REMORA
Energy Research and Forecasting: An Atmospheric Modeling Code
REMORA.H
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1 #ifndef REMORA_H_
2 #define REMORA_H_
3 
4 #include <string>
5 #include <limits>
6 #include <memory>
7 
8 #ifdef _OPENMP
9 #include <omp.h>
10 #endif
11 
12 #include <AMReX_AmrCore.H>
13 #include <AMReX_BCRec.H>
14 #include <AMReX_InterpFaceRegister.H>
15 
16 #include <AMReX_ParallelDescriptor.H>
17 #include <AMReX_ParmParse.H>
18 #include <AMReX_MultiFabUtil.H>
19 #include <AMReX_FillPatchUtil.H>
20 #include <AMReX_VisMF.H>
21 #include <AMReX_PhysBCFunct.H>
22 #include <AMReX_YAFluxRegister.H>
23 #include <AMReX_ErrorList.H>
24 
25 #ifdef AMREX_MEM_PROFILING
26 #include <AMReX_MemProfiler.H>
27 #endif
28 
29 #include <REMORA_Math.H>
30 #include <REMORA_PhysBCFunct.H>
31 #include <IndexDefines.H>
32 #include <TimeInterpolatedData.H>
33 #include <DataStruct.H>
34 #include <Derive.H>
35 
36 #ifdef REMORA_USE_PARTICLES
37 #include "ParticleData.H"
38 #endif
39 
40 #ifdef REMORA_USE_NETCDF
41 #include "NCInterface.H"
42 #endif
43 
44 #include <iostream>
45 
46 #ifdef AMREX_LAZY
47 #include <AMReX_Lazy.H>
48 #endif
49 
50 namespace InterpType {
51  enum {
52  PCInterp = 0,
53  NodeBilinear,
54  CellConservativeLinear,
55  CellBilinear,
56  CellQuadratic,
57  CellConservativeProtected,
58  CellConservativeQuartic
59  };
60 }
61 
62 template<typename V, typename T>
63 bool containerHasElement(const V& iterable, const T& query) {
64  return std::find(iterable.begin(), iterable.end(), query) != iterable.end();
65 }
66 
67 class REMORA
68  : public amrex::AmrCore
69 {
70 public:
71 
72  ////////////////
73  // public member functions
74 
75  /**
76  * constructor - reads in parameters from inputs file
77  * - sizes multilevel arrays and data structures
78  */
79  REMORA ();
80  virtual ~REMORA();
81 
82  /** Advance solution to final time */
83  void Evolve ();
84 
85  /** Tag cells for refinement */
86  virtual void ErrorEst (int lev, amrex::TagBoxArray& tags, amrex::Real time, int ngrow) override;
87 
88  /** Initialize multilevel data */
89  void InitData ();
90 
91  /** Init (NOT restart or regrid) */
92  void init_only (int lev, amrex::Real time);
93 
94  /** Restart */
95  void restart ();
96 
97  /** Called after every level 0 timestep */
98  void post_timestep (int nstep, amrex::Real time, amrex::Real dt_lev);
99 
100  // Diagnostics
101 
102  /** Integrate conserved quantities for diagnostics */
103  void sum_integrated_quantities(amrex::Real time);
104 
105  /* Perform the volume-weighted sum */
106  amrex::Real
107  volWgtSumMF(int lev,
108  const amrex::MultiFab& mf, int comp, bool local, bool finemask);
109 
110  /* Decide if it is time to take an action */
111  bool is_it_time_for_action(int nstep, amrex::Real time, amrex::Real dt,
112  int action_interval, amrex::Real action_per);
113 
114  /** Make a new level using provided BoxArray and DistributionMapping and
115  * fill with interpolated coarse level data.
116  * Overrides the pure virtual function in AmrCore
117  */
118  virtual void MakeNewLevelFromCoarse (int lev, amrex::Real time, const amrex::BoxArray& ba,
119  const amrex::DistributionMapping& dm) override;
120 
121  /** Remake an existing level using provided BoxArray and DistributionMapping and
122  * fill with existing fine and coarse data.
123  * Overrides the pure virtual function in AmrCore
124  */
125  virtual void RemakeLevel (int lev, amrex::Real time, const amrex::BoxArray& ba,
126  const amrex::DistributionMapping& dm) override;
127 
128  /** Delete level data
129  * Overrides the pure virtual function in AmrCore
130  */
131  virtual void ClearLevel (int lev) override;
132 
133  /** Make a new level from scratch using provided BoxArray and DistributionMapping.
134  * Only used during initialization.
135  * Overrides the pure virtual function in AmrCore
136  */
137  virtual void MakeNewLevelFromScratch (int lev, amrex::Real time, const amrex::BoxArray& ba,
138  const amrex::DistributionMapping& dm) override;
139 
140  /** compute dt from CFL considerations */
141  amrex::Real estTimeStep (int lev) const;
142 
143  /** Interface for advancing the data at one level by one "slow" timestep */
144  void remora_advance(int level,
145  amrex::MultiFab& cons_old, amrex::MultiFab& cons_new,
146  amrex::MultiFab& xvel_old, amrex::MultiFab& yvel_old, amrex::MultiFab& zvel_old,
147  amrex::MultiFab& xvel_new, amrex::MultiFab& yvel_new, amrex::MultiFab& zvel_new,
148  amrex::MultiFab& source,
149  const amrex::Geometry fine_geom,
150  const amrex::Real dt, const amrex::Real time);
151 
152  /** Make mask to zero out covered cells*/
153  amrex::MultiFab& build_fine_mask(int lev);
154 
155  /** write plotfile to disk */
156  void WritePlotFile (int which, amrex::Vector<std::string> plot_var_names);
157 
158  void WriteMultiLevelPlotfileWithBathymetry (const std::string &plotfilename,
159  int nlevels,
160  const amrex::Vector<const amrex::MultiFab*> &mf,
161  const amrex::Vector<const amrex::MultiFab*> &mf_nd,
162  const amrex::Vector<std::string> &varnames,
163  amrex::Real time,
164  const amrex::Vector<int> &level_steps,
165  const std::string &versionName = "HyperCLaw-V1.1",
166  const std::string &levelPrefix = "Level_",
167  const std::string &mfPrefix = "Cell",
168  const amrex::Vector<std::string>& extra_dirs = amrex::Vector<std::string>()) const;
169 
170 
171  void WriteGenericPlotfileHeaderWithBathymetry (std::ostream &HeaderFile,
172  int nlevels,
173  const amrex::Vector<amrex::BoxArray> &bArray,
174  const amrex::Vector<std::string> &varnames,
175  amrex::Real time,
176  const amrex::Vector<int> &level_steps,
177  const std::string &versionName,
178  const std::string &levelPrefix,
179  const std::string &mfPrefix) const;
180 
181  std::string pp_prefix {"remora"};
182 
183  amrex::Vector<amrex::MultiFab*> cons_old;
184  amrex::Vector<amrex::MultiFab*> xvel_old;
185  amrex::Vector<amrex::MultiFab*> yvel_old;
186  amrex::Vector<amrex::MultiFab*> zvel_old;
187 
188  amrex::Vector<amrex::MultiFab*> cons_new;
189  amrex::Vector<amrex::MultiFab*> xvel_new;
190  amrex::Vector<amrex::MultiFab*> yvel_new;
191  amrex::Vector<amrex::MultiFab*> zvel_new;
192 
193  // Program state data is represented by vectors of pointers to AMReX Multifabs.
