ERF
Energy Research and Forecasting: An Atmospheric Modeling Code
ERF.H
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1 #ifndef ERF_H_
2 #define ERF_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_Print.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 #include <AMReX_EBFabFactory.H>
25 #include <AMReX_EBMultiFabUtil.H>
26 
27 #include <ERF_EB.H>
28 
29 #ifdef ERF_USE_FFT
30 #include <AMReX_FFT_Poisson.H>
31 #endif
32 
33 #ifdef AMREX_MEM_PROFILING
34 #include <AMReX_MemProfiler.H>
35 #endif
36 
37 #include "ERF_ProbCommon.H"
38 
39 #include <ERF_IndexDefines.H>
40 #include <ERF_DataStruct.H>
41 #include <ERF_TurbPertStruct.H>
42 #include <ERF_InputSoundingData.H>
43 #include <ERF_InputSpongeData.H>
44 #include <ERF_SurfaceLayer.H>
45 #include <ERF_Derive.H>
46 #include <ERF_ReadBndryPlanes.H>
47 #include <ERF_WriteBndryPlanes.H>
48 #include <ERF_MRI.H>
49 #include <ERF_PhysBCFunct.H>
50 #include <ERF_FillPatcher.H>
51 #include <ERF_SampleData.H>
52 #include <ERF_ForestDrag.H>
53 
54 #ifdef ERF_USE_PARTICLES
55 #include "ERF_ParticleData.H"
56 #endif
57 
58 #include "ERF_EulerianMicrophysics.H"
59 #include "ERF_LagrangianMicrophysics.H"
60 #include "ERF_LandSurface.H"
61 
62 #ifdef ERF_USE_WINDFARM
63 #include "ERF_WindFarm.H"
64 #endif
65 
66 #include <ERF_RadiationModels.H>
67 
68 #ifdef ERF_USE_SHOC
69 #include "ERF_ShocInterface.H"
70 #endif
71 
72 #ifdef ERF_USE_P3
73 #include "ERF_P3Interface.H"
74 #endif
75 
76 #include <iostream>
77 
78 #ifdef AMREX_LAZY
79 #include <AMReX_Lazy.H>
80 #endif
81 
82 #ifndef AMREX_USE_MPI
83 using amrex::MPI_COMM_WORLD;
84 using amrex::MPI_Comm;
85 #endif
86 
87 #ifdef ERF_USE_MULTIBLOCK
88 class MultiBlockContainer;
89 #endif
90 
91 /**
92  * Enum of possible interpolation types between coarse/fine
93 */
94 AMREX_ENUM(StateInterpType,
95  FullState, Perturbational
96 );
97 
98 /**
99  * Enum of possible plotfile types
100 */
101 AMREX_ENUM(PlotFileType,
102  None, Amrex, Netcdf
103 );
104 
105 /**
106  * Main class in ERF code, instantiated from main.cpp
107 */
108 
109 class ERF
110  : public amrex::AmrCore
111 {
112 public:
113 
114  ////////////////
115  // public member functions
116 
117  // constructor - reads in parameters from inputs file
118  // - sizes multilevel arrays and data structures
119  ERF ();
120  ~ERF () override;
121 
122  void ERF_shared ();
123 
124  // Declare a default move constructor so we ensure the destructor is
125  // not called when we return an object of this class by value
126  ERF (ERF&&) noexcept = delete;
127 
128  // Declare a default move assignment operator
129  ERF& operator=(ERF&& other) noexcept = delete;
130 
131  // Delete the copy constructor
132  ERF (const ERF& other) = delete;
133  //
134  // Delete the copy assignment operator
135  ERF& operator=(const ERF& other) = delete;
136 
137  // Advance solution to final time
138  void Evolve ();
139 
140  // Tag cells for refinement
141  void ErrorEst (int lev, amrex::TagBoxArray& tags, amrex::Real time, int ngrow) override;
142 
143  // Refinement criteria for hurricanes
144  void HurricaneTracker (int lev,
145  amrex::Real time,
146  const amrex::MultiFab& U_new,
147  const amrex::MultiFab& V_new,
148  const amrex::MultiFab& W_new,
149  const amrex::Real velmag_threshold,
150  amrex::TagBoxArray* tags = nullptr);
151 
152  void HurricaneTrackerInitial (int lev,
153  const amrex::MultiFab& U_new,
154  const amrex::MultiFab& V_new,
155  const amrex::MultiFab& W_new,
156  const amrex::Real velmag_threshold,
157  amrex::TagBoxArray* tags = nullptr);
158 
159  void HurricaneTrackerNotInitial (int lev, amrex::TagBoxArray* tags = nullptr);
160 
161  // Hurricane track line output as VTKPolyline
162  amrex::Vector<std::array<amrex::Real, 2>> hurricane_track_xy;
163  amrex::Vector<std::array<amrex::Real, 2>> hurricane_eye_track_xy,
164  hurricane_eye_track_latlon,
165  hurricane_maxvel_vs_time,
166  hurricane_tracker_circle;
167  amrex::Vector<amrex::MultiFab> weather_forecast_data_1, weather_forecast_data_2;
168  amrex::Vector<amrex::Vector<amrex::MultiFab>> forecast_state_1,
169  forecast_state_2,
170  forecast_state_interp;
171  std::string MakeVTKFilename(int nstep);
172  std::string MakeVTKFilename_TrackerCircle(int nstep);
173  std::string MakeVTKFilename_EyeTracker_xy(int nstep);
174  std::string MakeFilename_EyeTracker_latlon(int nstep);
175  std::string MakeFilename_EyeTracker_maxvel(int nstep);
176  void WriteVTKPolyline(const std::string& filename,
177  amrex::Vector<std::array<amrex::Real, 2>>& points_xy);
178 
179  void WriteLinePlot(const std::string& filename,
180  amrex::Vector<std::array<amrex::Real, 2>>& points_xy);
181 
182  // Initialize multilevel data
183  void InitData ();
184 
185  // Initialize multilevel data before MultiBlock
186  void InitData_pre ();
187 
188  // Initialize multilevel data after MultiBlock
189  void InitData_post ();
190 
191  void WriteMyEBSurface ();
192 
193  // Compute the divergence -- whether EB, no-terrain, flat terrain or general terrain
194  void compute_divergence (int lev, amrex::MultiFab& rhs, amrex::Array<amrex::MultiFab const*,AMREX_SPACEDIM> rho0_u_const,
195  amrex::Geometry const& geom_at_lev);
196 
197  // Project the velocities to be divergence-free -- this is only relevant if anelastic == 1
198  void project_velocity (int lev, amrex::Real dt);
199  void project_momenta (int lev, amrex::Real dt, amrex::Vector<amrex::MultiFab >& vars);
200 
201  // Project the velocities to be divergence-free with a thin body
202  void project_velocity_tb (int lev, amrex::Real dt, amrex::Vector<amrex::MultiFab >& vars);
203 
204  // Calculate wall distance by solving a Poisson equation
205  void poisson_wall_dist (int lev);
206 
207  void make_subdomains(const amrex::BoxList& ba, amrex::Vector<amrex::BoxArray>& bins);
208 
209 #ifdef ERF_USE_FFT
210  void solve_with_fft (int lev, const amrex::Box& subdomain,
211  amrex::MultiFab& rhs, amrex::MultiFab& p,
212  amrex::Array<amrex::MultiFab,AMREX_SPACEDIM>& fluxes);
213 #endif
214  void solve_with_EB_mlmg (int lev, amrex::Vector<amrex::MultiFab>& rhs, amrex::Vector<amrex::MultiFab>& p,
215  amrex::Vector<amrex::Array<amrex::MultiFab,AMREX_SPACEDIM>>& fluxes);
216 
217  void solve_with_gmres (int lev, const amrex::Box& subdomain,
218  amrex::MultiFab& rhs, amrex::MultiFab& p,
219  amrex::Array<amrex::MultiFab,AMREX_SPACEDIM>& fluxes,
220  amrex::MultiFab& ax_sub, amrex::MultiFab& ay_sub,
221  amrex::MultiFab& az_sub,
222  amrex::MultiFab& /*dJ_sub*/, amrex::MultiFab& znd_sub);
223 
224  void solve_with_mlmg (int lev, amrex::Vector<amrex::MultiFab>& rhs, amrex::Vector<amrex::MultiFab>& p,
225  amrex::Vector<amrex::Array<amrex::MultiFab,AMREX_SPACEDIM>>& fluxes);
226 
227  void ImposeBCsOnPhi (int lev, amrex::MultiFab& phi, const amrex::Box& subdomain);
228 
229  // Define the projection bc's based on the domain bc types
230  amrex::Array<amrex::LinOpBCType,AMREX_SPACEDIM>
231  get_projection_bc (amrex::Orientation::Side side) const noexcept;
232  bool projection_has_dirichlet (amrex::Array<amrex::LinOpBCType,AMREX_SPACEDIM> bcs) const;
233 
234  // Init (NOT restart or regrid)
235  void init_only (int lev, amrex::Real time);
236 
237  // Restart
238  void restart ();
239 
240  // Check for NaNs and other bad stuff
241  void check_state_for_nans(amrex::MultiFab const& S);
242  void check_vels_for_nans(amrex::MultiFab const& xvel, amrex::MultiFab const& yvel, amrex::MultiFab const& zvel);
243  void check_for_negative_theta (amrex::MultiFab& S);
244  void check_for_low_temp (amrex::MultiFab& S);
245 
246  // Is it time to write a plotfile or checkpoint?
247  bool writeNow (const amrex::Real cur_time, const int nstep, const int plot_int,
248  const amrex::Real plot_per, const amrex::Real dt_0, amrex::Real& last_file_time);
249 
250  // Called after every level 0 timestep
251  void post_timestep (int nstep, amrex::Real time, amrex::Real dt_lev);
252 
253  // Diagnostics
254  void sum_integrated_quantities (amrex::Real time);
255  void sum_derived_quantities (amrex::Real time);
256  void sum_energy_quantities (amrex::Real time);
257 
258  void write_1D_profiles (amrex::Real time);
259  void write_1D_profiles_stag (amrex::Real time);
260 
261  amrex::Real cloud_fraction (amrex::Real time);
262 
263  // Fill the physical boundary conditions for cell-centered velocity (diagnostic only)
264  void FillBdyCCVels (amrex::Vector<amrex::MultiFab>& mf_cc_vel, int levc=0);
265 
266  void sample_points (int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab& mf);
267  void sample_lines (int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab& mf);
268 
269  void derive_diag_profiles (amrex::Real time,
270  amrex::Gpu::HostVector<amrex::Real>& h_avg_u , amrex::Gpu::HostVector<amrex::Real>& h_avg_v,
271  amrex::Gpu::HostVector<amrex::Real>& h_avg_w , amrex::Gpu::HostVector<amrex::Real>& h_avg_rho,
272  amrex::Gpu::HostVector<amrex::Real>& h_avg_th , amrex::Gpu::HostVector<amrex::Real>& h_avg_ksgs,
273  amrex::Gpu::HostVector<amrex::Real>& h_avg_Kmv , amrex::Gpu::HostVector<amrex::Real>& h_avg_Khv,
274  amrex::Gpu::HostVector<amrex::Real>& h_avg_qv , amrex::Gpu::HostVector<amrex::Real>& h_avg_qc,
275  amrex::Gpu::HostVector<amrex::Real>& h_avg_qr ,
276  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqv , amrex::Gpu::HostVector<amrex::Real>& h_avg_wqc,
277  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqr ,
278  amrex::Gpu::HostVector<amrex::Real>& h_avg_qi , amrex::Gpu::HostVector<amrex::Real>& h_avg_qs,
279  amrex::Gpu::HostVector<amrex::Real>& h_avg_qg ,
280  amrex::Gpu::HostVector<amrex::Real>& h_avg_uu , amrex::Gpu::HostVector<amrex::Real>& h_avg_uv,
281  amrex::Gpu::HostVector<amrex::Real>& h_avg_uw,
282  amrex::Gpu::HostVector<amrex::Real>& h_avg_vv , amrex::Gpu::HostVector<amrex::Real>& h_avg_vw,
283  amrex::Gpu::HostVector<amrex::Real>& h_avg_ww,
284  amrex::Gpu::HostVector<amrex::Real>& h_avg_uth , amrex::Gpu::HostVector<amrex::Real>& h_avg_vth,
285  amrex::Gpu::HostVector<amrex::Real>& h_avg_wth, amrex::Gpu::HostVector<amrex::Real>& h_avg_thth,
286  amrex::Gpu::HostVector<amrex::Real>& h_avg_ku, amrex::Gpu::HostVector<amrex::Real>& h_avg_kv,
287  amrex::Gpu::HostVector<amrex::Real>& h_avg_kw,
288  amrex::Gpu::HostVector<amrex::Real>& h_avg_p,
289  amrex::Gpu::HostVector<amrex::Real>& h_avg_pu, amrex::Gpu::HostVector<amrex::Real>& h_avg_pv,
290  amrex::Gpu::HostVector<amrex::Real>& h_avg_pw, amrex::Gpu::HostVector<amrex::Real>& h_avg_wthv);
291  void derive_diag_profiles_stag (amrex::Real time,
292  amrex::Gpu::HostVector<amrex::Real>& h_avg_u , amrex::Gpu::HostVector<amrex::Real>& h_avg_v,
293  amrex::Gpu::HostVector<amrex::Real>& h_avg_w , amrex::Gpu::HostVector<amrex::Real>& h_avg_rho,
294  amrex::Gpu::HostVector<amrex::Real>& h_avg_th , amrex::Gpu::HostVector<amrex::Real>& h_avg_ksgs,
295  amrex::Gpu::HostVector<amrex::Real>& h_avg_Kmv , amrex::Gpu::HostVector<amrex::Real>& h_avg_Khv,
296  amrex::Gpu::HostVector<amrex::Real>& h_avg_qv , amrex::Gpu::HostVector<amrex::Real>& h_avg_qc,
297  amrex::Gpu::HostVector<amrex::Real>& h_avg_qr ,
298  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqv , amrex::Gpu::HostVector<amrex::Real>& h_avg_wqc,
299  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqr ,
300  amrex::Gpu::HostVector<amrex::Real>& h_avg_qi , amrex::Gpu::HostVector<amrex::Real>& h_avg_qs,
301  amrex::Gpu::HostVector<amrex::Real>& h_avg_qg ,
302  amrex::Gpu::HostVector<amrex::Real>& h_avg_uu , amrex::Gpu::HostVector<amrex::Real>& h_avg_uv,
303  amrex::Gpu::HostVector<amrex::Real>& h_avg_uw,
304  amrex::Gpu::HostVector<amrex::Real>& h_avg_vv , amrex::Gpu::HostVector<amrex::Real>& h_avg_vw,
305  amrex::Gpu::HostVector<amrex::Real>& h_avg_ww,
306  amrex::Gpu::HostVector<amrex::Real>& h_avg_uth , amrex::Gpu::HostVector<amrex::Real>& h_avg_vth,
307  amrex::Gpu::HostVector<amrex::Real>& h_avg_wth, amrex::Gpu::HostVector<amrex::Real>& h_avg_thth,
308  amrex::Gpu::HostVector<amrex::Real>& h_avg_ku, amrex::Gpu::HostVector<amrex::Real>& h_avg_kv,
309  amrex::Gpu::HostVector<amrex::Real>& h_avg_kw,
310  amrex::Gpu::HostVector<amrex::Real>& h_avg_p,
311  amrex::Gpu::HostVector<amrex::Real>& h_avg_pu, amrex::Gpu::HostVector<amrex::Real>& h_avg_pv,
312  amrex::Gpu::HostVector<amrex::Real>& h_avg_pw, amrex::Gpu::HostVector<amrex::Real>& h_avg_wthv);
313 
314  void derive_stress_profiles (amrex::Gpu::HostVector<amrex::Real>& h_avg_tau11, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau12,
315  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau13, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau22,
316  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau23, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau33,
317  amrex::Gpu::HostVector<amrex::Real>& h_avg_hfx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_q1fx3,
318  amrex::Gpu::HostVector<amrex::Real>& h_avg_q2fx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_diss);
319  void derive_stress_profiles_stag (amrex::Gpu::HostVector<amrex::Real>& h_avg_tau11, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau12,
320  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau13, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau22,
321  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau23, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau33,
322  amrex::Gpu::HostVector<amrex::Real>& h_avg_hfx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_q1fx3,
323  amrex::Gpu::HostVector<amrex::Real>& h_avg_q2fx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_diss);
324 
325  // Perform the volume-weighted sum
326  amrex::Real
327  volWgtSumMF (int lev, const amrex::MultiFab& mf, int comp,
328  const amrex::MultiFab& dJ, const amrex::MultiFab& mfx, const amrex::MultiFab& mfy,
329  bool finemask, bool local = true);
330 
331  // Decide if it is time to take an action
332  static bool is_it_time_for_action (int nstep, amrex::Real time, amrex::Real dt,
333  int action_interval, amrex::Real action_per);
334 
335  // Make a new level using provided BoxArray and DistributionMapping and
336  // fill with interpolated coarse level data.
337  // overrides the pure virtual function in AmrCore
338  void MakeNewLevelFromCoarse (int lev, amrex::Real time, const amrex::BoxArray& ba,
339  const amrex::DistributionMapping& dm) override;
340 
341  // Remake an existing level using provided BoxArray and DistributionMapping and
342  // fill with existing fine and coarse data.
343  // overrides the pure virtual function in AmrCore
344  void RemakeLevel (int lev, amrex::Real time, const amrex::BoxArray& ba,
345  const amrex::DistributionMapping& dm) override;
346 
347  // Delete level data
348  // overrides the pure virtual function in AmrCore
349  void ClearLevel (int lev) override;
350 
351  // Make a new level from scratch using provided BoxArray and DistributionMapping.
