REMORA
Regional Modeling of Oceans Refined Adaptively
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REMORA_Checkpoint.cpp
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1#include <REMORA.H>
2#include "AMReX_PlotFileUtil.H"
3
4using namespace amrex;
5
6// utility to skip to next line in Header
7void
8REMORA::GotoNextLine (std::istream& is)
9{
10 constexpr std::streamsize bl_ignore_max { 100000 };
11 is.ignore(bl_ignore_max, '\n');
12}
13
14void
15REMORA::WriteCheckpointFile ()
16{
17
18 // chk00010 write a checkpoint file with this root directory
19 // chk00010/Header this contains information you need to save (e.g., finest_level, t_new, etc.) and also
20 // the BoxArrays at each level
21 // chk00010/Level_0/
22 // chk00010/Level_1/
23 // etc. these subdirectories will hold the MultiFab data at each level of refinement
24
25 // checkpoint file name, e.g., chk00010
26 const std::string& checkpointname = amrex::Concatenate(check_file,istep[0],file_min_digits);
27
28 amrex::Print() << "Writing checkpoint " << checkpointname << "\n";
29
30 const int nlevels = finest_level+1;
31
32 // ---- prebuild a hierarchy of directories
33 // ---- dirName is built first. if dirName exists, it is renamed. then build
34 // ---- dirName/subDirPrefix_0 .. dirName/subDirPrefix_nlevels-1
35 // ---- if callBarrier is true, call ParallelDescriptor::Barrier()
36 // ---- after all directories are built
37 // ---- ParallelDescriptor::IOProcessor() creates the directories
38 amrex::PreBuildDirectorHierarchy(checkpointname, "Level_", nlevels, true);
39
40 // write Header file
41 if (ParallelDescriptor::IOProcessor()) {
42
43 std::string HeaderFileName(checkpointname + "/Header");
44 VisMF::IO_Buffer io_buffer(VisMF::IO_Buffer_Size);
45 std::ofstream HeaderFile;
46 HeaderFile.rdbuf()->pubsetbuf(io_buffer.dataPtr(), io_buffer.size());
47 HeaderFile.open(HeaderFileName.c_str(), std::ofstream::out |
48 std::ofstream::trunc |
49 std::ofstream::binary);
50 if( ! HeaderFile.good()) {
51 amrex::FileOpenFailed(HeaderFileName);
52 }
53
54 HeaderFile.precision(17);
55
56 // write out title line
57 HeaderFile << "Checkpoint file for REMORA\n";
58
59 // write out finest_level
60 HeaderFile << finest_level << "\n";
61
62 // write the number of components
63 // for each variable we store
64
65 // conservative, cell-centered vars
66 HeaderFile << ncons << "\n";
67
68 // x-velocity on faces
69 HeaderFile << 1 << "\n";
70
71 // y-velocity on faces
72 HeaderFile << 1 << "\n";
73
74 // z-velocity on faces
75 HeaderFile << 1 << "\n";
76
77 HeaderFile << 2 << "\n";
78
79 HeaderFile << 2 << "\n";
80
81 HeaderFile << 3 << "\n";
82
83 HeaderFile << 3 << "\n";
84
85 // write out array of istep
86 for (int i = 0; i < istep.size(); ++i) {
87 HeaderFile << istep[i] << " ";
88 }
89 HeaderFile << "\n";
90
91 // write out array of dt
92 for (int i = 0; i < dt.size(); ++i) {
93 HeaderFile << dt[i] << " ";
94 }
95 HeaderFile << "\n";
96
97 // write out array of t_new, which counts from start_time
98 for (int i = 0; i < t_new.size(); ++i) {
99 HeaderFile << t_new[i] << " ";
100 }
101 HeaderFile << "\n";
102
103 // write the BoxArray at each level
104 for (int lev = 0; lev <= finest_level; ++lev) {
105 boxArray(lev).writeOn(HeaderFile);
106 HeaderFile << '\n';
107 }
108
109 // start_time, the origin t_new counts from. Last, so a reader that predates it
110 // stops before it; a checkpoint without it holds t_new on the model clock.
