,0));
386
387 resize_stuff(lev);
388
389 vec_Zt_avg1[lev].reset(new MultiFab(ba2d ,dm,1,IntVect(NGROW+1,NGROW+1,0))); //2d, average of the free surface (zeta)
390 vec_h[lev].reset(new MultiFab(ba2d ,dm,2,IntVect(NGROW+1,NGROW+1,0))); //2d, bathymetry
391 vec_ubar[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,3,IntVect(NGROW,NGROW,0)));
392 vec_vbar[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,3,IntVect(NGROW,NGROW,0)));
393
394 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)
395 vec_rv[lev].reset(new MultiFab(convert(ba,IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS v
396
397 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)
398 vec_rv2d[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0))); // RHS v
399
400 init_masks(lev, ba, dm);
401 init_stuff(lev, ba, dm);
402
403 init_only(lev, time);
404
405#ifdef REMORA_USE_PARTICLES
406 if (restart_chkfile.empty()) {
407 if (lev == 0) {
408 initializeTracers((ParGDBBase*)GetParGDB(),vec_z_phys_nd);
409 } else {
410 particleData.Redistribute();
411 }
412 }
413#endif
414}
415
416/**
417 * @param[in ] lev level do operate on
418 */
419void REMORA::resize_stuff(int lev)
420{
421 vec_z_phys_nd.resize(lev+1);
422
423 vec_h_full_domain.resize(hires_grid_level+1);
424
425 vec_h.resize(lev+1);
426 vec_Zt_avg1.resize(lev+1);
427 vec_z_w.resize(lev+1);
428 vec_z_r.resize(lev+1);
429 vec_Hz.resize(lev+1);
430 vec_Huon.resize(lev+1);
431 vec_Hvom.resize(lev+1);
432 vec_Akv.resize(lev+1);
433 vec_Akt.resize(lev+1);
434 vec_visc2_p.resize(lev+1);
435 vec_visc2_r.resize(lev+1);
436 vec_diff2.resize(lev+1);
437 vec_ru.resize(lev+1);
438 vec_rv.resize(lev+1);
439 vec_ru2d.resize(lev+1);
440 vec_rv2d.resize(lev+1);
441 vec_rufrc.resize(lev+1);
442 vec_rvfrc.resize(lev+1);
443 vec_sustr.resize(lev+1);
444 vec_svstr.resize(lev+1);
445 vec_btflx.resize(lev+1);
446 vec_stflx.resize(lev+1);
447 vec_btflux.resize(lev+1);
448 vec_stflux.resize(lev+1);
449 vec_lrflx.resize(lev+1);
450 vec_longwave_down.resize(lev+1);
451 vec_lhflx.resize(lev+1);
452 vec_shflx.resize(lev+1);
453 vec_rain.resize(lev+1);
454 vec_evap.resize(lev+1);
455 vec_rdrag.resize(lev+1);
456 vec_rdrag2.resize(lev+1);
457 vec_ZoBot.resize(lev+1);
458 vec_bustr.resize(lev+1);
459 vec_bvstr.resize(lev+1);
460 vec_uwind.resize(lev+1);
461 vec_vwind.resize(lev+1);
462 vec_Tair.resize(lev+1);
463 vec_qair.resize(lev+1);
464 vec_Pair.resize(lev+1);
465 vec_srflx.resize(lev+1);
466 vec_cloud.resize(lev+1);
467 vec_EminusP.resize(lev+1);
468 vec_alpha.resize(lev+1);
469 vec_beta.resize(lev+1);
470
471 vec_DU_avg1.resize(lev+1);
472 vec_DU_avg2.resize(lev+1);
473 vec_DV_avg1.resize(lev+1);
474 vec_DV_avg2.resize(lev+1);
475 vec_rubar.resize(lev+1);
476 vec_rvbar.resize(lev+1);
477 vec_rzeta.resize(lev+1);
478 vec_ubar.resize(lev+1);
479 vec_vbar.resize(lev+1);
480 vec_zeta.resize(lev+1);
481 vec_zeta_full_domain.resize(hires_init_level+1);
482 vec_mskr.resize(lev+1);
483 vec_msku.resize(lev+1);
484 vec_mskv.resize(lev+1);
485 vec_mskp.resize(lev+1);
486 vec_mskr3d.resize(lev+1);
487 vec_sstore.resize(lev+1);
488
489 vec_cons_full_domain.resize(hires_init_level+1);
490 vec_xvel_full_domain.resize(hires_init_level+1);
491 vec_yvel_full_domain.resize(hires_init_level+1);
492
493 vec_pm.resize(lev+1);
494 vec_pn.resize(lev+1);
495 vec_fcor.resize(lev+1);
496 vec_pm_full_domain.resize(hires_grid_level+1);
497 vec_pn_full_domain.resize(hires_grid_level+1);
498
499 vec_xr.resize(lev+1);
500 vec_yr.resize(lev+1);
501 vec_xu.resize(lev+1);
502 vec_yu.resize(lev+1);
503 vec_xv.resize(lev+1);
504 vec_yv.resize(lev+1);
505 vec_xp.resize(lev+1);
506 vec_yp.resize(lev+1);
507 vec_lonp.resize(lev+1);
508 vec_latp.resize(lev+1);
509
510 vec_dndx.resize(lev+1);
511 vec_dmde.resize(lev+1);
512
513 vec_rhoS.resize(lev+1);
514 vec_rhoA.resize(lev+1);
515 vec_bvf.resize(lev+1);
516
517 vec_tke.resize(lev+1);
518 vec_gls.resize(lev+1);
519 vec_Lscale.resize(lev+1);
520 vec_Akk.resize(lev+1);
521 vec_Akp.resize(lev+1);
522
523 vec_river_position.resize(lev+1);
524
525 if (lev==0) vec_nudg_coeff.resize(num_bdy_vars());
526
527 vec_nudg_coeff[BdyVars::u].resize(lev+1);
528 vec_nudg_coeff[BdyVars::v].resize(lev+1);
529 for (int icomp = 0; icomp < ncons; ++icomp) {
530 vec_nudg_coeff[BdyVars::cons(icomp)].resize(lev+1);
531 }
532 vec_nudg_coeff[bdy_ubar()].resize(lev+1);
533 vec_nudg_coeff[bdy_vbar()].resize(lev+1);
534 vec_nudg_coeff[bdy_zeta()].resize(lev+1);
535}
536
537/**
538 * @param[in ] lev level to operate on
539 * @param[in ] ba BoxArray for the level
540 * @param[in ] dm DistributionMapping for the level
541 */
542void REMORA::init_masks (int lev, const BoxArray& ba, const DistributionMapping& dm)