352  // Only used during initialization.
353  // overrides the pure virtual function in AmrCore
354  void MakeNewLevelFromScratch (int lev, amrex::Real time, const amrex::BoxArray& ba,
355  const amrex::DistributionMapping& dm) override;
356 
357  // compute dt from CFL considerations
358  amrex::Real estTimeStep (int lev, long& dt_fast_ratio) const;
359 
360 #ifdef ERF_USE_WW3_COUPLING
361  //amrex::Print() << " About to call send_to_ww3 from ERF.H" << std::endl;
362  void send_to_ww3(int lev);
363  //amrex::Print() << " About to call read_waves from ERF.H" << std::endl;
364  void read_waves(int lev);
365  //void send_to_ww3 (int lev);
366  //void read_waves (int lev);
367 
368  //void send_to_ww3 (int lev);
369 #endif
370 
371  // Interface for advancing the data at one level by one "slow" timestep
372  void advance_dycore (int level,
373  amrex::Vector<amrex::MultiFab>& state_old,
374  amrex::Vector<amrex::MultiFab>& state_new,
375  amrex::MultiFab& xvel_old, amrex::MultiFab& yvel_old, amrex::MultiFab& zvel_old,
376  amrex::MultiFab& xvel_new, amrex::MultiFab& yvel_new, amrex::MultiFab& zvel_new,
377  amrex::MultiFab& source, amrex::MultiFab& xmom_src,
378  amrex::MultiFab& ymom_src, amrex::MultiFab& zmom_src,
379  amrex::MultiFab& buoyancy, amrex::Geometry fine_geom,
380  amrex::Real dt, amrex::Real time);
381 
382  void advance_microphysics (int lev,
383  amrex::MultiFab& cons_in,
384  const amrex::Real& dt_advance,
385  const int& iteration,
386  const amrex::Real& time);
387 
388  void advance_lsm (int lev,
389  amrex::MultiFab& cons_in,
390  amrex::MultiFab& xvel_in,
391  amrex::MultiFab& yvel_in,
392  const amrex::Real& dt_advance);
393 
394  void advance_radiation (int lev,
395  amrex::MultiFab& cons_in,
396  const amrex::Real& dt_advance);
397 
398 #ifdef ERF_USE_SHOC
399  void compute_shoc_tendencies (int lev,
400  amrex::MultiFab* cons,
401  amrex::MultiFab* xvel,
402  amrex::MultiFab* yvel,
403  amrex::MultiFab* zvel,
404  amrex::Real* w_subsid,
405  amrex::MultiFab* tau13,
406  amrex::MultiFab* tau23,
407  amrex::MultiFab* hfx3,
408  amrex::MultiFab* qfx3,
409  amrex::MultiFab* eddyDiffs,
410  amrex::MultiFab* z_phys_nd,
411  const amrex::Real& dt_advance);
412 #endif
413 
414 #ifdef ERF_USE_P3
415  void compute_p3_tendencies (int lev,
416  amrex::MultiFab& cons_in,
417  amrex::MultiFab& source,
418  const amrex::Real& dt_advance);
419 #endif
420 
421  void build_fine_mask (int lev, amrex::MultiFab& fine_mask);
422 
423  void MakeHorizontalAverages ();
424  void MakeDiagnosticAverage (amrex::Vector<amrex::Real>& h_havg, amrex::MultiFab& S, int n);
425  void derive_upwp (amrex::Vector<amrex::Real>& h_havg);
426 
427  // Write plotfile to disk
428  void Write3DPlotFile (int which, PlotFileType plotfile_type, amrex::Vector<std::string> plot_var_names);
429  void Write2DPlotFile (int which, PlotFileType plotfile_type, amrex::Vector<std::string> plot_var_names);
430 
431  // Write subvolume of data into a different "plotfile"
432  void WriteSubvolume (int isub, amrex::Vector<std::string> subvol_var_names);
433 
434  void WriteMultiLevelPlotfileWithTerrain (const std::string &plotfilename,
435  int nlevels,
436  const amrex::Vector<const amrex::MultiFab*> &mf,
437  const amrex::Vector<const amrex::MultiFab*> &mf_nd,
438  const amrex::Vector<std::string> &varnames,
439  const amrex::Vector<amrex::Geometry>& my_geom,
440  amrex::Real time,
441  const amrex::Vector<int> &level_steps,
442  const amrex::Vector<amrex::IntVect>& my_ref_ratio,
443  const std::string &versionName = "HyperCLaw-V1.1",
444  const std::string &levelPrefix = "Level_",
445  const std::string &mfPrefix = "Cell",
446  const amrex::Vector<std::string>& extra_dirs = amrex::Vector<std::string>()) const;
447 
448 
449  void WriteGenericPlotfileHeaderWithTerrain (std::ostream &HeaderFile,
450  int nlevels,
451  const amrex::Vector<amrex::BoxArray> &bArray,
452  const amrex::Vector<std::string> &varnames,
453  const amrex::Vector<amrex::Geometry>& my_geom,
454  amrex::Real time,
455  const amrex::Vector<int> &level_steps,
456  const amrex::Vector<amrex::IntVect>& my_ref_ratio,
457  const std::string &versionName,
458  const std::string &levelPrefix,
459  const std::string &mfPrefix) const;
460 
461  void erf_enforce_hse (int lev,
462  amrex::MultiFab& dens, amrex::MultiFab& pres, amrex::MultiFab& pi,
463  amrex::MultiFab& th, amrex::MultiFab& qv,
464  std::unique_ptr<amrex::MultiFab>& z_cc);
465 
466 #ifdef ERF_USE_NETCDF
467  //! Write a timestep to 1D vertical column output for coupling
468  void writeToNCColumnFile (int lev,
469  const std::string& colfile_name, amrex::Real xloc, amrex::Real yloc,
470  amrex::Real time);
471 #endif //ERF_USE_NETCDF
472 
473  void init_from_input_sounding (int lev);
474 
475  void init_immersed_forcing (int lev);
476 
477  void input_sponge (int lev);
478 
479  void init_from_hse (int lev);
480 
481  void init_thin_body (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm);
482 
483  void FillForecastStateMultiFabs(const int lev,
484  const std::string& filename,
485  const std::unique_ptr<amrex::MultiFab>& z_phys_nd,
486  amrex::Vector<amrex::Vector<amrex::MultiFab>>& weather_forecast_data);
487 
488  void WeatherDataInterpolation(const int nlevs,
489  const amrex::Real time,
490  amrex::Vector<std::unique_ptr<amrex::MultiFab>>& z_phys_nd,
491  bool regrid_forces_file_read);
492 
493 #ifdef ERF_USE_MULTIBLOCK
494  // constructor used when ERF is created by a multiblock driver
495  // calls AmrCore constructor -> AmrMesh constructor
496  ERF (const amrex::RealBox& rb, int max_level_in,
497  const amrex::Vector<int>& n_cell_in, int coord,
498  const amrex::Vector<amrex::IntVect>& ref_ratio,
499  const amrex::Array<int,AMREX_SPACEDIM>& is_per,
500  std::string prefix);
501 
502  // Advance a block specified number of time steps
503  void Evolve_MB (int MBstep, int max_block_step);
504 
505  // get the current time values and dt
506  amrex::Real get_t_old (int lev) { return t_old[lev]; }
507  amrex::Real get_t_new (int lev) { return t_new[lev]; }
508  amrex::Real get_dt (int lev) { return dt[lev]; }
509 
510  // Set parmparse prefix for MultiBlock
511  void SetParmParsePrefix (std::string name) { pp_prefix = name; }
512 
513  // Set 'this' from multiblock container
514  void SetMultiBlockPointer (MultiBlockContainer *mbc) { m_mbc = mbc; }
515 
516  // Public data copy for MB
517  std::vector<amrex::Box> domain_p;
518 
519  // Primary solution data data containers
520  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_new;
521  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_old;
522 
523  // Velocity time averaged field
524  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vel_t_avg;
525  amrex::Vector<amrex::Real> t_avg_cnt;
526 #endif
527 
528  std::string pp_prefix {"erf"};
529 
530  void fill_from_bndryregs (const amrex::Vector<amrex::MultiFab*>& mfs,
531  amrex::Real time);
532 
533 #ifdef ERF_USE_NETCDF
534  // Version in which we always set the velocity values but don't set theta
535  void fill_from_realbdy (const amrex::Vector<amrex::MultiFab*>& mfs,
536  amrex::Real time,
537  bool cons_only,
538  int icomp_cons,
539  int ncomp_cons,
540  amrex::IntVect ngvect_cons,
541  amrex::IntVect ngvect_vels);
542 
543  // Version in which we only set the boundary value if inflowing, includes theta
544  void fill_from_realbdy_upwind (const amrex::Vector<amrex::MultiFab*>& mfs,
545  amrex::Real time,
546  bool cons_only,
547  int icomp_cons,
548  int ncomp_cons,
549  amrex::IntVect ngvect_cons,
550  amrex::IntVect ngvect_vels);
551 #endif
552 
553 #ifdef ERF_USE_NETCDF
554  void init_from_wrfinput (int lev,
555  amrex::MultiFab& mf_C1H,
556  amrex::MultiFab& mf_C2H,
557  amrex::MultiFab& mf_MUB,
558  amrex::MultiFab& mf_PSFC);
559  void init_from_metgrid (int lev);
560  void init_from_ncfile (int lev);
561 #endif // ERF_USE_NETCDF
562 
563 #ifdef ERF_USE_WINDFARM
564  void init_windfarm(int lev);
565  void advance_windfarm (const amrex::Geometry& a_geom,
566  const amrex::Real& dt_advance,
567  amrex::MultiFab& cons_in,
568  amrex::MultiFab& U_old, amrex::MultiFab& V_old, amrex::MultiFab& W_old,
569  amrex::MultiFab& mf_vars_windfarm,
570  const amrex::MultiFab& mf_Nturb,
571  const amrex::MultiFab& mf_SMark,
572  const amrex::Real& time);
573 #endif
574 
575  void MakeEBGeometry ();
576  void make_eb_box ();
577  void make_eb_regular ();
578 
579  // more flexible version of AverageDown() that lets you average down across multiple levels
580  void AverageDownTo (int crse_lev, int scomp, int ncomp); // NOLINT
581 
582  // write checkpoint file to disk
583  void WriteCheckpointFile () const;
584 
585  // read checkpoint file from disk
586  void ReadCheckpointFile ();
587 
588  // read checkpoint file from disk -- called after instantiating m_SurfaceLayer
589  void ReadCheckpointFileSurfaceLayer ();
590 
591  void init_zphys (int lev, amrex::Real time);
592  void remake_zphys (int lev, amrex::Real time, std::unique_ptr<amrex::MultiFab>& temp_zphys_nd);
593  void update_terrain_arrays (int lev);
594 
595 private:
596 
597  ///////////////////////////
598  // private member functions
599  ///////////////////////////
600 
601  // read in some parameters from inputs file
602  void ReadParameters ();
603  void ParameterSanityChecks ();
604 
605  // set covered coarse cells/faces to be the average of overlying fine cells/faces
606  void AverageDown ();
607 
608  void update_diffusive_arrays (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm);
609 
610  void Construct_ERFFillPatchers (int lev);
611 
612  void Define_ERFFillPatchers (int lev);
613 
614  void init1DArrays ();
615 
616  void init_bcs ();
617 
618  void init_custom (int lev);
619 
620  void init_uniform (int lev);
621 
622  void init_stuff (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm,
623  amrex::Vector<amrex::MultiFab>& lev_new, amrex::Vector<amrex::MultiFab>& lev_old,
624  amrex::MultiFab& tmp_base_state,
625  std::unique_ptr<amrex::MultiFab>& tmp_zphys_nd);
626 
627  // Initialize the Turbulent perturbation
628  void turbPert_update (const int lev, const amrex::Real dt);
629  void turbPert_amplitude (const int lev);
630 
631  // Initialize the integrator object
632  void initialize_integrator (int lev, amrex::MultiFab& cons_mf, amrex::MultiFab& vel_mf);
633 
634  // Create the physbcs objects
635  void make_physbcs (int lev);
636 
637  // Initialize the microphysics object
638  void initializeMicrophysics (const int&);
639 
640 #ifdef ERF_USE_WINDFARM
641  // Initialize the windfarm object
642  void initializeWindFarm (const int&);
643 #endif
644 
645  // Compute a vector of new MultiFabs by copying from valid region and filling ghost cells
646  //
647  // NOTE: FillPatch takes in an empty MF, and returns cell-centered + velocities (not momenta)
648  //
649  // This one works only at level = 0 (base state does not change)
650  void FillPatchCrseLevel (int lev, amrex::Real time,
651  const amrex::Vector<amrex::MultiFab*>& mfs_vel,
652  bool cons_only=false);
653 
654  // This one works only at level > 0 (base state does change)
655  void FillPatchFineLevel (int lev, amrex::Real time,
656  const amrex::Vector<amrex::MultiFab*>& mfs_vel,
657  const amrex::Vector<amrex::MultiFab*>& mfs_mom,
658  const amrex::MultiFab& old_base_state,
659  const amrex::MultiFab& new_base_state,
660  bool fillset=true, bool cons_only=false);
661 
662  // Compute new multifabs by copying data from valid region and filling ghost cells.
663  // Unlike FillPatch, FillIntermediatePatch will use the supplied multifabs instead of fine level data.
664  // This is to support filling boundary cells at an intermediate time between old/new times
665  // on the fine level when valid data at a specific time is already available (such as
666  // at each RK stage when integrating between initial and final times at a given level).
667  //
668  // NOTE: FillIntermediatePatch takes in updated momenta, and returns both updated velocity and momenta
669  //
670  void FillIntermediatePatch (int lev, amrex::Real time,
671  const amrex::Vector<amrex::MultiFab*>& mfs_vel,
672  const amrex::Vector<amrex::MultiFab*>& mfs_mom,
673  int ng_cons, int ng_vel, bool cons_only, int icomp_cons, int ncomp_cons);
674 
675  // Fill all multifabs (and all components) in a vector of multifabs corresponding to the
676  // grid variables defined in vars_old and vars_new just as FillCoarsePatch.
677  void FillCoarsePatch (int lev, amrex::Real time);
678 
679  // advance a level by dt
680  // includes a recursive call for finer levels
681  void timeStep (int lev, amrex::Real time, int iteration);
682 
683  // advance a single level for a single time step
684  void Advance (int lev, amrex::Real time, amrex::Real dt_lev, int iteration, int ncycle);
685 
686  //! Initialize HSE
687  void initHSE ();
688  void initHSE (int lev);
689 
690  //! Initialize Rayleigh damping profiles
691  void initRayleigh ();
692 
693  //! Initialize sponge profiles
694  void initSponge ();
695 
696  //! Set Rayleigh mean profiles from input sounding
697  void setRayleighRefFromSounding (bool restarting);
698 
699  //! Set sponge mean profiles from input sounding
700  void setSpongeRefFromSounding (bool restarting);
701 
702  // a wrapper for estTimeStep()
703  void ComputeDt (int step = -1);
704 
705  // get plotfile name
706  [[nodiscard]] std::string PlotFileName (int lev) const;
707 
708  // set plotfile variable names
709  static amrex::Vector<std::string> PlotFileVarNames (amrex::Vector<std::string> plot_var_names);
710 
711  // set which variables and derived quantities go into plotfiles
712  void setPlotVariables (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
713  void setPlotVariables2D (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
714  // append variables to plot
715  void appendPlotVariables (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
716 
717  void setSubVolVariables (const std::string& pp_subvol_var_names, amrex::Vector<std::string>& subvol_var_names);
718 
719 #ifdef ERF_USE_NETCDF
720  //! Create 1D vertical column output for coupling
721  void createNCColumnFile (int lev,
722  const std::string& colfile_name, amrex::Real xloc, amrex::Real yloc);
723 
724  // Copy from the NC*fabs into the MultiFabs holding the boundary data
725  void init_from_wrfbdy (amrex::Vector<amrex::FArrayBox*> x_vel_lateral,
726  amrex::Vector<amrex::FArrayBox*> y_vel_lateral,
727  amrex::Vector<amrex::FArrayBox*> z_vel_lateral,
728  amrex::Vector<amrex::FArrayBox*> T_lateral);
729 
730  static amrex::Real start_bdy_time;
731  static amrex::Real start_low_time;
732 
733  static amrex::Real bdy_time_interval;
734  static amrex::Real low_time_interval;
735 
736  // *** *** FArrayBox's for holding the SURFACE data
737  // amrex::IArrayBox NC_IVGTYP_fab; // Vegetation type (IVGTYP); Discrete numbers;
738  // amrex::FArrayBox NC_z0_fab; // Surface Roughness, z0 = z0 (IVGTYP)
739  // amrex::FArrayBox NC_PSFC_fab; // Surface pressure
740 
741  // TODO: Clarify the relation between SST and TSK
742  // amrex::FArrayBox NC_SST_fab; // Sea Surface Temperature; Defined even for land area
743  // amrex::FArrayBox NC_TSK_fab; // Surface Skin Temperature; Appears to be same as SST...
