ERF
Energy Research and Forecasting: An Atmospheric Modeling Code
ERF.H
Go to the documentation of this file.
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  amrex::Real EvolveOneStep (amrex::Real time, amrex::Real dt_request);
140 
141  void PackAtmosphericStates (amrex::Vector<amrex::MultiFab*>& states, amrex::Real time);
142  void ApplyOceanSurfaceState (const amrex::Vector<amrex::MultiFab*>& state, amrex::Real time);
143 
144  // Tag cells for refinement
145  void ErrorEst (int lev, amrex::TagBoxArray& tags, amrex::Real time, int ngrow) override;
146 
147  // Refinement criteria for hurricanes
148  void HurricaneTracker (int lev,
149  amrex::Real time,
150  const amrex::MultiFab& cc_vel,
151  const amrex::Real velmag_threshold,
152  amrex::TagBoxArray* tags = nullptr);
153 
154  bool FindInitialEye (int lev,
155  const amrex::MultiFab& cc_vel,
156  const amrex::Real velmag_threshold,
157  amrex::Real& eye_x, amrex::Real& eye_y);
158 
159  // Hurricane track line output as VTKPolyline
160  amrex::Vector<std::array<amrex::Real, 2>> hurricane_track_xy;
161  amrex::Vector<std::array<amrex::Real, 2>> hurricane_eye_track_xy,
162  hurricane_eye_track_latlon,
163  hurricane_maxvel_vs_time,
164  hurricane_minpressure_vs_time,
165  hurricane_tracker_circle;
166  amrex::Vector<amrex::MultiFab> weather_forecast_data_1, weather_forecast_data_2;
167  amrex::Vector<amrex::Vector<amrex::MultiFab>> forecast_state_1,
168  forecast_state_2,
169  forecast_state_interp;
170  amrex::Vector<amrex::MultiFab> surface_state_1,
171  surface_state_2,
172  surface_state_interp;
173 
174  amrex::Vector<amrex::Vector<amrex::MultiFab>> bckgnd_state;
175 
176  std::string MakeVTKFilename(int nstep);
177  std::string MakeVTKFilename_TrackerCircle(int nstep);
178  std::string MakeVTKFilename_EyeTracker_xy(int nstep);
179  std::string MakeFilename_EyeTracker_latlon(int nstep);
180  std::string MakeFilename_EyeTracker_maxvel(int nstep);
181  std::string MakeFilename_EyeTracker_minpressure(int nstep);
182  void WriteVTKPolyline(const std::string& filename,
183  amrex::Vector<std::array<amrex::Real, 2>>& points_xy);
184 
185  void WriteLinePlot(const std::string& filename,
186  amrex::Vector<std::array<amrex::Real, 2>>& points_xy);
187 
188  // Initialize multilevel data
189  void InitData ();
190 
191  // Initialize multilevel data before MultiBlock
192  void InitData_pre ();
193 
194  // Initialize multilevel data after MultiBlock
195  void InitData_post ();
196 
197  // Interpolate 2D arrays lat_m, lon_m, sinPhi, cosPhi
198  void Interp2DArrays (int lev, const amrex::BoxArray& my_ba2d, const amrex::DistributionMapping& my_dm);
199 
200  void WriteMyEBSurface ();
201 
202  // Compute the divergence -- whether EB, no-terrain, flat terrain or general terrain
203  void compute_divergence (int lev, amrex::MultiFab& rhs, amrex::Array<amrex::MultiFab const*,AMREX_SPACEDIM> rho0_u_const,
204  amrex::Geometry const& geom_at_lev);
205 
206  // Project the velocities to be divergence-free -- this is only relevant if anelastic == 1
207  void project_initial_velocity (int lev, amrex::Real time, amrex::Real dt);
208  void project_momenta (int lev, amrex::Real l_time, amrex::Real l_dt, amrex::Vector<amrex::MultiFab >& vars);
209 
210  // Project the velocities to be divergence-free with a thin body
211  void project_velocity_tb (int lev, amrex::Real dt, amrex::Vector<amrex::MultiFab >& vars);
212 
213  // Calculate wall distance by solving a Poisson equation
214  void poisson_wall_dist (int lev);
215 
216  void make_subdomains(const amrex::BoxList& ba, amrex::Vector<amrex::BoxArray>& bins);
217 
218 #ifdef ERF_USE_FFT
219  void build_fft_solvers (int lev);
220  void solve_with_fft (int lev, int isub, const amrex::Box& subdomain,
221  amrex::MultiFab& rhs, amrex::MultiFab& p,
222  amrex::Array<amrex::MultiFab,AMREX_SPACEDIM>& fluxes);
223 #endif
224  void solve_with_gmres (int lev, const amrex::Box& subdomain,
225  amrex::MultiFab& rhs, amrex::MultiFab& p,
226  amrex::Array<amrex::MultiFab,AMREX_SPACEDIM>& fluxes,
227  amrex::MultiFab& ax_sub, amrex::MultiFab& ay_sub,
228  amrex::MultiFab& az_sub,
229  amrex::MultiFab& /*dJ_sub*/, amrex::MultiFab& znd_sub);
230 
231  void ImposeBCsOnPhi (int lev, amrex::MultiFab& phi, const amrex::Box& subdomain);
232 
233  // Init (NOT restart or regrid)
234  void init_only (int lev, amrex::Real time);
235 
236  // Restart
237  void restart ();
238 
239  // Check for NaNs and other bad stuff
240  void check_state_for_nans(amrex::MultiFab const& S);
241  void check_vels_for_nans(amrex::MultiFab const& xvel, amrex::MultiFab const& yvel, amrex::MultiFab const& zvel);
242  void check_for_negative_theta (amrex::MultiFab& S);
243  void check_for_low_temp (amrex::MultiFab& S);
244 
245  void compute_max_pressure_gradient_diagnostic(int lev);
246 
247  // Is it time to write a plotfile or checkpoint?