543{
544 BoxList bl2d = ba.boxList();
545 for (auto& b : bl2d) {
546 b.setRange(2,0);
547 }
548
549 BoxArray ba2d(std::move(bl2d));
550 vec_mskr[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
551 vec_msku[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW+1,NGROW+1,0)));
552 vec_mskv[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW+1,NGROW+1,0)));
553 vec_mskp[lev].reset(new MultiFab(convert(ba2d,IntVect(1,1,0)),dm,1,IntVect(NGROW+1,NGROW+1,0)));
554
555 vec_mskr3d[lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0)));
556
557 vec_mskr[lev]->setVal(one);
558 vec_msku[lev]->setVal(one);
559 vec_mskv[lev]->setVal(one);
560 vec_mskp[lev]->setVal(one);
561
562 vec_mskr3d[lev]->setVal(one);
563}
564
565/**
566 * @param[in ] lev level to operate on
567 * @param[in ] ba BoxArray for the level
568 * @param[in ] dm DistributionMapping for the level
569 */
570void REMORA::init_stuff (int lev, const BoxArray& ba, const DistributionMapping& dm)
571{
572 // ********************************************************************************************
573 // Initialize the boundary conditions
574 // ********************************************************************************************
575 physbcs[lev] = std::make_unique<REMORAPhysBCFunct> (lev, geom[lev], domain_bcs_type, domain_bcs_type_d,
576 m_bc_extdir_vals, ncons);
577
578 BoxList bl2d = ba.boxList();
579 for (auto& b : bl2d) {
580 b.setRange(2,0);
581 }
582 BoxArray ba2d(std::move(bl2d));
583
584 BoxList bl1d = ba.boxList();
585 for (auto& b : bl1d) {
586 b.setRange(0,0);
587 b.setRange(1,0);
588 }
589 BoxArray ba1d(std::move(bl1d));
590
591 BoxArray ba_nd(ba);
592 ba_nd.surroundingNodes();
593 BoxArray ba_w(ba);
594 ba_w.surroundingNodes(2);
595
596 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
597 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)
598 vec_z_r[lev].reset (new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0))); // z at r points (cell center)
599 vec_Hz[lev].reset (new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,NGROW+1))); // like in ROMS, thickness of cell in z
600
601 vec_Huon[lev].reset (new MultiFab(convert(ba,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0))); // mass flux for u component
602 vec_Hvom[lev].reset (new MultiFab(convert(ba,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0))); // mass flux for v component
603
604 vec_Akv[lev].reset (new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0))); // vertical mixing coefficient (.in)
605 // NAT components, not ncons: vertical mixing coefficients exist for the active tracers
606 // alone, and passive tracers mix with the salinity one. See akt_comp().
607 vec_Akt[lev].reset (new MultiFab(convert(ba,IntVect(0,0,1)),dm,NAT,IntVect(NGROW,NGROW,0))); // vertical mixing coefficient (.in)
608
609 // check dimensionality
610 vec_visc2_p[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); // harmonic viscosity at psi points -- difference to 3d?
611 vec_visc2_r[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); // harmonic viscosity at rho points
612 vec_diff2[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0))); // harmonic diffusivity temperature/salt
613
614 //2d, (incl advection terms and surface/bottom stresses, integral over the whole column, k=0)
615 vec_rufrc[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,2,IntVect(NGROW,NGROW,0)));
616 vec_rvfrc[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,2,IntVect(NGROW,NGROW,0))); //2d, same as above but v
617
618 vec_sustr[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0))); //2d, surface stress
619 vec_svstr[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0))); //2d
620
621 if (solverChoice.bottom_stress_type == BottomStressType::linear) {
622 //2d, linear drag coefficient [m/s], defined at rho, somehow related to rdrg
623 vec_rdrag[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
624 } else if (solverChoice.bottom_stress_type == BottomStressType::quadratic) {
625 vec_rdrag2[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
626 }
627
628 if (solverChoice.bottom_stress_type == BottomStressType::logarithmic ||
629 solverChoice.vert_mixing_type == VertMixingType::GLS) {
630 vec_ZoBot[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
631 }
632
633 vec_bustr[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0))); //2d, bottom stress
634 vec_bvstr[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
635
636 //all 2d -- all associated with the 2D advance
637 //2d DU: sum(height[incl free surface?] * u)
638 vec_DU_avg1[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
639
640 //2d like above, but correct(or)?