744 
745  // Vectors (over time) of Vector (over variables) of FArrayBoxs for holding the data read from the wrfbdy NetCDF file
746  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_xlo;
747  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_xhi;
748  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_ylo;
749  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_yhi;
750 
751  amrex::Vector<amrex::Vector<amrex::FArrayBox>> low_data_zlo;
752 
753  // Maximum value of terrain read in from wrfinput at level 0
754  amrex::Real z_top = 0.;
755 
756 #endif // ERF_USE_NETCDF
757 
758  amrex::Vector<std::unique_ptr<amrex::MultiFab>> lat_m, lon_m; // Latitude and Longitude on the grid
759 
760  amrex::Vector<std::unique_ptr<amrex::MultiFab>> sinPhi_m, cosPhi_m; // Coriolis factors on the grid
761 
762  // Struct for working with the sounding data we take as an input
763  InputSoundingData input_sounding_data;
764 
765  // Struct for working with the sponge data we take as an input
766  InputSpongeData input_sponge_data;
767 
768  // Vector (6 planes) of DeviceVectors (ncell in plane) for Dirichlet BC data
769  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> xvel_bc_data;
770  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> yvel_bc_data;
771  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> zvel_bc_data;
772  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> th_bc_data;
773 
774  // Function to read and populate above vectors (if input file exists)
775  void init_Dirichlet_bc_data (const std::string input_file);
776 
777  // Read the file passed to amr.restart and use it as an initial condition for
778  // the current simulation. Supports a different number of components and
779  // ghost cells.
780  void InitializeFromFile ();
781 
782  // Initialize the new-time data at a level from the initial_data MultiFab
783  void InitializeLevelFromData (int lev, const amrex::MultiFab& initial_data);
784 
785  // utility to skip to next line in Header
786  static void GotoNextLine (std::istream& is);
787 
788  // Single level functions called by advance()
789  void post_update (amrex::MultiFab& state_mf, amrex::Real time, const amrex::Geometry& geom);
790  void fill_rhs (amrex::MultiFab& rhs_mf, const amrex::MultiFab& state_mf, amrex::Real time, const amrex::Geometry& geom);
791 
792  ////////////////
793  // private data members
794 
795  std::unique_ptr<ProblemBase> prob = nullptr; // problem-specific functions
796 
797  amrex::Vector<int> num_boxes_at_level; // how many boxes specified at each level by tagging criteria
798  amrex::Vector<int> num_files_at_level; // how many wrfinput files specified at each level
799  amrex::Vector<amrex::Vector<amrex::Box>> boxes_at_level; // the boxes specified at each level by tagging criteria
800 
801  amrex::Vector<int> istep; // which step?
802  amrex::Vector<int> nsubsteps; // how many substeps on each level?
803 
804  // keep track of old time, new time, and time step at each level
805  amrex::Vector<amrex::Real> t_new;
806  amrex::Vector<amrex::Real> t_old;
807  amrex::Vector<amrex::Real> dt;
808  amrex::Vector<long> dt_mri_ratio;
809 
810 #ifndef ERF_USE_MULTIBLOCK
811  // Array of multifabs to store the solution at each level of refinement;
812  // after advancing a level we use "swap".
813  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_new;
814  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_old;
815 
816  // Pressure gradient at each level
817  amrex::Vector<amrex::Vector<amrex::MultiFab> > gradp;
818 
819  // Velocity time averaged field
820  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vel_t_avg;
821  amrex::Vector<amrex::Real> t_avg_cnt;
822 #endif
823  amrex::Vector<std::unique_ptr<MRISplitIntegrator<amrex::Vector<amrex::MultiFab> > > > mri_integrator_mem;
824 
825  // Used for anelastic or when we impose an initial projection
826  amrex::Vector<amrex::MultiFab> pp_inc;
827 
828  // Used only for fast substepping
829  amrex::Vector<amrex::MultiFab> lagged_delta_rt;
830  amrex::Vector<amrex::MultiFab> avg_xmom;
831  amrex::Vector<amrex::MultiFab> avg_ymom;
832  amrex::Vector<amrex::MultiFab> avg_zmom;
833 
834  // Vector over levels of routines to impose physical boundary conditions
835  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_cons>> physbcs_cons;
836  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_u>> physbcs_u;
837  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_v>> physbcs_v;
838  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_w>> physbcs_w;
839  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_base>> physbcs_base;
840 
841  // Store primitive variable for MOST BC
842  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Theta_prim;
843  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Qv_prim;
844  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Qr_prim;
845 
846  // Scratch space for time integrator
847  amrex::Vector<amrex::MultiFab> rU_old;
848  amrex::Vector<amrex::MultiFab> rU_new;
849  amrex::Vector<amrex::MultiFab> rV_old;
850  amrex::Vector<amrex::MultiFab> rV_new;
851  amrex::Vector<amrex::MultiFab> rW_old;
852  amrex::Vector<amrex::MultiFab> rW_new;
853 
854  // amrex::Vector<amrex::MultiFab> xmom_crse_rhs;
855  // amrex::Vector<amrex::MultiFab> ymom_crse_rhs;
856  amrex::Vector<amrex::MultiFab> zmom_crse_rhs;
857 
858  std::unique_ptr<Microphysics> micro;
859  amrex::Vector<amrex::Vector<amrex::MultiFab*>> qmoist; // (lev,ncomp) rain_accum, snow_accum, graup_accum
860 
861  // Variables for wind farm parametrization models
862 
863 #ifdef ERF_USE_WINDFARM
864  std::unique_ptr<WindFarm> windfarm;
865  amrex::Vector<amrex::MultiFab> Nturb;
866  amrex::Vector<amrex::MultiFab> vars_windfarm; // Fitch: Vabs, Vabsdt, dudt, dvdt, dTKEdt
867  // EWP: dudt, dvdt, dTKEdt
868 
869  amrex::Vector<amrex::MultiFab> SMark; // A multifab that holds an integer corresponding
870  // to the number of the wind turbine to sample
871  // velocity upstream of the turbine
872 #endif
873 
874  LandSurface lsm;
875  amrex::Vector<std::string> lsm_data_name; // (ncomp)
876  amrex::Vector<amrex::Vector<amrex::MultiFab*>> lsm_data; // (lev,ncomp)
877  amrex::Vector<std::string> lsm_flux_name; // (ncomp)
878  amrex::Vector<amrex::Vector<amrex::MultiFab*>> lsm_flux; // (lev,ncomp)
879 
880  amrex::Vector<std::unique_ptr<IRadiation>> rad; // Radiation model at each level
881  amrex::Vector<std::unique_ptr<amrex::MultiFab>> qheating_rates; // radiation heating rate source terms (SW, LW)
882  amrex::Vector<std::unique_ptr<amrex::MultiFab>> rad_fluxes; // radiation fluxes (SW up/dn, LW up/dn)
883 #ifdef ERF_USE_SHOC
884  amrex::Vector<std::unique_ptr<SHOCInterface>> shoc_interface; // SHOC model at each level
885 #endif
886 
887 #ifdef ERF_USE_P3
888  amrex::Vector<std::unique_ptr<P3Interface>> p3_interface; // P3 model at each level
889 #endif
890 
891  // Containers for additional SLM inputs
892  amrex::Vector<std::unique_ptr<amrex::MultiFab>> sw_lw_fluxes; // Direct SW (visible, NIR), Diffuse SW (visible, NIR), LW flux
893  amrex::Vector<std::unique_ptr<amrex::MultiFab>> solar_zenith; // Solar zenith angle
894 
895  bool plot_rad = false;
896  int rad_datalog_int = -1;
897 
898  // Fillpatcher classes for coarse-fine boundaries
899  int cf_width{0};
900  int cf_set_width{0};
901  amrex::Vector<ERFFillPatcher> FPr_c;
902  amrex::Vector<ERFFillPatcher> FPr_u;
903  amrex::Vector<ERFFillPatcher> FPr_v;
904  amrex::Vector<ERFFillPatcher> FPr_w;
905 
906  // Diffusive stresses and Smag
907  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> Tau;
908  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> Tau_corr; // correction to tau for implicit
909  amrex::Vector<std::unique_ptr<amrex::MultiFab>> eddyDiffs_lev;
910  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SmnSmn_lev;
911 
912  // Sea Surface Temps, Skin Temperature and Land Masks (lev, ntimes)
913  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> sst_lev;
914  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> tsk_lev;
915  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::iMultiFab>>> lmask_lev;
916 
917  // Land grid types and urban fraction
918  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::iMultiFab>>> land_type_lev;
919  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::iMultiFab>>> soil_type_lev;
920  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> urb_frac_lev;
921 
922  // Other SFS terms
923  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_hfx1_lev, SFS_hfx2_lev, SFS_hfx3_lev;
924  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_diss_lev;
925  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_q1fx1_lev, SFS_q1fx2_lev, SFS_q1fx3_lev;
926  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_q2fx3_lev;
927 
928  // Grid stretching
929  amrex::Vector<amrex::Vector<amrex::Real>> zlevels_stag; // nominal height levels
930 
931  // Data structures for terrain-fitted coordinates
932  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_nd;
933  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_cc;
934 
935  amrex::Vector<std::unique_ptr<amrex::MultiFab>> detJ_cc;
936  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ax;
937  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ay;
938  amrex::Vector<std::unique_ptr<amrex::MultiFab>> az;
939 
940  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_nd_src;
941  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_cc_src;
942  amrex::Vector<std::unique_ptr<amrex::MultiFab>> detJ_cc_src;
943  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ax_src;
944  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ay_src;
945  amrex::Vector<std::unique_ptr<amrex::MultiFab>> az_src;
946 
947  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_nd_new;
948  amrex::Vector<std::unique_ptr<amrex::MultiFab>> detJ_cc_new;
949 
950  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_t_rk;
951 
952  // Data structures for terrain immersed forcing
953  amrex::Vector<std::unique_ptr<amrex::MultiFab>> terrain_blanking;
954 
955  // Wall distance function
956  amrex::Vector<std::unique_ptr<amrex::MultiFab>> walldist;
957 
958  // Map scale factors -- vector across levels of vector across types
959  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> mapfac;
960 
961  // Mask to be used to identify cells covered by finer level (if level > 0)
962  amrex::Vector<std::unique_ptr<amrex::MultiFab>> fine_mask;
963 
964  amrex::Vector<amrex::Vector<amrex::Real>> stretched_dz_h;
965  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> stretched_dz_d;
966 
967  amrex::Vector<amrex::MultiFab> base_state;
968  amrex::Vector<amrex::MultiFab> base_state_new;
969 
970  // Wave coupling data
971  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Hwave;
972  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Lwave;
973  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Hwave_onegrid;
974  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Lwave_onegrid;
975  bool finished_wave = false;
976 
977  // array of flux registers
978  amrex::Vector<amrex::YAFluxRegister*> advflux_reg;
979 
980  // A BCRec is essentially a 2*DIM integer array storing the boundary
981  // condition type at each lo/hi walls in each direction. We have one BCRec
982  // for each component of the cell-centered variables and each velocity component.
983  amrex::Vector <amrex::BCRec> domain_bcs_type;
984  amrex::Gpu::DeviceVector<amrex::BCRec> domain_bcs_type_d;
985 
986  // We store these so that we can print them out in the job_info file
987  amrex::Array<std::string,2*AMREX_SPACEDIM> domain_bc_type;
988 
989  // These hold the Dirichlet values at walls which need them ...
990  amrex::Array<amrex::Array<amrex::Real, AMREX_SPACEDIM*2>, AMREX_SPACEDIM+NBCVAR_max> m_bc_extdir_vals;
991 
992  // These hold the Neumann values at walls which need them ...
993  amrex::Array<amrex::Array<amrex::Real, AMREX_SPACEDIM*2>, AMREX_SPACEDIM+NBCVAR_max> m_bc_neumann_vals;
994 
995  // These are the "physical" boundary condition types (e.g. "inflow")
996  amrex::GpuArray<ERF_BC, AMREX_SPACEDIM*2> phys_bc_type;
997 
998  // These are the masks for the thin immersed body
999  amrex::Vector<std::unique_ptr<amrex::iMultiFab>> xflux_imask;
1000  amrex::Vector<std::unique_ptr<amrex::iMultiFab>> yflux_imask;
1001  amrex::Vector<std::unique_ptr<amrex::iMultiFab>> zflux_imask;
1002  //amrex::Vector<std::unique_ptr<amrex::iMultiFab>> overset_imask;
1003 
1004  // These are the body forces that result from the thin immersed body
1005  amrex::Vector<std::unique_ptr<amrex::MultiFab>> thin_xforce;
1006  amrex::Vector<std::unique_ptr<amrex::MultiFab>> thin_yforce;
1007  amrex::Vector<std::unique_ptr<amrex::MultiFab>> thin_zforce;
1008 
1009  static int last_plot3d_file_step_1;
1010  static int last_plot3d_file_step_2;
1011  static int last_plot2d_file_step_1;
1012  static int last_plot2d_file_step_2;
1013  static int last_check_file_step;
1014 
1015  static amrex::Real last_plot3d_file_time_1;
1016  static amrex::Real last_plot3d_file_time_2;
1017  static amrex::Real last_plot2d_file_time_1;
1018  static amrex::Real last_plot2d_file_time_2;
1019  static amrex::Real last_check_file_time;
1020 
1021  amrex::Vector<int> last_subvol_step;
1022  amrex::Vector<amrex::Real> last_subvol_time;
1023 
1024  static bool plot_file_on_restart;
1025 
1026  // Output control
1027  const int datwidth = 14;
1028  const int datprecision = 6;
1029  const int timeprecision = 13; // e.g., 1-yr LES: 31,536,000 s with dt ~ 0.01 ==> min prec = 10
1030  // epoch time for 2030-01-01 00:00:00 is 1,893,456,000 s with dt ~ 0.01 ==> min prec = 12
1031 
1032  ////////////////
1033  // runtime parameters
1034 
1035  // Maximum number of steps
1036  int max_step = -1;
1037 
1038  // Start and stop times
1039  static amrex::Real start_time;
1040  static amrex::Real stop_time;
1041 
1042  bool use_datetime = false;
1043  const std::string datetime_format = "%Y-%m-%d %H:%M:%S"; // ISO 8601 standard
1044 
1045  // if >= 0 we restart from a checkpoint
1046  std::string restart_chkfile = "";
1047 
1048  // Time step controls
1049  static amrex::Real cfl;
1050  static amrex::Real sub_cfl;
1051  static amrex::Real init_shrink;
1052  static amrex::Real change_max;
1053  static amrex::Real dt_max_initial;
1054  static amrex::Real dt_max;
1055 
1056  // Fixed dt at each level (only used if positive)
1057  amrex::Vector<amrex::Real> fixed_dt;
1058  amrex::Vector<amrex::Real> fixed_fast_dt;
1059  static int fixed_mri_dt_ratio;
1060 
1061  // how often each level regrids the higher levels of refinement
1062  // (after a level advances that many time steps)
1063  int regrid_int = -1;
1064 
1065  // Should we regrid level 0 after restart if Ngrids < Nprocs or
1066  // max_grid_size has changed?