194  // There is one pointer per level
195 
196  /** Bathymetry data (2D, positive valued, h in ROMS) **/
197  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_hOfTheConfusingName;
198 
199  /** Width of cells in the vertical (z-) direction (3D, Hz in ROMS) */
200  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_Hz;
201  /** u-volume flux (3D) */
202  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_Huon;
203  /** v-volume flux (3D) */
204  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_Hvom;
205  /** u velocity RHS (3D, includes horizontal and vertical advection) */
206  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_ru;
207  /** v velocity RHS (3D, includes horizontal and vertical advection) */
208  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_rv;
209  /** u velocity RHS, integrated, including advection and bottom/surface stresses (2D) */
210  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_rufrc;
211  /** v velocity RHS, integrated, including advection and bottom/surface stresses (2D) */
212  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_rvfrc;
213  /** Vertical viscosity coefficient (3D), set in .in file */
214  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_Akv;
215  /** Vertical diffusion coefficient (3D), set in .in file */
216  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_Akt;
217  /** Harmonic viscosity devined on the psi points (corners of horizontal grid cells) */
218  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_visc2_p;
219  /** Harmonic viscosity devined on the rho points (centers) */
220  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_visc2_r;
221  /** Harmonic diffusivity for temperature / salinity */
222  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_diff2;
223 
224  /** x coordinates at rho points (cell centers) */
225  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_x_r;
226 
227  /** y coordinates at rho points (cell centers) */
228  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_y_r;
229 
230  /** z coordinates at rho points (cell centers) */
231  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_z_r;
232 
233  /** z coordinates at w points (faces between z-cells) */
234  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_z_w;
235 
236  /** Scaled vertical coordinate (range [0,1]) that transforms to z, defined at rho points (cell centers) */
237  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_s_r;
238 
239  /** z coordinates at psi points (cell nodes) **/
240  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_z_phys_nd;
241 
242  /** Average of the free surface, zeta (2D) */
243  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_Zt_avg1;
244 
245  /** Surface stress in the u direction */
246  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_sustr;
247 
248  /** Surface stress in the v direction */
249  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_svstr;
250 
251  /** Linear drag coefficient [m/s], defined at rho points */
252  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_rdrag;
253 
254  /** Bottom stress in the u direction */
255  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_bustr;
256 
257  /** Bottom stress in the v direction */
258  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_bvstr;
259 
260  /** time average of barotropic x velocity flux (2D) */
261  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_DU_avg1;
262  /** correct time average of barotropic x velocity flux for coupling (2D) */
263  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_DU_avg2;
264  /** time average of barotropic y velocity flux */
265  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_DV_avg1;
266  /** correct time average of barotropic y velocity flux for coupling (2D) */
267  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_DV_avg2;
268  /** barotropic x velocity for the RHS (2D) */
269  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_rubar;
270  /** barotropic y velocity for the RHS (2D) */
271  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_rvbar;
272  /** free surface height for the RHS (2D) */
273  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_rzeta;
274  /** barotropic x velocity (2D) */
275  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_ubar;
276  /** barotropic y velocity (2D) */
277  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_vbar;
278  /** free surface height (2D) */
279  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_zeta;
280 
281  /** map factor (2D) */
282  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_pm;
283 
284  /** map factor (2D) */
285  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_pn;
286 
287  /** coriolis factor (2D) */
288  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_fcor;
289 
290  /** saltstore, tempstore, etc*/
291  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_sstore;
292 
293  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_visc3d_r;
294 
295  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_rhoS;
296  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vec_rhoA;
297 
298  amrex::Vector<amrex::Real> vec_weight1;
299  amrex::Vector<amrex::Real> vec_weight2;
300 
301  /** advance a single level for a single time step */
302  void Advance (int lev, amrex::Real time, amrex::Real dt_lev, int iteration, int ncycle);
303 
304  /** Set everything up for a step on a level */
305  void setup_step(int lev, amrex::Real time, amrex::Real dt_lev);
306 
307  /** 3D advance on a single level */
308  void advance_3d_ml (int lev, amrex::Real dt_lev);
309 
310  /** 2D advance, one predictor/corrector step */
311  void advance_2d_onestep (int lev, amrex::Real dt_lev, amrex::Real dtfast_lev, int my_iif, int nfast_counter);
312 
313  /** Perform a 2D predictor (predictor_2d_step=True) or corrector (predictor_2d_step=False) step */
314  void advance_2d (int lev,
315  amrex::MultiFab const* mf_rhoS,
316  amrex::MultiFab const* mf_rhoA,
317  amrex::MultiFab * mf_ru,
318  amrex::MultiFab * mf_rv,
319  amrex::MultiFab * mf_rufrc,
320  amrex::MultiFab * mf_rvfrc,
321  amrex::MultiFab * mf_Zt_avg1,
322  std::unique_ptr<amrex::MultiFab>& mf_DU_avg1,
323  std::unique_ptr<amrex::MultiFab>& mf_DU_avg2,
324  std::unique_ptr<amrex::MultiFab>& mf_DV_avg1,
325  std::unique_ptr<amrex::MultiFab>& mf_DV_avg2,
326  std::unique_ptr<amrex::MultiFab>& mf_rubar,
327  std::unique_ptr<amrex::MultiFab>& mf_rvbar,
328  std::unique_ptr<amrex::MultiFab>& mf_rzeta,
329  std::unique_ptr<amrex::MultiFab>& mf_ubar,
330  std::unique_ptr<amrex::MultiFab>& mf_vbar,
331  amrex::MultiFab * mf_zeta,
332  amrex::MultiFab const* mf_h,
333  amrex::MultiFab const* mf_pm,
334  amrex::MultiFab const* mf_pn,
335  amrex::MultiFab const* mf_fcor,
336  amrex::MultiFab const* mf_visc2_p,
337  amrex::MultiFab const* mf_visc2_r,
338  const amrex::Real dtfast_lev,
339  const bool predictor_2d_step,
340  const bool first_2d_step, int my_iif,
341  int & next_indx1);
342 
343  /** Advance the 3D variables */
344  void advance_3d (int lev,
345  amrex::MultiFab& mf_cons,
346  amrex::MultiFab& mf_u , amrex::MultiFab& mf_v,
347  amrex::MultiFab* mf_sstore,
348  amrex::MultiFab* mf_ru , amrex::MultiFab* mf_rv,
349  std::unique_ptr<amrex::MultiFab>& mf_DU_avg1,
350  std::unique_ptr<amrex::MultiFab>& mf_DU_avg2,
351  std::unique_ptr<amrex::MultiFab>& mf_DV_avg1,
352  std::unique_ptr<amrex::MultiFab>& mf_DV_avg2,
353  std::unique_ptr<amrex::MultiFab>& mf_ubar,
354  std::unique_ptr<amrex::MultiFab>& mf_vbar,
355  std::unique_ptr<amrex::MultiFab>& mf_Akv,
356  std::unique_ptr<amrex::MultiFab>& mf_Akt,
357  std::unique_ptr<amrex::MultiFab>& mf_Hz,
358  std::unique_ptr<amrex::MultiFab>& mf_Huon,
359  std::unique_ptr<amrex::MultiFab>& mf_Hvom,
360  std::unique_ptr<amrex::MultiFab>& mf_z_w,
361  amrex::MultiFab const* mf_h,
362  amrex::MultiFab const* mf_pm,
363  amrex::MultiFab const* mf_pn,
364  const int N,
365  const amrex::Real dt_lev);
366 
367  /** Wrapper function for prestep */
368  void prestep (int lev,
369  amrex::MultiFab& mf_uold, amrex::MultiFab& mf_vold,
370  amrex::MultiFab& mf_u, amrex::MultiFab& mf_v,
371  amrex::MultiFab* mf_ru,
372  amrex::MultiFab* mf_rv,
373  amrex::MultiFab& S_old,
374  amrex::MultiFab& S_new,
375  amrex::MultiFab& mf_W, amrex::MultiFab& mf_DC,
376  /* MF mf_FC? */
377  const amrex::MultiFab* mf_z_r,
378  const amrex::MultiFab* mf_z_w,
379  const amrex::MultiFab* mf_h,
380  const amrex::MultiFab* mf_pm,
381  const amrex::MultiFab* mf_pn,
382  const amrex::MultiFab* mf_sustr,
383  const amrex::MultiFab* mf_svstr,
384  const amrex::MultiFab* mf_bustr,
385  const amrex::MultiFab* mf_bvstr,
386  const int iic, const int nfirst,
387  const int nnew, int nstp, int nrhs,
388  int N, const amrex::Real dt_lev);
389 
390  /** Prestep calculations for the tracers */
391  void prestep_t_advection (const amrex::Box& tbx,
392  const amrex::Box& gbx,
393  const amrex::Array4<amrex::Real >& tempold,
394  const amrex::Array4<amrex::Real >& tempcache,
395  const amrex::Array4<amrex::Real >& Hz,
396  const amrex::Array4<amrex::Real >& Huon,
397  const amrex::Array4<amrex::Real >& Hvom,
398  const amrex::Array4<amrex::Real >& W,
399  const amrex::Array4<amrex::Real >& DC,
400  const amrex::Array4<amrex::Real >& FC,
401  const amrex::Array4<amrex::Real >& sstore,
402  const amrex::Array4<amrex::Real const>& z_w,
403  const amrex::Array4<amrex::Real const>& h,
404  const amrex::Array4<amrex::Real const>& pm,
405  const amrex::Array4<amrex::Real const>& pn,
406  int iic, int ntfirst, int nrhs, int N,
407  const amrex::Real dt_lev);
408 
409  void rhs_t_3d (const amrex::Box& bx,
410  const amrex::Box& gbx,
411  const amrex::Array4<amrex::Real >& t,
412  const amrex::Array4<amrex::Real const>& tempstore,
413  const amrex::Array4<amrex::Real const>& Huon,
414  const amrex::Array4<amrex::Real const>& Hvom,
415  const amrex::Array4<amrex::Real const>& Hz,
416  const amrex::Array4<amrex::Real const>& pn,
417  const amrex::Array4<amrex::Real const>& pm,
418  const amrex::Array4<amrex::Real const>& W,
419  const amrex::Array4<amrex::Real >& FC,
420  int nrhs, int nnew, int N, const amrex::Real dt_lev);
421 
422  /** Calculation of the RHS */
423  void rhs_uv_3d (const amrex::Box& xbx,
424  const amrex::Box& ybx,
425  const amrex::Array4<amrex::Real const>& uold,
426  const amrex::Array4<amrex::Real const>& vold,
427  const amrex::Array4<amrex::Real >& ru,
428  const amrex::Array4<amrex::Real >& rv,
429  const amrex::Array4<amrex::Real >& rufrc,