641 vec_DU_avg2[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
642
643 vec_DV_avg1[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
644 vec_DV_avg2[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
645
646 vec_rubar[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,4,IntVect(NGROW,NGROW,0))); // 2d RHS ubar
647 vec_rvbar[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,4,IntVect(NGROW,NGROW,0)));
648 vec_rzeta[lev].reset(new MultiFab(ba2d,dm,4,IntVect(NGROW,NGROW,0))); // 2d RHS zeta
649
650 // 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
651 vec_zeta[lev].reset(new MultiFab(ba2d,dm,3,IntVect(NGROW+1,NGROW+1,0))); // 2d free surface
652
653 vec_pm[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+2,0)));
654 vec_pn[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+2,NGROW+1,0)));
655 vec_fcor[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
656
657 vec_xr[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
658 vec_yr[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
659
660 vec_xu[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
661 vec_yu[lev].reset(new MultiFab(convert(ba2d,IntVect(1,0,0)),dm,1,IntVect(NGROW,NGROW,0)));
662 vec_xv[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
663 vec_yv[lev].reset(new MultiFab(convert(ba2d,IntVect(0,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
664 vec_xp[lev].reset(new MultiFab(convert(ba2d,IntVect(1,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
665 vec_yp[lev].reset(new MultiFab(convert(ba2d,IntVect(1,1,0)),dm,1,IntVect(NGROW,NGROW,0)));
666
667 if (solverChoice.use_curvilinear_grid) {
668 vec_dndx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
669 vec_dmde[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
670 }
671
672 // tempstore, saltstore, etc
673 vec_sstore[lev].reset(new MultiFab(ba,dm,ncons,IntVect(NGROW,NGROW,0)));
674
675 vec_rhoS[lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW,NGROW,0)));
676 vec_rhoA[lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW,NGROW,0)));
677 vec_bvf[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0)));
678
679 vec_tke[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,3,IntVect(NGROW,NGROW,0)));
680 vec_gls[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,3,IntVect(NGROW,NGROW,0)));
681 vec_Lscale[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0)));
682 vec_Akk[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0)));
683 vec_Akp[lev].reset(new MultiFab(convert(ba,IntVect(0,0,1)),dm,1,IntVect(NGROW,NGROW,0)));
684
685 // surface/bottom tracer fluxes for update
686 vec_stflx[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0)));
687 vec_btflx[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0)));
688 // surface/bottom tracer fluxes to be filled by inputs
689 vec_stflux[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0)));
690 vec_btflux[lev].reset(new MultiFab(ba2d,dm,ncons,IntVect(NGROW,NGROW,0)));
691
692 if (solverChoice.bulk_fluxes || solverChoice.atm2ocn_flux_mode) {
693 vec_uwind[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, surface wind u
694 vec_vwind[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, surface wind v
695 vec_Tair[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, air temperature
696 vec_qair[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, specific humidity
697 vec_Pair[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, air pressure
698 vec_srflx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, shortwave radiation flux
699 vec_longwave_down[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, external longwave radiation flux
700 vec_cloud[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, cloud cover fraction
701 vec_EminusP[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0))); //2d, evaporation minus precipitation
702 vec_alpha[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
703 vec_beta[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
704 vec_lrflx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
705 vec_lhflx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
706 vec_shflx[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
707 vec_rain[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
708 vec_evap[lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
709
710 vec_uwind[lev]->setVal(solverChoice.Uwind);
711 vec_vwind[lev]->setVal(solverChoice.Vwind);
712 vec_Tair[lev]->setVal(solverChoice.Tair);
713 vec_qair[lev]->setVal(solverChoice.Hair); // Hair can be specific humidity or RH
714 vec_Pair[lev]->setVal(solverChoice.Pair);
715 vec_srflx[lev]->setVal(solverChoice.srflux);
716 vec_longwave_down[lev]->setVal(solverChoice.longwave_rad);
717 vec_cloud[lev]->setVal(solverChoice.cloud);
718 vec_EminusP[lev]->setVal(solverChoice.EminusP);
719 vec_rain[lev]->setVal(solverChoice.rain);
720
721 // Set flux vars that will be computed in bulk_fluxes to zero so initial plotting works
722 vec_stflx[lev]->setVal(zero);
723 vec_lhflx[lev]->setVal(zero);
724 vec_shflx[lev]->setVal(zero);
725 vec_lrflx[lev]->setVal(zero); // possibly this should be set to longwave_rad like longwave_down
726 vec_evap[lev]->setVal(zero);
727 }
728
729 if (solverChoice.do_rivers) {
730 vec_river_position[lev].reset(new iMultiFab(ba2d,dm,1,IntVect(NGROW,NGROW,0)));
731 vec_river_position[lev]->setVal(-1);
732 }
733
734 vec_nudg_coeff[BdyVars::u][lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0)));
735 vec_nudg_coeff[BdyVars::v][lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0)));