1067  bool regrid_level_0_on_restart = false;
1068 
1069  // plotfile prefix and frequency
1070  std::string plot3d_file_1 {"plt_1_"};
1071  std::string plot3d_file_2 {"plt_2_"};
1072  std::string plot2d_file_1 {"plt2d_1_"};
1073  std::string plot2d_file_2 {"plt2d_2_"};
1074  std::string subvol_file {"subvol"};
1075  bool m_expand_plotvars_to_unif_rr = false;
1076  int m_plot3d_int_1 = -1;
1077  int m_plot3d_int_2 = -1;
1078  int m_plot2d_int_1 = -1;
1079  int m_plot2d_int_2 = -1;
1080 
1081  amrex::Vector<int> m_subvol_int;
1082  amrex::Vector<amrex::Real> m_subvol_per;
1083 
1084  amrex::Real m_plot3d_per_1 = -1.0;
1085  amrex::Real m_plot3d_per_2 = -1.0;
1086  amrex::Real m_plot2d_per_1 = -1.0;
1087  amrex::Real m_plot2d_per_2 = -1.0;
1088  bool m_plot_face_vels = false;
1089 
1090  bool plot_lsm = false;
1091 
1092  // other sampling output control
1093  int profile_int = -1;
1094  bool destag_profiles = true;
1095 
1096  // Checkpoint type, prefix and frequency
1097  std::string check_file {"chk"};
1098  int m_check_int = -1;
1099  amrex::Real m_check_per = -1.0;
1100 
1101  amrex::Vector<std::string> subvol3d_var_names;
1102 
1103  amrex::Vector<std::string> plot3d_var_names_1;
1104  amrex::Vector<std::string> plot3d_var_names_2;
1105  amrex::Vector<std::string> plot2d_var_names_1;
1106  amrex::Vector<std::string> plot2d_var_names_2;
1107  const amrex::Vector<std::string> cons_names {"density", "rhotheta", "rhoKE", "rhoadv_0",
1108  "rhoQ1", "rhoQ2", "rhoQ3",
1109  "rhoQ4", "rhoQ5", "rhoQ6"};
1110 
1111  // **************************************************************************************
1112  // NOTE: The order of variable names here **MUST MATCH THE ORDER** in IO/ERF_Plotfile.cpp
1113  // **************************************************************************************
1114  const amrex::Vector<std::string> derived_names {"soundspeed", "temp", "theta", "KE", "scalar",
1115  "vorticity_x","vorticity_y","vorticity_z",
1116  "magvel", "divU",
1117  "pres_hse", "dens_hse", "theta_hse", "pressure", "pert_pres", "pert_dens",
1118  "eq_pot_temp",
1119 #ifdef ERF_USE_WINDFARM
1120  "num_turb", "SMark0", "SMark1",
1121 #endif
1122  "dpdx", "dpdy", "dpdz", "pres_hse_x", "pres_hse_y",
1123  "z_phys", "detJ", "mapfac", "lat_m", "lon_m",
1124  // Time averaged velocity
1125  "u_t_avg", "v_t_avg", "w_t_avg", "umag_t_avg",
1126  // eddy viscosity
1127  "nut",
1128  // eddy diffusivity of momentum
1129  "Kmv","Kmh",
1130  // eddy diffusivity of heat
1131  "Khv","Khh",
1132  // turbulence lengthscale
1133  "Lturb",
1134  // wall distance
1135  "walldist",
1136  // dissipation
1137  "diss",
1138  // moisture vars
1139  "moist_density", "qv", "qc", "qi", "qrain", "qsnow", "qgraup", "qt", "qn", "qp", "qsat",
1140  "rain_accum", "snow_accum", "graup_accum", "reflectivity", "max_reflectivity",
1141  // Terrain IB mask
1142  "terrain_IB_mask",
1143  // EB variables
1144  "volfrac"
1145 #ifdef ERF_COMPUTE_ERROR
1146  // error vars
1147  ,"xvel_err", "yvel_err", "zvel_err", "pp_err"
1148 #endif
1149  ,"qsrc_sw", "qsrc_lw"
1150  };
1151 
1152  // **************************************************************************************
1153  // NOTE: The order of variable names here **MUST MATCH THE ORDER** in IO/ERF_Plotfile.cpp
1154  // **************************************************************************************
1155  const amrex::Vector<std::string> derived_names_2d {
1156  "z_surf", "landmask", "mapfac", "lat_m", "lon_m",
1157  "u_star", "w_star", "t_star", "q_star", "Olen", "pblh",
1158  "t_surf", "q_surf", "z0", "OLR", "sens_flux", "laten_flux",
1159  "surf_pres"
1160  };
1161 
1162  // **************************************************************************************
1163  // NOTE: The order of variable names here **MUST MATCH THE ORDER** in IO/ERF_WriteSubVolume.cpp
1164  // **************************************************************************************
1165  const amrex::Vector<std::string> derived_subvol_names {"soundspeed", "temp", "theta", "KE", "scalar"};
1166 
1167  // algorithm choices
1168  static SolverChoice solverChoice;
1169 
1170  // Turbulent perturbation structure
1171  TurbulentPerturbation turbPert;
1172 
1173 #ifdef ERF_USE_PARTICLES
1174  // Particle container with all particle species
1175  ParticleData particleData;
1176 
1177  // variables and functions for tracers particles
1178  bool m_use_tracer_particles; /*!< tracer particles that advect with flow with optional sedimentation */
1179 
1180  /*! Read tracer and hydro particles parameters */
1181  void readTracersParams();
1182 
1183  /*! Initialize tracer and hydro particles */
1184  void initializeTracers ( amrex::ParGDBBase*,
1185  const amrex::Vector<std::unique_ptr<amrex::MultiFab>>&,
1186  const amrex::Real time);
1187 
1188  /*! Restart tracer and hydro particles */
1189  void restartTracers ( amrex::ParGDBBase*, const std::string& );
1190 
1191  /*! Evolve tracers and hydro particles */
1192  void evolveTracers( int,
1193  amrex::Real,
1194  amrex::Vector<amrex::Vector<amrex::MultiFab>>&,
1195  const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& );
1196 
1197 #endif
1198 
1199 #ifdef ERF_USE_MULTIBLOCK
1200  MultiBlockContainer *m_mbc = nullptr;
1201 #endif
1202 
1203  static int verbose;
1204  static int mg_verbose;
1205  static bool use_fft;
1206 
1207  static int check_for_nans;
1208 
1209  // Diagnostic output interval
1210  static int sum_interval;
1211  static int pert_interval;
1212  static amrex::Real sum_per;
1213 
1214  // Write in native AMReX or NetCDF format for each plotfile
1215  static PlotFileType plotfile3d_type_1;
1216  static PlotFileType plotfile3d_type_2;
1217  static PlotFileType plotfile2d_type_1;
1218  static PlotFileType plotfile2d_type_2;
1219 
1220  static StateInterpType interpolation_type;
1221 
1222  // sponge_type: "input_sponge"
1223  static std::string sponge_type;
1224 
1225  // NetCDF initialization (wrfinput) file
1226  static amrex::Vector<amrex::Vector<std::string>> nc_init_file;
1227  static amrex::Vector<amrex::Vector<int>> have_read_nc_init_file;
1228 
1229  // NetCDF initialization (wrfbdy/met_em) file
1230  static std::string nc_bdy_file;
1231  int real_width{0};
1232  int real_set_width{0};
1233  bool real_extrap_w{true};
1234 
1235  // NetCDF initialization of zlo boundary values
1236  static std::string nc_low_file;
1237 
1238  // Options for vertical interpolation of met_em*.nc data.
1239  bool metgrid_debug_quiescent{false};
1240  bool metgrid_debug_isothermal{false};
1241  bool metgrid_debug_dry{false};
1242  bool metgrid_debug_psfc{false};
1243  bool metgrid_debug_msf{false};
1244  bool metgrid_interp_theta{false};
1245  bool metgrid_basic_linear{false};
1246  bool metgrid_use_below_sfc{true};
1247  bool metgrid_use_sfc{true};
1248  bool metgrid_retain_sfc{false};
1249  amrex::Real metgrid_proximity{500.0};
1250  int metgrid_order{2};
1251  int metgrid_force_sfc_k{6};
1252 
1253  amrex::Vector<amrex::BoxArray> ba1d;
1254  amrex::Vector<amrex::BoxArray> ba2d;
1255  std::unique_ptr<amrex::MultiFab> mf_C1H;
1256  std::unique_ptr<amrex::MultiFab> mf_C2H;
1257  std::unique_ptr<amrex::MultiFab> mf_MUB;
1258 
1259  amrex::Vector<std::unique_ptr<amrex::MultiFab>> mf_PSFC;
1260 
1261  // 1D CDF output (for ingestion in AMR-Wind)
1262  static int output_1d_column;
1263  static int column_interval;
1264  static amrex::Real column_per;
1265  static amrex::Real column_loc_x;
1266  static amrex::Real column_loc_y;
1267  static std::string column_file_name;
1268 
1269  // 2D BndryRegister output (for ingestion in AMR-Wind)
1270  static int output_bndry_planes;
1271  static int bndry_output_planes_interval;
1272  static amrex::Real bndry_output_planes_per;
1273  static amrex::Real bndry_output_planes_start_time;
1274 
1275  // 2D BndryRegister input
1276  static int input_bndry_planes;
1277 
1278  static int ng_dens_hse;
1279  static int ng_pres_hse;
1280 
1281  // Custom source terms
1282  amrex::Vector< amrex::Vector<amrex::Real> > h_rhotheta_src;
1283  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_rhotheta_src;
1284 
1285  amrex::Vector< amrex::Vector<amrex::Real> > h_rhoqt_src;
1286  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_rhoqt_src;
1287 
1288  amrex::Vector< amrex::Vector<amrex::Real> > h_w_subsid;
1289  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_w_subsid;
1290 
1291  amrex::Vector< amrex::Vector<amrex::Real> > h_u_geos;
1292  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_u_geos;
1293 
1294  amrex::Vector< amrex::Vector<amrex::Real> > h_v_geos;
1295  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_v_geos;
1296 
1297  // Function to read and populate above host vectors (if input file exists)
1298  void init_geo_wind_profile (const std::string input_file,
1299  amrex::Vector<amrex::Real>& u_geos,
1300  amrex::Gpu::DeviceVector<amrex::Real>& u_geos_d,
1301  amrex::Vector<amrex::Real>& v_geos,
1302  amrex::Gpu::DeviceVector<amrex::Real>& v_geos_d,
1303  const amrex::Geometry& lgeom,
1304  const amrex::Vector<amrex::Real>& zlev_stag);
1305 
1306  // This is a vector over levels of vectors across quantities of Vectors
1307  amrex::Vector<amrex::Vector<amrex::Vector<amrex::Real> > > h_rayleigh_ptrs;
1308  amrex::Vector<amrex::Vector<amrex::Vector<amrex::Real> > > h_sponge_ptrs;
1309 
1310  // These are vectors over levels of Vectors
1311  amrex::Vector<amrex::Vector<amrex::Real> > h_sinesq_ptrs;
1312  amrex::Vector<amrex::Vector<amrex::Real> > h_sinesq_stag_ptrs;
1313 
1314  // This is a vector over levels of vectors across quantities of DeviceVectors
1315  amrex::Vector<amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > > d_rayleigh_ptrs;
1316  amrex::Vector<amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > > d_sponge_ptrs;
1317 
1318  // These are vectors over levels of DeviceVectors
1319  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_sinesq_ptrs;
1320  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_sinesq_stag_ptrs;
1321 
1322  amrex::Vector<amrex::Real> h_havg_density;
1323  amrex::Vector<amrex::Real> h_havg_temperature;
1324  amrex::Vector<amrex::Real> h_havg_pressure;
1325  amrex::Vector<amrex::Real> h_havg_qv;
1326  amrex::Vector<amrex::Real> h_havg_qc;
1327 
1328  amrex::Gpu::DeviceVector<amrex::Real> d_havg_density;
1329  amrex::Gpu::DeviceVector<amrex::Real> d_havg_temperature;
1330  amrex::Gpu::DeviceVector<amrex::Real> d_havg_pressure;
1331  amrex::Gpu::DeviceVector<amrex::Real> d_havg_qv;
1332  amrex::Gpu::DeviceVector<amrex::Real> d_havg_qc;
1333 
1334  void refinement_criteria_setup ();
1335 
1336  std::unique_ptr<WriteBndryPlanes> m_w2d = nullptr;
1337  std::unique_ptr<ReadBndryPlanes> m_r2d = nullptr;
1338  std::unique_ptr<SurfaceLayer> m_SurfaceLayer = nullptr;
1339  amrex::Vector<std::unique_ptr<ForestDrag>> m_forest_drag;
1340 
1341  //
1342  // Holds info for dynamically generated tagging criteria
1343  //
1344  static amrex::Vector<amrex::AMRErrorTag> ref_tags;
1345 
1346  amrex::Vector<amrex::Vector<amrex::BoxArray>> subdomains;
1347 
1348  amrex::Vector<amrex::Real> dz_min;
1349 
1350  static AMREX_FORCE_INLINE
1351  int
1352  ComputeGhostCells (const SolverChoice& sc)
1353  {
1354  int ngrow = 0;
1355 
1356  if (sc.use_num_diff)
1357  {
1358  ngrow = 3;
1359  } else {
1360  if (
1361  (sc.advChoice.dycore_horiz_adv_type == AdvType::Centered_6th)
1362  || (sc.advChoice.dycore_vert_adv_type == AdvType::Centered_6th)
1363  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Centered_6th)
1364  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Centered_6th)
1365  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Centered_6th)
1366  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Centered_6th) )
1367  { ngrow = 3; }
1368  else if (
1369  (sc.advChoice.dycore_horiz_adv_type == AdvType::Upwind_5th)
1370  || (sc.advChoice.dycore_vert_adv_type == AdvType::Upwind_5th)
1371  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Upwind_5th)
1372  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Upwind_5th)
1373  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Upwind_5th)
1374  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Upwind_5th) )
1375  { ngrow = 3; }
1376  else if (
1377  (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_5)
1378  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_5)
1379  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_5)
1380  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_5)
1381  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_5Z)
1382  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_5Z)
1383  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_5Z)
1384  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_5Z) )
1385  { ngrow = 3; }
1386  else if (
1387  (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_7)
1388  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_7)
1389  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_7)
1390  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_7)
1391  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_7Z)
1392  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_7Z)
1393  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_7Z)
1394  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_7Z) )
1395  { ngrow = 4; }
1396  else
1397  {
1398  if (sc.terrain_type == TerrainType::EB){
1399  ngrow = 3;
1400  } else {
1401  ngrow = 2;
1402  }
1403  }
1404  }
1405 
1406  return ngrow;
1407  }
1408 
1409  AMREX_FORCE_INLINE
1410  amrex::YAFluxRegister* getAdvFluxReg (int lev)
1411  {
1412  return advflux_reg[lev];
1413  }
1414 
1415  AMREX_FORCE_INLINE
1416  std::ostream&
1417  DataLog (int i)
1418  {
1419  return *datalog[i];
1420  }
1421 
1422  AMREX_FORCE_INLINE
1423  std::ostream&
1424  DerDataLog (int i)
1425  {
1426  return *der_datalog[i];
1427  }
1428 
1429  AMREX_FORCE_INLINE
1430  int
1431  NumDataLogs () noexcept
1432  {
1433  return datalog.size();
1434  }
1435 
1436  AMREX_FORCE_INLINE
1437  int
1438  NumDerDataLogs () noexcept
1439  {
1440  return der_datalog.size();
1441  }
1442 
1443 
1444  AMREX_FORCE_INLINE
1445  std::ostream&
1446  SamplePointLog (int i)
1447  {
1448  return *sampleptlog[i];
1449  }
1450 
1451  AMREX_FORCE_INLINE
1452  int
1453  NumSamplePointLogs () noexcept
1454  {
1455  return sampleptlog.size();
1456  }
1457 
1458  AMREX_FORCE_INLINE
1459  std::ostream&
1460  SampleLineLog (int i)
1461  {
1462  return *samplelinelog[i];
1463  }
1464 
1465  AMREX_FORCE_INLINE
1466  int
1467  NumSampleLineLogs () noexcept
1468  {
1469  return samplelinelog.size();
1470  }
1471 
1472  amrex::IntVect&
1473  SamplePoint (int i)
1474  {
1475  return samplepoint[i];
1476  }
1477 
1478  AMREX_FORCE_INLINE
1479  int
1480  NumSamplePoints () noexcept
1481  {
1482  return samplepoint.size();
1483  }
1484 
1485  amrex::IntVect&
1486  SampleLine (int i)
1487  {
1488  return sampleline[i];
1489  }
1490 
1491  AMREX_FORCE_INLINE
1492  int
1493  NumSampleLines () noexcept
1494  {
1495  return sampleline.size();
1496  }
1497 
1498  static amrex::Real startCPUTime;
1499  static amrex::Real previousCPUTimeUsed;
1500 
1501  static amrex::Real
1502  getCPUTime ()
1503  {
1504  int numCores = amrex::ParallelDescriptor::NProcs();
1505 #ifdef _OPENMP
1506  numCores = numCores * omp_get_max_threads();
1507 #endif
1508 
1509  amrex::Real T =
1510  numCores * (amrex::ParallelDescriptor::second() - startCPUTime) +
1511  previousCPUTimeUsed;
1512 
1513  return T;
1514  }
1515 
1516  void setRecordDataInfo (int i, const std::string& filename) // NOLINT
1517  {
1518  if (amrex::ParallelDescriptor::IOProcessor())
1519  {
1520  datalog[i] = std::make_unique<std::fstream>();
1521  datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1522  if (!datalog[i]->good()) {
1523  amrex::FileOpenFailed(filename);
1524  }
1525  }
1526  amrex::ParallelDescriptor::Barrier("ERF::setRecordDataInfo");
1527  }
1528 
1529  void setRecordDerDataInfo (int i, const std::string& filename) // NOLINT
1530  {
1531  if (amrex::ParallelDescriptor::IOProcessor())
1532  {
1533  der_datalog[i] = std::make_unique<std::fstream>();
1534  der_datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1535  if (!der_datalog[i]->good()) {
1536  amrex::FileOpenFailed(filename);
1537  }
1538  }
1539  amrex::ParallelDescriptor::Barrier("ERF::setRecordDerDataInfo");
1540  }
1541 
1542  void setRecordEnergyDataInfo (int i, const std::string& filename) // NOLINT
1543  {
1544  if (amrex::ParallelDescriptor::IOProcessor())
1545  {
1546  tot_e_datalog[i] = std::make_unique<std::fstream>();
1547  tot_e_datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1548  if (!tot_e_datalog[i]->good()) {
1549  amrex::FileOpenFailed(filename);
1550  }
1551  }
1552  amrex::ParallelDescriptor::Barrier("ERF::setRecordEnergyDataInfo");
1553  }
1554 
1555  void setRecordSamplePointInfo (int i, int lev, amrex::IntVect& cell, const std::string& filename) // NOLINT
1556  {
1557  amrex::MultiFab dummy(grids[lev],dmap[lev],1,0);
1558  for (amrex::MFIter mfi(dummy); mfi.isValid(); ++mfi)
1559  {
1560  const amrex::Box& bx = mfi.validbox();
1561  if (bx.contains(cell)) {
1562  sampleptlog[i] = std::make_unique<std::fstream>();
1563  sampleptlog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1564  if (!sampleptlog[i]->good()) {
1565  amrex::FileOpenFailed(filename);
1566  }
1567  }
1568  }
1569  amrex::ParallelDescriptor::Barrier("ERF::setRecordSamplePointInfo");
1570  }
1571 
1572  void setRecordSampleLineInfo (int i, int lev, amrex::IntVect& cell, const std::string& filename) // NOLINT
1573  {
1574  amrex::MultiFab dummy(grids[lev],dmap[lev],1,0);
1575  for (amrex::MFIter mfi(dummy); mfi.isValid(); ++mfi)
1576  {
1577  const amrex::Box& bx = mfi.validbox();
1578  if (bx.contains(cell)) {
1579  samplelinelog[i] = std::make_unique<std::fstream>();
1580  samplelinelog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1581  if (!samplelinelog[i]->good()) {
1582  amrex::FileOpenFailed(filename);
1583  }
1584  }
1585  }
1586  amrex::ParallelDescriptor::Barrier("ERF::setRecordSampleLineInfo");
1587  }
1588 
1589  // Data sampler for line and plane output
1590  int line_sampling_interval = -1;
1591  int plane_sampling_interval = -1;
1592  amrex::Real line_sampling_per = -1.0;
1593  amrex::Real plane_sampling_per = -1.0;
1594  std::unique_ptr<LineSampler> line_sampler = nullptr;
1595  std::unique_ptr<PlaneSampler> plane_sampler = nullptr;
1596 
1597  amrex::Vector<std::unique_ptr<std::fstream> > datalog;
1598  amrex::Vector<std::unique_ptr<std::fstream> > der_datalog;
1599  amrex::Vector<std::unique_ptr<std::fstream> > tot_e_datalog;
1600  amrex::Vector<std::string> datalogname;
1601  amrex::Vector<std::string> der_datalogname;
1602  amrex::Vector<std::string> tot_e_datalogname;
1603 
1604  amrex::Vector<std::unique_ptr<std::fstream> > sampleptlog;
1605  amrex::Vector<std::string> sampleptlogname;
1606  amrex::Vector<amrex::IntVect> samplepoint;
1607 
1608  amrex::Vector<std::unique_ptr<std::fstream> > samplelinelog;
1609  amrex::Vector<std::string> samplelinelogname;
1610  amrex::Vector<amrex::IntVect> sampleline;
1611 
1612  //! The filename of the ith datalog file.