111 HeaderFile << "start_time " << start_time << "\n";
112 }
113
114 // write the MultiFab data to, e.g., chk00010/Level_0/
115 // Here we make copies of the MultiFab with no ghost cells
116 for (int lev = 0; lev <= finest_level; ++lev)
117 {
118 BoxList bl2d = grids[lev].boxList();
119 for (auto& b : bl2d) {
120 b.setRange(2,0);
121 }
122 BoxArray ba2d(std::move(bl2d));
123
124 MultiFab cons(grids[lev],dmap[lev],ncons,cons_new[lev]->nGrowVect());
125 MultiFab::Copy(cons,*cons_new[lev],0,0,ncons,cons_new[lev]->nGrowVect());
126 VisMF::Write(cons, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Cell"));
127
128 MultiFab::Copy(cons,*cons_old[lev],0,0,ncons,cons_old[lev]->nGrowVect());
129 VisMF::Write(cons, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Cell_old"));
130
131 MultiFab xvel(convert(grids[lev],IntVect(1,0,0)),dmap[lev],1,xvel_new[lev]->nGrowVect());
132 MultiFab::Copy(xvel,*xvel_new[lev],0,0,1,xvel_new[lev]->nGrowVect());
133 VisMF::Write(xvel, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "XFace"));
134
135 MultiFab::Copy(xvel,*xvel_old[lev],0,0,1,xvel_old[lev]->nGrowVect());
136 VisMF::Write(xvel, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "XFace_old"));
137
138 MultiFab yvel(convert(grids[lev],IntVect(0,1,0)),dmap[lev],1,yvel_new[lev]->nGrowVect());
139 MultiFab::Copy(yvel,*yvel_new[lev],0,0,1,yvel_new[lev]->nGrowVect());
140 VisMF::Write(yvel, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "YFace"));
141
142 MultiFab::Copy(yvel,*yvel_old[lev],0,0,1,yvel_old[lev]->nGrowVect());
143 VisMF::Write(yvel, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "YFace_old"));
144
145 MultiFab zvel(convert(grids[lev],IntVect(0,0,1)),dmap[lev],1,zvel_new[lev]->nGrowVect());
146 MultiFab::Copy(zvel,*zvel_new[lev],0,0,1,zvel_new[lev]->nGrowVect());
147 VisMF::Write(zvel, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "ZFace"));
148
149 MultiFab::Copy(zvel,*zvel_old[lev],0,0,1,zvel_old[lev]->nGrowVect());
150 VisMF::Write(zvel, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "ZFace_old"));
151
152 MultiFab mf_ru(convert(grids[lev],IntVect(1,0,0)),dmap[lev],2,(vec_ru[lev])->nGrowVect());
153 MultiFab::Copy(mf_ru,*vec_ru[lev],0,0,2,(vec_ru[lev])->nGrowVect());
154 VisMF::Write(mf_ru, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "XRHS"));
155
156 MultiFab mf_rv(convert(grids[lev],IntVect(0,1,0)),dmap[lev],2,(vec_rv[lev])->nGrowVect());
157 MultiFab::Copy(mf_rv,*vec_rv[lev],0,0,2,(vec_rv[lev])->nGrowVect());
158 VisMF::Write(mf_rv, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "YRHS"));
159
160 MultiFab mf_ubar(convert(ba2d,IntVect(1,0,0)),dmap[lev],3,(vec_ubar[lev])->nGrowVect());
161 MultiFab::Copy(mf_ubar,*(vec_ubar[lev]),0,0,3,(vec_ubar[lev])->nGrowVect());
162 VisMF::Write(mf_ubar, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "XBar"));
163
164 MultiFab mf_vbar(convert(ba2d,IntVect(0,1,0)),dmap[lev],3,(vec_vbar[lev])->nGrowVect());
165 MultiFab::Copy(mf_vbar,*(vec_vbar[lev]),0,0,3,(vec_vbar[lev])->nGrowVect());
166 VisMF::Write(mf_vbar, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "YBar"));
167
168 MultiFab mf_ru2d(convert(ba2d,IntVect(1,0,0)),dmap[lev],2,(vec_ru2d[lev])->nGrowVect());