736 for (int icomp = 0; icomp < ncons; ++icomp) {
737 vec_nudg_coeff[BdyVars::cons(icomp)][lev].reset(new MultiFab(ba,dm,1,IntVect(NGROW+1,NGROW+1,0)));
738 }
739 vec_nudg_coeff[bdy_ubar()][lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
740 vec_nudg_coeff[bdy_vbar()][lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
741 vec_nudg_coeff[bdy_zeta()][lev].reset(new MultiFab(ba2d,dm,1,IntVect(NGROW+1,NGROW+1,0)));
742
743 set_weights(lev);
744
745 vec_DU_avg1[lev]->setVal(zero);
746 vec_DU_avg2[lev]->setVal(zero);
747 vec_DV_avg1[lev]->setVal(zero);
748 vec_DV_avg2[lev]->setVal(zero);
749 vec_rubar[lev]->setVal(zero);
750 vec_rvbar[lev]->setVal(zero);
751 vec_rzeta[lev]->setVal(zero);
752
753 // Initialize these vars even if we aren't using GLS to
754 // avoid issues on e.g. checkpoint
755 vec_tke[lev]->setVal(solverChoice.gls_Kmin);
756 vec_gls[lev]->setVal(solverChoice.gls_Pmin);
757 vec_Lscale[lev]->setVal(zero);
758 vec_Akk[lev]->setVal(solverChoice.Akk_bak);
759 vec_Akp[lev]->setVal(solverChoice.Akp_bak);
760
761 vec_stflx[lev]->setVal(zero);
762 vec_btflx[lev]->setVal(zero);
763 vec_stflux[lev]->setVal(zero);
764 vec_btflux[lev]->setVal(zero);
765 vec_sustr[lev]->setVal(zero);
766 vec_svstr[lev]->setVal(zero);
767
768 // NOTE: Used to set vec_pm and vec_pn to 1e34 here to make foextrap work
769 // when init_type = real. However, this does not appear to be necessary so removing
770
771 // Set initial linear drag coefficient
772 if (solverChoice.bottom_stress_type == BottomStressType::linear) {
773 vec_rdrag[lev]->setVal(solverChoice.rdrag);
774 } else if (solverChoice.bottom_stress_type == BottomStressType::quadratic) {
775 vec_rdrag2[lev]->setVal(solverChoice.rdrag2);
776 }
777
778 if (solverChoice.bottom_stress_type == BottomStressType::logarithmic ||
779 solverChoice.vert_mixing_type == VertMixingType::GLS) {
780 vec_ZoBot[lev]->setVal(solverChoice.Zob);
781 }
782
783
784 // ********************************************************************************************
785 // Create the REMORAFillPatcher object
786 // ********************************************************************************************
787 if (lev > 0 && cf_width >= 0) {
788 Construct_REMORAFillPatchers(lev);
789 Define_REMORAFillPatchers(lev);
790 }
791}
792
793/**
794 * Delete level data. Overrides the pure virtual function in AmrCore
795 *
796 * @param[in ] lev level to operate on
797 */
798void
799REMORA::ClearLevel (int lev)
800{
801 delete cons_new[lev]; delete xvel_new[lev]; delete yvel_new[lev]; delete zvel_new[lev];
802 delete cons_old[lev]; delete xvel_old[lev]; delete yvel_old[lev]; delete zvel_old[lev];
803}
804
805/**
806 * @param[in ] lev level to operate on
807 */
808void
809REMORA::set_grid_scale (int lev)
810{
811 // Even if we're using high-resolution grid initialization, don't set it up with average-down
812 if (solverChoice.ic_type == IC_Type::analytic) {
813 if (solverChoice.grid_scale_type == GridScaleType::constant) {
814 const auto dxi = Geom(lev).InvCellSize();
815 vec_pm[lev]->setVal(dxi[0]); vec_pm[lev]->FillBoundary(geom[lev].periodicity());
816 vec_pn[lev]->setVal(dxi[1]); vec_pn[lev]->FillBoundary(geom[lev].periodicity());
817 } else if (solverChoice.grid_scale_type == GridScaleType::analytic) {
818 prob->init_analytic_grid_scale(lev, Geom(lev), solverChoice, *this, *vec_pm[lev].get(), *vec_pn[lev].get());
819 vec_pm[lev]->FillBoundary(geom[lev].periodicity());
820 vec_pn[lev]->FillBoundary(geom[lev].periodicity());
821 }
822 set_grid_coords_from_grid_scale(lev);
823#ifdef REMORA_USE_NETCDF
824 } else if (solverChoice.ic_type == IC_Type::netcdf) {
825 if (lev == 0 && hires_grid_level < 0) {
826 init_grid_vars_from_netcdf(lev);
827 } else if (lev > hires_grid_level) {
828 Real dummy_time = zero;
829 FillCoarsePatch(lev,dummy_time,vec_pm[lev].get(), vec_pm[lev-1].get(), foextrap_bc());
830 FillCoarsePatch(lev,dummy_time,vec_pn[lev].get(), vec_pn[lev-1].get(), foextrap_bc());
831
832 int rrx = ref_ratio[lev-1][0];
833 int rry = ref_ratio[lev-1][1];
834 // pm and pn need to be rescaled by the refinement ratio
835 for ( MFIter mfi(*vec_pm[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
836 {
837 Array4<Real> const& pm = vec_pm[lev]->array(mfi);
838 Array4<Real> const& pn = vec_pn[lev]->array(mfi);
839 Box ubx = mfi.growntilebox(IntVect(NGROW+1,NGROW+2,0));
840 Box vbx = mfi.growntilebox(IntVect(NGROW+2,NGROW+1,0));
841 ParallelFor(ubx, [=] AMREX_GPU_DEVICE (int i, int j, int ) {
842 pm(i,j,0) = pm(i,j,0) * (rrx);
843 });
844 ParallelFor(vbx, [=] AMREX_GPU_DEVICE (int i, int j, int ) {
845 pn(i,j,0) = pn(i,j,0) * (rry);
846 });
847 }
848 set_grid_coords_from_grid_scale(lev);
849 } else {
850 set_grid_vars_averaged_down(lev);
851 set_grid_coords_from_grid_scale(lev);
852 }
853#endif
854 }
855 if (solverChoice.use_curvilinear_grid) {
856 set_curvilinear_terms_from_grid_scale(lev);
857 }
858}
859
860/**
861 * @param[in ]lev level to operate on
862 */
863void
864REMORA::set_grid_coords_from_grid_scale (int lev) {
865 for ( MFIter mfi(*vec_xr[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
866 {
867 Array4<const Real> const& pm = vec_pm[lev]->const_array(mfi);
868 Array4<const Real> const& pn = vec_pn[lev]->const_array(mfi);
869 Array4<Real> const& xr = vec_xr[lev]->array(mfi);
870 Array4<Real> const& yr = vec_yr[lev]->array(mfi);
871 Array4<Real> const& xu = vec_xu[lev]->array(mfi);
872 Array4<Real> const& yu = vec_yu[lev]->array(mfi);
873 Array4<Real> const& xv = vec_xv[lev]->array(mfi);
874 Array4<Real> const& yv = vec_yv[lev]->array(mfi);
875 Array4<Real> const& xp = vec_xp[lev]->array(mfi);