248  // Note that "cur_time" is always in double precision
249  bool writeNow (double cur_time, const int nstep, const int plot_int,
250  const amrex::Real plot_per, const amrex::Real dt_0, amrex::Real& last_file_time);
251 
252  // Called after every level 0 timestep
253  void post_timestep (int nstep, double time, amrex::Real dt_lev);
254 
255  // Diagnostics
256  void sum_integrated_quantities (double time);
257  void sum_derived_quantities (double time);
258  void sum_energy_quantities (double time);
259 
260  void write_1D_profiles (double time);
261  void write_1D_profiles_stag (double time);
262 
263  amrex::Real cloud_fraction (double time);
264 
265  // Fill the physical boundary conditions for cell-centered velocity (diagnostic only)
266  void FillBdyCCVels (amrex::MultiFab& mf_cc_vel, amrex::Geometry& lev_geom);
267 
268  void sample_points (int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab& mf);
269  void sample_lines (int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab& mf);
270 
271  void derive_diag_profiles (double time,
272  amrex::Gpu::HostVector<amrex::Real>& h_avg_u , amrex::Gpu::HostVector<amrex::Real>& h_avg_v,
273  amrex::Gpu::HostVector<amrex::Real>& h_avg_w , amrex::Gpu::HostVector<amrex::Real>& h_avg_rho,
274  amrex::Gpu::HostVector<amrex::Real>& h_avg_th , amrex::Gpu::HostVector<amrex::Real>& h_avg_ksgs,
275  amrex::Gpu::HostVector<amrex::Real>& h_avg_Kmv , amrex::Gpu::HostVector<amrex::Real>& h_avg_Khv,
276  amrex::Gpu::HostVector<amrex::Real>& h_avg_qv , amrex::Gpu::HostVector<amrex::Real>& h_avg_qc,
277  amrex::Gpu::HostVector<amrex::Real>& h_avg_qr ,
278  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqv , amrex::Gpu::HostVector<amrex::Real>& h_avg_wqc,
279  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqr ,
280  amrex::Gpu::HostVector<amrex::Real>& h_avg_qi , amrex::Gpu::HostVector<amrex::Real>& h_avg_qs,
281  amrex::Gpu::HostVector<amrex::Real>& h_avg_qg ,
282  amrex::Gpu::HostVector<amrex::Real>& h_avg_uu , amrex::Gpu::HostVector<amrex::Real>& h_avg_uv,
283  amrex::Gpu::HostVector<amrex::Real>& h_avg_uw,
284  amrex::Gpu::HostVector<amrex::Real>& h_avg_vv , amrex::Gpu::HostVector<amrex::Real>& h_avg_vw,
285  amrex::Gpu::HostVector<amrex::Real>& h_avg_ww,
286  amrex::Gpu::HostVector<amrex::Real>& h_avg_uth , amrex::Gpu::HostVector<amrex::Real>& h_avg_vth,
287  amrex::Gpu::HostVector<amrex::Real>& h_avg_wth, amrex::Gpu::HostVector<amrex::Real>& h_avg_thth,
288  amrex::Gpu::HostVector<amrex::Real>& h_avg_ku, amrex::Gpu::HostVector<amrex::Real>& h_avg_kv,
289  amrex::Gpu::HostVector<amrex::Real>& h_avg_kw,
290  amrex::Gpu::HostVector<amrex::Real>& h_avg_p,
291  amrex::Gpu::HostVector<amrex::Real>& h_avg_pu, amrex::Gpu::HostVector<amrex::Real>& h_avg_pv,
292  amrex::Gpu::HostVector<amrex::Real>& h_avg_pw, amrex::Gpu::HostVector<amrex::Real>& h_avg_wthv);
293  void derive_diag_profiles_stag (double time,
294  amrex::Gpu::HostVector<amrex::Real>& h_avg_u , amrex::Gpu::HostVector<amrex::Real>& h_avg_v,
295  amrex::Gpu::HostVector<amrex::Real>& h_avg_w , amrex::Gpu::HostVector<amrex::Real>& h_avg_rho,
296  amrex::Gpu::HostVector<amrex::Real>& h_avg_th , amrex::Gpu::HostVector<amrex::Real>& h_avg_ksgs,
297  amrex::Gpu::HostVector<amrex::Real>& h_avg_Kmv , amrex::Gpu::HostVector<amrex::Real>& h_avg_Khv,
298  amrex::Gpu::HostVector<amrex::Real>& h_avg_qv , amrex::Gpu::HostVector<amrex::Real>& h_avg_qc,
299  amrex::Gpu::HostVector<amrex::Real>& h_avg_qr ,
300  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqv , amrex::Gpu::HostVector<amrex::Real>& h_avg_wqc,
301  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqr ,
302  amrex::Gpu::HostVector<amrex::Real>& h_avg_qi , amrex::Gpu::HostVector<amrex::Real>& h_avg_qs,
303  amrex::Gpu::HostVector<amrex::Real>& h_avg_qg ,
304  amrex::Gpu::HostVector<amrex::Real>& h_avg_uu , amrex::Gpu::HostVector<amrex::Real>& h_avg_uv,
305  amrex::Gpu::HostVector<amrex::Real>& h_avg_uw,
306  amrex::Gpu::HostVector<amrex::Real>& h_avg_vv , amrex::Gpu::HostVector<amrex::Real>& h_avg_vw,
307  amrex::Gpu::HostVector<amrex::Real>& h_avg_ww,
308  amrex::Gpu::HostVector<amrex::Real>& h_avg_uth , amrex::Gpu::HostVector<amrex::Real>& h_avg_vth,
309  amrex::Gpu::HostVector<amrex::Real>& h_avg_wth, amrex::Gpu::HostVector<amrex::Real>& h_avg_thth,
310  amrex::Gpu::HostVector<amrex::Real>& h_avg_ku, amrex::Gpu::HostVector<amrex::Real>& h_avg_kv,
311  amrex::Gpu::HostVector<amrex::Real>& h_avg_kw,
312  amrex::Gpu::HostVector<amrex::Real>& h_avg_p,
313  amrex::Gpu::HostVector<amrex::Real>& h_avg_pu, amrex::Gpu::HostVector<amrex::Real>& h_avg_pv,
314  amrex::Gpu::HostVector<amrex::Real>& h_avg_pw, amrex::Gpu::HostVector<amrex::Real>& h_avg_wthv);
315 
316  void derive_stress_profiles (amrex::Gpu::HostVector<amrex::Real>& h_avg_tau11, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau12,
317  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau13, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau22,
318  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau23, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau33,
319  amrex::Gpu::HostVector<amrex::Real>& h_avg_hfx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_q1fx3,
320  amrex::Gpu::HostVector<amrex::Real>& h_avg_q2fx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_diss);
321  void derive_stress_profiles_stag (amrex::Gpu::HostVector<amrex::Real>& h_avg_tau11, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau12,
322  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau13, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau22,
323  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau23, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau33,
324  amrex::Gpu::HostVector<amrex::Real>& h_avg_hfx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_q1fx3,
325  amrex::Gpu::HostVector<amrex::Real>& h_avg_q2fx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_diss);
326 
327  // Perform the volume-weighted sum
328  amrex::Real
329  volWgtSumMF (int lev, const amrex::MultiFab& mf, int comp,
330  const amrex::MultiFab& dJ, const amrex::MultiFab& mfx, const amrex::MultiFab& mfy,
331  bool finemask, bool local = true);
332 
333  void
334  volWgtColumnSum (int lev, const amrex::MultiFab& mf, int comp,
335  amrex::MultiFab& mf_2d, const amrex::MultiFab& dJ);
336 
337  // Decide if it is time to take an action
338  static bool is_it_time_for_action (int nstep, double time, amrex::Real dt,
339  int action_interval, amrex::Real action_per);
340 
341  // Make a new level using provided BoxArray and DistributionMapping and
342  // fill with interpolated coarse level data.
343  // overrides the pure virtual function in AmrCore
344  void MakeNewLevelFromCoarse (int lev, amrex::Real time, const amrex::BoxArray& ba,
345  const amrex::DistributionMapping& dm) override;
346 
347  // Remake an existing level using provided BoxArray and DistributionMapping and
348  // fill with existing fine and coarse data.
349  // overrides the pure virtual function in AmrCore
350  void RemakeLevel (int lev, amrex::Real time, const amrex::BoxArray& ba,
351  const amrex::DistributionMapping& dm) override;
352 
353  // Delete level data
354  // overrides the pure virtual function in AmrCore
355  void ClearLevel (int lev) override;
356 
357  // Make a new level from scratch using provided BoxArray and DistributionMapping.
358  // Only used during initialization.