169 MultiFab::Copy(mf_ru2d,*(vec_ru2d[lev]),0,0,2,(vec_ru2d[lev])->nGrowVect());
170 VisMF::Write(mf_ru2d, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "XRHS2d"));
171
172 MultiFab mf_rv2d(convert(ba2d,IntVect(0,1,0)),dmap[lev],2,(vec_rv2d[lev])->nGrowVect());
173 MultiFab::Copy(mf_rv2d,*(vec_rv2d[lev]),0,0,2,(vec_rv2d[lev])->nGrowVect());
174 VisMF::Write(mf_rv2d, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "YRHS2d"));
175
176 MultiFab mf_mskr(ba2d,dmap[lev],1,(vec_mskr[lev])->nGrowVect());
177 MultiFab::Copy(mf_mskr,*(vec_mskr[lev]),0,0,1,(vec_mskr[lev])->nGrowVect());
178 VisMF::Write(mf_mskr, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Mskr"));
179
180 MultiFab mf_msku(convert(ba2d,IntVect(1,0,0)),dmap[lev],1,(vec_msku[lev])->nGrowVect());
181 MultiFab::Copy(mf_msku,*(vec_msku[lev]),0,0,1,(vec_msku[lev])->nGrowVect());
182 VisMF::Write(mf_msku, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Msku"));
183
184 MultiFab mf_mskv(convert(ba2d,IntVect(0,1,0)),dmap[lev],1,(vec_mskv[lev])->nGrowVect());
185 MultiFab::Copy(mf_mskv,*(vec_mskv[lev]),0,0,1,(vec_mskv[lev])->nGrowVect());
186 VisMF::Write(mf_mskv, amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Mskv"));
187
188 if (solverChoice.bottom_stress_type == BottomStressType::linear) {
189 VisMF::Write(*(vec_rdrag[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "rdrag"));
190 } else if (solverChoice.bottom_stress_type == BottomStressType::quadratic) {
191 VisMF::Write(*(vec_rdrag2[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "rdrag2"));
192 }
193
194 if (solverChoice.bottom_stress_type == BottomStressType::logarithmic ||
195 solverChoice.vert_mixing_type == VertMixingType::GLS) {
196 VisMF::Write(*(vec_ZoBot[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "ZoBot"));
197 }
198
199 VisMF::Write(*(vec_DU_avg1[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "DU_avg1"));
200 VisMF::Write(*(vec_DU_avg2[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "DU_avg2"));
201 VisMF::Write(*(vec_DV_avg1[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "DV_avg1"));
202 VisMF::Write(*(vec_DV_avg2[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "DV_avg2"));
203
204 VisMF::Write(*(vec_zeta[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "zeta"));
205 VisMF::Write(*(vec_Zt_avg1[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Zt_avg1"));
206
207 VisMF::Write(*(vec_h[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "h"));
208
209 VisMF::Write(*(vec_tke[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "tke"));
210 VisMF::Write(*(vec_gls[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "gls"));
211 VisMF::Write(*(vec_Lscale[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Lscale"));
212 VisMF::Write(*(vec_Akk[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Akk"));
213 VisMF::Write(*(vec_Akp[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Akp"));
214 VisMF::Write(*(vec_Akv[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Akv"));
215 VisMF::Write(*(vec_Akt[lev]), amrex::MultiFabFileFullPrefix(lev, checkpointname, "Level_", "Akt"));
216 }
217
218#ifdef REMORA_USE_PARTICLES
219 particleData.Checkpoint(checkpointname);
220#endif
221}
222
223void
224REMORA::ReadCheckpointFile ()