1613  [[nodiscard]] std::string DataLogName (int i) const noexcept { return datalogname[i]; }
1614  [[nodiscard]] std::string DerDataLogName (int i) const noexcept { return der_datalogname[i]; }
1615 
1616  //! The filename of the ith sampleptlog file.
1617  [[nodiscard]] std::string SamplePointLogName (int i) const noexcept { return sampleptlogname[i]; }
1618 
1619  //! The filename of the ith samplelinelog file.
1620  [[nodiscard]] std::string SampleLineLogName (int i) const noexcept { return samplelinelogname[i]; }
1621 
1622  // array of EB objects
1623  amrex::Vector<std::unique_ptr<eb_>> eb;
1624 
1625  [[nodiscard]] eb_ const& get_eb (int lev) const noexcept {
1626  AMREX_ASSERT(lev >= 0 && lev < eb.size() && eb[lev] != nullptr);
1627  return *eb[lev];
1628  }
1629 
1630  [[nodiscard]] amrex::EBFArrayBoxFactory const&
1631  EBFactory (int lev) const noexcept {
1632  return *(eb[lev]->get_const_factory());
1633  }
1634 
1635  [[nodiscard]] static int nghost_eb_basic ()
1636  { return 5; }
1637 
1638  // We need 5 for doing StateRedistribution; otherwise 4 would be enough
1639  [[nodiscard]] static int nghost_eb_volume ()
1640  { return 5; }
1641 
1642  [[nodiscard]] static int nghost_eb_full ()
1643  { return 4; }
1644 
1645 #ifdef ERF_USE_FFT
1646  amrex::Vector<std::unique_ptr<amrex::FFT::Poisson<amrex::MultiFab>>> m_3D_poisson;
1647  amrex::Vector<std::unique_ptr<amrex::FFT::PoissonHybrid<amrex::MultiFab>>> m_2D_poisson;
1648 #endif
1649 
1650 public:
1651  void writeJobInfo (const std::string& dir) const;
1652  static void writeBuildInfo (std::ostream& os);
1653 
1654  static void print_banner(MPI_Comm /*comm*/, std::ostream& /*out*/);
1655  static void print_usage(MPI_Comm /*comm*/, std::ostream& /*out*/);
1656  static void print_error(MPI_Comm /*comm*/, const std::string& msg);
1657  static void print_summary(std::ostream&);
1658  static void print_tpls(std::ostream& /*out*/);
1659 };
1660 
1661 #endif
AMREX_ENUM
AMREX_ENUM(StateInterpType, FullState, Perturbational)
RayleighDampingType::None
@ None
ERF_DataStruct.H
tau23
@ tau23
Definition: ERF_DataStruct.H:31
tau13
@ tau13
Definition: ERF_DataStruct.H:31
ERF_Derive.H
ERF_EB.H
ERF_EulerianMicrophysics.H
Contains the Eulerian microphysics class.
ERF_FillPatcher.H
ERF_ForestDrag.H
out
struct @19 out
ERF_IndexDefines.H
NBCVAR_max
#define NBCVAR_max
Definition: ERF_IndexDefines.H:29
AdvType::Weno_7
@ Weno_7
AdvType::Weno_7Z
@ Weno_7Z
AdvType::Upwind_5th
@ Upwind_5th
AdvType::Centered_6th
@ Centered_6th
AdvType::Weno_5Z
@ Weno_5Z
AdvType::Weno_5
@ Weno_5
ERF_InputSoundingData.H
ERF_InputSpongeData.H
ERF_LagrangianMicrophysics.H
Contains the Lagrangian microphysics class.
ERF_LandSurface.H
ERF_MRI.H
ERF_ParticleData.H
ERF_PhysBCFunct.H
ERF_ProbCommon.H
ERF_RadiationModels.H
ERF_ReadBndryPlanes.H
ERF_SampleData.H
ERF_ShocInterface.H
Real
amrex::Real Real
Definition: ERF_ShocInterface.H:19
ERF_SurfaceLayer.H
ERF_TurbPertStruct.H
ERF_WindFarm.H
ERF_WriteBndryPlanes.H
ERF
Definition: ERF.H:111
ERF::MakeHorizontalAverages
void MakeHorizontalAverages()
Definition: ERF.cpp:2610
ERF::rU_new
amrex::Vector< amrex::MultiFab > rU_new
Definition: ERF.H:848
ERF::last_check_file_step
static int last_check_file_step
Definition: ERF.H:1013
ERF::walldist
amrex::Vector< std::unique_ptr< amrex::MultiFab > > walldist
Definition: ERF.H:956
ERF::h_sponge_ptrs
amrex::Vector< amrex::Vector< amrex::Vector< amrex::Real > > > h_sponge_ptrs
Definition: ERF.H:1308
ERF::initRayleigh
void initRayleigh()
Initialize Rayleigh damping profiles.
Definition: ERF_InitRayleigh.cpp:14
ERF::start_time
static amrex::Real start_time
Definition: ERF.H:1039
ERF::metgrid_basic_linear
bool metgrid_basic_linear
Definition: ERF.H:1245
ERF::boxes_at_level
amrex::Vector< amrex::Vector< amrex::Box > > boxes_at_level
Definition: ERF.H:799
ERF::samplelinelogname
amrex::Vector< std::string > samplelinelogname
Definition: ERF.H:1609
ERF::MakeEBGeometry
void MakeEBGeometry()
ERF::max_step
int max_step
Definition: ERF.H:1036
ERF::metgrid_debug_msf
bool metgrid_debug_msf
Definition: ERF.H:1243
ERF::DerDataLog
AMREX_FORCE_INLINE std::ostream & DerDataLog(int i)
Definition: ERF.H:1424
ERF::mapfac
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > mapfac
Definition: ERF.H:959
ERF::FillBdyCCVels
void FillBdyCCVels(amrex::Vector< amrex::MultiFab > &mf_cc_vel, int levc=0)
Definition: ERF_FillBdyCCVels.cpp:11
ERF::setRayleighRefFromSounding
void setRayleighRefFromSounding(bool restarting)
Set Rayleigh mean profiles from input sounding.
Definition: ERF_InitRayleigh.cpp:94
ERF::mri_integrator_mem
amrex::Vector< std::unique_ptr< MRISplitIntegrator< amrex::Vector< amrex::MultiFab > > > > mri_integrator_mem
Definition: ERF.H:823
ERF::d_sinesq_stag_ptrs
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_sinesq_stag_ptrs
Definition: ERF.H:1320
ERF::check_vels_for_nans
void check_vels_for_nans(amrex::MultiFab const &xvel, amrex::MultiFab const &yvel, amrex::MultiFab const &zvel)
Definition: ERF.cpp:2883
ERF::Evolve
void Evolve()
Definition: ERF.cpp:538
ERF::avg_xmom
amrex::Vector< amrex::MultiFab > avg_xmom
Definition: ERF.H:830
ERF::d_rhotheta_src
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_rhotheta_src
Definition: ERF.H:1283
ERF::pp_inc
amrex::Vector< amrex::MultiFab > pp_inc
Definition: ERF.H:826
ERF::last_plot2d_file_time_2
static amrex::Real last_plot2d_file_time_2
Definition: ERF.H:1018
ERF::make_eb_box
void make_eb_box()
ERF::FPr_u
amrex::Vector< ERFFillPatcher > FPr_u
Definition: ERF.H:902
ERF::cloud_fraction
amrex::Real cloud_fraction(amrex::Real time)
Definition: ERF_WriteScalarProfiles.cpp:451
ERF::sampleline
amrex::Vector< amrex::IntVect > sampleline
Definition: ERF.H:1610
ERF::subvol3d_var_names
amrex::Vector< std::string > subvol3d_var_names
Definition: ERF.H:1101
ERF::SFS_q1fx3_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q1fx3_lev
Definition: ERF.H:925
ERF::Hwave_onegrid
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Hwave_onegrid
Definition: ERF.H:973
ERF::vars_new
amrex::Vector< amrex::Vector< amrex::MultiFab > > vars_new
Definition: ERF.H:813
ERF::ERF
ERF(ERF &&) noexcept=delete
ERF::NumSampleLineLogs
AMREX_FORCE_INLINE int NumSampleLineLogs() noexcept
Definition: ERF.H:1467
ERF::print_tpls
static void print_tpls(std::ostream &)
Definition: ERF_ConsoleIO.cpp:137
ERF::dz_min
amrex::Vector< amrex::Real > dz_min
Definition: ERF.H:1348
ERF::m_plot2d_per_1
amrex::Real m_plot2d_per_1
Definition: ERF.H:1086
ERF::lagged_delta_rt
amrex::Vector< amrex::MultiFab > lagged_delta_rt
Definition: ERF.H:829
ERF::plane_sampling_per
amrex::Real plane_sampling_per
Definition: ERF.H:1593
ERF::DataLogName
std::string DataLogName(int i) const noexcept
The filename of the ith datalog file.
Definition: ERF.H:1613
ERF::plot2d_file_2
std::string plot2d_file_2
Definition: ERF.H:1073
ERF::thin_yforce
amrex::Vector< std::unique_ptr< amrex::MultiFab > > thin_yforce
Definition: ERF.H:1006
ERF::ErrorEst
void ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real time, int ngrow) override
Definition: ERF_Tagging.cpp:20
ERF::SFS_hfx3_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_hfx3_lev
Definition: ERF.H:923
ERF::sw_lw_fluxes
amrex::Vector< std::unique_ptr< amrex::MultiFab > > sw_lw_fluxes
Definition: ERF.H:892
ERF::h_w_subsid
amrex::Vector< amrex::Vector< amrex::Real > > h_w_subsid
Definition: ERF.H:1288
ERF::print_banner
static void print_banner(MPI_Comm, std::ostream &)
Definition: ERF_ConsoleIO.cpp:60
ERF::last_plot2d_file_time_1
static amrex::Real last_plot2d_file_time_1
Definition: ERF.H:1017
ERF::datalog
amrex::Vector< std::unique_ptr< std::fstream > > datalog
Definition: ERF.H:1597
ERF::sum_per
static amrex::Real sum_per
Definition: ERF.H:1212
ERF::MakeFilename_EyeTracker_maxvel
std::string MakeFilename_EyeTracker_maxvel(int nstep)
Definition: ERF_Write1DProfiles.cpp:629
ERF::FPr_v
amrex::Vector< ERFFillPatcher > FPr_v
Definition: ERF.H:903
ERF::derived_names_2d
const amrex::Vector< std::string > derived_names_2d
Definition: ERF.H:1155
ERF::cf_set_width
int cf_set_width
Definition: ERF.H:900
ERF::previousCPUTimeUsed
static amrex::Real previousCPUTimeUsed
Definition: ERF.H:1499
ERF::setPlotVariables
void setPlotVariables(const std::string &pp_plot_var_names, amrex::Vector< std::string > &plot_var_names)
Definition: ERF_Plotfile.cpp:24
ERF::d_havg_temperature
amrex::Gpu::DeviceVector< amrex::Real > d_havg_temperature
Definition: ERF.H:1329
ERF::last_plot2d_file_step_2
static int last_plot2d_file_step_2
Definition: ERF.H:1012
ERF::fill_from_bndryregs
void fill_from_bndryregs(const amrex::Vector< amrex::MultiFab * > &mfs, amrex::Real time)
Definition: ERF_BoundaryConditionsBndryReg.cpp:13
ERF::timeprecision
const int timeprecision
Definition: ERF.H:1029
ERF::setRecordDataInfo
void setRecordDataInfo(int i, const std::string &filename)
Definition: ERF.H:1516
ERF::SFS_hfx1_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_hfx1_lev
Definition: ERF.H:923
ERF::hurricane_eye_track_xy
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_eye_track_xy
Definition: ERF.H:163
ERF::ba2d
amrex::Vector< amrex::BoxArray > ba2d
Definition: ERF.H:1254
ERF::m_bc_extdir_vals
amrex::Array< amrex::Array< amrex::Real, AMREX_SPACEDIM *2 >, AMREX_SPACEDIM+NBCVAR_max > m_bc_extdir_vals
Definition: ERF.H:990
ERF::init_from_input_sounding
void init_from_input_sounding(int lev)
Definition: ERF_InitFromInputSounding.cpp:52
ERF::erf_enforce_hse
void erf_enforce_hse(int lev, amrex::MultiFab &dens, amrex::MultiFab &pres, amrex::MultiFab &pi, amrex::MultiFab &th, amrex::MultiFab &qv, std::unique_ptr< amrex::MultiFab > &z_cc)
Definition: ERF_Init1D.cpp:164
ERF::gradp
amrex::Vector< amrex::Vector< amrex::MultiFab > > gradp
Definition: ERF.H:817
ERF::plot3d_file_1
std::string plot3d_file_1
Definition: ERF.H:1070
ERF::FillPatchCrseLevel
void FillPatchCrseLevel(int lev, amrex::Real time, const amrex::Vector< amrex::MultiFab * > &mfs_vel, bool cons_only=false)
Definition: ERF_FillPatch.cpp:282
ERF::get_eb
eb_ const & get_eb(int lev) const noexcept
Definition: ERF.H:1625
ERF::d_havg_qv
amrex::Gpu::DeviceVector< amrex::Real > d_havg_qv
Definition: ERF.H:1331
ERF::column_loc_y
static amrex::Real column_loc_y
Definition: ERF.H:1266
ERF::plot_file_on_restart
static bool plot_file_on_restart
Definition: ERF.H:1024
ERF::mg_verbose
static int mg_verbose
Definition: ERF.H:1204
ERF::ReadParameters
void ReadParameters()
Definition: ERF.cpp:2084
ERF::PlotFileVarNames
static amrex::Vector< std::string > PlotFileVarNames(amrex::Vector< std::string > plot_var_names)
Definition: ERF_Plotfile.cpp:295
ERF::forecast_state_interp
amrex::Vector< amrex::Vector< amrex::MultiFab > > forecast_state_interp
Definition: ERF.H:170
ERF::InitializeFromFile
void InitializeFromFile()
ERF::physbcs_cons
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_cons > > physbcs_cons
Definition: ERF.H:835
ERF::project_velocity_tb
void project_velocity_tb(int lev, amrex::Real dt, amrex::Vector< amrex::MultiFab > &vars)
Definition: ERF_PoissonSolve_tb.cpp:20
ERF::mf_PSFC
amrex::Vector< std::unique_ptr< amrex::MultiFab > > mf_PSFC
Definition: ERF.H:1259
ERF::ERF
ERF()
Definition: ERF.cpp:127
ERF::init_Dirichlet_bc_data
void init_Dirichlet_bc_data(const std::string input_file)
Definition: ERF_InitBCs.cpp:652
ERF::~ERF
~ERF() override
ERF::z_phys_nd_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_nd_src
Definition: ERF.H:940
ERF::detJ_cc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > detJ_cc
Definition: ERF.H:935
ERF::lsm_flux_name
amrex::Vector< std::string > lsm_flux_name
Definition: ERF.H:877
ERF::WriteMyEBSurface
void WriteMyEBSurface()
Definition: ERF_EBWriteSurface.cpp:5
ERF::z_phys_cc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_cc
Definition: ERF.H:933
ERF::eb
amrex::Vector< std::unique_ptr< eb_ > > eb
Definition: ERF.H:1623
ERF::eddyDiffs_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > eddyDiffs_lev
Definition: ERF.H:909
ERF::solverChoice
static SolverChoice solverChoice
Definition: ERF.H:1168
ERF::FPr_c
amrex::Vector< ERFFillPatcher > FPr_c
Definition: ERF.H:901
ERF::plot_rad
bool plot_rad
Definition: ERF.H:895
ERF::hurricane_tracker_circle
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_tracker_circle
Definition: ERF.H:166
ERF::use_fft
static bool use_fft
Definition: ERF.H:1205
ERF::FillForecastStateMultiFabs
void FillForecastStateMultiFabs(const int lev, const std::string &filename, const std::unique_ptr< amrex::MultiFab > &z_phys_nd, amrex::Vector< amrex::Vector< amrex::MultiFab >> &weather_forecast_data)
Definition: ERF_WeatherDataInterpolation.cpp:64
ERF::m_plot_face_vels
bool m_plot_face_vels
Definition: ERF.H:1088
ERF::hurricane_maxvel_vs_time
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_maxvel_vs_time
Definition: ERF.H:165
ERF::base_state_new
amrex::Vector< amrex::MultiFab > base_state_new
Definition: ERF.H:968
ERF::plot3d_file_2
std::string plot3d_file_2
Definition: ERF.H:1071
ERF::az