430  const amrex::Array4<amrex::Real >& rvfrc,
431  const amrex::Array4<amrex::Real const>& sustr,
432  const amrex::Array4<amrex::Real const>& svstr,
433  const amrex::Array4<amrex::Real const>& bustr,
434  const amrex::Array4<amrex::Real const>& bvstr,
435  const amrex::Array4<amrex::Real const>& Huon,
436  const amrex::Array4<amrex::Real const>& Hvom,
437  const amrex::Array4<amrex::Real const>& pm,
438  const amrex::Array4<amrex::Real const>& pn,
439  const amrex::Array4<amrex::Real const>& W,
440  const amrex::Array4<amrex::Real >& FC,
441  int nrhs, int N);
442 
443  void rhs_uv_2d (const amrex::Box& xbx,
444  const amrex::Box& ybx,
445  const amrex::Array4<amrex::Real const>& uold,
446  const amrex::Array4<amrex::Real const>& vold,
447  const amrex::Array4<amrex::Real >& ru,
448  const amrex::Array4<amrex::Real >& rv,
449  const amrex::Array4<amrex::Real const>& Duon,
450  const amrex::Array4<amrex::Real const>& Dvom,
451  const int nrhs);
452 
453  void rho_eos (const amrex::Box& bx,
454  const amrex::Array4<amrex::Real const>& state,
455  const amrex::Array4<amrex::Real >& rho,
456  const amrex::Array4<amrex::Real >& rhoA,
457  const amrex::Array4<amrex::Real >& rhoS,
458  const amrex::Array4<amrex::Real const>& Hz,
459  const amrex::Array4<amrex::Real const>& z_w,
460  const amrex::Array4<amrex::Real const>& h,
461  const int N);
462 
463  void prsgrd (const amrex::Box& bx,
464  const amrex::Box& gbx,
465  const amrex::Box& utbx,
466  const amrex::Box& vtbx,
467  const amrex::Array4<amrex::Real >& ru,
468  const amrex::Array4<amrex::Real >& rv,
469  const amrex::Array4<amrex::Real const>& pn,
470  const amrex::Array4<amrex::Real const>& pm,
471  const amrex::Array4<amrex::Real const>& rho,
472  const amrex::Array4<amrex::Real >& FC,
473  const amrex::Array4<amrex::Real const>& Hz,
474  const amrex::Array4<amrex::Real const>& z_r,
475  const amrex::Array4<amrex::Real const>& z_w,
476  const int nrhs, const int N);
477 
478  /** Update velocities or tracers with diffusion/viscosity
479  * as the last part of the prestep */
480  void prestep_diffusion (const amrex::Box& bx,
481  const amrex::Box& gbx,
482  const int ioff, const int joff,
483  const amrex::Array4<amrex::Real >& vel,
484  const amrex::Array4<amrex::Real const>& vel_old,
485  const amrex::Array4<amrex::Real >& rvel,
486  const amrex::Array4<amrex::Real const>& Hz,
487  const amrex::Array4<amrex::Real const>& Akv,
488  const amrex::Array4<amrex::Real >& DC,
489  const amrex::Array4<amrex::Real >& FC,
490  const amrex::Array4<amrex::Real const>& sstr,
491  const amrex::Array4<amrex::Real const>& bstr,
492  const amrex::Array4<amrex::Real const>& z_r,
493  const amrex::Array4<amrex::Real const>& pm,
494  const amrex::Array4<amrex::Real const>& pn,
495  const int iic, const int ntfirst, const int nnew, int nstp, int nrhs, int N,
496  const amrex::Real lambda, const amrex::Real dt_lev);
497 
498  void vert_visc_3d (const amrex::Box& bx,
499  const int ioff, const int joff,
500  const amrex::Array4<amrex::Real >& phi,
501  const amrex::Array4<amrex::Real const>& Hz,
502  const amrex::Array4<amrex::Real >& Hzk,
503  const amrex::Array4<amrex::Real >& AK,
504  const amrex::Array4<amrex::Real >& Akv,
505  const amrex::Array4<amrex::Real >& BC,
506  const amrex::Array4<amrex::Real >& DC,
507  const amrex::Array4<amrex::Real >& FC,
508  const amrex::Array4<amrex::Real >& CF,
509  const int nnew, const int N,
510  const amrex::Real dt_lev);
511 
512  void update_massflux_3d (const amrex::Box& bx,
513  const int ioff, const int joff,
514  const amrex::Array4<amrex::Real >& phi,
515  const amrex::Array4<amrex::Real >& phibar,
516  const amrex::Array4<amrex::Real >& Hphi,
517  const amrex::Array4<amrex::Real const>& Hz,
518  const amrex::Array4<amrex::Real const>& pm_or_pn,
519  const amrex::Array4<amrex::Real const>& Dphi1,
520  const amrex::Array4<amrex::Real const>& Dphi2,
521  const amrex::Array4<amrex::Real >& DC,
522  const amrex::Array4<amrex::Real >& FC,
523  const int nnew);
524 
525  void vert_mean_3d (const amrex::Box& bx,
526  const int ioff, const int joff,
527  const amrex::Array4<amrex::Real >& phi,
528  const amrex::Array4<amrex::Real const>& Hz,
529  const amrex::Array4<amrex::Real const>& Dphi_avg1,
530  const amrex::Array4<amrex::Real >& DC,
531  const amrex::Array4<amrex::Real >& CF,
532  const amrex::Array4<amrex::Real const>& dxlen,
533  const int nnew, const int N);
534 
535  /** Harmonic viscosity */
536  void uv3dmix (const amrex::Box& xbx,
537  const amrex::Box& ybx,
538  const amrex::Array4<amrex::Real >& u,
539  const amrex::Array4<amrex::Real >& v,
540  const amrex::Array4<amrex::Real const>& uold,
541  const amrex::Array4<amrex::Real const>& vold,
542  const amrex::Array4<amrex::Real >& rufrc,
543  const amrex::Array4<amrex::Real >& rvfrc,
544  const amrex::Array4<amrex::Real const>& visc2_p,
545  const amrex::Array4<amrex::Real const>& visc2_r,
546  const amrex::Array4<amrex::Real const>& Hz,
547  const amrex::Array4<amrex::Real const>& pm,
548  const amrex::Array4<amrex::Real const>& pn,
549  int nrhs, int nnew,
550  const amrex::Real dt_lev);
551 
552  /** Harmonic diffusivity for tracers */
553  void t3dmix (const amrex::Box& bx,
554  const amrex::Array4<amrex::Real >& state,
555  const amrex::Array4<amrex::Real const>& diff2,
556  const amrex::Array4<amrex::Real const>& Hz,
557  const amrex::Array4<amrex::Real const>& pm,
558  const amrex::Array4<amrex::Real const>& pn,
559  const amrex::Real dt_lev,
560  const int ncomp);
561 
562  void coriolis (const amrex::Box& xbx,
563  const amrex::Box& ybx,
564  const amrex::Array4<amrex::Real const>& uold,
565  const amrex::Array4<amrex::Real const>& vold,
566  const amrex::Array4<amrex::Real >& ru,
567  const amrex::Array4<amrex::Real >& rv,
568  const amrex::Array4<amrex::Real const>& Hz,
569  const amrex::Array4<amrex::Real const>& fomn,
570  int nrhs, int nr);
571 
572  void set_2darrays (int lev);
573 
574  void set_bathymetry (int lev);
575 
576  void set_coriolis (int lev);
577 
578  void stretch_transform (int lev);
579 
580  void set_vmix (int lev);
581 
582  void set_smflux (int lev, amrex::Real time);
583 
584  void set_hmixcoef (int lev);
585 
586  void set_drag (int lev);
587 
588  void set_weights (int lev);
589 
590  // Fill a new MultiFab by copying in phi from valid region and filling ghost cells
591  void FillPatch (int lev, amrex::Real time,
592  amrex::MultiFab& mf_to_be_filled,
593  amrex::Vector<amrex::MultiFab*> const& mfs,
594  const int bdy_var_type = BdyVars::null);
595 
596  void fill_from_bdyfiles (amrex::MultiFab& mf_to_fill,
597  const amrex::Real time,
598  const int bdy_var_type);
599 
600  void init_beta_plane_coriolis (int lev);
601 
602 #ifdef REMORA_USE_NETCDF
603  static int total_nc_plot_file_step;
604 #endif
605 
606 private:
607 
608  ///////////////////////////
609  // private member functions
610  ///////////////////////////
611 
612  /** read in some parameters from inputs file */
613  void ReadParameters();
614 
615  /** set covered coarse cells to be the average of overlying fine cells */
616  void AverageDown ();
617 
618  void init1DArrays();
619 
620  void init_bcs();
621 
622  void init_custom(int lev);
623 
624  void init_stuff (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm);
625 
626  void resize_stuff (int lev);
627 
628  /** more flexible version of AverageDown() that lets you average down across multiple levels */
629  void AverageDownTo (int crse_lev);
630 
631  /** fill an entire multifab by interpolating from the coarser level
632  * this comes into play when a new level of refinement appears
633  */
634  void FillCoarsePatch (int lev, amrex::Real time, amrex::MultiFab* mf_fine, amrex::MultiFab* mf_crse);
635 
636  /** utility to copy in data from old and/or new state into another multifab */
637  TimeInterpolatedData GetDataAtTime (int lev, amrex::Real time);
638 
639  /** advance a level by dt, includes a recursive call for finer levels */
640  void timeStep (int lev, amrex::Real time, int iteration);
641 
642  /** advance all levels by dt, loops over finer levels */
643  void timeStepML (amrex::Real time, int iteration);
644 
645  //! Initialize HSE
646  void initHSE();
647 
648  //! Initialize Rayleigh damping profiles
649  void initRayleigh();
650 
651  /** a wrapper for estTimeStep() */
652  void ComputeDt ();
653 
654  /** get plotfile name */
655  std::string PlotFileName (int lev) const;
656 
657  /** set plotfile variables names */
658  amrex::Vector<std::string> PlotFileVarNames (amrex::Vector<std::string> plot_var_names) const;
659 
660  /** set which variables and derived quantities go into plotfiles */
661  void setPlotVariables (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
662 
663 
664 #ifdef REMORA_USE_NETCDF
665  //! Write plotfile using NETCDF
666  void WriteNCPlotFile(int istep) const;
667  void WriteNCPlotFile_which(int istep, int lev, int which_subdomain,
668  bool not_empty, ncutils::NCFile& ncf) const;
669 
670  //! Write MultiFab in NetCDF format
671  void WriteNCMultiFab (const amrex::FabArray<amrex::FArrayBox> &fab,
672  const std::string& name,
673  bool set_ghost = false) const;
674 
675  //! Read MultiFab in NetCDF format
676  void ReadNCMultiFab (amrex::FabArray<amrex::FArrayBox> &fab,
677  const std::string &name,
678  int coordinatorProc = amrex::ParallelDescriptor::IOProcessorNumber(),
679  int allow_empty_mf = 0);
680 
681  // Vectors (over time) of Vector (over variables) of FArrayBoxs for holding the data read from the wrfbdy NetCDF file
682  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_xlo;
683  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_xhi;
684  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_ylo;
685  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_yhi;
686 
687  amrex::Real start_bdy_time;
688  amrex::Real bdy_time_interval;
689 
690  static bool write_history_file;
691 
692  int bdy_width{0};
693  int bdy_set_width{0};
694 
695  void init_data_from_netcdf (int lev);
696  void init_bdry_from_netcdf ();
697  void init_bathymetry_from_netcdf (int lev);
698  void init_coriolis_from_netcdf (int lev);
699 #endif // REMORA_USE_NETCDF
700 
701  // write checkpoint file to disk
702  void WriteCheckpointFile () const;
703 
704  // read checkpoint file from disk
705  void ReadCheckpointFile ();
706 
707  // Read the file passed to amr.restart and use it as an initial condition for
708  // the current simulation. Supports a different number of components and
709  // ghost cells.