876 Array4<Real> const& yp = vec_yp[lev]->array(mfi);
877
878 Box bx = mfi.growntilebox(IntVect(NGROW,NGROW,0));
879 ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int)
880 {
881 xr(i,j,0) = (i + Real(0.5)) / pm(i,j,0);
882 yr(i,j,0) = (j + Real(0.5)) / pn(i,j,0);
883 });
884
885 ParallelFor(mfi.tilebox(IntVect(1,0,0),IntVect(NGROW,NGROW,0)), [=] AMREX_GPU_DEVICE (int i, int j, int)
886 {
887 xu(i,j,0) = i / pm(i,j,0);
888 yu(i,j,0) = (j + Real(0.5)) / pn(i,j,0);
889 });
890
891 ParallelFor(mfi.tilebox(IntVect(0,1,0),IntVect(NGROW,NGROW,0)), [=] AMREX_GPU_DEVICE (int i, int j, int)
892 {
893 xv(i,j,0) = (i + Real(0.5)) / pm(i,j,0);
894 yv(i,j,0) = j / pn(i,j,0);
895 });
896
897 ParallelFor(mfi.tilebox(IntVect(1,1,0),IntVect(NGROW,NGROW,0)), [=] AMREX_GPU_DEVICE (int i, int j, int)
898 {
899 xp(i,j,0) = i / pm(i,j,0);
900 yp(i,j,0) = j / pn(i,j,0);
901 });
902 }
903}
904
905/**
906 * @param[in ]lev level to operate on
907 */
908void
909REMORA::set_curvilinear_terms_from_grid_scale (int lev) {
910 for ( MFIter mfi(*vec_dndx[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
911 {
912 Array4<const Real> const& pm = vec_pm[lev]->const_array(mfi);
913 Array4<const Real> const& pn = vec_pn[lev]->const_array(mfi);
914 Array4<Real> const& dndx = vec_dndx[lev]->array(mfi);
915 Array4<Real> const& dmde = vec_dmde[lev]->array(mfi);
916
917 Box bx = mfi.growntilebox(IntVect(NGROW,NGROW,0));
918 ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int)
919 {
920 dndx(i,j,0) = Real(0.5) * (one / pn(i+1,j ,0) - one / pn(i-1,j ,0));
921 dmde(i,j,0) = Real(0.5) * (one / pm(i ,j+1,0) - one / pm(i ,j-1,0));
922 });
923 }
924}
925
926/**
927 * @param[in ] lev level to operate on
928 * @param[in ] apply_eminusp whether to apply the evaporation-minus-precipitation correction to Zt_avg1
929 */
930void
931REMORA::set_zeta_to_Ztavg (int lev, bool apply_eminusp)
932{
933 BL_PROFILE("REMORA::set_zeta_to_Ztavg()");
934 std::unique_ptr<MultiFab>& mf_zeta = vec_zeta[lev];
935 std::unique_ptr<MultiFab>& mf_Zt_avg1 = vec_Zt_avg1[lev];
936 if (solverChoice.eminusp_correct_ssh && apply_eminusp) {
937 for ( MFIter mfi(*vec_zeta[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
938 {
939 Array4<Real> const& Zt_avg1 = (mf_Zt_avg1)->array(mfi);
940 Array4<const Real> const& evap = vec_evap[lev]->const_array(mfi);
941 Array4<const Real> const& rain = vec_rain[lev]->const_array(mfi);
942 Array4<const Real> const& EminusP = vec_EminusP[lev]->const_array(mfi);
943 bool use_EminusP_from_input = solverChoice.eminusp &&
944 solverChoice.bulk_flux_type[BulkFlux::EminusP] != BulkForcingType::computed;
945
946 Box bx2 = mfi.growntilebox(IntVect(NGROW,NGROW,0));// bx2.grow(IntVect(NGROW,NGROW,0));
947
948 Real cff = dt[lev] / rhow;
949 Real dt_lev = dt[lev];
950
951 ParallelFor(bx2, [=] AMREX_GPU_DEVICE (int i, int j, int )
952 {
953 if (use_EminusP_from_input) {
954 // EminusP is treated as a kinematic freshwater flux (m/s).
955 Zt_avg1(i,j,0) = Zt_avg1(i,j,0) - EminusP(i,j,0) * dt_lev;
956 } else {
957 Zt_avg1(i,j,0) = Zt_avg1(i,j,0) - (evap(i,j,0) - rain(i,j,0)) * cff;
958 }
959 });
960 }
961 }
962 Gpu::streamSynchronize();
963
964 vec_Zt_avg1[lev]->FillBoundary(geom[lev].periodicity());
965
966 for ( MFIter mfi(*vec_zeta[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
967 {
968 Box bx3 = mfi.tilebox(); bx3.grow(IntVect(NGROW+1,NGROW+1,0));
969 Array4<Real> const& zeta = mf_zeta->array(mfi);
970 Array4<Real> const& Zt_avg1 = (mf_Zt_avg1)->array(mfi);
971
972 ParallelFor(bx3, 3, [=] AMREX_GPU_DEVICE (int i, int j, int , int n)
973 {
974 zeta(i,j,0,n) = Zt_avg1(i,j,0);
975 });
976 }
977}
978
979/**
980 * @param[in ] lev level to operate on
981 */
982void
983REMORA::update_mskp (int lev)
984{
985 for ( MFIter mfi(*vec_mskr[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
986 {
987 Array4<const Real> const& mskr = vec_mskr[lev]->const_array(mfi);
988 Array4< Real> const& mskp = vec_mskp[lev]->array(mfi);
989
990 Box bx = mfi.tilebox(); bx.grow(IntVect(1,1,0)); bx.makeSlab(2,0);
991
992 Real cff1 = one;
993 Real cff2 = two;
994
995 ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int)
996 {
997 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))) {
998 mskp(i,j,0) = one;
999 } 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))) {
1000 mskp(i,j,0) = cff1;
1001 } 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))) {
1002 mskp(i,j,0) = cff1;
1003 } 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))) {
1004 mskp(i,j,0) = cff1;
1005 } 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))) {
1006 mskp(i,j,0) = cff1;
1007 } 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))) {
1008 mskp(i,j,0) = cff2;
1009 } 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))) {
1010 mskp(i,j,0) = cff2;
1011 } 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))) {
1012 mskp(i,j,0) = cff2;
1013 } 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))) {
1014 mskp(i,j,0) = cff2;
1015 } else {
1016 mskp(i,j,0) = zero;
1017 }
1018
1019 });
1020 }
1021}
1022
1023/**
1024 * @param[in ] lev level to operate on
1025 */
1026void
1027REMORA::calculate_nodal_masks (int lev)
1028{
1029 for ( MFIter mfi(*vec_mskr[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
1030 {
1031 Array4<const Real> const& mskr = vec_mskr[lev]->const_array(mfi);
1032 Array4< Real> const& msku = vec_msku[lev]->array(mfi);
1033 Array4< Real> const& mskv = vec_mskv[lev]->array(mfi);
1034 Array4< Real> const& mskp = vec_mskp[lev]->array(mfi);
1035
1036 Box bx = mfi.tilebox(); bx.grow(IntVect(1,1,0)); bx.makeSlab(2,0);