359  // overrides the pure virtual function in AmrCore
360  void MakeNewLevelFromScratch (int lev, amrex::Real time, const amrex::BoxArray& ba,
361  const amrex::DistributionMapping& dm) override;
362 
363  // compute dt from CFL considerations
364  amrex::Real estTimeStep (int lev, long& dt_fast_ratio) const;
365 
366 #ifdef ERF_USE_WW3_COUPLING
367  //amrex::Print() << " About to call send_to_ww3 from ERF.H" << std::endl;
368  void send_to_ww3(int lev);
369  //amrex::Print() << " About to call read_waves from ERF.H" << std::endl;
370  void read_waves(int lev);
371  //void send_to_ww3 (int lev);
372  //void read_waves (int lev);
373 
374  //void send_to_ww3 (int lev);
375 #endif
376 
377  // Interface for advancing the data at one level by one "slow" timestep
378  void advance_dycore (int level,
379  amrex::Vector<amrex::MultiFab>& state_old,
380  amrex::Vector<amrex::MultiFab>& state_new,
381  amrex::MultiFab& xvel_old, amrex::MultiFab& yvel_old, amrex::MultiFab& zvel_old,
382  amrex::MultiFab& xvel_new, amrex::MultiFab& yvel_new, amrex::MultiFab& zvel_new,
383  amrex::MultiFab& source, amrex::MultiFab& xmom_src,
384  amrex::MultiFab& ymom_src, amrex::MultiFab& zmom_src,
385  amrex::MultiFab& buoyancy, amrex::Geometry fine_geom,
386  amrex::Real dt, amrex::Real time);
387 
388  void advance_microphysics (int lev,
389  amrex::MultiFab& cons_in,
390  const amrex::Real& dt_advance,
391  const int& iteration,
392  const amrex::Real& time);
393 
394  void advance_lsm (int lev,
395  amrex::MultiFab& cons_in,
396  amrex::MultiFab& xvel_in,
397  amrex::MultiFab& yvel_in,
398  const amrex::Real& time,
399  const amrex::Real& dt_advance);
400 
401  void advance_radiation (int lev,
402  amrex::MultiFab& cons_in,
403  const amrex::Real& dt_advance);
404 
405 #ifdef ERF_USE_SHOC
406  void compute_shoc_tendencies (int lev,
407  amrex::MultiFab* cons,
408  amrex::MultiFab* xvel,
409  amrex::MultiFab* yvel,
410  amrex::MultiFab* zvel,
411  amrex::Real* w_subsid,
412  amrex::MultiFab* tau13,
413  amrex::MultiFab* tau23,
414  amrex::MultiFab* hfx3,
415  amrex::MultiFab* qfx3,
416  amrex::MultiFab* eddyDiffs,
417  amrex::MultiFab* z_phys_nd,
418  const amrex::Real& dt_advance);
419 #endif
420 
421 #ifdef ERF_USE_P3
422  void compute_p3_tendencies (int lev,
423  amrex::MultiFab& cons_in,
424  amrex::MultiFab& source,
425  const amrex::Real& dt_advance);
426 #endif
427 
428  void build_fine_mask (int lev, amrex::MultiFab& fine_mask);
429 
430  void MakeHorizontalAverages ();
431  void MakeDiagnosticAverage (amrex::Vector<amrex::Real>& h_havg, amrex::MultiFab& S, int n);
432  void derive_upwp (amrex::Vector<amrex::Real>& h_havg);
433 
434  // Write plotfile to disk
435  void Write3DPlotFile (int which, PlotFileType plotfile_type, amrex::Vector<std::string> plot_var_names);
436  void Write2DPlotFile (int which, PlotFileType plotfile_type, amrex::Vector<std::string> plot_var_names);
437 
438  // Write subvolume of data into a different "plotfile"
439  void WriteSubvolume (int isub, amrex::Vector<std::string> subvol_var_names);
440 
441  void WriteMultiLevelPlotfileWithTerrain (const std::string &plotfilename,
442  int nlevels,
443  const amrex::Vector<const amrex::MultiFab*> &mf,
444  const amrex::Vector<const amrex::MultiFab*> &mf_nd,
445  const amrex::Vector<std::string> &varnames,
446  const amrex::Vector<amrex::Geometry>& my_geom,
447  amrex::Real time,
448  const amrex::Vector<int> &level_steps,
449  const amrex::Vector<amrex::IntVect>& my_ref_ratio,
450  const std::string &versionName = "HyperCLaw-V1.1",
451  const std::string &levelPrefix = "Level_",
452  const std::string &mfPrefix = "Cell",
453  const amrex::Vector<std::string>& extra_dirs = amrex::Vector<std::string>()) const;
454 
455 
456  void WriteGenericPlotfileHeaderWithTerrain (std::ostream &HeaderFile,
457  int nlevels,
458  const amrex::Vector<amrex::BoxArray> &bArray,
459  const amrex::Vector<std::string> &varnames,
460  const amrex::Vector<amrex::Geometry>& my_geom,
461  amrex::Real time,
462  const amrex::Vector<int> &level_steps,
463  const amrex::Vector<amrex::IntVect>& my_ref_ratio,
464  const std::string &versionName,
465  const std::string &levelPrefix,
466  const std::string &mfPrefix) const;
467 
468  void erf_enforce_hse (int lev,
469  amrex::MultiFab& dens, amrex::MultiFab& pres, amrex::MultiFab& pi,
470  amrex::MultiFab& th, amrex::MultiFab& qv,
471  std::unique_ptr<amrex::MultiFab>& z_cc);
472 
473 #ifdef ERF_USE_NETCDF
474  //! Write a timestep to 1D vertical column output for coupling
475  void writeToNCColumnFile (int lev,
476  const std::string& colfile_name, amrex::Real xloc, amrex::Real yloc,
477  amrex::Real time);
478 #endif //ERF_USE_NETCDF
479 
480  void init_from_input_sounding (int lev);
481 
482  void init_immersed_forcing (int lev);
483 
484  void input_sponge (int lev);
485 
486  void init_from_hse (int lev);
487 
488  void init_thin_body (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm);
489 
490  void FillForecastStateMultiFabs(const int lev,
491  const std::string& filename,
492  const std::unique_ptr<amrex::MultiFab>& z_phys_nd,
493  amrex::Vector<amrex::Vector<amrex::MultiFab>>& forecast_state);
494 
495  void FillSurfaceStateMultiFabs(const int lev,
496  const std::string& filename,
497  amrex::Vector<amrex::MultiFab>& surface_state);
498 
499 
500  void WeatherDataInterpolation(const int nlevs,
501  const amrex::Real time,
502  amrex::Vector<std::unique_ptr<amrex::MultiFab>>& z_phys_nd,
503  bool regrid_forces_file_read);
504 
505  void SurfaceDataInterpolation(const int nlevs,
506  const amrex::Real time,
507  amrex::Vector<std::unique_ptr<amrex::MultiFab>>& z_phys_nd,
508  bool regrid_forces_file_read);
509 
510  void create_background_state_for_ensemble (int lev,
511  amrex::MultiFab& mf_cc_pert,
512  amrex::MultiFab& cons_pert,
513  amrex::MultiFab& xvel_pert,
514  amrex::MultiFab& yvel_pert,
515  amrex::MultiFab& zvel_pert);
516 
517  void create_random_perturbations (const int lev,
518  amrex::MultiFab& mf_cc_pert);
519 
520  void apply_gaussian_smoothing_to_perturbations (const int lev,
521  amrex::MultiFab& mf_cc_pert);
522 
523  void ComputeAndWriteEnsemblePerturbations();
524 
525  void PerformDataAssimilation(int da_iter);
526 
527  void init_custom (int lev);
528 
529 #ifdef ERF_USE_MULTIBLOCK
530  // constructor used when ERF is created by a multiblock driver
531  // calls AmrCore constructor -> AmrMesh constructor
532  ERF (const amrex::RealBox& rb, int max_level_in,
533  const amrex::Vector<int>& n_cell_in, int coord,
534  const amrex::Vector<amrex::IntVect>& ref_ratio,
535  const amrex::Array<int,AMREX_SPACEDIM>& is_per,
536  std::string prefix);
537 
538  // Advance a block specified number of time steps
539  void Evolve_MB (int MBstep, int max_block_step);
540 
541  // Set parmparse prefix for MultiBlock
542  void SetParmParsePrefix (std::string name) { pp_prefix = name; }
543 
544  // Set 'this' from multiblock container
545  void SetMultiBlockPointer (MultiBlockContainer *mbc) { m_mbc = mbc; }
546 
547  // Public data copy for MB
548  std::vector<amrex::Box> domain_p;
549 
550  // Primary solution data data containers
551  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_new;
552  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_old;
553 
554  // Pressure gradient at each level
555  amrex::Vector<amrex::Vector<amrex::MultiFab> > gradp;
556 
557  // Velocity time averaged field
558  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vel_t_avg;
559  amrex::Vector<amrex::Real> t_avg_cnt;
560 #endif
561 
562  std::string pp_prefix {"erf"};
563 
564  void fill_from_bndryregs (const amrex::Vector<amrex::MultiFab*>& mfs,
565  amrex::Real time);
566 
567 #ifdef ERF_USE_NETCDF
568  // Version in which we always set the velocity values but don't set theta
569  void fill_from_realbdy (const amrex::Vector<amrex::MultiFab*>& mfs,
570  amrex::Real time,
571  bool cons_only,
572  int icomp_cons,
573  int ncomp_cons,
574  amrex::IntVect ngvect_cons,
575  amrex::IntVect ngvect_vels);
576 #endif
577 
578 #ifdef ERF_USE_NETCDF
579  void init_from_wrfinput (int lev, amrex::MultiFab& mf_PSFC);