710  void InitializeFromFile ();
711 
712  // Initialize the new-time data at a level from the initial_data MultiFab
713  void InitializeLevelFromData (int lev, const amrex::MultiFab& initial_data);
714 
715  // utility to skip to next line in Header
716  static void GotoNextLine (std::istream& is);
717 
718  // Single level functions called by advance()
719  void post_update (amrex::MultiFab& state_mf, const amrex::Real time, const amrex::Geometry& geom);
720  void fill_rhs (amrex::MultiFab& rhs_mf, const amrex::MultiFab& state_mf, const amrex::Real time, const amrex::Geometry& geom);
721 
722  ////////////////
723  // private data members
724 
725  amrex::Vector<int> num_boxes_at_level; // how many boxes specified at each level by tagging criteria
726  amrex::Vector<int> num_files_at_level; // how many wrfinput files specified at each level
727  amrex::Vector<amrex::Vector<amrex::Box>> boxes_at_level; // the boxes specified at each level by tagging criteria
728 
729  amrex::Vector<int> istep; // which step?
730  amrex::Vector<int> nsubsteps; // how many substeps on each level?
731 
732  // keep track of old time, new time, and time step at each level
733  amrex::Vector<amrex::Real> t_new;
734  amrex::Vector<amrex::Real> t_old;
735  amrex::Vector<amrex::Real> dt;
736 
737  amrex::Vector<std::unique_ptr<REMORAPhysBCFunct>> physbcs;
738  // array of multifabs to store the solution at each level of refinement
739  // after advancing a level we use "swap".
740 
741  amrex::Vector<std::unique_ptr<amrex::MultiFab>> mapfac_m;
742  amrex::Vector<std::unique_ptr<amrex::MultiFab>> mapfac_u;
743  amrex::Vector<std::unique_ptr<amrex::MultiFab>> mapfac_v;
744 
745  amrex::Vector<std::unique_ptr<amrex::MultiFab>> sst;
746 
747  // array of flux registers
748  amrex::Vector<amrex::YAFluxRegister*> advflux_reg;
749 
750  // A BCRec is essentially a 2*DIM integer array storing the boundary
751  // condition type at each lo/hi walls in each direction. We have one BCRec
752  // for each component of the cell-centered variables and each velocity component.
753  amrex::Vector <amrex::BCRec> domain_bcs_type;
754  amrex::Gpu::DeviceVector<amrex::BCRec> domain_bcs_type_d;
755 
756  // We store these so that we can print them out in the job_info file
757  amrex::Array<std::string,2*AMREX_SPACEDIM> domain_bc_type;
758 
759  // These hold the Dirichlet values at walls which need them ...
760  amrex::Array<amrex::Array<amrex::Real, AMREX_SPACEDIM*2>,AMREX_SPACEDIM+NCONS> m_bc_extdir_vals;
761 
762  // These are the "physical" boundary condition types (e.g. "inflow")
763  amrex::GpuArray<REMORA_BC, AMREX_SPACEDIM*2> phys_bc_type;
764 
765  int last_plot_file_step_1;
766  int last_plot_file_step_2;
767 
768  int last_check_file_step;
769  int plot_file_on_restart = 1;
770 
771  ////////////////
772  // runtime parameters
773 
774  // maximum number of steps and stop time
775  int max_step = std::numeric_limits<int>::max();
776  amrex::Real stop_time = std::numeric_limits<amrex::Real>::max();
777 
778  // if >= 0 we restart from a checkpoint
779  std::string restart_chkfile = "";
780 
781  // Time step controls
782  static amrex::Real cfl;
783  static amrex::Real init_shrink;
784  static amrex::Real change_max;
785 
786  // Fixed dt for level 0 timesteps (only used if positive)
787  static amrex::Real fixed_dt;
788  static amrex::Real fixed_fast_dt;
789  static int fixed_ndtfast_ratio;
790  int nfast;
791 
792  // Whether to substep fine levels in time
793  int do_substep;
794 
795  // how often each level regrids the higher levels of refinement
796  // (after a level advances that many time steps)
797  int regrid_int = 2;
798 
799  // plotfile prefix and frequency
800  std::string plot_file_1 {"plt_1_"};
801  std::string plot_file_2 {"plt_2_"};
802  int plot_int_1 = -1;
803  int plot_int_2 = -1;
804 
805  // Checkpoint type, prefix and frequency
806  std::string check_file {"chk"};
807  int check_int = -1;
808 
809  amrex::Vector<std::string> plot_var_names_1;
810  amrex::Vector<std::string> plot_var_names_2;
811  const amrex::Vector<std::string> cons_names {"temp", "salt", "scalar"};
812 
813  // Note that the order of variable names here must match the order in Derive.cpp
814 #ifdef REMORA_USE_PARTICLES
815  const amrex::Vector<std::string> derived_names {"dpdx", "dpdy" ,"tracer_particle_count"};
816 #else
817  const amrex::Vector<std::string> derived_names {"dpdx", "dpdy"};
818 #endif
819 
820 
821  // algorithm choices
822  static SolverChoice solverChoice;
823 
824 #ifdef REMORA_USE_PARTICLES
825  // Particle info
826  static ParticleData particleData;
827 #endif
828 
829  static int verbose;
830 
831  // flag to turn tracer particle generation on/off
832  static bool use_tracer_particles;
833 
834  // Diagnostic output interval
835  static int sum_interval;
836  static amrex::Real sum_per;
837 
838  // Native or NetCDF
839  static PlotfileType plotfile_type;
840 
841  // NetCDF initialization files for solution and grid
842  static amrex::Vector<amrex::Vector<std::string>> nc_init_file;
843  static amrex::Vector<amrex::Vector<std::string>> nc_grid_file;
844 
845  // NetCDF file of time series of boundary data
846  static std::string nc_bdry_file;
847 
848  // Text input_sounding file
849  static std::string input_sounding_file;
850 
851  // 1D CDF output (for ingestion in AMR-Wind)
852  static int output_1d_column;
853  static int column_interval;
854  static amrex::Real column_per;
855  static amrex::Real column_loc_x;
856  static amrex::Real column_loc_y;
857  static std::string column_file_name;
858 
859  // 2D BndryRegister output (for ingestion in AMR-Wind)
860  static int output_bndry_planes;
861  static int bndry_output_planes_interval;
862  static amrex::Real bndry_output_planes_per;
863  static amrex::Real bndry_output_planes_start_time;
864 
865  // 2D BndryRegister input
866  static int input_bndry_planes;
867 
868  amrex::Vector<amrex::Real> h_havg_density;
869  amrex::Vector<amrex::Real> h_havg_temperature;
870  amrex::Vector<amrex::Real> h_havg_pressure;
871  amrex::Gpu::DeviceVector<amrex::Real> d_havg_density;
872  amrex::Gpu::DeviceVector<amrex::Real> d_havg_temperature;
873  amrex::Gpu::DeviceVector<amrex::Real> d_havg_pressure;
874 
875  void refinement_criteria_setup();
876 
877  //
878  // Holds info for dynamically generated tagging criteria
879  //
880  static amrex::Vector<amrex::AMRErrorTag> ref_tags;
881 
882  //
883  // Build a mask that zeroes out values on a coarse level underlying
884  // grids on the next finest level
885  //
886  amrex::MultiFab fine_mask;
887 
888  AMREX_FORCE_INLINE
889  int
890  ComputeGhostCells(const int& spatial_order) {
891  int nGhostCells;
892 
893  switch (spatial_order) {
894  case 2:
895  nGhostCells = 2; // We need this many to compute the eddy viscosity in the ghost cells
896  break;
897  case 3:
898  nGhostCells = 2;
899  break;
900  case 4:
901  nGhostCells = 2;
902  break;
903  case 5:
904  nGhostCells = 3;
905  break;
906  case 6:
907  nGhostCells = 3;
908  break;
909  default:
910  amrex::Error("Must specify spatial order to be 2,3,4,5 or 6");
911  }
912 
913  return nGhostCells;
914  }
915 
916  AMREX_FORCE_INLINE
917  amrex::YAFluxRegister* getAdvFluxReg (int lev)
918  {
919  return advflux_reg[lev];
920  }
921 
922  AMREX_FORCE_INLINE
923  std::ostream&
924  DataLog (int i)
925  {
926  return *datalog[i];
927  }
928 
929  AMREX_FORCE_INLINE
930  int
931  NumDataLogs () noexcept
932  {
933  return datalog.size();
934  }
935 
936  static amrex::Real startCPUTime;
937  static amrex::Real previousCPUTimeUsed;
938 
939  amrex::Real
940  getCPUTime() const
941  {
942  int numCores = amrex::ParallelDescriptor::NProcs();
943 #ifdef _OPENMP