1037
1038 ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int)
1039 {
1040 msku(i,j,0) = mskr(i-1,j ,0) * mskr(i,j,0);
1041 mskv(i,j,0) = mskr(i ,j-1,0) * mskr(i,j,0);
1042 mskp(i,j,0) = mskr(i-1,j-1,0) * mskr(i,j,0) * mskr(i-1,j,0) * mskr(i,j-1,0);
1043 });
1044 }
1045}
1046
1047/**
1048 * @param[in ] lev level to operate on
1049 */
1050void
1051REMORA::fill_3d_masks (int lev)
1052{
1053 for ( MFIter mfi(*vec_mskr3d[lev], TilingIfNotGPU()); mfi.isValid(); ++mfi )
1054 {
1055 Array4<const Real> const& mskr = vec_mskr[lev]->const_array(mfi);
1056 Array4< Real> const& mskr3d = vec_mskr3d[lev]->array(mfi);
1057
1058 Box bx = mfi.tilebox(); bx.grow(IntVect(1,1,0));
1059
1060 ParallelFor(bx, [=] AMREX_GPU_DEVICE (int i, int j, int k)
1061 {
1062 mskr3d(i,j,k) = mskr(i,j,0);
1063 });
1064 }
1065}
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
cff1
Real cff1
Definition REMORA_InitAnalyticBiology_BioToy.H:2
cff2
Real cff2
Definition REMORA_InitAnalyticBiology_BioToy.H:3
dxi
const auto dxi
Definition REMORA_InitAnalyticGridScale_BoundaryLayer.H:4
time
Real time
Definition REMORA_InitAnalyticSMFlux_ChannelTest.H:1
REMORA_prob_common.H
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:509
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:750
REMORA::foextrap_periodic_bc
int foextrap_periodic_bc() const noexcept
Definition REMORA.H:1320
REMORA::ncons
int ncons
Number of conserved scalars in the state (temperature + salt + passive scalars + biology tracers)
Definition REMORA.H:1644
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:554
REMORA::vec_rv2d
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rv2d
v velocity RHS (2D, includes horizontal and vertical advection)
Definition REMORA.H:424
REMORA::vec_evap
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_evap
evaporation rate [kg/m^2/s]
Definition REMORA.H:505
REMORA::zvel_bc
int zvel_bc() const noexcept
Definition REMORA.H:1315
REMORA::xvel_bc
int xvel_bc() const noexcept
Definition REMORA.H:1313
REMORA::domain_bcs_type
amrex::Vector< amrex::BCRec > domain_bcs_type
vector (over BCVars) of BCRecs
Definition REMORA.H:1578
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:1027
REMORA::vec_fcor
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_fcor
coriolis factor (2D)
Definition REMORA.H:577
REMORA::vec_btflux
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_btflux
Bottom tracer flux; input arrays.
Definition REMORA.H:500
REMORA::vec_rubar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rubar
barotropic x velocity for the RHS (2D)
Definition REMORA.H:541
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:397
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:406
REMORA::vec_pm
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pm
horizontal scaling factor: 1 / dx (2D)
Definition REMORA.H:568
REMORA::vec_ZoBot
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ZoBot
Bottom roughness length [m], defined at rho points.
Definition REMORA.H:525
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:535
REMORA::vec_lrflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_lrflx
longwave radiation
Definition REMORA.H:485
REMORA::vec_yv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_yv
y_grid on v-points (2D)
Definition REMORA.H:592
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:386
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:78
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:909
REMORA::vec_vwind
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_vwind
Wind in the v direction, defined at rho-points.
Definition REMORA.H:474
REMORA::prob
std::unique_ptr< ProblemBase > prob
Pointer to container of analytical functions for problem definition.
Definition REMORA.H:1542
REMORA::vec_mskr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskr
land/sea mask at cell centers (2D)
Definition REMORA.H:557
REMORA::Construct_REMORAFillPatchers
void Construct_REMORAFillPatchers(int lev)
Construct FillPatchers.
Definition REMORA.cpp:522
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:526
REMORA::vec_rain
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rain
precipitation rate [kg/m^2/s]
Definition REMORA.H:503
REMORA::vec_tke
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_tke
Turbulent kinetic energy.
Definition REMORA.H:632
REMORA::vec_stflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_stflx
Surface tracer flux; working arrays.
Definition REMORA.H:494
REMORA::vec_gls
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_gls
Turbulent generic length scale.
Definition REMORA.H:634
REMORA::vec_sustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sustr
Surface stress in the u direction.
Definition REMORA.H:467
REMORA::vec_yp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_yp
y_grid on psi-points (2D)
Definition REMORA.H:597
REMORA::vec_xr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_xr
x_grid on rho points (2D)
Definition REMORA.H:580
REMORA::yvel_bc
int yvel_bc() const noexcept
Definition REMORA.H:1314
REMORA::vec_ru2d
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ru2d
u velocity RHS (2D, includes horizontal and vertical advection)
Definition REMORA.H:422
REMORA::ClearLevel
virtual void ClearLevel(int lev) override
Delete level data Overrides the pure virtual function in AmrCore.
Definition REMORA_make_new_level.cpp:799
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:392
REMORA::ComputeGhostCells
AMREX_FORCE_INLINE int ComputeGhostCells(const int &spatial_order)
Helper function to determine number of ghost cells.