580  void init_from_metgrid (int lev);
581  void init_from_ncfile (int lev);
582 #endif // ERF_USE_NETCDF
583 
584 #ifdef ERF_USE_WINDFARM
585  void init_windfarm(int lev);
586  void advance_windfarm (const amrex::Geometry& a_geom,
587  const amrex::Real& dt_advance,
588  amrex::MultiFab& cons_in,
589  amrex::MultiFab& U_old,
590  amrex::MultiFab& V_old,
591  amrex::MultiFab& W_old,
592  amrex::MultiFab& mf_vars_windfarm,
593  const amrex::MultiFab& mf_Nturb,
594  const amrex::MultiFab& mf_SMark,
595  const amrex::Real& time);
596 #endif
597 
598  void MakeEBGeometry ();
599  void make_eb_box ();
600  void make_eb_regular ();
601 
602  // more flexible version of AverageDown() that lets you average down across multiple levels
603  void AverageDownTo (int crse_lev,
604  int scomp,
605  int ncomp,
606  bool do_perturbational_and_momenta = true); // NOLINT
607 
608  /*! \brief Conservation-preserving fine→coarse average of moist state components
609  * (RhoTheta and the contiguous moist q range) using detJ/mfac weighting,
610  * reusing AverageDownTo with perturbational/momenta handling disabled. */
611  void AverageDownMoistStateTo (int crse_lev);
612 
613  // Write checkpoint file to disk
614  void WriteCheckpointFile () const;
615 
616  // Read checkpoint file from disk
617  void ReadCheckpointFile ();
618 
619  // Read only velocities from checkpoint file
620  void ReadVelsOnlyFromCheckpointFile (int lev_to_fill, std::string& chkfile);
621 
622  // read checkpoint file from disk -- called after instantiating m_SurfaceLayer
623  void ReadCheckpointFileSurfaceLayer ();
624 
625  void init_zphys (int lev, amrex::Real elapsed_time);
626  void remake_zphys (int lev, std::unique_ptr<amrex::MultiFab>& temp_zphys_nd);
627  void update_terrain_arrays (int lev);
628 
629 private:
630 
631  ///////////////////////////
632  // private member functions
633  ///////////////////////////
634 
635  // read in some parameters from inputs file
636  void ReadParameters ();
637  void ParameterSanityChecks ();
638 
639  // set covered coarse cells/faces to be the average of overlying fine cells/faces
640  void AverageDown ();
641 
642  void update_diffusive_arrays (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm);
643 
644  void Construct_ERFFillPatchers (int lev);
645 
646  void Define_ERFFillPatchers (int lev);
647 
648  void init1DArrays ();
649 
650  void init_bcs ();
651  void init_phys_bcs (bool& rho_read, bool& read_prim_theta);
652 
653  void init_stuff (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm,
654  amrex::Vector<amrex::MultiFab>& lev_new, amrex::Vector<amrex::MultiFab>& lev_old,
655  amrex::MultiFab& tmp_base_state,
656  std::unique_ptr<amrex::MultiFab>& tmp_zphys_nd);
657 
658  // Initialize the Turbulent perturbation
659  void turbPert_update (const int lev, const amrex::Real dt);
660  void turbPert_amplitude (const int lev);
661 
662  // Initialize the integrator object
663  void initialize_integrator (int lev, amrex::MultiFab& cons_mf, amrex::MultiFab& vel_mf);
664 
665  // Create the physbcs objects
666  void make_physbcs (int lev);
667 
668  // Initialize the microphysics object
669  void initializeMicrophysics (const int&);
670 
671 #ifdef ERF_USE_WINDFARM
672  // Initialize the windfarm object
673  void initializeWindFarm (const int&);
674 #endif
675 
676  // Compute a vector of new MultiFabs by copying from valid region and filling ghost cells
677  //
678  // NOTE: FillPatch takes in an empty MF, and returns cell-centered + velocities (not momenta)
679  //
680  // This one works only at level = 0 (base state does not change)
681  void FillPatchCrseLevel (int lev, double time,
682  const amrex::Vector<amrex::MultiFab*>& mfs_vel,
683  bool cons_only=false);
684 
685  // This one works only at level > 0 (base state does change)
686  void FillPatchFineLevel (int lev, double time,
687  const amrex::Vector<amrex::MultiFab*>& mfs_vel,
688  const amrex::Vector<amrex::MultiFab*>& mfs_mom,
689  const amrex::MultiFab& old_base_state,
690  const amrex::MultiFab& new_base_state,
691  bool fillset=true, bool cons_only=false);
692 
693  // Compute new multifabs by copying data from valid region and filling ghost cells.
694  // Unlike FillPatch, FillIntermediatePatch will use the supplied multifabs instead of fine level data.
695  // This is to support filling boundary cells at an intermediate time between old/new times
696  // on the fine level when valid data at a specific time is already available (such as
697  // at each RK stage when integrating between initial and final times at a given level).
698  //
699  // NOTE: FillIntermediatePatch takes in updated momenta, and returns both updated velocity and momenta
700  //
701  void FillIntermediatePatch (int lev, amrex::Real time,
702  const amrex::Vector<amrex::MultiFab*>& mfs_vel,
703  const amrex::Vector<amrex::MultiFab*>& mfs_mom,
704  int ng_cons, int ng_vel, bool cons_only, int icomp_cons, int ncomp_cons);
705 
706  // Fill all multifabs (and all components) in a vector of multifabs corresponding to the
707  // grid variables defined in vars_old and vars_new just as FillCoarsePatch.
708  void FillCoarsePatch (int lev, amrex::Real time);
709 
710  // advance a level by dt
711  // includes a recursive call for finer levels
712  void timeStep (int lev, double time, int iteration);
713 
714  // advance a single level for a single time step
715  void Advance (int lev, amrex::Real time, amrex::Real dt_lev, int iteration, int ncycle);
716 
717  //! Initialize HSE
718  void initHSE ();
719  void initHSE (int lev);
720 
721  //! Initialize Rayleigh damping profiles at a level
722  void initRayleigh_at_level (const int& lev);
723 
724  //! Initialize sponge profiles
725  void initSponge ();
726 
727  //! Set Rayleigh mean profiles from input sounding
728  void setRayleighRefFromSounding (bool restarting);
729 
730  //! Set sponge mean profiles from input sounding
731  void setSpongeRefFromSounding (bool restarting);
732 
733  // a wrapper for estTimeStep()
734  void ComputeDt (int step = -1, double cur_time_d = 0.0);
735 
736  // get plotfile name
737  [[nodiscard]] std::string PlotFileName (int lev) const;
738 
739  // set plotfile variable names
740  static amrex::Vector<std::string> PlotFileVarNames (amrex::Vector<std::string> plot_var_names);
741 
742  // set which variables and derived quantities go into plotfiles
743  void setPlotVariables (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
744  void setPlotVariables2D (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
745  // append variables to plot
746  void appendPlotVariables (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
747 
748  void setSubVolVariables (const std::string& pp_subvol_var_names, amrex::Vector<std::string>& subvol_var_names);
749 
750 #ifdef ERF_USE_NETCDF
751  //! Create 1D vertical column output for coupling
752  void createNCColumnFile (int lev,
753  const std::string& colfile_name, amrex::Real xloc, amrex::Real yloc);
754 
755  // Copy from the NC*fabs into the MultiFabs holding the boundary data
756  void init_from_wrfbdy (amrex::Vector<amrex::FArrayBox*> x_vel_lateral,
757  amrex::Vector<amrex::FArrayBox*> y_vel_lateral,
758  amrex::Vector<amrex::FArrayBox*> z_vel_lateral,
759  amrex::Vector<amrex::FArrayBox*> T_lateral);
760 
761  static amrex::Real start_bdy_time;
762  static amrex::Real final_bdy_time;
763 
764  static amrex::Real start_low_time;
765  static amrex::Real final_low_time;
766 
767  static amrex::Real bdy_time_interval;
768  static amrex::Real low_time_interval;
769 
770  // *** *** FArrayBox's for holding the SURFACE data
771  // amrex::IArrayBox NC_IVGTYP_fab; // Vegetation type (IVGTYP); Discrete numbers;
772  // amrex::FArrayBox NC_z0_fab; // Surface Roughness, z0 = z0 (IVGTYP)
773  // amrex::FArrayBox NC_PSFC_fab; // Surface pressure
774 
775  // TODO: Clarify the relation between SST and TSK
776  // amrex::FArrayBox NC_SST_fab; // Sea Surface Temperature; Defined even for land area
777  // amrex::FArrayBox NC_TSK_fab; // Surface Skin Temperature; Appears to be same as SST...