225{
226 amrex::Print() << "Restart from checkpoint " << restart_chkfile << "\n";
227
228 // Header
229 std::string File(restart_chkfile + "/Header");
230
231 VisMF::IO_Buffer io_buffer(VisMF::GetIOBufferSize());
232
233 Vector<char> fileCharPtr;
234 ParallelDescriptor::ReadAndBcastFile(File, fileCharPtr);
235 std::string fileCharPtrString(fileCharPtr.dataPtr());
236 std::istringstream is(fileCharPtrString, std::istringstream::in);
237
238 std::string line, word;
239
240 int chk_ncomp;
241
242 // read in title line
243 std::getline(is, line);
244
245 // read in finest_level
246 is >> finest_level;
247 GotoNextLine(is);
248
249 if (finest_level > max_level) {
250 amrex::Abort("Checkpoint file has more levels than amr.max_level");
251 }
252
253 // read the number of components
254 // for each variable we store
255
256 // conservative, cell-centered vars
257 is >> chk_ncomp;
258 GotoNextLine(is);
259 if (chk_ncomp != ncons) {
260 // The tracer count comes from remora.nscalar or, when a biology model is
261 // active, from that model's tracer list, so name both rather than only the
262 // input a biology run never sets.
263 amrex::Abort("Checkpoint holds " + std::to_string(chk_ncomp) +
264 " cell-centered components but this run has " + std::to_string(ncons) +
265 ". The count is set by remora.nscalar and by remora.biology_model; "
266 "both must match the run the checkpoint came from.");
267 }
268
269 // x-velocity on faces
270 is >> chk_ncomp;
271 GotoNextLine(is);
272 AMREX_ASSERT(chk_ncomp == 1);
273
274 // y-velocity on faces
275 is >> chk_ncomp;
276 GotoNextLine(is);
277 AMREX_ASSERT(chk_ncomp == 1);
278
279 // z-velocity on faces
280 is >> chk_ncomp;
281 GotoNextLine(is);
282 AMREX_ASSERT(chk_ncomp == 1);
283
284 is >> chk_ncomp;
285 GotoNextLine(is);
286 AMREX_ASSERT(chk_ncomp == 2);
287
288 is >> chk_ncomp;
289 GotoNextLine(is);
290 AMREX_ASSERT(chk_ncomp == 2);
291
292 is >> chk_ncomp;
293 GotoNextLine(is);
294 AMREX_ASSERT(chk_ncomp == 3);
295
296 is >> chk_ncomp;
297 GotoNextLine(is);
298 AMREX_ASSERT(chk_ncomp == 3);
299
300 // read in array of istep
301 std::getline(is, line);
302 {
303 std::istringstream lis(line);
304 int i = 0;
305 while (lis >> word && i < istep.size()) {
306 istep[i++] = std::stoi(word);
307 }
308 }
309
310 // read in array of dt
311 std::getline(is, line);
312 {
313 std::istringstream lis(line);
314 int i = 0;
315 while (lis >> word && i < dt.size()) {
316#ifdef AMREX_USE_FLOAT
317 dt[i++] = std::stof(word);
318#else
319 dt[i++] = std::stod(word);
320#endif
321 }
322 }
323
324 // read in array of t_new. Kept in double until the origin it counts from is known.
325 Vector<double> chk_t_new(t_new.size(), 0.0);
326 std::getline(is, line);
327 {
328 std::istringstream lis(line);
329 int i = 0;
330 while (lis >> word && i < chk_t_new.size()) {
331 chk_t_new[i++] = std::stod(word);
332 }
333 }
334
335 // read in the BoxArray at each level
336 Vector<BoxArray> chk_ba(finest_level+1);
337 for (int lev = 0; lev <= finest_level; ++lev) {
338 chk_ba[lev].readFrom(is);
339 GotoNextLine(is);
340 }
341
342 // The origin the checkpoint's t_new counts from. A checkpoint written before
343 // model time was split has no such line and holds t_new on the model clock.