Definition REMORA.H:1839
REMORA::vec_sstore
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sstore
additional scratch space for calculations on temp, salt, etc
Definition REMORA.H:612
REMORA::vec_xv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_xv
x_grid on v-points (2D)
Definition REMORA.H:590
REMORA::init_only
void init_only(int lev, amrex::Real time)
Init (NOT restart or regrid)
Definition REMORA.cpp:1320
REMORA::init_set_vmix
void init_set_vmix(int lev)
Initialize vertical mixing coefficients from file or analytic.
Definition REMORA.cpp:825
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:809
REMORA::set_coriolis
void set_coriolis(int lev)
Initialize Coriolis factor from file or analytic.
Definition REMORA.cpp:796
REMORA::foextrap_bc
int foextrap_bc() const noexcept
Definition REMORA.H:1321
REMORA::vec_Lscale
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Lscale
Vertical mixing turbulent length scale.
Definition REMORA.H:636
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:412
REMORA::vec_Akt
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akt
Vertical diffusion coefficient (3D)
Definition REMORA.H:432
REMORA::vec_msku
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_msku
land/sea mask at x-faces (2D)
Definition REMORA.H:559
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:428
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:572
REMORA::xvel_old
amrex::Vector< amrex::MultiFab * > xvel_old
multilevel data container for last step's x velocities (u in ROMS)
Definition REMORA.H:379
REMORA::yvel_new
amrex::Vector< amrex::MultiFab * > yvel_new
multilevel data container for current step's y velocities (v in ROMS)
Definition REMORA.H:390
REMORA::vec_uwind
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_uwind
Wind in the u direction, defined at rho-points.
Definition REMORA.H:472
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:426
REMORA::zeta_bc
int zeta_bc() const noexcept
Definition REMORA.H:1318
REMORA::Define_REMORAFillPatchers
void Define_REMORAFillPatchers(int lev)
Define FillPatchers.
Definition REMORA.cpp:571
REMORA::num_bdy_vars
int num_bdy_vars() const noexcept
Definition REMORA.H:1332
REMORA::vec_shflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_shflx
sensible heat flux
Definition REMORA.H:491
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:434
REMORA::vec_dmde
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_dmde
d(1/m)/d(eta)
Definition REMORA.H:609
REMORA::vec_rvbar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rvbar
barotropic y velocity for the RHS (2D)
Definition REMORA.H:543
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:383
REMORA::vec_z_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_r
z coordinates at rho points (cell centers)
Definition REMORA.H:441
REMORA::xvel_new
amrex::Vector< amrex::MultiFab * > xvel_new
multilevel data container for current step's x velocities (u in ROMS)
Definition REMORA.H:388
REMORA::vec_lhflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_lhflx
latent heat flux
Definition REMORA.H:489
REMORA::vec_mskp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskp
land/sea mask at cell corners (2D)
Definition REMORA.H:563
REMORA::bdy_zeta
int bdy_zeta() const noexcept
Definition REMORA.H:1331
REMORA::vec_bvf
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bvf
Brunt-Vaisala frequency (3D)
Definition REMORA.H:619
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:166
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:601
REMORA::vec_mskv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskv
land/sea mask at y-faces (2D)
Definition REMORA.H:561
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:542
REMORA::physbcs
amrex::Vector< std::unique_ptr< REMORAPhysBCFunct > > physbcs
Vector (over level) of functors to apply physical boundary conditions.
Definition REMORA.H:1566
REMORA::fill_3d_masks
void fill_3d_masks(int lev)
Copy maskr to all z levels.
Definition REMORA_make_new_level.cpp:1051
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:411
REMORA::vec_rhoS
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoS
density perturbation
Definition REMORA.H:615
REMORA::init_riv_pos_from_netcdf
void init_riv_pos_from_netcdf(int lev)
Definition REMORA_init_from_netcdf.cpp:1011
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:436
REMORA::update_mskp
void update_mskp(int lev)
Set psi-point mask to be consistent with rho-point mask.
Definition REMORA_make_new_level.cpp:983
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:399
REMORA::vec_svstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_svstr
Surface stress in the v direction.
Definition REMORA.H:469
REMORA::vec_Huon
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Huon
u-volume flux (3D)
Definition REMORA.H:414
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:409
REMORA::yvel_old
amrex::Vector< amrex::MultiFab * > yvel_old
multilevel data container for last step's y velocities (v in ROMS)
Definition REMORA.H:381
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:570
REMORA::vec_rhoA
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoA
vertically-averaged density
Definition REMORA.H:617
REMORA::vec_DV_avg1
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_DV_avg1
time average of barotropic y velocity flux
Definition REMORA.H:537
REMORA::hires_init_level
int hires_init_level
Which level the high resolution initialization data is at.
Definition REMORA.H:1787
REMORA::bdy_vbar
int bdy_vbar() const noexcept
Definition REMORA.H:1330
REMORA::t_new
amrex::Vector< amrex::Real > t_new
new time at each level
Definition REMORA.H:1556
REMORA::solverChoice
static SolverChoice solverChoice
Container for algorithmic choices.
Definition REMORA.H:1717
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:864
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:419
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:1494
REMORA::vec_Akk
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akk
Turbulent kinetic energy vertical diffusion coefficient.
Definition REMORA.H:638
REMORA::vec_rdrag2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rdrag2
Quadratic drag coefficient [unitless], defined at rho points.
Definition REMORA.H:523
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:931
REMORA::vec_ru
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ru
u velocity RHS (3D, includes horizontal and vertical advection)
Definition REMORA.H:418
REMORA::bdy_ubar
int bdy_ubar() const noexcept
Definition REMORA.H:1329
REMORA::vec_xp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_xp
x_grid on psi-points (2D)
Definition REMORA.H:595
REMORA::vec_longwave_down
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_longwave_down
Downward longwave radiation.
Definition REMORA.H:487
REMORA::vec_zeta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_zeta
free surface height (2D)
Definition REMORA.H:551
REMORA::ubar_bc
int ubar_bc() const noexcept
Definition REMORA.H:1316
REMORA::vec_vbar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_vbar
barotropic y velocity (2D)
Definition REMORA.H:549
REMORA::FillCoarsePatchPC
void FillCoarsePatchPC(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 using the piecewise constant interpol...