778 
779  // Vectors (over time) of Vector (over variables) of FArrayBoxs for holding the data read from the wrfbdy NetCDF file
780  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_xlo;
781  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_xhi;
782  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_ylo;
783  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_yhi;
784 
785  amrex::Vector<amrex::Vector<amrex::FArrayBox>> low_data_zlo;
786 
787  // Maximum value of terrain read in from wrfinput at level 0
788  amrex::Real z_top = zero;
789 
790 #endif // ERF_USE_NETCDF
791 
792  amrex::Vector<std::unique_ptr<amrex::MultiFab>> lat_m, lon_m; // Latitude and Longitude on the grid
793 
794  amrex::Vector<std::unique_ptr<amrex::MultiFab>> sinPhi_m, cosPhi_m; // Coriolis factors on the grid
795 
796  // Struct for working with the sounding data we take as an input
797  InputSoundingData input_sounding_data;
798 
799  // Struct for working with the sponge data we take as an input
800  InputSpongeData input_sponge_data;
801 
802  // Vector (6 planes) of DeviceVectors (ncell in plane) for Dirichlet BC data
803  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> xvel_bc_data;
804  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> yvel_bc_data;
805  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> zvel_bc_data;
806  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> th_bc_data;
807 
808  // Function to read and populate above vectors (if input file exists)
809  void init_Dirichlet_bc_data (const std::string input_file);
810 
811  // Read the file passed to amr.restart and use it as an initial condition for
812  // the current simulation. Supports a different number of components and
813  // ghost cells.
814  void InitializeFromFile ();
815 
816  // Initialize the new-time data at a level from the initial_data MultiFab
817  void InitializeLevelFromData (int lev, const amrex::MultiFab& initial_data);
818 
819  // utility to skip to next line in Header
820  static void GotoNextLine (std::istream& is);
821 
822  // Single level functions called by advance()
823  void post_update (amrex::MultiFab& state_mf, amrex::Real time, const amrex::Geometry& geom);
824  void fill_rhs (amrex::MultiFab& rhs_mf, const amrex::MultiFab& state_mf, amrex::Real time, const amrex::Geometry& geom);
825 
826  ////////////////
827  // private data members
828 
829  std::unique_ptr<ProblemBase> prob = nullptr; // problem-specific functions
830 
831  amrex::Vector<int> num_boxes_at_level; // how many boxes specified at each level by tagging criteria
832  amrex::Vector<int> num_files_at_level; // how many wrfinput files specified at each level
833  amrex::Vector<amrex::Vector<amrex::Box>> boxes_at_level; // the boxes specified at each level by tagging criteria
834 
835  amrex::Vector<int> istep; // which step?
836  amrex::Vector<int> nsubsteps; // how many substeps on each level?
837 
838  // keep track of old time, new time, and time step at each level
839  amrex::Vector<amrex::Real> t_new;
840  amrex::Vector<amrex::Real> t_old;
841  amrex::Vector<amrex::Real> dt;
842  amrex::Vector<long> dt_mri_ratio;
843 
844 #ifndef ERF_USE_MULTIBLOCK
845  // Array of multifabs to store the solution at each level of refinement;
846  // after advancing a level we use "swap".
847  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_new;
848  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_old;
849 
850  // Pressure gradient at each level
851  amrex::Vector<amrex::Vector<amrex::MultiFab> > gradp;
852 
853  // Velocity time averaged field
854  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vel_t_avg;
855  amrex::Vector<amrex::Real> t_avg_cnt;
856 #endif
857  amrex::Vector<std::unique_ptr<MRISplitIntegrator<amrex::Vector<amrex::MultiFab> > > > mri_integrator_mem;
858 
859  // Used for anelastic or when we impose an initial projection
860  amrex::Vector<amrex::MultiFab> pp_inc;
861 
862  // Used only for fast substepping
863  amrex::Vector<amrex::MultiFab> lagged_delta_rt;
864  amrex::Vector<amrex::MultiFab> avg_xmom;
865  amrex::Vector<amrex::MultiFab> avg_ymom;
866  amrex::Vector<amrex::MultiFab> avg_zmom;
867 
868  // Vector over levels of routines to impose physical boundary conditions
869  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_cons>> physbcs_cons;
870  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_u>> physbcs_u;
871  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_v>> physbcs_v;
872  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_w>> physbcs_w;
873  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_base>> physbcs_base;
874 
875  // Store primitive variable for MOST BC
876  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Theta_prim;
877  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Qv_prim;
878  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Qr_prim;
879 
880  // Scratch space for time integrator
881  amrex::Vector<amrex::MultiFab> rU_old;
882  amrex::Vector<amrex::MultiFab> rU_new;
883  amrex::Vector<amrex::MultiFab> rV_old;
884  amrex::Vector<amrex::MultiFab> rV_new;
885  amrex::Vector<amrex::MultiFab> rW_old;
886  amrex::Vector<amrex::MultiFab> rW_new;
887 
888  // amrex::Vector<amrex::MultiFab> xmom_crse_rhs;
889  // amrex::Vector<amrex::MultiFab> ymom_crse_rhs;
890  amrex::Vector<amrex::MultiFab> zmom_crse_rhs;
891 
892  std::unique_ptr<Microphysics> micro;
893  amrex::Vector<amrex::Vector<amrex::MultiFab*>> qmoist; // (lev,ncomp) rain_accum, snow_accum, graup_accum
894 
895  // Variables for wind farm parametrization models
896 
897 #ifdef ERF_USE_WINDFARM
898  std::unique_ptr<WindFarm> windfarm;
899  amrex::Vector<amrex::MultiFab> Nturb;
900  amrex::Vector<amrex::MultiFab> vars_windfarm; // Fitch: Vabs, Vabsdt, dudt, dvdt, dTKEdt
901  // EWP: dudt, dvdt, dTKEdt
902 
903  amrex::Vector<amrex::MultiFab> SMark; // A multifab that holds an integer corresponding
904  // to the number of the wind turbine to sample
905  // velocity upstream of the turbine
906 #endif
907 
908  LandSurface lsm;
909  amrex::Vector<std::string> lsm_data_name; // (ncomp) -- e.g., sw_dn_dir/dif_vis/nir, lw_dn, cos_zen
910  amrex::Vector<amrex::Vector<amrex::MultiFab*>> lsm_data; // (lev,ncomp) Data for LSM coupling
911  amrex::Vector<std::string> lsm_flux_name; // (ncomp) -- e.g., hfx3, q1fx3, tau13, tau23
912  amrex::Vector<amrex::Vector<amrex::MultiFab*>> lsm_flux; // (lev,ncomp) Fluxes from LSM needed by DYCORE
913 
914  amrex::Vector<std::unique_ptr<IRadiation>> rad; // Radiation model at each level
915  amrex::Vector<std::unique_ptr<amrex::MultiFab>> qheating_rates; // radiation heating rate source terms (SW, LW) (DYCORE)
916  amrex::Vector<std::unique_ptr<amrex::MultiFab>> rad_fluxes; // radiation fluxes (SW up/dn, LW up/dn) (OUTPUT ONLY)
917 #ifdef ERF_USE_SHOC
918  amrex::Vector<std::unique_ptr<SHOCInterface>> shoc_interface; // SHOC model at each level
919 #endif
920 
921 #ifdef ERF_USE_P3
922  amrex::Vector<std::unique_ptr<P3Interface>> p3_interface; // P3 model at each level
923 #endif
924 
925  bool plot_rad = false;
926  int rad_datalog_int = -1;
927 
928  // Fillpatcher classes for coarse-fine boundaries
929  int cf_width{0};
930  int cf_set_width{0};
931  amrex::Vector<ERFFillPatcher> FPr_c;
932  amrex::Vector<ERFFillPatcher> FPr_u;
933  amrex::Vector<ERFFillPatcher> FPr_v;
934  amrex::Vector<ERFFillPatcher> FPr_w;
935 
936  // Diffusive stresses and Smag
937  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> Tau;
938  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> Tau_corr; // correction to tau for implicit