344 double chk_start_time = 0.0;
345 if (is >> word && word == "start_time") {
346 is >> chk_start_time;
347 }
348
349 // Rebase onto this run's start_time. Take t_new verbatim when the origin is
350 // unchanged, the usual case, so a restart reproduces the run it continues.
351 for (int lev = 0; lev < t_new.size(); ++lev) {
352 t_new[lev] = (chk_start_time == start_time)
353 ? static_cast<Real>(chk_t_new[lev])
354 : elapsed_time(chk_start_time + chk_t_new[lev]);
355 }
356
357 for (int lev = 0; lev <= finest_level; ++lev) {
358 // create a distribution mapping
359 DistributionMapping dm { chk_ba[lev], ParallelDescriptor::NProcs() };
360
361 MakeNewLevelFromScratch (lev, t_new[lev], chk_ba[lev], dm);
362 }
363
364 // read in the MultiFab data
365 for (int lev = 0; lev <= finest_level; ++lev)
366 {
367 BoxList bl2d = grids[lev].boxList();
368 for (auto& b : bl2d) {
369 b.setRange(2,0);
370 }
371 BoxArray ba2d(std::move(bl2d));
372
373 MultiFab cons(grids[lev],dmap[lev],ncons,cons_new[lev]->nGrowVect());
374 VisMF::Read(cons, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Cell"));
375 MultiFab::Copy(*cons_new[lev],cons,0,0,ncons,cons_new[lev]->nGrowVect());
376
377 VisMF::Read(cons, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Cell_old"));
378 MultiFab::Copy(*cons_old[lev],cons,0,0,ncons,cons_old[lev]->nGrowVect());
379
380 MultiFab xvel(convert(grids[lev],IntVect(1,0,0)),dmap[lev],1,xvel_new[lev]->nGrowVect());
381 VisMF::Read(xvel, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "XFace"));
382 MultiFab::Copy(*xvel_new[lev],xvel,0,0,1,xvel_new[lev]->nGrowVect());
383
384 VisMF::Read(xvel, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "XFace_old"));
385 MultiFab::Copy(*xvel_old[lev],xvel,0,0,1,xvel_old[lev]->nGrowVect());
386
387 MultiFab yvel(convert(grids[lev],IntVect(0,1,0)),dmap[lev],1,yvel_new[lev]->nGrowVect());
388 VisMF::Read(yvel, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "YFace"));
389 MultiFab::Copy(*yvel_new[lev],yvel,0,0,1,yvel_new[lev]->nGrowVect());
390
391 VisMF::Read(yvel, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "YFace_old"));
392 MultiFab::Copy(*yvel_old[lev],yvel,0,0,1,yvel_old[lev]->nGrowVect());
393
394 MultiFab zvel(convert(grids[lev],IntVect(0,0,1)),dmap[lev],1,zvel_new[lev]->nGrowVect());
395 VisMF::Read(zvel, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "ZFace"));
396 MultiFab::Copy(*zvel_new[lev],zvel,0,0,1,zvel_new[lev]->nGrowVect());
397
398 VisMF::Read(zvel, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "ZFace_old"));
399 MultiFab::Copy(*zvel_old[lev],zvel,0,0,1,zvel_old[lev]->nGrowVect());
400
401 MultiFab mf_ru(convert(grids[lev],IntVect(1,0,0)),dmap[lev],2,(vec_ru[lev])->nGrowVect());
402 VisMF::Read(mf_ru, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "XRHS"));
403 MultiFab::Copy(*(vec_ru[lev]),mf_ru,0,0,2,(vec_ru[lev])->nGrowVect());
404
405 MultiFab mf_rv(convert(grids[lev],IntVect(0,1,0)),dmap[lev],2,(vec_rv[lev])->nGrowVect());
406 VisMF::Read(mf_rv, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "YRHS"));
407 MultiFab::Copy(*(vec_rv[lev]),mf_rv,0,0,2,(vec_rv[lev])->nGrowVect());
408
409 MultiFab mf_ubar(convert(ba2d,IntVect(1,0,0)),dmap[lev],3,(vec_ubar[lev])->nGrowVect());
410 VisMF::Read(mf_ubar, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "XBar"));
411 MultiFab::Copy(*(vec_ubar[lev]),mf_ubar,0,0,3,(vec_ubar[lev])->nGrowVect());
412
413 MultiFab mf_vbar(convert(ba2d,IntVect(0,1,0)),dmap[lev],3,(vec_vbar[lev])->nGrowVect());
414 VisMF::Read(mf_vbar, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "YBar"));
415 MultiFab::Copy(*(vec_vbar[lev]),mf_vbar,0,0,3,(vec_vbar[lev])->nGrowVect());
416