amrex::Vector< std::unique_ptr< amrex::MultiFab > > az
Definition: ERF.H:938
ERF::regrid_int
int regrid_int
Definition: ERF.H:1063
ERF::fixed_dt
amrex::Vector< amrex::Real > fixed_dt
Definition: ERF.H:1057
ERF::write_1D_profiles_stag
void write_1D_profiles_stag(amrex::Real time)
Definition: ERF_Write1DProfiles_stag.cpp:25
ERF::WriteGenericPlotfileHeaderWithTerrain
void WriteGenericPlotfileHeaderWithTerrain(std::ostream &HeaderFile, int nlevels, const amrex::Vector< amrex::BoxArray > &bArray, const amrex::Vector< std::string > &varnames, const amrex::Vector< amrex::Geometry > &my_geom, amrex::Real time, const amrex::Vector< int > &level_steps, const amrex::Vector< amrex::IntVect > &my_ref_ratio, const std::string &versionName, const std::string &levelPrefix, const std::string &mfPrefix) const
Definition: ERF_Plotfile.cpp:1832
ERF::solve_with_gmres
void solve_with_gmres(int lev, const amrex::Box &subdomain, amrex::MultiFab &rhs, amrex::MultiFab &p, amrex::Array< amrex::MultiFab, AMREX_SPACEDIM > &fluxes, amrex::MultiFab &ax_sub, amrex::MultiFab &ay_sub, amrex::MultiFab &az_sub, amrex::MultiFab &, amrex::MultiFab &znd_sub)
Definition: ERF_SolveWithGMRES.cpp:12
ERF::d_sponge_ptrs
amrex::Vector< amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > > d_sponge_ptrs
Definition: ERF.H:1316
ERF::h_rhoqt_src
amrex::Vector< amrex::Vector< amrex::Real > > h_rhoqt_src
Definition: ERF.H:1285
ERF::dt_mri_ratio
amrex::Vector< long > dt_mri_ratio
Definition: ERF.H:808
ERF::Tau
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > Tau
Definition: ERF.H:907
ERF::vel_t_avg
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vel_t_avg
Definition: ERF.H:820
ERF::sum_energy_quantities
void sum_energy_quantities(amrex::Real time)
Definition: ERF_WriteScalarProfiles.cpp:312
ERF::SFS_q2fx3_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q2fx3_lev
Definition: ERF.H:926
ERF::dt_max
static amrex::Real dt_max
Definition: ERF.H:1054
ERF::lmask_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::iMultiFab > > > lmask_lev
Definition: ERF.H:915
ERF::NumSamplePointLogs
AMREX_FORCE_INLINE int NumSamplePointLogs() noexcept
Definition: ERF.H:1453
ERF::h_havg_pressure
amrex::Vector< amrex::Real > h_havg_pressure
Definition: ERF.H:1324
ERF::update_diffusive_arrays
void update_diffusive_arrays(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)
Definition: ERF_MakeNewArrays.cpp:516
ERF::verbose
static int verbose
Definition: ERF.H:1203
ERF::h_havg_qc
amrex::Vector< amrex::Real > h_havg_qc
Definition: ERF.H:1326
ERF::physbcs_w
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_w > > physbcs_w
Definition: ERF.H:838
ERF::nghost_eb_basic
static int nghost_eb_basic()
Definition: ERF.H:1635
ERF::Advance
void Advance(int lev, amrex::Real time, amrex::Real dt_lev, int iteration, int ncycle)
Definition: ERF_Advance.cpp:20
ERF::column_file_name
static std::string column_file_name
Definition: ERF.H:1267
ERF::samplelinelog
amrex::Vector< std::unique_ptr< std::fstream > > samplelinelog
Definition: ERF.H:1608
ERF::last_plot3d_file_time_2
static amrex::Real last_plot3d_file_time_2
Definition: ERF.H:1016
ERF::terrain_blanking
amrex::Vector< std::unique_ptr< amrex::MultiFab > > terrain_blanking
Definition: ERF.H:953
ERF::micro
std::unique_ptr< Microphysics > micro
Definition: ERF.H:858
ERF::m_plot2d_int_2
int m_plot2d_int_2
Definition: ERF.H:1079
ERF::base_state
amrex::Vector< amrex::MultiFab > base_state
Definition: ERF.H:967
ERF::getAdvFluxReg
AMREX_FORCE_INLINE amrex::YAFluxRegister * getAdvFluxReg(int lev)
Definition: ERF.H:1410
ERF::m_plot3d_int_1
int m_plot3d_int_1
Definition: ERF.H:1076
ERF::h_havg_density
amrex::Vector< amrex::Real > h_havg_density
Definition: ERF.H:1322
ERF::z_phys_nd_new
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_nd_new
Definition: ERF.H:947
ERF::fixed_fast_dt
amrex::Vector< amrex::Real > fixed_fast_dt
Definition: ERF.H:1058
ERF::derived_subvol_names
const amrex::Vector< std::string > derived_subvol_names
Definition: ERF.H:1165
ERF::metgrid_retain_sfc
bool metgrid_retain_sfc
Definition: ERF.H:1248
ERF::Qv_prim
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Qv_prim
Definition: ERF.H:843
ERF::sum_interval
static int sum_interval
Definition: ERF.H:1210
ERF::pert_interval
static int pert_interval
Definition: ERF.H:1211
ERF::line_sampling_per
amrex::Real line_sampling_per
Definition: ERF.H:1592
ERF::restart
void restart()
Definition: ERF.cpp:1885
ERF::last_plot3d_file_step_2
static int last_plot3d_file_step_2
Definition: ERF.H:1010
ERF::SFS_q1fx2_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q1fx2_lev
Definition: ERF.H:925
ERF::SampleLine
amrex::IntVect & SampleLine(int i)
Definition: ERF.H:1486
ERF::build_fine_mask
void build_fine_mask(int lev, amrex::MultiFab &fine_mask)
Definition: ERF_VolWgtSum.cpp:79
ERF::rV_new
amrex::Vector< amrex::MultiFab > rV_new
Definition: ERF.H:850
ERF::PlotFileName
std::string PlotFileName(int lev) const
ERF::write_1D_profiles
void write_1D_profiles(amrex::Real time)
Definition: ERF_Write1DProfiles.cpp:17
ERF::initialize_integrator
void initialize_integrator(int lev, amrex::MultiFab &cons_mf, amrex::MultiFab &vel_mf)
Definition: ERF_MakeNewArrays.cpp:775
ERF::thin_zforce
amrex::Vector< std::unique_ptr< amrex::MultiFab > > thin_zforce
Definition: ERF.H:1007
ERF::plot3d_var_names_2
amrex::Vector< std::string > plot3d_var_names_2
Definition: ERF.H:1104
ERF::domain_bcs_type
amrex::Vector< amrex::BCRec > domain_bcs_type
Definition: ERF.H:983
ERF::get_projection_bc
amrex::Array< amrex::LinOpBCType, AMREX_SPACEDIM > get_projection_bc(amrex::Orientation::Side side) const noexcept
Definition: ERF_SolveWithMLMG.cpp:17
ERF::Qr_prim
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Qr_prim
Definition: ERF.H:844
ERF::post_timestep
void post_timestep(int nstep, amrex::Real time, amrex::Real dt_lev)
Definition: ERF.cpp:689
ERF::mf_MUB
std::unique_ptr< amrex::MultiFab > mf_MUB
Definition: ERF.H:1257
ERF::pp_prefix
std::string pp_prefix
Definition: ERF.H:528
ERF::SampleLineLogName
std::string SampleLineLogName(int i) const noexcept
The filename of the ith samplelinelog file.
Definition: ERF.H:1620
ERF::sst_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > sst_lev
Definition: ERF.H:913
ERF::plot2d_var_names_1
amrex::Vector< std::string > plot2d_var_names_1
Definition: ERF.H:1105
ERF::thin_xforce
amrex::Vector< std::unique_ptr< amrex::MultiFab > > thin_xforce
Definition: ERF.H:1005
ERF::NumSamplePoints
AMREX_FORCE_INLINE int NumSamplePoints() noexcept
Definition: ERF.H:1480
ERF::mf_C2H
std::unique_ptr< amrex::MultiFab > mf_C2H
Definition: ERF.H:1256
ERF::metgrid_use_sfc
bool metgrid_use_sfc
Definition: ERF.H:1247
ERF::m_plot2d_per_2
amrex::Real m_plot2d_per_2
Definition: ERF.H:1087
ERF::bndry_output_planes_per
static amrex::Real bndry_output_planes_per
Definition: ERF.H:1272
ERF::setPlotVariables2D
void setPlotVariables2D(const std::string &pp_plot_var_names, amrex::Vector< std::string > &plot_var_names)
Definition: ERF_Plotfile.cpp:186
ERF::m_check_per
amrex::Real m_check_per
Definition: ERF.H:1099
ERF::init_custom
void init_custom(int lev)
Definition: ERF_InitCustom.cpp:26
ERF::rad
amrex::Vector< std::unique_ptr< IRadiation > > rad
Definition: ERF.H:880
ERF::prob
std::unique_ptr< ProblemBase > prob
Definition: ERF.H:795
ERF::num_files_at_level
amrex::Vector< int > num_files_at_level
Definition: ERF.H:798
ERF::WriteMultiLevelPlotfileWithTerrain
void WriteMultiLevelPlotfileWithTerrain(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, const amrex::Vector< amrex::Geometry > &my_geom, amrex::Real time, const amrex::Vector< int > &level_steps, const amrex::Vector< amrex::IntVect > &my_ref_ratio, 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: ERF_Plotfile.cpp:1745
ERF::init_bcs
void init_bcs()
Definition: ERF_InitBCs.cpp:20
ERF::profile_int
int profile_int
Definition: ERF.H:1093
ERF::metgrid_debug_quiescent
bool metgrid_debug_quiescent
Definition: ERF.H:1239
ERF::physbcs_u
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_u > > physbcs_u
Definition: ERF.H:836
ERF::t_new
amrex::Vector< amrex::Real > t_new
Definition: ERF.H:805
ERF::destag_profiles
bool destag_profiles
Definition: ERF.H:1094
ERF::stretched_dz_d
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > stretched_dz_d
Definition: ERF.H:965
ERF::th_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > th_bc_data
Definition: ERF.H:772
ERF::t_avg_cnt
amrex::Vector< amrex::Real > t_avg_cnt
Definition: ERF.H:821
ERF::FillPatchFineLevel
void FillPatchFineLevel(int lev, amrex::Real time, const amrex::Vector< amrex::MultiFab * > &mfs_vel, const amrex::Vector< amrex::MultiFab * > &mfs_mom, const amrex::MultiFab &old_base_state, const amrex::MultiFab &new_base_state, bool fillset=true, bool cons_only=false)
Definition: ERF_FillPatch.cpp:20
ERF::DerDataLogName
std::string DerDataLogName(int i) const noexcept
Definition: ERF.H:1614
ERF::remake_zphys
void remake_zphys(int lev, amrex::Real time, std::unique_ptr< amrex::MultiFab > &temp_zphys_nd)
Definition: ERF_MakeNewArrays.cpp:718
ERF::m_check_int
int m_check_int
Definition: ERF.H:1098
ERF::solar_zenith
amrex::Vector< std::unique_ptr< amrex::MultiFab > > solar_zenith
Definition: ERF.H:893
ERF::estTimeStep
amrex::Real estTimeStep(int lev, long &dt_fast_ratio) const
Definition: ERF_ComputeTimestep.cpp:54
ERF::sponge_type
static std::string sponge_type
Definition: ERF.H:1223
ERF::startCPUTime
static amrex::Real startCPUTime
Definition: ERF.H:1498
ERF::SFS_diss_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_diss_lev
Definition: ERF.H:924
ERF::d_sinesq_ptrs
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_sinesq_ptrs
Definition: ERF.H:1319
ERF::rU_old
amrex::Vector< amrex::MultiFab > rU_old
Definition: ERF.H:847
ERF::FillIntermediatePatch
void FillIntermediatePatch(int lev, amrex::Real time, const amrex::Vector< amrex::MultiFab * > &mfs_vel, const amrex::Vector< amrex::MultiFab * > &mfs_mom, int ng_cons, int ng_vel, bool cons_only, int icomp_cons, int ncomp_cons)
Definition: ERF_FillIntermediatePatch.cpp:28
ERF::t_old
amrex::Vector< amrex::Real > t_old
Definition: ERF.H:806
ERF::HurricaneTrackerNotInitial
void HurricaneTrackerNotInitial(int lev, amrex::TagBoxArray *tags=nullptr)
Definition: ERF_Tagging.cpp:601
ERF::NumSampleLines
AMREX_FORCE_INLINE int NumSampleLines() noexcept
Definition: ERF.H:1493
ERF::Theta_prim
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Theta_prim
Definition: ERF.H:842
ERF::init1DArrays
void init1DArrays()
ERF::z_t_rk
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_t_rk
Definition: ERF.H:950
ERF::check_for_nans
static int check_for_nans
Definition: ERF.H:1207
ERF::make_subdomains
void make_subdomains(const amrex::BoxList &ba, amrex::Vector< amrex::BoxArray > &bins)
Definition: ERF_MakeSubdomains.cpp:6
ERF::compute_divergence
void compute_divergence(int lev, amrex::MultiFab &rhs, amrex::Array< amrex::MultiFab const *, AMREX_SPACEDIM > rho0_u_const, amrex::Geometry const &geom_at_lev)
Definition: ERF_ComputeDivergence.cpp:10
ERF::MakeVTKFilename
std::string MakeVTKFilename(int nstep)
Definition: ERF_Write1DProfiles.cpp:574
ERF::fill_rhs
void fill_rhs(amrex::MultiFab &rhs_mf, const amrex::MultiFab &state_mf, amrex::Real time, const amrex::Geometry &geom)
ERF::appendPlotVariables
void appendPlotVariables(const std::string &pp_plot_var_names, amrex::Vector< std::string > &plot_var_names)
Definition: ERF_Plotfile.cpp:228
ERF::physbcs_v
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_v > > physbcs_v
Definition: ERF.H:837
ERF::column_per
static amrex::Real column_per
Definition: ERF.H:1264
ERF::tot_e_datalogname
amrex::Vector< std::string > tot_e_datalogname
Definition: ERF.H:1602
ERF::stop_time
static amrex::Real stop_time
Definition: ERF.H:1040
ERF::output_bndry_planes
static int output_bndry_planes
Definition: ERF.H:1270
ERF::d_v_geos
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_v_geos
Definition: ERF.H:1295
ERF::update_terrain_arrays
void update_terrain_arrays(int lev)
Definition: ERF_MakeNewArrays.cpp:758
ERF::nc_bdy_file
static std::string nc_bdy_file
Definition: ERF.H:1230
ERF::metgrid_interp_theta
bool metgrid_interp_theta
Definition: ERF.H:1244
ERF::nc_init_file
static amrex::Vector< amrex::Vector< std::string > > nc_init_file
Definition: ERF.H:1226
ERF::init_only
void init_only(int lev, amrex::Real time)
Definition: ERF.cpp:1947
ERF::input_bndry_planes
static int input_bndry_planes
Definition: ERF.H:1276
ERF::interpolation_type
static StateInterpType interpolation_type
Definition: ERF.H:1220
ERF::d_havg_qc
amrex::Gpu::DeviceVector< amrex::Real > d_havg_qc
Definition: ERF.H:1332
ERF::AverageDown
void AverageDown()
Definition: ERF_AverageDown.cpp:16
ERF::h_v_geos
amrex::Vector< amrex::Vector< amrex::Real > > h_v_geos
Definition: ERF.H:1294
ERF::projection_has_dirichlet
bool projection_has_dirichlet(amrex::Array< amrex::LinOpBCType, AMREX_SPACEDIM > bcs) const
Definition: ERF_PoissonSolve_tb.cpp:8