939  amrex::Vector<std::unique_ptr<amrex::MultiFab>> eddyDiffs_lev;
940  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SmnSmn_lev;
941 
942  // Sea Surface Temps, Skin Temperature and Land Masks (lev, ntimes)
943  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> sst_lev;
944  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> tsk_lev;
945  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::iMultiFab>>> lmask_lev;
946 
947  // Land grid types and urban fraction
948  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::iMultiFab>>> land_type_lev;
949  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::iMultiFab>>> soil_type_lev;
950  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> urb_frac_lev;
951 
952  // Other SFS terms
953  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_hfx1_lev, SFS_hfx2_lev, SFS_hfx3_lev;
954  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_diss_lev;
955  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_q1fx1_lev, SFS_q1fx2_lev, SFS_q1fx3_lev;
956  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_q2fx3_lev;
957 
958  // Diffusive fluxes for EB
959  // Tau_EB[level][component][grid_type]
960  amrex::Vector<amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>>> Tau_EB;
961  amrex::Vector<std::unique_ptr<amrex::MultiFab>> hfx3_EB;
962  amrex::Vector<std::unique_ptr<amrex::MultiFab>> qfx3_EB;
963 
964  // Grid stretching
965  amrex::Vector<amrex::Vector<amrex::Real>> zlevels_stag; // nominal height levels
966 
967  // Data structures for terrain-fitted coordinates
968  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_nd;
969  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_cc;
970 
971  amrex::Vector<std::unique_ptr<amrex::MultiFab>> detJ_cc;
972  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ax;
973  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ay;
974  amrex::Vector<std::unique_ptr<amrex::MultiFab>> az;
975 
976  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_nd_src;
977  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_cc_src;
978  amrex::Vector<std::unique_ptr<amrex::MultiFab>> detJ_cc_src;
979  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ax_src;
980  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ay_src;
981  amrex::Vector<std::unique_ptr<amrex::MultiFab>> az_src;
982 
983  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_nd_new;
984  amrex::Vector<std::unique_ptr<amrex::MultiFab>> detJ_cc_new;
985 
986  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_t_rk;
987 
988  // Data structures for terrain immersed forcing
989  amrex::Vector<std::unique_ptr<amrex::MultiFab>> terrain_blanking;
990 
991  // Wall distance function
992  amrex::Vector<std::unique_ptr<amrex::MultiFab>> walldist;
993 
994  // Map scale factors -- vector across levels of vector across types
995  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> mapfac;
996 
997  // Mask to be used to identify cells covered by finer level (if level > 0)
998  amrex::Vector<std::unique_ptr<amrex::MultiFab>> fine_mask;
999 
1000  amrex::Vector<amrex::Vector<amrex::Real>> stretched_dz_h;
1001  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> stretched_dz_d;
1002 
1003  amrex::Vector<amrex::MultiFab> base_state;
1004  amrex::Vector<amrex::MultiFab> base_state_new;
1005 
1006  // Wave coupling data
1007  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Hwave;
1008  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Lwave;
1009  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Hwave_onegrid;
1010  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Lwave_onegrid;
1011  bool finished_wave = false;
1012 
1013  // array of flux registers
1014  amrex::Vector<amrex::YAFluxRegister*> advflux_reg;
1015 
1016  // A BCRec is essentially a 2*DIM integer array storing the boundary
1017  // condition type at each lo/hi walls in each direction. We have one BCRec
1018  // for each component of the cell-centered variables and each velocity component.
1019  amrex::Vector <amrex::BCRec> domain_bcs_type;
1020  amrex::Gpu::DeviceVector<amrex::BCRec> domain_bcs_type_d;
1021 
1022  // We store these so that we can print them out in the job_info file
1023  amrex::Array<std::string,2*AMREX_SPACEDIM> domain_bc_type;
1024 
1025  // These hold the Dirichlet values at walls which need them ...
1026  amrex::Array<amrex::Array<amrex::Real, AMREX_SPACEDIM*2>, AMREX_SPACEDIM+NBCVAR_max> m_bc_extdir_vals;
1027 
1028  // These hold the Neumann values at walls which need them ...
1029  amrex::Array<amrex::Array<amrex::Real, AMREX_SPACEDIM*2>, AMREX_SPACEDIM+NBCVAR_max> m_bc_neumann_vals;
1030 
1031  // Per-face flag: non-reflecting inflow (extrapolate RhoTheta instead of prescribing)
1032  amrex::Array<bool, AMREX_SPACEDIM*2> m_bc_nonreflecting = {{false}};
1033 
1034  // These are the "physical" boundary condition types (e.g. "inflow")
1035  amrex::GpuArray<ERF_BC, AMREX_SPACEDIM*2> phys_bc_type;
1036 
1037  // These are the masks for the thin immersed body
1038  amrex::Vector<std::unique_ptr<amrex::iMultiFab>> xflux_imask;
1039  amrex::Vector<std::unique_ptr<amrex::iMultiFab>> yflux_imask;
1040  amrex::Vector<std::unique_ptr<amrex::iMultiFab>> zflux_imask;
1041  //amrex::Vector<std::unique_ptr<amrex::iMultiFab>> overset_imask;
1042 
1043  // These are the body forces that result from the thin immersed body
1044  amrex::Vector<std::unique_ptr<amrex::MultiFab>> thin_xforce;
1045  amrex::Vector<std::unique_ptr<amrex::MultiFab>> thin_yforce;
1046  amrex::Vector<std::unique_ptr<amrex::MultiFab>> thin_zforce;
1047 
1048  static int last_plot3d_file_step_1;
1049  static int last_plot3d_file_step_2;
1050  static int last_plot2d_file_step_1;
1051  static int last_plot2d_file_step_2;
1052  static int last_check_file_step;
1053 
1054  static amrex::Real last_plot3d_file_time_1;
1055  static amrex::Real last_plot3d_file_time_2;
1056  static amrex::Real last_plot2d_file_time_1;
1057  static amrex::Real last_plot2d_file_time_2;
1058  static amrex::Real last_check_file_time;
1059 
1060  amrex::Vector<int> last_subvol_step;
1061  amrex::Vector<amrex::Real> last_subvol_time;
1062 
1063  static bool plot_file_on_restart;
1064 
1065  // Output control
1066  const int datwidth = 14;
1067  const int datprecision = 6;
1068  const int timeprecision = 13; // e.g., 1-yr LES: 31,536,000 s with dt ~ amrex::Real(0.01) ==> min prec = 10
1069  // epoch time for 2030-01-01 00:00:00 is 1,893,456,000 s with dt ~ amrex::Real(0.01) ==> min prec = 12
1070 
1071  ////////////////
1072  // runtime parameters
1073 
1074  // Maximum number of steps
1075  int max_step = -1;
1076 
1077  // Start and stop times
1078  static amrex::Real start_time;
1079  static amrex::Real stop_time;
1080 
1081  bool use_datetime = false;
1082  const std::string datetime_format = "%Y-%m-%d %H:%M:%S"; // ISO 8601 standard
1083 
1084  // if >= 0 we restart from a checkpoint
1085  std::string restart_chkfile = "";
1086 
1087  // Time step controls
1088  static amrex::Real cfl;
1089  static amrex::Real sub_cfl;
1090  static amrex::Real init_shrink;
1091  static amrex::Real change_max;
1092  static amrex::Real dt_max_initial;
1093  static amrex::Real dt_max;
1094 
1095  // Fixed dt at each level (only used if positive)
1096  amrex::Vector<amrex::Real> fixed_dt;
1097  amrex::Vector<amrex::Real> fixed_fast_dt;
1098  static int fixed_mri_dt_ratio;
1099 
1100  // how often each level regrids the higher levels of refinement
1101  // (after a level advances that many time steps)
1102  int regrid_int = -1;
1103 
1104  // Should we regrid level 0 after restart if Ngrids < Nprocs or
1105  // max_grid_size has changed?