944  numCores = numCores * omp_get_max_threads();
945 #endif
946 
947  amrex::Real T =
948  numCores * (amrex::ParallelDescriptor::second() - startCPUTime) +
949  previousCPUTimeUsed;
950 
951  return T;
952  }
953 
954  void setRecordDataInfo (int i, const std::string& filename)
955  {
956  if (amrex::ParallelDescriptor::IOProcessor())
957  {
958  datalog[i] = std::make_unique<std::fstream>();
959  datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
960  if (!datalog[i]->good()) {
961  amrex::FileOpenFailed(filename);
962  }
963  }
964  amrex::ParallelDescriptor::Barrier("REMORA::setRecordDataInfo");
965  }
966 
967  amrex::Vector<std::unique_ptr<std::fstream> > datalog;
968  amrex::Vector<std::string> datalogname;
969 
970  //! The filename of the ith datalog file.
971  const std::string DataLogName (int i) const noexcept { return datalogname[i]; }
972 
973 public:
974  void writeJobInfo(const std::string& dir) const;
975  static void writeBuildInfo(std::ostream& os);
976 };
977 
978 #endif
PlotfileType
PlotfileType
Definition: DataStruct.H:37
NCONS
#define NCONS
Definition: IndexDefines.H:11
containerHasElement
bool containerHasElement(const V &iterable, const T &query)
Definition: REMORA.H:63
REMORA_Math.H
REMORA_PhysBCFunct.H
REMORA
Definition: REMORA.H:69
REMORA::plotfile_type
static PlotfileType plotfile_type
Definition: REMORA.H:839
REMORA::cons_names
const amrex::Vector< std::string > cons_names
Definition: REMORA.H:811
REMORA::GotoNextLine
static void GotoNextLine(std::istream &is)
Definition: Checkpoint.cpp:8
REMORA::bndry_output_planes_interval
static int bndry_output_planes_interval
Definition: REMORA.H:861
REMORA::nfast
int nfast
Definition: REMORA.H:790
REMORA::column_interval
static int column_interval
Definition: REMORA.H:853
REMORA::plot_var_names_1
amrex::Vector< std::string > plot_var_names_1
Definition: REMORA.H:809
REMORA::rhs_uv_2d
void rhs_uv_2d(const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &Duon, const amrex::Array4< amrex::Real const > &Dvom, const int nrhs)
Definition: REMORA_rhs_uv_2d.cpp:20
REMORA::m_bc_extdir_vals
amrex::Array< amrex::Array< amrex::Real, AMREX_SPACEDIM *2 >, AMREX_SPACEDIM+NCONS > m_bc_extdir_vals
Definition: REMORA.H:760
REMORA::fixed_dt
static amrex::Real fixed_dt
Definition: REMORA.H:787
REMORA::prestep_diffusion
void prestep_diffusion(const amrex::Box &bx, const amrex::Box &gbx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &vel, const amrex::Array4< amrex::Real const > &vel_old, const amrex::Array4< amrex::Real > &rvel, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &Akv, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &sstr, const amrex::Array4< amrex::Real const > &bstr, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const int iic, const int ntfirst, const int nnew, int nstp, int nrhs, int N, const amrex::Real lambda, const amrex::Real dt_lev)
Definition: REMORA_prestep_diffusion.cpp:19
REMORA::getAdvFluxReg
AMREX_FORCE_INLINE amrex::YAFluxRegister * getAdvFluxReg(int lev)
Definition: REMORA.H:917
REMORA::init_bcs
void init_bcs()
Definition: REMORA_init_bcs.cpp:9
REMORA::domain_bcs_type
amrex::Vector< amrex::BCRec > domain_bcs_type
Definition: REMORA.H:753
REMORA::rhs_t_3d
void rhs_t_3d(const amrex::Box &bx, const amrex::Box &gbx, const amrex::Array4< amrex::Real > &t, const amrex::Array4< amrex::Real const > &tempstore, const amrex::Array4< amrex::Real const > &Huon, const amrex::Array4< amrex::Real const > &Hvom, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &W, const amrex::Array4< amrex::Real > &FC, int nrhs, int nnew, int N, const amrex::Real dt_lev)
Definition: REMORA_rhs_t_3d.cpp:25
REMORA::previousCPUTimeUsed
static amrex::Real previousCPUTimeUsed
Definition: REMORA.H:937
REMORA::vec_fcor
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_fcor
Definition: REMORA.H:288
REMORA::vec_hOfTheConfusingName
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_hOfTheConfusingName
Definition: REMORA.H:197
REMORA::vec_rubar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rubar
Definition: REMORA.H:269
REMORA::vec_pm
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pm
Definition: REMORA.H:282
REMORA::fine_mask
amrex::MultiFab fine_mask
Definition: REMORA.H:886
REMORA::init_shrink
static amrex::Real init_shrink
Definition: REMORA.H:783
REMORA::vec_DU_avg2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_DU_avg2
Definition: REMORA.H:263
REMORA::plot_int_2
int plot_int_2
Definition: REMORA.H:803
REMORA::cons_new
amrex::Vector< amrex::MultiFab * > cons_new
Definition: REMORA.H:188
REMORA::MakeNewLevelFromCoarse
virtual void MakeNewLevelFromCoarse(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: REMORA_make_new_level.cpp:18
REMORA::stretch_transform
void stretch_transform(int lev)
Definition: DepthStretchTransform.H:12
REMORA::advance_2d
void advance_2d(int lev, amrex::MultiFab const *mf_rhoS, amrex::MultiFab const *mf_rhoA, amrex::MultiFab *mf_ru, amrex::MultiFab *mf_rv, amrex::MultiFab *mf_rufrc, amrex::MultiFab *mf_rvfrc, amrex::MultiFab *mf_Zt_avg1, std::unique_ptr< amrex::MultiFab > &mf_DU_avg1, std::unique_ptr< amrex::MultiFab > &mf_DU_avg2, std::unique_ptr< amrex::MultiFab > &mf_DV_avg1, std::unique_ptr< amrex::MultiFab > &mf_DV_avg2, std::unique_ptr< amrex::MultiFab > &mf_rubar, std::unique_ptr< amrex::MultiFab > &mf_rvbar, std::unique_ptr< amrex::MultiFab > &mf_rzeta, std::unique_ptr< amrex::MultiFab > &mf_ubar, std::unique_ptr< amrex::MultiFab > &mf_vbar, amrex::MultiFab *mf_zeta, amrex::MultiFab const *mf_h, amrex::MultiFab const *mf_pm, amrex::MultiFab const *mf_pn, amrex::MultiFab const *mf_fcor, amrex::MultiFab const *mf_visc2_p, amrex::MultiFab const *mf_visc2_r, const amrex::Real dtfast_lev, const bool predictor_2d_step, const bool first_2d_step, int my_iif, int &next_indx1)
Definition: REMORA_advance_2d.cpp:37
REMORA::prestep_t_advection
void prestep_t_advection(const amrex::Box &tbx, const amrex::Box &gbx, const amrex::Array4< amrex::Real > &tempold, const amrex::Array4< amrex::Real > &tempcache, const amrex::Array4< amrex::Real > &Hz, const amrex::Array4< amrex::Real > &Huon, const amrex::Array4< amrex::Real > &Hvom, const amrex::Array4< amrex::Real > &W, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real > &sstore, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &h, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, int iic, int ntfirst, int nrhs, int N, const amrex::Real dt_lev)
Definition: REMORA_prestep_t_advection.cpp:10
REMORA::sum_interval
static int sum_interval
Definition: REMORA.H:835
REMORA::stop_time
amrex::Real stop_time
Definition: REMORA.H:776
REMORA::bndry_output_planes_start_time
static amrex::Real bndry_output_planes_start_time
Definition: REMORA.H:863
REMORA::do_substep
int do_substep
Definition: REMORA.H:793
REMORA::plot_var_names_2
amrex::Vector< std::string > plot_var_names_2
Definition: REMORA.H:810
REMORA::Evolve
void Evolve()
Definition: REMORA.cpp:142
REMORA::ReadCheckpointFile
void ReadCheckpointFile()
Definition: Checkpoint.cpp:214
REMORA::writeJobInfo
void writeJobInfo(const std::string &dir) const
Definition: writeJobInfo.cpp:7
REMORA::vec_sustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sustr
Definition: REMORA.H:246
REMORA::ClearLevel
virtual void ClearLevel(int lev) override
Definition: REMORA_make_new_level.cpp:327
REMORA::datalogname
amrex::Vector< std::string > datalogname
Definition: REMORA.H:968
REMORA::zvel_new
amrex::Vector< amrex::MultiFab * > zvel_new
Definition: REMORA.H:191
REMORA::plot_int_1
int plot_int_1
Definition: REMORA.H:802
REMORA::ComputeGhostCells
AMREX_FORCE_INLINE int ComputeGhostCells(const int &spatial_order)
Definition: REMORA.H:890
REMORA::vec_sstore
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_sstore