417 MultiFab mf_ru2d(convert(ba2d,IntVect(1,0,0)),dmap[lev],2,(vec_ru2d[lev])->nGrowVect());
418 VisMF::Read(mf_ru2d, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "XRHS2d"));
419 MultiFab::Copy(*(vec_ru2d[lev]),mf_ru2d,0,0,2,(vec_ru2d[lev])->nGrowVect());
420
421 MultiFab mf_rv2d(convert(ba2d,IntVect(0,1,0)),dmap[lev],2,(vec_rv2d[lev])->nGrowVect());
422 VisMF::Read(mf_rv2d, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "YRHS2d"));
423 MultiFab::Copy(*(vec_rv2d[lev]),mf_rv2d,0,0,2,(vec_rv2d[lev])->nGrowVect());
424
425 MultiFab mf_mskr(ba2d,dmap[lev],1,(vec_mskr[lev])->nGrowVect());
426 VisMF::Read(mf_mskr, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Mskr"));
427 MultiFab::Copy(*(vec_mskr[lev]),mf_mskr,0,0,1,(vec_mskr[lev])->nGrowVect());
428
429 MultiFab mf_msku(convert(ba2d,IntVect(1,0,0)),dmap[lev],1,(vec_msku[lev])->nGrowVect());
430 VisMF::Read(mf_msku, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Msku"));
431 MultiFab::Copy(*(vec_msku[lev]),mf_msku,0,0,1,(vec_msku[lev])->nGrowVect());
432
433 MultiFab mf_mskv(convert(ba2d,IntVect(0,1,0)),dmap[lev],1,(vec_mskv[lev])->nGrowVect());
434 VisMF::Read(mf_mskv, amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Mskv"));
435 MultiFab::Copy(*(vec_mskv[lev]),mf_mskv,0,0,1,(vec_mskv[lev])->nGrowVect());
436
437 if (solverChoice.bottom_stress_type == BottomStressType::linear) {
438 VisMF::Read(*(vec_rdrag[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "rdrag"));
439 } else if (solverChoice.bottom_stress_type == BottomStressType::quadratic) {
440 VisMF::Read(*(vec_rdrag2[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "rdrag2"));
441 }
442
443 if (solverChoice.bottom_stress_type == BottomStressType::logarithmic ||
444 solverChoice.vert_mixing_type == VertMixingType::GLS) {
445 VisMF::Read(*(vec_ZoBot[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "ZoBot"));
446 }
447
448 VisMF::Read(*(vec_DU_avg1[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "DU_avg1"));
449 VisMF::Read(*(vec_DU_avg2[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "DU_avg2"));
450 VisMF::Read(*(vec_DV_avg1[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "DV_avg1"));
451 VisMF::Read(*(vec_DV_avg2[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "DV_avg2"));
452
453 VisMF::Read(*(vec_zeta[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "zeta"));
454 VisMF::Read(*(vec_Zt_avg1[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Zt_avg1"));
455
456 VisMF::Read(*(vec_h[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "h"));
457
458 VisMF::Read(*(vec_tke[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "tke"));
459 VisMF::Read(*(vec_gls[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "gls"));
460 VisMF::Read(*(vec_Lscale[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Lscale"));
461 VisMF::Read(*(vec_Akk[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Akk"));
462 VisMF::Read(*(vec_Akp[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Akp"));
463 VisMF::Read(*(vec_Akt[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Akt"));
464 VisMF::Read(*(vec_Akv[lev]), amrex::MultiFabFileFullPrefix(lev, restart_chkfile, "Level_", "Akv"));
465
466 stretch_transform(lev);
467
468 }
469
470#ifdef REMORA_USE_PARTICLES
471 particleData.Restart((amrex::ParGDBBase*)GetParGDB(),restart_chkfile);
472#endif
473}
BottomStressType::logarithmic
@ logarithmic
BottomStressType::linear
@ linear
BottomStressType::quadratic
@ quadratic
VertMixingType::GLS
@ GLS
setVal
mf_h setVal(geomdata.ProbHi(2))
REMORA::GotoNextLine
static void GotoNextLine(std::istream &is)
utility to skip to next line in Header
Definition REMORA_Checkpoint.cpp:8
REMORA::ncons
int ncons