1106  bool regrid_level_0_on_restart = false;
1107 
1108  // plotfile prefix and frequency
1109  std::string plot3d_file_1 {"plt_1_"};
1110  std::string plot3d_file_2 {"plt_2_"};
1111  std::string plot2d_file_1 {"plt2d_1_"};
1112  std::string plot2d_file_2 {"plt2d_2_"};
1113  std::string subvol_file {"subvol"};
1114  bool m_expand_plotvars_to_unif_rr = false;
1115  int m_plot3d_int_1 = -1;
1116  int m_plot3d_int_2 = -1;
1117  int m_plot2d_int_1 = -1;
1118  int m_plot2d_int_2 = -1;
1119 
1120  amrex::Vector<int> m_subvol_int;
1121  amrex::Vector<amrex::Real> m_subvol_per;
1122 
1123  amrex::Real m_plot3d_per_1 = -one;
1124  amrex::Real m_plot3d_per_2 = -one;
1125  amrex::Real m_plot2d_per_1 = -one;
1126  amrex::Real m_plot2d_per_2 = -one;
1127  bool m_plot_face_vels = false;
1128 
1129  bool plot_lsm = false;
1130 
1131  // other sampling output control
1132  int profile_int = -1;
1133  bool destag_profiles = true;
1134 
1135  // Checkpoint type, prefix and frequency
1136  std::string check_file {"chk"};
1137  int m_check_int = -1;
1138  amrex::Real m_check_per = -one;
1139 
1140  amrex::Vector<std::string> subvol3d_var_names;
1141 
1142  amrex::Vector<std::string> plot3d_var_names_1;
1143  amrex::Vector<std::string> plot3d_var_names_2;
1144  amrex::Vector<std::string> plot2d_var_names_1;
1145  amrex::Vector<std::string> plot2d_var_names_2;
1146  const amrex::Vector<std::string> cons_names {"density", "rhotheta", "rhoKE", "rhoadv_0",
1147  "rhoQ1", "rhoQ2", "rhoQ3",
1148  "rhoQ4", "rhoQ5", "rhoQ6",
1149  "rhoQ7", "rhoQ8", "rhoQ9",
1150  "rhoQ10", "rhoQ11"};
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 {"temp", "theta", "KE", "scalar", "soundspeed",
1156  "reflectivity","max_reflectivity", "precipitable", "mucape",
1157  "vorticity_x","vorticity_y","vorticity_z",
1158  "helicity", "local_helicity",
1159  "magvel", "divU",
1160  "pres_hse", "dens_hse", "theta_hse", "pressure", "pert_pres", "pert_dens",
1161  "buoyancy", "eq_pot_temp", "VPD",
1162 #ifdef ERF_USE_WINDFARM
1163  "num_turb", "SMark0", "SMark1",
1164 #endif
1165  "dpdx", "dpdy", "dpdz", "pres_hse_x", "pres_hse_y",
1166  "z_phys", "detJ", "mapfac", "lat_m", "lon_m",
1167  // Time averaged velocity
1168  "u_t_avg", "v_t_avg", "w_t_avg", "umag_t_avg",
1169  // eddy viscosity
1170  "nut",
1171  // eddy diffusivity of momentum
1172  "Kmv","Kmh",
1173  // eddy diffusivity of heat
1174  "Khv","Khh",
1175  // turbulence lengthscale
1176  "Lturb",
1177  // wall distance
1178  "walldist",
1179  // dissipation
1180  "diss",
1181  // moisture vars
1182  "moist_density", "qv", "qc", "qi", "qrain", "qsnow", "qgraup",
1183  "qt", "qn", "qp", "qsat", "nc", "ni", "nr", "ns", "ng",
1184  "rain_accum", "snow_accum", "graup_accum",
1185  "rel_humidity", "condensation_rate",
1186  // Terrain IB mask
1187  "terrain_IB_mask",
1188  // EB variables
1189  "volfrac"
1190 #ifdef ERF_COMPUTE_ERROR
1191  // error vars
1192  ,"xvel_err", "yvel_err", "zvel_err", "pp_err"
1193 #endif
1194  ,"qsrc_sw", "qsrc_lw"
1195  };
1196 
1197  // **************************************************************************************
1198  // NOTE: The order of variable names here **MUST MATCH THE ORDER** in IO/ERF_Plotfile.cpp
1199  // **************************************************************************************
1200  const amrex::Vector<std::string> derived_names_2d {
1201  "z_surf", "landmask", "mapfac", "lat_m", "lon_m",
1202  "u_star", "w_star", "t_star", "q_star", "Olen", "pblh",
1203  "t_surf", "q_surf", "z0", "OLR", "sens_flux", "laten_flux",
1204  "surf_pres", "integrated_qv"
1205  };
1206 
1207  // **************************************************************************************
1208  // NOTE: The order of variable names here **MUST MATCH THE ORDER** in IO/ERF_WriteSubVolume.cpp
1209  // **************************************************************************************
1210  const amrex::Vector<std::string> derived_subvol_names {"soundspeed", "temp", "theta", "KE", "scalar"};
1211 
1212  // algorithm choices
1213  static SolverChoice solverChoice;
1214 
1215  // Turbulent perturbation structure
1216  TurbulentPerturbation turbPert;
1217 
1218 #ifdef ERF_USE_PARTICLES
1219  // Particle container with all particle species
1220  ParticleData particleData;
1221 
1222  // variables and functions for tracers particles
1223  bool m_use_tracer_particles; /*!< tracer particles that advect with flow with optional sedimentation */
1224 
1225  /*! Read tracer and hydro particles parameters */
1226  void readTracersParams();
1227 
1228  /*! Initialize tracer and hydro particles */
1229  void initializeTracers ( amrex::ParGDBBase*,
1230  const amrex::Vector<std::unique_ptr<amrex::MultiFab>>&,
1231  const amrex::Real time);
1232 
1233  /*! Restart tracer and hydro particles */
1234  void restartTracers ( amrex::ParGDBBase*, const std::string& );
1235 
1236  /*! Evolve tracers and hydro particles */
1237  void evolveTracers( int,
1238  amrex::Real,
1239  amrex::Vector<amrex::Vector<amrex::MultiFab>>&,
1240  const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& );
1241 
1242 #endif
1243 
1244 #ifdef ERF_USE_MULTIBLOCK
1245  MultiBlockContainer *m_mbc = nullptr;
1246 #endif
1247 
1248  static int verbose;
1249  static int mg_verbose;
1250  static bool use_fft;
1251 
1252  static int check_for_nans;
1253 
1254  // Diagnostic output interval
1255  static int sum_interval;
1256  static int pert_interval;
1257  static amrex::Real sum_per;
1258 
1259  // Write in native AMReX or NetCDF format for each plotfile
1260  static PlotFileType plotfile3d_type_1;
1261  static PlotFileType plotfile3d_type_2;
1262  static PlotFileType plotfile2d_type_1;
1263  static PlotFileType plotfile2d_type_2;
1264 
1265  int file_name_digits = 5;
1266  bool use_real_time_in_pltname = false;
1267 
1268  static StateInterpType interpolation_type;
1269 
1270  // NetCDF initialization (wrfinput) file
1271  static amrex::Vector<amrex::Vector<std::string>> nc_init_file;
1272  static amrex::Vector<amrex::Vector<int>> have_read_nc_init_file;
1273 
1274  // NetCDF initialization (wrfbdy/met_em) file
1275  static std::string nc_bdy_file;
1276  int real_width{0};
1277  bool real_extrap_w{true};
1278 
1279  // NetCDF initialization of zlo boundary values
1280  static std::string nc_low_file;
1281 
1282  // Options for vertical interpolation of met_em*.nc data.