Definition: REMORA.H:291
REMORA::column_loc_x
static amrex::Real column_loc_x
Definition: REMORA.H:855
REMORA::init_only
void init_only(int lev, amrex::Real time)
Definition: REMORA.cpp:447
REMORA::init1DArrays
void init1DArrays()
REMORA::set_coriolis
void set_coriolis(int lev)
Definition: REMORA.cpp:396
REMORA::boxes_at_level
amrex::Vector< amrex::Vector< amrex::Box > > boxes_at_level
Definition: REMORA.H:727
REMORA::ref_tags
static amrex::Vector< amrex::AMRErrorTag > ref_tags
Definition: REMORA.H:880
REMORA::vec_Hz
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Hz
Definition: REMORA.H:200
REMORA::vec_Akt
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akt
Definition: REMORA.H:216
REMORA::vec_rvfrc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rvfrc
Definition: REMORA.H:212
REMORA::column_loc_y
static amrex::Real column_loc_y
Definition: REMORA.H:856
REMORA::check_file
std::string check_file
Definition: REMORA.H:806
REMORA::startCPUTime
static amrex::Real startCPUTime
Definition: REMORA.H:936
REMORA::set_smflux
void set_smflux(int lev, amrex::Real time)
Definition: REMORA.cpp:438
REMORA::xvel_old
amrex::Vector< amrex::MultiFab * > xvel_old
Definition: REMORA.H:184
REMORA::vec_x_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_x_r
Definition: REMORA.H:225
REMORA::yvel_new
amrex::Vector< amrex::MultiFab * > yvel_new
Definition: REMORA.H:190
REMORA::vec_rufrc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rufrc
Definition: REMORA.H:210
REMORA::fixed_fast_dt
static amrex::Real fixed_fast_dt
Definition: REMORA.H:788
REMORA::regrid_int
int regrid_int
Definition: REMORA.H:797
REMORA::mapfac_u
amrex::Vector< std::unique_ptr< amrex::MultiFab > > mapfac_u
Definition: REMORA.H:742
REMORA::uv3dmix
void uv3dmix(const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real > &u, const amrex::Array4< amrex::Real > &v, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &rufrc, const amrex::Array4< amrex::Real > &rvfrc, const amrex::Array4< amrex::Real const > &visc2_p, const amrex::Array4< amrex::Real const > &visc2_r, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, int nrhs, int nnew, const amrex::Real dt_lev)
Definition: REMORA_uv3dmix.cpp:6
REMORA::output_bndry_planes
static int output_bndry_planes
Definition: REMORA.H:860
REMORA::vec_weight2
amrex::Vector< amrex::Real > vec_weight2
Definition: REMORA.H:299
REMORA::last_plot_file_step_2
int last_plot_file_step_2
Definition: REMORA.H:766
REMORA::vec_visc2_p
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_visc2_p
Definition: REMORA.H:218
REMORA::set_drag
void set_drag(int lev)
REMORA::build_fine_mask
amrex::MultiFab & build_fine_mask(int lev)
Definition: REMORA_SumIQ.cpp:115
REMORA::vec_rvbar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rvbar
Definition: REMORA.H:271
REMORA::num_files_at_level
amrex::Vector< int > num_files_at_level
Definition: REMORA.H:726
REMORA::advance_2d_onestep
void advance_2d_onestep(int lev, amrex::Real dt_lev, amrex::Real dtfast_lev, int my_iif, int nfast_counter)
Definition: REMORA_advance_2d_onestep.cpp:6
REMORA::AverageDownTo
void AverageDownTo(int crse_lev)
Definition: REMORA.cpp:641
REMORA::post_timestep
void post_timestep(int nstep, amrex::Real time, amrex::Real dt_lev)
Definition: REMORA.cpp:231
REMORA::max_step
int max_step
Definition: REMORA.H:775
REMORA::zvel_old
amrex::Vector< amrex::MultiFab * > zvel_old
Definition: REMORA.H:186
REMORA::plot_file_2
std::string plot_file_2
Definition: REMORA.H:801
REMORA::vec_z_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_r
Definition: REMORA.H:231
REMORA::mapfac_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > mapfac_m
Definition: REMORA.H:741
REMORA::WritePlotFile
void WritePlotFile(int which, amrex::Vector< std::string > plot_var_names)
Definition: Plotfile.cpp:99
REMORA::h_havg_temperature
amrex::Vector< amrex::Real > h_havg_temperature
Definition: REMORA.H:869
REMORA::num_boxes_at_level
amrex::Vector< int > num_boxes_at_level
Definition: REMORA.H:725
REMORA::xvel_new
amrex::Vector< amrex::MultiFab * > xvel_new
Definition: REMORA.H:189
REMORA::refinement_criteria_setup
void refinement_criteria_setup()
Definition: REMORA_Tagging.cpp:39
REMORA::remora_advance
void remora_advance(int level, amrex::MultiFab &cons_old, amrex::MultiFab &cons_new, amrex::MultiFab &xvel_old, amrex::MultiFab &yvel_old, amrex::MultiFab &zvel_old, amrex::MultiFab &xvel_new, amrex::MultiFab &yvel_new, amrex::MultiFab &zvel_new, amrex::MultiFab &source, const amrex::Geometry fine_geom, const amrex::Real dt, const amrex::Real time)
REMORA::last_check_file_step
int last_check_file_step
Definition: REMORA.H:768
REMORA::rhs_uv_3d
void rhs_uv_3d(const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real > &rufrc, const amrex::Array4< amrex::Real > &rvfrc, const amrex::Array4< amrex::Real const > &sustr, const amrex::Array4< amrex::Real const > &svstr, const amrex::Array4< amrex::Real const > &bustr, const amrex::Array4< amrex::Real const > &bvstr, const amrex::Array4< amrex::Real const > &Huon, const amrex::Array4< amrex::Real const > &Hvom, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &W, const amrex::Array4< amrex::Real > &FC, int nrhs, int N)
Definition: REMORA_rhs_uv_3d.cpp:31
REMORA::init_beta_plane_coriolis
void init_beta_plane_coriolis(int lev)
Definition: REMORA_init.cpp:54
REMORA::set_vmix
void set_vmix(int lev)
Definition: REMORA.cpp:418
REMORA::RemakeLevel
virtual void RemakeLevel(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: REMORA_make_new_level.cpp:49
REMORA::vert_mean_3d
void vert_mean_3d(const amrex::Box &bx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &phi, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &Dphi_avg1, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &CF, const amrex::Array4< amrex::Real const > &dxlen, const int nnew, const int N)
Definition: REMORA_vert_mean_3d.cpp:10
REMORA::nsubsteps
amrex::Vector< int > nsubsteps
Definition: REMORA.H:730
REMORA::physbcs
amrex::Vector< std::unique_ptr< REMORAPhysBCFunct > > physbcs
Definition: REMORA.H:737
REMORA::ComputeDt
void ComputeDt()
Definition: REMORA_ComputeTimestep.cpp:8
REMORA::WriteGenericPlotfileHeaderWithBathymetry
void WriteGenericPlotfileHeaderWithBathymetry(std::ostream &HeaderFile, int nlevels, const amrex::Vector< amrex::BoxArray > &bArray, const amrex::Vector< std::string > &varnames, amrex::Real time, const amrex::Vector< int > &level_steps, const std::string &versionName, const std::string &levelPrefix, const std::string &mfPrefix) const
Definition: Plotfile.cpp:390
REMORA::writeBuildInfo
static void writeBuildInfo(std::ostream &os)
Definition: writeJobInfo.cpp:135
REMORA::init_custom
void init_custom(int lev)
Definition: REMORA_init.cpp:13
REMORA::ErrorEst
virtual void ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real time, int ngrow) override
Definition: REMORA_Tagging.cpp:15
REMORA::plot_file_1
std::string plot_file_1
Definition: REMORA.H:800
REMORA::getCPUTime
amrex::Real getCPUTime() const
Definition: REMORA.H:940
REMORA::InitData
void InitData()
Definition: REMORA.cpp:260
REMORA::istep
amrex::Vector< int > istep
Definition: REMORA.H:729
REMORA::t3dmix
void t3dmix(const amrex::Box &bx, const amrex::Array4< amrex::Real > &state, const amrex::Array4< amrex::Real const > &diff2, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Real dt_lev, const int ncomp)
Definition: REMORA_t3dmix.cpp:6
REMORA::setRecordDataInfo
void setRecordDataInfo(int i, const std::string &filename)
Definition: REMORA.H:954
REMORA::advance_3d_ml
void advance_3d_ml(int lev, amrex::Real dt_lev)
Definition: REMORA_advance_3d_ml.cpp:6
REMORA::DataLogName
const std::string DataLogName(int i) const noexcept
The filename of the ith datalog file.