ERF::regrid_level_0_on_restart
bool regrid_level_0_on_restart
Definition: ERF.H:1067
ERF::Lwave_onegrid
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Lwave_onegrid
Definition: ERF.H:974
ERF::input_sounding_data
InputSoundingData input_sounding_data
Definition: ERF.H:763
ERF::d_rhoqt_src
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_rhoqt_src
Definition: ERF.H:1286
ERF::h_sinesq_ptrs
amrex::Vector< amrex::Vector< amrex::Real > > h_sinesq_ptrs
Definition: ERF.H:1311
ERF::Write2DPlotFile
void Write2DPlotFile(int which, PlotFileType plotfile_type, amrex::Vector< std::string > plot_var_names)
Definition: ERF_Plotfile.cpp:1921
ERF::d_havg_density
amrex::Gpu::DeviceVector< amrex::Real > d_havg_density
Definition: ERF.H:1328
ERF::init_from_hse
void init_from_hse(int lev)
Definition: ERF_InitFromHSE.cpp:32
ERF::datetime_format
const std::string datetime_format
Definition: ERF.H:1043
ERF::advflux_reg
amrex::Vector< amrex::YAFluxRegister * > advflux_reg
Definition: ERF.H:978
ERF::metgrid_force_sfc_k
int metgrid_force_sfc_k
Definition: ERF.H:1251
ERF::h_rhotheta_src
amrex::Vector< amrex::Vector< amrex::Real > > h_rhotheta_src
Definition: ERF.H:1282
ERF::setSubVolVariables
void setSubVolVariables(const std::string &pp_subvol_var_names, amrex::Vector< std::string > &subvol_var_names)
Definition: ERF_WriteSubvolume.cpp:8
ERF::ng_pres_hse
static int ng_pres_hse
Definition: ERF.H:1279
ERF::bndry_output_planes_start_time
static amrex::Real bndry_output_planes_start_time
Definition: ERF.H:1273
ERF::real_extrap_w
bool real_extrap_w
Definition: ERF.H:1233
ERF::cfl
static amrex::Real cfl
Definition: ERF.H:1049
ERF::fine_mask
amrex::Vector< std::unique_ptr< amrex::MultiFab > > fine_mask
Definition: ERF.H:962
ERF::project_velocity
void project_velocity(int lev, amrex::Real dt)
Definition: ERF_PoissonSolve.cpp:10
ERF::solve_with_mlmg
void solve_with_mlmg(int lev, amrex::Vector< amrex::MultiFab > &rhs, amrex::Vector< amrex::MultiFab > &p, amrex::Vector< amrex::Array< amrex::MultiFab, AMREX_SPACEDIM >> &fluxes)
Definition: ERF_SolveWithMLMG.cpp:40
ERF::domain_bcs_type_d
amrex::Gpu::DeviceVector< amrex::BCRec > domain_bcs_type_d
Definition: ERF.H:984
ERF::m_forest_drag
amrex::Vector< std::unique_ptr< ForestDrag > > m_forest_drag
Definition: ERF.H:1339
ERF::datwidth
const int datwidth
Definition: ERF.H:1027
ERF::derive_diag_profiles_stag
void derive_diag_profiles_stag(amrex::Real time, amrex::Gpu::HostVector< amrex::Real > &h_avg_u, amrex::Gpu::HostVector< amrex::Real > &h_avg_v, amrex::Gpu::HostVector< amrex::Real > &h_avg_w, amrex::Gpu::HostVector< amrex::Real > &h_avg_rho, amrex::Gpu::HostVector< amrex::Real > &h_avg_th, amrex::Gpu::HostVector< amrex::Real > &h_avg_ksgs, amrex::Gpu::HostVector< amrex::Real > &h_avg_Kmv, amrex::Gpu::HostVector< amrex::Real > &h_avg_Khv, amrex::Gpu::HostVector< amrex::Real > &h_avg_qv, amrex::Gpu::HostVector< amrex::Real > &h_avg_qc, amrex::Gpu::HostVector< amrex::Real > &h_avg_qr, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqv, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqc, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqr, amrex::Gpu::HostVector< amrex::Real > &h_avg_qi, amrex::Gpu::HostVector< amrex::Real > &h_avg_qs, amrex::Gpu::HostVector< amrex::Real > &h_avg_qg, amrex::Gpu::HostVector< amrex::Real > &h_avg_uu, amrex::Gpu::HostVector< amrex::Real > &h_avg_uv, amrex::Gpu::HostVector< amrex::Real > &h_avg_uw, amrex::Gpu::HostVector< amrex::Real > &h_avg_vv, amrex::Gpu::HostVector< amrex::Real > &h_avg_vw, amrex::Gpu::HostVector< amrex::Real > &h_avg_ww, amrex::Gpu::HostVector< amrex::Real > &h_avg_uth, amrex::Gpu::HostVector< amrex::Real > &h_avg_vth, amrex::Gpu::HostVector< amrex::Real > &h_avg_wth, amrex::Gpu::HostVector< amrex::Real > &h_avg_thth, amrex::Gpu::HostVector< amrex::Real > &h_avg_ku, amrex::Gpu::HostVector< amrex::Real > &h_avg_kv, amrex::Gpu::HostVector< amrex::Real > &h_avg_kw, amrex::Gpu::HostVector< amrex::Real > &h_avg_p, amrex::Gpu::HostVector< amrex::Real > &h_avg_pu, amrex::Gpu::HostVector< amrex::Real > &h_avg_pv, amrex::Gpu::HostVector< amrex::Real > &h_avg_pw, amrex::Gpu::HostVector< amrex::Real > &h_avg_wthv)
Definition: ERF_Write1DProfiles_stag.cpp:296
ERF::ba1d
amrex::Vector< amrex::BoxArray > ba1d
Definition: ERF.H:1253
ERF::input_sponge_data
InputSpongeData input_sponge_data
Definition: ERF.H:766
ERF::subdomains
amrex::Vector< amrex::Vector< amrex::BoxArray > > subdomains
Definition: ERF.H:1346
ERF::check_state_for_nans
void check_state_for_nans(amrex::MultiFab const &S)
Definition: ERF.cpp:2860
ERF::restart_chkfile
std::string restart_chkfile
Definition: ERF.H:1046
ERF::metgrid_use_below_sfc
bool metgrid_use_below_sfc
Definition: ERF.H:1246
ERF::init_zphys
void init_zphys(int lev, amrex::Real time)
Definition: ERF_MakeNewArrays.cpp:641
ERF::sampleptlogname
amrex::Vector< std::string > sampleptlogname
Definition: ERF.H:1605
ERF::xvel_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > xvel_bc_data
Definition: ERF.H:769
ERF::InitData_pre
void InitData_pre()
Definition: ERF.cpp:901
ERF::SamplePoint
amrex::IntVect & SamplePoint(int i)
Definition: ERF.H:1473
ERF::use_datetime
bool use_datetime
Definition: ERF.H:1042
ERF::hurricane_track_xy
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_track_xy
Definition: ERF.H:162
ERF::h_u_geos
amrex::Vector< amrex::Vector< amrex::Real > > h_u_geos
Definition: ERF.H:1291
ERF::InitializeLevelFromData
void InitializeLevelFromData(int lev, const amrex::MultiFab &initial_data)
ERF::subvol_file
std::string subvol_file
Definition: ERF.H:1074
ERF::m_subvol_per
amrex::Vector< amrex::Real > m_subvol_per
Definition: ERF.H:1082
ERF::rad_datalog_int
int rad_datalog_int
Definition: ERF.H:896
ERF::sum_derived_quantities
void sum_derived_quantities(amrex::Real time)
Definition: ERF_WriteScalarProfiles.cpp:177
ERF::sum_integrated_quantities
void sum_integrated_quantities(amrex::Real time)
Definition: ERF_WriteScalarProfiles.cpp:15
ERF::datalogname
amrex::Vector< std::string > datalogname
Definition: ERF.H:1600
ERF::initHSE
void initHSE()
Initialize HSE.
Definition: ERF_Init1D.cpp:146
ERF::column_loc_x
static amrex::Real column_loc_x
Definition: ERF.H:1265
ERF::ax
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ax
Definition: ERF.H:936
ERF::z_phys_nd
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_nd
Definition: ERF.H:932
ERF::MakeDiagnosticAverage
void MakeDiagnosticAverage(amrex::Vector< amrex::Real > &h_havg, amrex::MultiFab &S, int n)
Definition: ERF.cpp:2716
ERF::metgrid_proximity
amrex::Real metgrid_proximity
Definition: ERF.H:1249
ERF::volWgtSumMF
amrex::Real volWgtSumMF(int lev, const amrex::MultiFab &mf, int comp, const amrex::MultiFab &dJ, const amrex::MultiFab &mfx, const amrex::MultiFab &mfy, bool finemask, bool local=true)
Definition: ERF_VolWgtSum.cpp:20
ERF::setRecordDerDataInfo
void setRecordDerDataInfo(int i, const std::string &filename)
Definition: ERF.H:1529
ERF::h_havg_temperature
amrex::Vector< amrex::Real > h_havg_temperature
Definition: ERF.H:1323
ERF::advance_dycore
void advance_dycore(int level, amrex::Vector< amrex::MultiFab > &state_old, amrex::Vector< amrex::MultiFab > &state_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, amrex::MultiFab &xmom_src, amrex::MultiFab &ymom_src, amrex::MultiFab &zmom_src, amrex::MultiFab &buoyancy, amrex::Geometry fine_geom, amrex::Real dt, amrex::Real time)
Definition: ERF_AdvanceDycore.cpp:38
ERF::sampleptlog
amrex::Vector< std::unique_ptr< std::fstream > > sampleptlog
Definition: ERF.H:1604
ERF::poisson_wall_dist
void poisson_wall_dist(int lev)
Definition: ERF_PoissonWallDist.cpp:20
ERF::hurricane_eye_track_latlon
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_eye_track_latlon
Definition: ERF.H:164
ERF::detJ_cc_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > detJ_cc_src
Definition: ERF.H:942
ERF::d_havg_pressure
amrex::Gpu::DeviceVector< amrex::Real > d_havg_pressure
Definition: ERF.H:1330
ERF::plot2d_file_1
std::string plot2d_file_1
Definition: ERF.H:1072
ERF::der_datalogname
amrex::Vector< std::string > der_datalogname
Definition: ERF.H:1601
ERF::SmnSmn_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SmnSmn_lev
Definition: ERF.H:910
ERF::derived_names
const amrex::Vector< std::string > derived_names
Definition: ERF.H:1114
ERF::MakeVTKFilename_TrackerCircle
std::string MakeVTKFilename_TrackerCircle(int nstep)
Definition: ERF_Write1DProfiles.cpp:587
ERF::ay_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ay_src
Definition: ERF.H:944
ERF::sample_points
void sample_points(int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab &mf)
Definition: ERF_WriteScalarProfiles.cpp:527
ERF::DataLog
AMREX_FORCE_INLINE std::ostream & DataLog(int i)
Definition: ERF.H:1417
ERF::writeJobInfo
void writeJobInfo(const std::string &dir) const
Definition: ERF_WriteJobInfo.cpp:10
ERF::solve_with_EB_mlmg
void solve_with_EB_mlmg(int lev, amrex::Vector< amrex::MultiFab > &rhs, amrex::Vector< amrex::MultiFab > &p, amrex::Vector< amrex::Array< amrex::MultiFab, AMREX_SPACEDIM >> &fluxes)
Definition: ERF_SolveWithEBMLMG.cpp:19
ERF::MakeVTKFilename_EyeTracker_xy
std::string MakeVTKFilename_EyeTracker_xy(int nstep)
Definition: ERF_Write1DProfiles.cpp:601
ERF::ComputeDt
void ComputeDt(int step=-1)
Definition: ERF_ComputeTimestep.cpp:11
ERF::nsubsteps
amrex::Vector< int > nsubsteps
Definition: ERF.H:802
ERF::yflux_imask
amrex::Vector< std::unique_ptr< amrex::iMultiFab > > yflux_imask
Definition: ERF.H:1000
ERF::rW_new
amrex::Vector< amrex::MultiFab > rW_new
Definition: ERF.H:852
ERF::weather_forecast_data_2
amrex::Vector< amrex::MultiFab > weather_forecast_data_2
Definition: ERF.H:167
ERF::lon_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > lon_m
Definition: ERF.H:758
ERF::m_w2d
std::unique_ptr< WriteBndryPlanes > m_w2d
Definition: ERF.H:1336
ERF::SampleLineLog
AMREX_FORCE_INLINE std::ostream & SampleLineLog(int i)
Definition: ERF.H:1460
ERF::lsm_flux
amrex::Vector< amrex::Vector< amrex::MultiFab * > > lsm_flux
Definition: ERF.H:878
ERF::plot3d_var_names_1
amrex::Vector< std::string > plot3d_var_names_1
Definition: ERF.H:1103
ERF::SamplePointLogName
std::string SamplePointLogName(int i) const noexcept
The filename of the ith sampleptlog file.
Definition: ERF.H:1617
ERF::turbPert_update
void turbPert_update(const int lev, const amrex::Real dt)
Definition: ERF_InitTurbPert.cpp:12
ERF::InitData_post
void InitData_post()
Definition: ERF.cpp:980
ERF::refinement_criteria_setup
void refinement_criteria_setup()
Definition: ERF_Tagging.cpp:274
ERF::nghost_eb_volume
static int nghost_eb_volume()
Definition: ERF.H:1639
ERF::metgrid_debug_dry
bool metgrid_debug_dry
Definition: ERF.H:1241
ERF::ComputeGhostCells
static AMREX_FORCE_INLINE int ComputeGhostCells(const SolverChoice &sc)
Definition: ERF.H:1352
ERF::bndry_output_planes_interval
static int bndry_output_planes_interval
Definition: ERF.H:1271
ERF::init_geo_wind_profile
void init_geo_wind_profile(const std::string input_file, amrex::Vector< amrex::Real > &u_geos, amrex::Gpu::DeviceVector< amrex::Real > &u_geos_d, amrex::Vector< amrex::Real > &v_geos, amrex::Gpu::DeviceVector< amrex::Real > &v_geos_d, const amrex::Geometry &lgeom, const amrex::Vector< amrex::Real > &zlev_stag)
Definition: ERF_InitGeowind.cpp:10
ERF::ERF_shared
void ERF_shared()
Definition: ERF.cpp:142
ERF::plot2d_var_names_2
amrex::Vector< std::string > plot2d_var_names_2
Definition: ERF.H:1106
ERF::WeatherDataInterpolation
void WeatherDataInterpolation(const int nlevs, const amrex::Real time, amrex::Vector< std::unique_ptr< amrex::MultiFab >> &z_phys_nd, bool regrid_forces_file_read)
Definition: ERF_WeatherDataInterpolation.cpp:347
ERF::Tau_corr
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > Tau_corr
Definition: ERF.H:908
ERF::WriteSubvolume
void WriteSubvolume(int isub, amrex::Vector< std::string > subvol_var_names)
Definition: ERF_WriteSubvolume.cpp:144
ERF::nghost_eb_full
static int nghost_eb_full()
Definition: ERF.H:1642
ERF::RemakeLevel
void RemakeLevel(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: ERF_MakeNewLevel.cpp:515
ERF::GotoNextLine
static void GotoNextLine(std::istream &is)
Definition: ERF_Checkpoint.cpp:16
ERF::MakeNewLevelFromScratch
void MakeNewLevelFromScratch(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: ERF_MakeNewLevel.cpp:25
ERF::init_stuff
void init_stuff(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm, amrex::Vector< amrex::MultiFab > &lev_new, amrex::Vector< amrex::MultiFab > &lev_old, amrex::MultiFab &tmp_base_state, std::unique_ptr< amrex::MultiFab > &tmp_zphys_nd)
Definition: ERF_MakeNewArrays.cpp:24
ERF::zmom_crse_rhs
amrex::Vector< amrex::MultiFab > zmom_crse_rhs
Definition: ERF.H:856
ERF::metgrid_debug_isothermal
bool metgrid_debug_isothermal
Definition: ERF.H:1240
ERF::lsm_data_name
amrex::Vector< std::string > lsm_data_name
Definition: ERF.H:875
ERF::initSponge
void initSponge()
Initialize sponge profiles.