Definition REMORA_FillPatch.cpp:377
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:533
REMORA::vec_alpha
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_alpha
Thermal expansion coefficient (3D)
Definition REMORA.H:621
REMORA::vec_ubar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ubar
barotropic x velocity (2D)
Definition REMORA.H:547
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:377
REMORA::vec_bustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bustr
Bottom stress in the u direction.
Definition REMORA.H:528
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:395
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())
Fill a new MultiFab by copying in phi from valid region and filling ghost cells.
Definition REMORA_FillPatch.cpp:30
REMORA::vbar_bc
int vbar_bc() const noexcept
Definition REMORA.H:1317
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:539
REMORA::set_hmixcoef
void set_hmixcoef(int lev)
Initialize horizontal mixing coefficients.
Definition REMORA.cpp:886
REMORA::vec_yu
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_yu
y_grid on u-points (2D)
Definition REMORA.H:587
REMORA::vec_dndx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_dndx
d(1/n)/d(xi)
Definition REMORA.H:607
REMORA::vec_bvstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bvstr
Bottom stress in the v direction.
Definition REMORA.H:530
REMORA::vec_rzeta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rzeta
free surface height for the RHS (2D)
Definition REMORA.H:545
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:461
REMORA::vec_xu
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_xu
x_grid on u-points (2D)
Definition REMORA.H:585
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:574
REMORA::vec_nudg_coeff
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > vec_nudg_coeff
Climatology nudging coefficients.
Definition REMORA.H:643
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:570
REMORA::vec_Akv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akv
Vertical viscosity coefficient (3D)
Definition REMORA.H:430
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:349
REMORA::vec_stflux
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_stflux
Surface tracer flux; input arrays.
Definition REMORA.H:496
REMORA::vec_rdrag
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rdrag
Linear drag coefficient [m/s], defined at rho points.
Definition REMORA.H:521
REMORA::vec_cloud
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_cloud
cloud cover fraction [0-1], defined at rho-points
Definition REMORA.H:507
REMORA::vec_Zt_avg1
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Zt_avg1
Average of the free surface, zeta (2D)
Definition REMORA.H:464
REMORA::restart_chkfile
std::string restart_chkfile
If set, restart from this checkpoint file.
Definition REMORA.H:1630
REMORA::vec_rv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rv
v velocity RHS (3D, includes horizontal and vertical advection)
Definition REMORA.H:420
REMORA::vec_btflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_btflx
Bottom tracer flux; working arrays.
Definition REMORA.H:498
REMORA::cf_width
int cf_width
Nudging width at coarse-fine interface.
Definition REMORA.H:1504
REMORA::vec_beta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_beta
Saline contraction coefficient (3D)
Definition REMORA.H:623
REMORA::t_old
amrex::Vector< amrex::Real > t_old
old time at each level
Definition REMORA.H:1558
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:565
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:1586
REMORA::vec_srflx
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_srflx
Shortwave radiation flux [W/m²], defined at rho-points.
Definition REMORA.H:483
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:733
REMORA::dt
amrex::Vector< amrex::Real > dt
time step at each level
Definition REMORA.H:1560
REMORA::vec_Pair
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Pair
Air pressure [mb], defined at rho-points.
Definition REMORA.H:480
REMORA::domain_bcs_type_d
amrex::Gpu::DeviceVector< amrex::BCRec > domain_bcs_type_d
GPU vector (over BCVars) of BCRecs.
Definition REMORA.H:1580
REMORA::vec_qair
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_qair
Specific humidity [kg/kg], defined at rho-points.
Definition REMORA.H:478
REMORA::hires_grid_level
int hires_grid_level
Which level the high resolution bathymetry is at.
Definition REMORA.H:1780
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:444
REMORA::vec_Tair
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Tair
Air temperature [°C], defined at rho-points.
Definition REMORA.H:476
REMORA::vec_yr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_yr
y_grid on rho points (2D)
Definition REMORA.H:582
REMORA::vec_Hvom
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Hvom
v-volume flux (3D)
Definition REMORA.H:416
REMORA::vec_Akp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akp
Turbulent length scale vertical diffusion coefficient.
Definition REMORA.H:640
REMORA::vec_diff2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_diff2
Harmonic diffusivity for temperature / salinity.
Definition REMORA.H:438
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:604
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::cloud
amrex::Real cloud
Definition REMORA_DataStruct.H:986
SolverChoice::rdrag2
amrex::Real rdrag2
Definition REMORA_DataStruct.H:953
SolverChoice::Akk_bak
amrex::Real Akk_bak
Definition REMORA_DataStruct.H:1030
SolverChoice::EminusP
amrex::Real EminusP
Definition REMORA_DataStruct.H:1005
SolverChoice::bottom_stress_type
BottomStressType bottom_stress_type
Definition REMORA_DataStruct.H:930
SolverChoice::longwave_rad
amrex::Real longwave_rad
Definition REMORA_DataStruct.H:1003
SolverChoice::srflux
amrex::Real srflux
Definition REMORA_DataStruct.H:998
SolverChoice::gls_Kmin
amrex::Real gls_Kmin
Definition REMORA_DataStruct.H:1018
SolverChoice::rdrag
amrex::Real rdrag
Definition REMORA_DataStruct.H:951
SolverChoice::vert_mixing_type
VertMixingType vert_mixing_type
Definition REMORA_DataStruct.H:936
SolverChoice::bulk_flux_type
std::array< BulkForcingType, BulkFlux::NumTypes > bulk_flux_type
Definition REMORA_DataStruct.H:869
SolverChoice::grid_scale_type
GridScaleType grid_scale_type
Definition REMORA_DataStruct.H:943
SolverChoice::gls_Pmin
amrex::Real gls_Pmin
Definition REMORA_DataStruct.H:1019
SolverChoice::Akp_bak
amrex::Real Akp_bak
Definition REMORA_DataStruct.H:1031