Definition: REMORA.H:971
REMORA::d_havg_temperature
amrex::Gpu::DeviceVector< amrex::Real > d_havg_temperature
Definition: REMORA.H:872
REMORA::h_havg_pressure
amrex::Vector< amrex::Real > h_havg_pressure
Definition: REMORA.H:870
REMORA::DataLog
AMREX_FORCE_INLINE std::ostream & DataLog(int i)
Definition: REMORA.H:924
REMORA::vec_rhoS
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoS
Definition: REMORA.H:295
REMORA::vec_visc2_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_visc2_r
Definition: REMORA.H:220
REMORA::sst
amrex::Vector< std::unique_ptr< amrex::MultiFab > > sst
Definition: REMORA.H:745
REMORA::vec_svstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_svstr
Definition: REMORA.H:249
REMORA::vec_Huon
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Huon
Definition: REMORA.H:202
REMORA::REMORA
REMORA()
Definition: REMORA.cpp:61
REMORA::change_max
static amrex::Real change_max
Definition: REMORA.H:784
REMORA::WriteMultiLevelPlotfileWithBathymetry
void WriteMultiLevelPlotfileWithBathymetry(const std::string &plotfilename, int nlevels, const amrex::Vector< const amrex::MultiFab * > &mf, const amrex::Vector< const amrex::MultiFab * > &mf_nd, const amrex::Vector< std::string > &varnames, amrex::Real time, const amrex::Vector< int > &level_steps, const std::string &versionName="HyperCLaw-V1.1", const std::string &levelPrefix="Level_", const std::string &mfPrefix="Cell", const amrex::Vector< std::string > &extra_dirs=amrex::Vector< std::string >()) const
Definition: Plotfile.cpp:305
REMORA::FillCoarsePatch
void FillCoarsePatch(int lev, amrex::Real time, amrex::MultiFab *mf_fine, amrex::MultiFab *mf_crse)
Definition: REMORA_FillPatch.cpp:176
REMORA::pp_prefix
std::string pp_prefix
Definition: REMORA.H:181
REMORA::set_bathymetry
void set_bathymetry(int lev)
Definition: REMORA.cpp:372
REMORA::use_tracer_particles
static bool use_tracer_particles
Definition: REMORA.H:832
REMORA::initHSE
void initHSE()
Initialize HSE.
REMORA::yvel_old
amrex::Vector< amrex::MultiFab * > yvel_old
Definition: REMORA.H:185
REMORA::init_stuff
void init_stuff(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)
Definition: REMORA_make_new_level.cpp:191
REMORA::GetDataAtTime
TimeInterpolatedData GetDataAtTime(int lev, amrex::Real time)
Definition: REMORA_FillPatch.cpp:115
REMORA::Advance
void Advance(int lev, amrex::Real time, amrex::Real dt_lev, int iteration, int ncycle)
Definition: REMORA_Advance.cpp:7
REMORA::vec_rhoA
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rhoA
Definition: REMORA.H:296
REMORA::d_havg_pressure
amrex::Gpu::DeviceVector< amrex::Real > d_havg_pressure
Definition: REMORA.H:873
REMORA::vec_DV_avg1
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_DV_avg1
Definition: REMORA.H:265
REMORA::h_havg_density
amrex::Vector< amrex::Real > h_havg_density
Definition: REMORA.H:868
REMORA::last_plot_file_step_1
int last_plot_file_step_1
Definition: REMORA.H:765
REMORA::mapfac_v
amrex::Vector< std::unique_ptr< amrex::MultiFab > > mapfac_v
Definition: REMORA.H:743
REMORA::advflux_reg
amrex::Vector< amrex::YAFluxRegister * > advflux_reg
Definition: REMORA.H:748
REMORA::t_new
amrex::Vector< amrex::Real > t_new
Definition: REMORA.H:733
REMORA::d_havg_density
amrex::Gpu::DeviceVector< amrex::Real > d_havg_density
Definition: REMORA.H:871
REMORA::solverChoice
static SolverChoice solverChoice
Definition: REMORA.H:822
REMORA::resize_stuff
void resize_stuff(int lev)
Definition: REMORA_make_new_level.cpp:137
REMORA::ReadParameters
void ReadParameters()
Definition: REMORA.cpp:484
REMORA::vec_visc3d_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_visc3d_r
Definition: REMORA.H:293
REMORA::vec_ru
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ru
Definition: REMORA.H:206
REMORA::sum_integrated_quantities
void sum_integrated_quantities(amrex::Real time)
Definition: REMORA_SumIQ.cpp:9
REMORA::vec_weight1
amrex::Vector< amrex::Real > vec_weight1
Definition: REMORA.H:298
REMORA::fill_from_bdyfiles
void fill_from_bdyfiles(amrex::MultiFab &mf_to_fill, const amrex::Real time, const int bdy_var_type)
REMORA::prestep
void prestep(int lev, amrex::MultiFab &mf_uold, amrex::MultiFab &mf_vold, amrex::MultiFab &mf_u, amrex::MultiFab &mf_v, amrex::MultiFab *mf_ru, amrex::MultiFab *mf_rv, amrex::MultiFab &S_old, amrex::MultiFab &S_new, amrex::MultiFab &mf_W, amrex::MultiFab &mf_DC, const amrex::MultiFab *mf_z_r, const amrex::MultiFab *mf_z_w, const amrex::MultiFab *mf_h, const amrex::MultiFab *mf_pm, const amrex::MultiFab *mf_pn, const amrex::MultiFab *mf_sustr, const amrex::MultiFab *mf_svstr, const amrex::MultiFab *mf_bustr, const amrex::MultiFab *mf_bvstr, const int iic, const int nfirst, const int nnew, int nstp, int nrhs, int N, const amrex::Real dt_lev)
Definition: REMORA_prestep.cpp:34
REMORA::vec_zeta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_zeta
Definition: REMORA.H:279
REMORA::vec_vbar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_vbar
Definition: REMORA.H:277
REMORA::vec_y_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_y_r
Definition: REMORA.H:228
REMORA::vec_DU_avg1
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_DU_avg1
Definition: REMORA.H:261
REMORA::plot_file_on_restart
int plot_file_on_restart
Definition: REMORA.H:769
REMORA::set_2darrays
void set_2darrays(int lev)
Definition: REMORA_init.cpp:82
REMORA::vec_ubar
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_ubar
Definition: REMORA.H:275
REMORA::fill_rhs
void fill_rhs(amrex::MultiFab &rhs_mf, const amrex::MultiFab &state_mf, const amrex::Real time, const amrex::Geometry &geom)
REMORA::InitializeLevelFromData
void InitializeLevelFromData(int lev, const amrex::MultiFab &initial_data)
REMORA::cons_old
amrex::Vector< amrex::MultiFab * > cons_old
Definition: REMORA.H:183
REMORA::vec_bustr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bustr
Definition: REMORA.H:255
REMORA::NumDataLogs
AMREX_FORCE_INLINE int NumDataLogs() noexcept
Definition: REMORA.H:931
REMORA::volWgtSumMF
amrex::Real volWgtSumMF(int lev, const amrex::MultiFab &mf, int comp, bool local, bool finemask)
Definition: REMORA_SumIQ.cpp:89
REMORA::vert_visc_3d
void vert_visc_3d(const amrex::Box &bx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &phi, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real > &Hzk, const amrex::Array4< amrex::Real > &AK, const amrex::Array4< amrex::Real > &Akv, const amrex::Array4< amrex::Real > &BC, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real > &CF, const int nnew, const int N, const amrex::Real dt_lev)
Definition: REMORA_vert_visc_3d.cpp:10
REMORA::is_it_time_for_action
bool is_it_time_for_action(int nstep, amrex::Real time, amrex::Real dt, int action_interval, amrex::Real action_per)
Definition: REMORA_SumIQ.cpp:143
REMORA::PlotFileName
std::string PlotFileName(int lev) const
REMORA::vec_DV_avg2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_DV_avg2
Definition: REMORA.H:267
REMORA::set_hmixcoef
void set_hmixcoef(int lev)
Definition: REMORA.cpp:427
REMORA::domain_bc_type
amrex::Array< std::string, 2 *AMREX_SPACEDIM > domain_bc_type
Definition: REMORA.H:757
REMORA::column_file_name
static std::string column_file_name
Definition: REMORA.H:857
REMORA::estTimeStep
amrex::Real estTimeStep(int lev) const
Definition: REMORA_ComputeTimestep.cpp:40
REMORA::vec_bvstr
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_bvstr
Definition: REMORA.H:258
REMORA::timeStep
void timeStep(int lev, amrex::Real time, int iteration)