Definition: ERF_InitSponge.cpp:35
ERF::plane_sampler
std::unique_ptr< PlaneSampler > plane_sampler
Definition: ERF.H:1595
ERF::check_for_low_temp
void check_for_low_temp(amrex::MultiFab &S)
Definition: ERF.cpp:2910
ERF::der_datalog
amrex::Vector< std::unique_ptr< std::fstream > > der_datalog
Definition: ERF.H:1598
ERF::have_read_nc_init_file
static amrex::Vector< amrex::Vector< int > > have_read_nc_init_file
Definition: ERF.H:1227
ERF::m_plot3d_per_2
amrex::Real m_plot3d_per_2
Definition: ERF.H:1085
ERF::advance_lsm
void advance_lsm(int lev, amrex::MultiFab &cons_in, amrex::MultiFab &xvel_in, amrex::MultiFab &yvel_in, const amrex::Real &dt_advance)
Definition: ERF_AdvanceLSM.cpp:5
ERF::tot_e_datalog
amrex::Vector< std::unique_ptr< std::fstream > > tot_e_datalog
Definition: ERF.H:1599
ERF::sinPhi_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > sinPhi_m
Definition: ERF.H:760
ERF::derive_diag_profiles
void derive_diag_profiles(amrex::Real time, amrex::Gpu::HostVector< amrex::Real > &h_avg_u, amrex::Gpu::HostVector< amrex::Real > &h_avg_v, amrex::Gpu::HostVector< amrex::Real > &h_avg_w, amrex::Gpu::HostVector< amrex::Real > &h_avg_rho, amrex::Gpu::HostVector< amrex::Real > &h_avg_th, amrex::Gpu::HostVector< amrex::Real > &h_avg_ksgs, amrex::Gpu::HostVector< amrex::Real > &h_avg_Kmv, amrex::Gpu::HostVector< amrex::Real > &h_avg_Khv, amrex::Gpu::HostVector< amrex::Real > &h_avg_qv, amrex::Gpu::HostVector< amrex::Real > &h_avg_qc, amrex::Gpu::HostVector< amrex::Real > &h_avg_qr, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqv, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqc, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqr, amrex::Gpu::HostVector< amrex::Real > &h_avg_qi, amrex::Gpu::HostVector< amrex::Real > &h_avg_qs, amrex::Gpu::HostVector< amrex::Real > &h_avg_qg, amrex::Gpu::HostVector< amrex::Real > &h_avg_uu, amrex::Gpu::HostVector< amrex::Real > &h_avg_uv, amrex::Gpu::HostVector< amrex::Real > &h_avg_uw, amrex::Gpu::HostVector< amrex::Real > &h_avg_vv, amrex::Gpu::HostVector< amrex::Real > &h_avg_vw, amrex::Gpu::HostVector< amrex::Real > &h_avg_ww, amrex::Gpu::HostVector< amrex::Real > &h_avg_uth, amrex::Gpu::HostVector< amrex::Real > &h_avg_vth, amrex::Gpu::HostVector< amrex::Real > &h_avg_wth, amrex::Gpu::HostVector< amrex::Real > &h_avg_thth, amrex::Gpu::HostVector< amrex::Real > &h_avg_ku, amrex::Gpu::HostVector< amrex::Real > &h_avg_kv, amrex::Gpu::HostVector< amrex::Real > &h_avg_kw, amrex::Gpu::HostVector< amrex::Real > &h_avg_p, amrex::Gpu::HostVector< amrex::Real > &h_avg_pu, amrex::Gpu::HostVector< amrex::Real > &h_avg_pv, amrex::Gpu::HostVector< amrex::Real > &h_avg_pw, amrex::Gpu::HostVector< amrex::Real > &h_avg_wthv)
Definition: ERF_Write1DProfiles.cpp:190
ERF::HurricaneTrackerInitial
void HurricaneTrackerInitial(int lev, const amrex::MultiFab &U_new, const amrex::MultiFab &V_new, const amrex::MultiFab &W_new, const amrex::Real velmag_threshold, amrex::TagBoxArray *tags=nullptr)
Definition: ERF_Tagging.cpp:502
ERF::real_width
int real_width
Definition: ERF.H:1231
ERF::MakeNewLevelFromCoarse
void MakeNewLevelFromCoarse(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: ERF_MakeNewLevel.cpp:292
ERF::last_subvol_step
amrex::Vector< int > last_subvol_step
Definition: ERF.H:1021
ERF::ax_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ax_src
Definition: ERF.H:943
ERF::urb_frac_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > urb_frac_lev
Definition: ERF.H:920
ERF::z_phys_cc_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_cc_src
Definition: ERF.H:941
ERF::input_sponge
void input_sponge(int lev)
Definition: ERF_InitSponge.cpp:17
ERF::d_u_geos
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_u_geos
Definition: ERF.H:1292
ERF::Define_ERFFillPatchers
void Define_ERFFillPatchers(int lev)
Definition: ERF.cpp:2788
ERF::NumDataLogs
AMREX_FORCE_INLINE int NumDataLogs() noexcept
Definition: ERF.H:1431
ERF::plotfile3d_type_2
static PlotFileType plotfile3d_type_2
Definition: ERF.H:1216
ERF::setRecordEnergyDataInfo
void setRecordEnergyDataInfo(int i, const std::string &filename)
Definition: ERF.H:1542
ERF::turbPert
TurbulentPerturbation turbPert
Definition: ERF.H:1171
ERF::rW_old
amrex::Vector< amrex::MultiFab > rW_old
Definition: ERF.H:851
ERF::forecast_state_2
amrex::Vector< amrex::Vector< amrex::MultiFab > > forecast_state_2
Definition: ERF.H:169
ERF::check_for_negative_theta
void check_for_negative_theta(amrex::MultiFab &S)
Definition: ERF.cpp:2945
ERF::ImposeBCsOnPhi
void ImposeBCsOnPhi(int lev, amrex::MultiFab &phi, const amrex::Box &subdomain)
Definition: ERF_ImposeBCsOnPhi.cpp:12
ERF::FillCoarsePatch
void FillCoarsePatch(int lev, amrex::Real time)
Definition: ERF_FillCoarsePatch.cpp:21
ERF::ClearLevel
void ClearLevel(int lev) override
Definition: ERF_MakeNewLevel.cpp:742
ERF::m_SurfaceLayer
std::unique_ptr< SurfaceLayer > m_SurfaceLayer
Definition: ERF.H:1338
ERF::plotfile2d_type_2
static PlotFileType plotfile2d_type_2
Definition: ERF.H:1218
ERF::plane_sampling_interval
int plane_sampling_interval
Definition: ERF.H:1591
ERF::ref_tags
static amrex::Vector< amrex::AMRErrorTag > ref_tags
Definition: ERF.H:1344
ERF::make_physbcs
void make_physbcs(int lev)
Definition: ERF_MakeNewArrays.cpp:797
ERF::d_w_subsid
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_w_subsid
Definition: ERF.H:1289
ERF::FPr_w
amrex::Vector< ERFFillPatcher > FPr_w
Definition: ERF.H:904
ERF::real_set_width
int real_set_width
Definition: ERF.H:1232
ERF::SFS_hfx2_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_hfx2_lev
Definition: ERF.H:923
ERF::WriteLinePlot
void WriteLinePlot(const std::string &filename, amrex::Vector< std::array< amrex::Real, 2 >> &points_xy)
Definition: ERF_Write1DProfiles.cpp:690
ERF::soil_type_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::iMultiFab > > > soil_type_lev
Definition: ERF.H:919
ERF::writeNow
bool writeNow(const amrex::Real cur_time, const int nstep, const int plot_int, const amrex::Real plot_per, const amrex::Real dt_0, amrex::Real &last_file_time)
Definition: ERF.cpp:2839
ERF::zlevels_stag
amrex::Vector< amrex::Vector< amrex::Real > > zlevels_stag
Definition: ERF.H:929
ERF::NumDerDataLogs
AMREX_FORCE_INLINE int NumDerDataLogs() noexcept
Definition: ERF.H:1438
ERF::EBFactory
amrex::EBFArrayBoxFactory const & EBFactory(int lev) const noexcept
Definition: ERF.H:1631
ERF::lsm_data
amrex::Vector< amrex::Vector< amrex::MultiFab * > > lsm_data
Definition: ERF.H:876
ERF::init_immersed_forcing
void init_immersed_forcing(int lev)
Definition: ERF_InitImmersedForcing.cpp:15
ERF::stretched_dz_h
amrex::Vector< amrex::Vector< amrex::Real > > stretched_dz_h
Definition: ERF.H:964
ERF::m_plot2d_int_1
int m_plot2d_int_1
Definition: ERF.H:1078
ERF::WriteCheckpointFile
void WriteCheckpointFile() const
Definition: ERF_Checkpoint.cpp:26
ERF::output_1d_column
static int output_1d_column
Definition: ERF.H:1262
ERF::metgrid_debug_psfc
bool metgrid_debug_psfc
Definition: ERF.H:1242
ERF::az_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > az_src
Definition: ERF.H:945
ERF::fixed_mri_dt_ratio
static int fixed_mri_dt_ratio
Definition: ERF.H:1059
ERF::dt
amrex::Vector< amrex::Real > dt
Definition: ERF.H:807
ERF::init_shrink
static amrex::Real init_shrink
Definition: ERF.H:1051
ERF::WriteVTKPolyline
void WriteVTKPolyline(const std::string &filename, amrex::Vector< std::array< amrex::Real, 2 >> &points_xy)
Definition: ERF_Write1DProfiles.cpp:643
ERF::Write3DPlotFile
void Write3DPlotFile(int which, PlotFileType plotfile_type, amrex::Vector< std::string > plot_var_names)
Definition: ERF_Plotfile.cpp:307
ERF::advance_radiation
void advance_radiation(int lev, amrex::MultiFab &cons_in, const amrex::Real &dt_advance)
Definition: ERF_AdvanceRadiation.cpp:5
ERF::dt_max_initial
static amrex::Real dt_max_initial
Definition: ERF.H:1053
ERF::is_it_time_for_action
static bool is_it_time_for_action(int nstep, amrex::Real time, amrex::Real dt, int action_interval, amrex::Real action_per)
Definition: ERF_WriteScalarProfiles.cpp:653
ERF::nc_low_file
static std::string nc_low_file
Definition: ERF.H:1236
ERF::d_rayleigh_ptrs
amrex::Vector< amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > > d_rayleigh_ptrs
Definition: ERF.H:1315
ERF::InitData
void InitData()
Definition: ERF.cpp:892
ERF::advance_microphysics
void advance_microphysics(int lev, amrex::MultiFab &cons_in, const amrex::Real &dt_advance, const int &iteration, const amrex::Real &time)
Definition: ERF_AdvanceMicrophysics.cpp:5
ERF::Lwave
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Lwave
Definition: ERF.H:972
ERF::cosPhi_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > cosPhi_m
Definition: ERF.H:760
ERF::ParameterSanityChecks
void ParameterSanityChecks()
Definition: ERF.cpp:2543
ERF::land_type_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::iMultiFab > > > land_type_lev
Definition: ERF.H:918
ERF::derive_stress_profiles
void derive_stress_profiles(amrex::Gpu::HostVector< amrex::Real > &h_avg_tau11, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau12, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau13, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau22, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau23, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau33, amrex::Gpu::HostVector< amrex::Real > &h_avg_hfx3, amrex::Gpu::HostVector< amrex::Real > &h_avg_q1fx3, amrex::Gpu::HostVector< amrex::Real > &h_avg_q2fx3, amrex::Gpu::HostVector< amrex::Real > &h_avg_diss)
Definition: ERF_Write1DProfiles.cpp:475
ERF::forecast_state_1
amrex::Vector< amrex::Vector< amrex::MultiFab > > forecast_state_1
Definition: ERF.H:168
ERF::cf_width
int cf_width
Definition: ERF.H:899
ERF::last_plot2d_file_step_1
static int last_plot2d_file_step_1
Definition: ERF.H:1011
ERF::zflux_imask
amrex::Vector< std::unique_ptr< amrex::iMultiFab > > zflux_imask
Definition: ERF.H:1001
ERF::m_expand_plotvars_to_unif_rr
bool m_expand_plotvars_to_unif_rr
Definition: ERF.H:1075
ERF::m_plot3d_per_1
amrex::Real m_plot3d_per_1
Definition: ERF.H:1084
ERF::Construct_ERFFillPatchers
void Construct_ERFFillPatchers(int lev)
Definition: ERF.cpp:2762
ERF::post_update
void post_update(amrex::MultiFab &state_mf, amrex::Real time, const amrex::Geometry &geom)
ERF::num_boxes_at_level
amrex::Vector< int > num_boxes_at_level
Definition: ERF.H:797
ERF::sub_cfl
static amrex::Real sub_cfl
Definition: ERF.H:1050
ERF::print_error
static void print_error(MPI_Comm, const std::string &msg)
Definition: ERF_ConsoleIO.cpp:43
ERF::ng_dens_hse
static int ng_dens_hse
Definition: ERF.H:1278
ERF::m_r2d
std::unique_ptr< ReadBndryPlanes > m_r2d
Definition: ERF.H:1337
ERF::ay
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ay
Definition: ERF.H:937
ERF::project_momenta
void project_momenta(int lev, amrex::Real dt, amrex::Vector< amrex::MultiFab > &vars)
Definition: ERF_PoissonSolve.cpp:44
ERF::qmoist
amrex::Vector< amrex::Vector< amrex::MultiFab * > > qmoist
Definition: ERF.H:859
ERF::SFS_q1fx1_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q1fx1_lev
Definition: ERF.H:925
ERF::getCPUTime
static amrex::Real getCPUTime()
Definition: ERF.H:1502
ERF::zvel_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > zvel_bc_data
Definition: ERF.H:771
ERF::derive_stress_profiles_stag
void derive_stress_profiles_stag(amrex::Gpu::HostVector< amrex::Real > &h_avg_tau11, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau12, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau13, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau22, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau23, amrex::Gpu::HostVector< amrex::Real > &h_avg_tau33, amrex::Gpu::HostVector< amrex::Real > &h_avg_hfx3, amrex::Gpu::HostVector< amrex::Real > &h_avg_q1fx3, amrex::Gpu::HostVector< amrex::Real > &h_avg_q2fx3, amrex::Gpu::HostVector< amrex::Real > &h_avg_diss)
Definition: ERF_Write1DProfiles_stag.cpp:605
ERF::lsm
LandSurface lsm
Definition: ERF.H:874
ERF::change_max
static amrex::Real change_max
Definition: ERF.H:1052
ERF::AverageDownTo
void AverageDownTo(int crse_lev, int scomp, int ncomp)
Definition: ERF_AverageDown.cpp:36
ERF::setRecordSampleLineInfo
void setRecordSampleLineInfo(int i, int lev, amrex::IntVect &cell, const std::string &filename)
Definition: ERF.H:1572
ERF::setSpongeRefFromSounding
void setSpongeRefFromSounding(bool restarting)
Set sponge mean profiles from input sounding.
Definition: ERF_InitSponge.cpp:65
ERF::avg_ymom
amrex::Vector< amrex::MultiFab > avg_ymom
Definition: ERF.H:831
ERF::line_sampling_interval
int line_sampling_interval
Definition: ERF.H:1590
ERF::h_sinesq_stag_ptrs
amrex::Vector< amrex::Vector< amrex::Real > > h_sinesq_stag_ptrs
Definition: ERF.H:1312
ERF::detJ_cc_new
amrex::Vector< std::unique_ptr< amrex::MultiFab > > detJ_cc_new
Definition: ERF.H:948
ERF::domain_bc_type
amrex::Array< std::string, 2 *AMREX_SPACEDIM > domain_bc_type
Definition: ERF.H:987
ERF::yvel_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > yvel_bc_data
Definition: ERF.H:770
ERF::init_uniform
void init_uniform(int lev)
Definition: ERF_InitUniform.cpp:17
ERF::writeBuildInfo
static void writeBuildInfo(std::ostream &os)
Definition: ERF_WriteJobInfo.cpp:144
ERF::phys_bc_type
amrex::GpuArray< ERF_BC, AMREX_SPACEDIM *2 > phys_bc_type
Definition: ERF.H:996
ERF::check_file
std::string check_file
Definition: ERF.H:1097
ERF::samplepoint
amrex::Vector< amrex::IntVect > samplepoint
Definition: ERF.H:1606
ERF::h_havg_qv
amrex::Vector< amrex::Real > h_havg_qv
Definition: ERF.H:1325
ERF::last_subvol_time
amrex::Vector< amrex::Real > last_subvol_time
Definition: ERF.H:1022
ERF::weather_forecast_data_1
amrex::Vector< amrex::MultiFab > weather_forecast_data_1
Definition: ERF.H:167
ERF::print_usage
static void print_usage(MPI_Comm, std::ostream &)
Definition: ERF_ConsoleIO.cpp:26
ERF::rV_old
amrex::Vector< amrex::MultiFab > rV_old
Definition: ERF.H:849
ERF::HurricaneTracker
void HurricaneTracker(int lev, amrex::Real time, const amrex::MultiFab &U_new, const amrex::MultiFab &V_new, const amrex::MultiFab &W_new, const amrex::Real velmag_threshold, amrex::TagBoxArray *tags=nullptr)
Definition: ERF_Tagging.cpp:632
ERF::lat_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > lat_m
Definition: ERF.H:758
ERF::h_rayleigh_ptrs
amrex::Vector< amrex::Vector< amrex::Vector< amrex::Real > > > h_rayleigh_ptrs
Definition: ERF.H:1307
ERF::make_eb_regular
void make_eb_regular()
ERF::last_check_file_time
static amrex::Real last_check_file_time
Definition: ERF.H:1019
ERF::mf_C1H
std::unique_ptr< amrex::MultiFab > mf_C1H
Definition: ERF.H:1255
ERF::last_plot3d_file_step_1
static int last_plot3d_file_step_1
Definition: ERF.H:1009
ERF::last_plot3d_file_time_1
static amrex::Real last_plot3d_file_time_1
Definition: ERF.H:1015
ERF::line_sampler
std::unique_ptr< LineSampler > line_sampler
Definition: ERF.H:1594
ERF::Hwave
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Hwave
Definition: ERF.H:971
ERF::istep
amrex::Vector< int > istep
Definition: ERF.H:801
ERF::datprecision
const int datprecision
Definition: ERF.H:1028
ERF::xflux_imask
amrex::Vector< std::unique_ptr< amrex::iMultiFab > > xflux_imask
Definition: ERF.H:999
ERF::derive_upwp
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Definition: ERF.H:1217
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Definition: ERF.H:1250
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Definition: ERF.H:975
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Definition: ERF_Checkpoint.cpp:448
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Definition: ERF.H:814
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Definition: ERF.H:839
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Definition: ERF_MakeNewLevel.cpp:787
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Definition: ERF.H:1215
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Definition: ERF.H:1081
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Definition: ERF.H:1446
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Definition: ERF_Write1DProfiles.cpp:615
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Definition: ERF.H:993
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Definition: ERF.H:914
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Definition: ERF.H:1555
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Definition: ERF.H:1263
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Definition: ERF.H:1077
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Definition: ERF.H:881
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Definition: ERF_InitTurbPert.cpp:32
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Definition: ERF_WriteScalarProfiles.cpp:563
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Definition: ERF.H:882
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Definition: ERF.cpp:1850
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Definition: ERF.H:1090
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Definition: ERF.H:832
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Definition: ERF.H:1107
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Definition: ERF_Checkpoint.cpp:1040
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Definition: ERF_TimeStep.cpp:17
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Definition: ERF_LandSurface.H:15
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Definition: ERF_EB.H:13
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Definition: ERF_Kessler.H:25
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Definition: ERF_Kessler.H:28
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Definition: ERF_IndexDefines.H:110
Vars::xvel
@ xvel
Definition: ERF_IndexDefines.H:141
Vars::cons
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Definition: ERF_IndexDefines.H:140
Vars::zvel
@ zvel
Definition: ERF_IndexDefines.H:143
Vars::yvel
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Definition: ERF_IndexDefines.H:142
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Definition: ERF_ConsoleIO.cpp:12
module_mp_morr_two_moment::pi
real(c_double), parameter, private pi
Definition: ERF_module_mp_morr_two_moment.F90:100
module_mp_morr_two_moment::isub
integer, private isub
Definition: ERF_module_mp_morr_two_moment.F90:164
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Definition: ERF_AdvStruct.H:423
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Definition: ERF_AdvStruct.H:420
AdvChoice::moistscal_vert_adv_type
AdvType moistscal_vert_adv_type
Definition: ERF_AdvStruct.H:424
AdvChoice::dryscal_horiz_adv_type
AdvType dryscal_horiz_adv_type
Definition: ERF_AdvStruct.H:421
AdvChoice::dycore_horiz_adv_type
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Definition: ERF_AdvStruct.H:419
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Definition: ERF_AdvStruct.H:422
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Definition: ERF_InputSoundingData.H:22
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Definition: ERF_InputSpongeData.H:19
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Definition: ERF_DataStruct.H:128
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Definition: ERF_DataStruct.H:1094
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Definition: ERF_DataStruct.H:991
SolverChoice::terrain_type
static TerrainType terrain_type
Definition: ERF_DataStruct.H:971
TurbulentPerturbation
Definition: ERF_TurbPertStruct.H:22