Number of conserved scalars in the state (temperature + salt + passive scalars + biology tracers)
Definition REMORA.H:1797
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_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_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::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::stretch_transform
void stretch_transform(int lev)
Calculate vertical stretched coordinates.
Definition REMORA_DepthStretchTransform.H:92
REMORA::vec_mskr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskr
land/sea mask at cell centers (2D)
Definition REMORA.H:584
REMORA::vec_tke
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_tke
Turbulent kinetic energy.
Definition REMORA.H:667
REMORA::ReadCheckpointFile
void ReadCheckpointFile()
read checkpoint file from disk
Definition REMORA_Checkpoint.cpp:224
REMORA::vec_gls
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_gls
Turbulent generic length scale.
Definition REMORA.H:669
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::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::start_time
double start_time
Time of the start of the simulation, in seconds on the model clock.
Definition REMORA.H:1780
REMORA::vec_Lscale
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Lscale
Vertical mixing turbulent length scale.
Definition REMORA.H:671
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::check_file
std::string check_file
Checkpoint file prefix.
Definition REMORA.H:1923
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::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::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::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_mskv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_mskv
land/sea mask at y-faces (2D)
Definition REMORA.H:588
REMORA::istep
amrex::Vector< int > istep
which step?
Definition REMORA.H:1689
REMORA::WriteCheckpointFile
void WriteCheckpointFile()
write checkpoint file to disk
Definition REMORA_Checkpoint.cpp:15
REMORA::file_min_digits
static int file_min_digits
Minimum number of digits in plotfile name or chunked history file.
Definition REMORA.H:1993
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::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::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::vec_Akk
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akk
Turbulent kinetic energy vertical diffusion coefficient.
Definition REMORA.H:673
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::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::vec_zeta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_zeta
free surface height (2D)
Definition REMORA.H:578
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_ubar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ubar
barotropic x velocity (2D)
Definition REMORA.H:574
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_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::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::elapsed_time
amrex::Real elapsed_time(double time) const noexcept
Elapsed time since start_time of a time on the model clock.
Definition REMORA.H:2176
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_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::dt
amrex::Vector< amrex::Real > dt
time step at each level
Definition REMORA.H:1704
REMORA::vec_Akp
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akp
Turbulent length scale vertical diffusion coefficient.
Definition REMORA.H:675
SolverChoice::bottom_stress_type
BottomStressType bottom_stress_type
Definition REMORA_DataStruct.H:946
SolverChoice::vert_mixing_type
VertMixingType vert_mixing_type
Definition REMORA_DataStruct.H:956