Definition: REMORA_TimeStep.cpp:9
REMORA::vec_rzeta
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rzeta
Definition: REMORA.H:273
REMORA::vec_z_phys_nd
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_phys_nd
Definition: REMORA.H:240
REMORA::AverageDown
void AverageDown()
Definition: REMORA.cpp:631
REMORA::fixed_ndtfast_ratio
static int fixed_ndtfast_ratio
Definition: REMORA.H:789
REMORA::update_massflux_3d
void update_massflux_3d(const amrex::Box &bx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &phi, const amrex::Array4< amrex::Real > &phibar, const amrex::Array4< amrex::Real > &Hphi, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm_or_pn, const amrex::Array4< amrex::Real const > &Dphi1, const amrex::Array4< amrex::Real const > &Dphi2, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &FC, const int nnew)
Definition: REMORA_update_massflux_3d.cpp:23
REMORA::timeStepML
void timeStepML(amrex::Real time, int iteration)
Definition: REMORA_TimeStepML.cpp:9
REMORA::input_bndry_planes
static int input_bndry_planes
Definition: REMORA.H:866
REMORA::set_weights
void set_weights(int lev)
Definition: REMORA_set_weights.cpp:10
REMORA::output_1d_column
static int output_1d_column
Definition: REMORA.H:852
REMORA::vec_pn
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_pn
Definition: REMORA.H:285
REMORA::datalog
amrex::Vector< std::unique_ptr< std::fstream > > datalog
Definition: REMORA.H:967
REMORA::vec_Akv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Akv
Definition: REMORA.H:214
REMORA::cfl
static amrex::Real cfl
Definition: REMORA.H:782
REMORA::post_update
void post_update(amrex::MultiFab &state_mf, const amrex::Real time, const amrex::Geometry &geom)
REMORA::MakeNewLevelFromScratch
virtual void MakeNewLevelFromScratch(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: REMORA_make_new_level.cpp:102
REMORA::verbose
static int verbose
Definition: REMORA.H:829
REMORA::setup_step
void setup_step(int lev, amrex::Real time, amrex::Real dt_lev)
Definition: REMORA_setup_step.cpp:7
REMORA::phys_bc_type
amrex::GpuArray< REMORA_BC, AMREX_SPACEDIM *2 > phys_bc_type
Definition: REMORA.H:763
REMORA::initRayleigh
void initRayleigh()
Initialize Rayleigh damping profiles.
REMORA::vec_rdrag
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rdrag
Definition: REMORA.H:252
REMORA::nc_bdry_file
static std::string nc_bdry_file
Definition: REMORA.H:846
REMORA::vec_Zt_avg1
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Zt_avg1
Definition: REMORA.H:243
REMORA::PlotFileVarNames
amrex::Vector< std::string > PlotFileVarNames(amrex::Vector< std::string > plot_var_names) const
Definition: Plotfile.cpp:87
REMORA::check_int
int check_int
Definition: REMORA.H:807
REMORA::restart_chkfile
std::string restart_chkfile
Definition: REMORA.H:779
REMORA::vec_rv
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_rv
Definition: REMORA.H:208
REMORA::derived_names
const amrex::Vector< std::string > derived_names
Definition: REMORA.H:817
REMORA::t_old
amrex::Vector< amrex::Real > t_old
Definition: REMORA.H:734
REMORA::FillPatch
void FillPatch(int lev, amrex::Real time, amrex::MultiFab &mf_to_be_filled, amrex::Vector< amrex::MultiFab * > const &mfs, const int bdy_var_type=BdyVars::null)
Definition: REMORA_FillPatch.cpp:16
REMORA::WriteCheckpointFile
void WriteCheckpointFile() const
Definition: Checkpoint.cpp:15
REMORA::rho_eos
void rho_eos(const amrex::Box &bx, const amrex::Array4< amrex::Real const > &state, const amrex::Array4< amrex::Real > &rho, const amrex::Array4< amrex::Real > &rhoA, const amrex::Array4< amrex::Real > &rhoS, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &h, const int N)
Definition: REMORA_rho_eos.cpp:20
REMORA::dt
amrex::Vector< amrex::Real > dt
Definition: REMORA.H:735
REMORA::sum_per
static amrex::Real sum_per
Definition: REMORA.H:836
REMORA::input_sounding_file
static std::string input_sounding_file
Definition: REMORA.H:849
REMORA::nc_grid_file
static amrex::Vector< amrex::Vector< std::string > > nc_grid_file
Definition: REMORA.H:843
REMORA::InitializeFromFile
void InitializeFromFile()
REMORA::coriolis
void coriolis(const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &fomn, int nrhs, int nr)
Definition: REMORA_coriolis.cpp:10
REMORA::bndry_output_planes_per
static amrex::Real bndry_output_planes_per
Definition: REMORA.H:862
REMORA::domain_bcs_type_d
amrex::Gpu::DeviceVector< amrex::BCRec > domain_bcs_type_d
Definition: REMORA.H:754
REMORA::~REMORA
virtual ~REMORA()
Definition: REMORA.cpp:136
REMORA::vec_z_w
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_z_w
Definition: REMORA.H:234
REMORA::nc_init_file
static amrex::Vector< amrex::Vector< std::string > > nc_init_file
Definition: REMORA.H:842
REMORA::restart
void restart()
Definition: REMORA.cpp:363
REMORA::prsgrd
void prsgrd(const amrex::Box &bx, const amrex::Box &gbx, const amrex::Box &utbx, const amrex::Box &vtbx, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &rho, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &z_w, const int nrhs, const int N)
Definition: REMORA_prsgrd.cpp:6
REMORA::column_per
static amrex::Real column_per
Definition: REMORA.H:854
REMORA::advance_3d
void advance_3d(int lev, amrex::MultiFab &mf_cons, amrex::MultiFab &mf_u, amrex::MultiFab &mf_v, amrex::MultiFab *mf_sstore, amrex::MultiFab *mf_ru, amrex::MultiFab *mf_rv, std::unique_ptr< amrex::MultiFab > &mf_DU_avg1, std::unique_ptr< amrex::MultiFab > &mf_DU_avg2, std::unique_ptr< amrex::MultiFab > &mf_DV_avg1, std::unique_ptr< amrex::MultiFab > &mf_DV_avg2, std::unique_ptr< amrex::MultiFab > &mf_ubar, std::unique_ptr< amrex::MultiFab > &mf_vbar, std::unique_ptr< amrex::MultiFab > &mf_Akv, std::unique_ptr< amrex::MultiFab > &mf_Akt, std::unique_ptr< amrex::MultiFab > &mf_Hz, std::unique_ptr< amrex::MultiFab > &mf_Huon, std::unique_ptr< amrex::MultiFab > &mf_Hvom, std::unique_ptr< amrex::MultiFab > &mf_z_w, amrex::MultiFab const *mf_h, amrex::MultiFab const *mf_pm, amrex::MultiFab const *mf_pn, const int N, const amrex::Real dt_lev)
Definition: REMORA_advance_3d.cpp:10
REMORA::vec_s_r
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_s_r
Definition: REMORA.H:237
REMORA::vec_Hvom
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_Hvom
Definition: REMORA.H:204
REMORA::vec_diff2
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vec_diff2
Definition: REMORA.H:222
REMORA::setPlotVariables
void setPlotVariables(const std::string &pp_plot_var_names, amrex::Vector< std::string > &plot_var_names)
Definition: Plotfile.cpp:9
ncutils::NCFile
Definition: NCInterface.H:285
BdyVars::u
@ u
Definition: IndexDefines.H:34
BdyVars::v
@ v
Definition: IndexDefines.H:35
BdyVars::null
@ null
Definition: IndexDefines.H:33
BdyVars::t
@ t
Definition: IndexDefines.H:36
InterpType
Definition: REMORA.H:50
InterpType::CellConservativeQuartic
@ CellConservativeQuartic
Definition: REMORA.H:58
InterpType::CellBilinear
@ CellBilinear
Definition: REMORA.H:55
InterpType::PCInterp
@ PCInterp
Definition: REMORA.H:52
InterpType::NodeBilinear
@ NodeBilinear
Definition: REMORA.H:53
InterpType::CellConservativeLinear
@ CellConservativeLinear
Definition: REMORA.H:54
InterpType::CellQuadratic
@ CellQuadratic
Definition: REMORA.H:56
InterpType::CellConservativeProtected
@ CellConservativeProtected
Definition: REMORA.H:57
ParticleData
Definition: ParticleData.H:19
SolverChoice
Definition: DataStruct.H:41
TimeInterpolatedData
Definition: TimeInterpolatedData.H:8