1283  bool metgrid_debug_quiescent{false};
1284  bool metgrid_debug_isothermal{false};
1285  bool metgrid_debug_dry{false};
1286  bool metgrid_debug_psfc{false};
1287  bool metgrid_debug_msf{false};
1288  bool metgrid_interp_theta{false};
1289  bool metgrid_basic_linear{false};
1290  bool metgrid_use_below_sfc{true};
1291  bool metgrid_use_sfc{true};
1292  bool metgrid_retain_sfc{false};
1293  amrex::Real metgrid_proximity{amrex::Real(500.0)};
1294  int metgrid_order{2};
1295  int metgrid_force_sfc_k{6};
1296 
1297  amrex::Vector<amrex::BoxArray> ba1d;
1298  amrex::Vector<amrex::BoxArray> ba2d;
1299 
1300  std::unique_ptr<amrex::MultiFab> wrf_C1H;
1301  std::unique_ptr<amrex::MultiFab> wrf_C2H;
1302  std::unique_ptr<amrex::MultiFab> wrf_MUB;
1303 
1304  // Base geopotential
1305  std::unique_ptr<amrex::MultiFab> wrf_PHB;
1306 
1307  amrex::Vector<std::unique_ptr<amrex::MultiFab>> mf_PSFC;
1308 
1309  // 1D CDF output (for ingestion in AMR-Wind)
1310  static int output_1d_column;
1311  static int column_interval;
1312  static amrex::Real column_per;
1313  static amrex::Real column_loc_x;
1314  static amrex::Real column_loc_y;
1315  static std::string column_file_name;
1316 
1317  // 2D BndryRegister output (for ingestion in AMR-Wind)
1318  static int output_bndry_planes;
1319  static int bndry_output_planes_interval;
1320  static amrex::Real bndry_output_planes_per;
1321  static amrex::Real bndry_output_planes_start_time;
1322 
1323  // 2D BndryRegister input
1324  static int input_bndry_planes;
1325 
1326  static int ng_dens_hse;
1327  static int ng_pres_hse;
1328 
1329  // Custom source terms
1330  amrex::Vector<std::unique_ptr<amrex::MultiFab>> rhotheta_src;
1331  amrex::Vector<std::unique_ptr<amrex::MultiFab>> rhoqt_src;
1332 
1333  amrex::Vector< amrex::Vector<amrex::Real> > h_w_subsid;
1334  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_w_subsid;
1335 
1336  amrex::Vector< amrex::Vector<amrex::Real> > h_u_geos;
1337  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_u_geos;
1338 
1339  amrex::Vector< amrex::Vector<amrex::Real> > h_v_geos;
1340  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_v_geos;
1341 
1342  // Function to read and populate above host vectors (if input file exists)
1343  void init_geo_wind_profile (const std::string input_file,
1344  amrex::Vector<amrex::Real>& u_geos,
1345  amrex::Gpu::DeviceVector<amrex::Real>& u_geos_d,
1346  amrex::Vector<amrex::Real>& v_geos,
1347  amrex::Gpu::DeviceVector<amrex::Real>& v_geos_d,
1348  const amrex::Geometry& lgeom,
1349  const amrex::Vector<amrex::Real>& zlev_stag);
1350 
1351  // This is a vector over levels of vectors across quantities of Vectors
1352  amrex::Vector<amrex::Vector<amrex::Vector<amrex::Real> > > h_rayleigh_ptrs;
1353  amrex::Vector<amrex::Vector<amrex::Vector<amrex::Real> > > h_sponge_ptrs;
1354 
1355  // These are vectors over levels of Vectors
1356  amrex::Vector<amrex::Vector<amrex::Real> > h_sinesq_ptrs;
1357  amrex::Vector<amrex::Vector<amrex::Real> > h_sinesq_stag_ptrs;
1358 
1359  // This is a vector over levels of vectors across quantities of DeviceVectors
1360  amrex::Vector<amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > > d_rayleigh_ptrs;
1361  amrex::Vector<amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > > d_sponge_ptrs;
1362 
1363  // These are vectors over levels of DeviceVectors
1364  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_sinesq_ptrs;
1365  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_sinesq_stag_ptrs;
1366 
1367  amrex::Vector<amrex::Real> h_havg_density;
1368  amrex::Vector<amrex::Real> h_havg_temperature;
1369  amrex::Vector<amrex::Real> h_havg_pressure;
1370  amrex::Vector<amrex::Real> h_havg_qv;
1371  amrex::Vector<amrex::Real> h_havg_qc;
1372 
1373  amrex::Gpu::DeviceVector<amrex::Real> d_havg_density;
1374  amrex::Gpu::DeviceVector<amrex::Real> d_havg_temperature;
1375  amrex::Gpu::DeviceVector<amrex::Real> d_havg_pressure;
1376  amrex::Gpu::DeviceVector<amrex::Real> d_havg_qv;
1377  amrex::Gpu::DeviceVector<amrex::Real> d_havg_qc;
1378 
1379  void refinement_criteria_setup ();
1380 
1381  std::unique_ptr<WriteBndryPlanes> m_w2d = nullptr;
1382  std::unique_ptr<ReadBndryPlanes> m_r2d = nullptr;
1383  std::unique_ptr<SurfaceLayer> m_SurfaceLayer = nullptr;
1384  amrex::Vector<std::unique_ptr<ForestDrag>> m_forest_drag;
1385 
1386  //
1387  // Holds info for dynamically generated tagging criteria
1388  //
1389  static amrex::Vector<amrex::AMRErrorTag> ref_tags;
1390 
1391  amrex::Vector<amrex::Vector<amrex::BoxArray>> subdomains;
1392 
1393  amrex::Vector<amrex::Real> dz_min;
1394 
1395  static AMREX_FORCE_INLINE
1396  int
1397  ComputeGhostCells (const SolverChoice& sc)
1398  {
1399  int ngrow = 0;
1400 
1401  if (sc.use_num_diff)
1402  {
1403  ngrow = 3;
1404  } else {
1405  if (
1406  (sc.advChoice.dycore_horiz_adv_type == AdvType::Centered_6th)
1407  || (sc.advChoice.dycore_vert_adv_type == AdvType::Centered_6th)
1408  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Centered_6th)
1409  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Centered_6th)
1410  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Centered_6th)
1411  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Centered_6th) )
1412  { ngrow = 3; }
1413  else if (
1414  (sc.advChoice.dycore_horiz_adv_type == AdvType::Upwind_5th)
1415  || (sc.advChoice.dycore_vert_adv_type == AdvType::Upwind_5th)
1416  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Upwind_5th)
1417  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Upwind_5th)
1418  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Upwind_5th)
1419  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Upwind_5th) )
1420  { ngrow = 3; }
1421  else if (
1422  (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_5)
1423  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_5)
1424  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_5)
1425  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_5)
1426  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_5Z)
1427  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_5Z)
1428  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_5Z)
1429  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_5Z) )
1430  { ngrow = 3; }
1431  else if (
1432  (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_7)
1433  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_7)
1434  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_7)
1435  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_7)
1436  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_7Z)
1437  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_7Z)
1438  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_7Z)
1439  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_7Z) )
1440  { ngrow = 4; }
1441  else
1442  {
1443  if (sc.terrain_type == TerrainType::EB){
1444  ngrow = 4;
1445  } else {
1446  ngrow = 2;
1447  }
1448  }
1449  }
1450 
1451  return ngrow;
1452  }
1453 
1454  AMREX_FORCE_INLINE
1455  amrex::YAFluxRegister* getAdvFluxReg (int lev)
1456  {
1457  return advflux_reg[lev];
1458  }
1459 
1460  AMREX_FORCE_INLINE
1461  std::ostream&
1462  DataLog (int i)
1463  {
1464  return *datalog[i];
1465  }
1466 
1467  AMREX_FORCE_INLINE
1468  std::ostream&
1469  DerDataLog (int i)
1470  {
1471  return *der_datalog[i];
1472  }
1473 
1474  AMREX_FORCE_INLINE
1475  int
1476  NumDataLogs () noexcept
1477  {
1478  return static_cast<int>(datalog.size());
1479  }
1480 
1481  AMREX_FORCE_INLINE
1482  int
1483  NumDerDataLogs () noexcept
1484  {
1485  return static_cast<int>(der_datalog.size());
1486  }
1487 
1488 
1489  AMREX_FORCE_INLINE
1490  std::ostream&
1491  SamplePointLog (int i)
1492  {
1493  return *sampleptlog[i];
1494  }
1495 
1496  AMREX_FORCE_INLINE
1497  int
1498  NumSamplePointLogs () noexcept
1499  {
1500  return static_cast<int>(sampleptlog.size());
1501  }
1502 
1503  AMREX_FORCE_INLINE
1504  std::ostream&
1505  SampleLineLog (int i)
1506  {
1507  return *samplelinelog[i];
1508  }
1509 
1510  AMREX_FORCE_INLINE
1511  int
1512  NumSampleLineLogs () noexcept
1513  {
1514  return static_cast<int>(samplelinelog.size());
1515  }
1516 
1517  amrex::IntVect&
1518  SamplePoint (int i)
1519  {
1520  return samplepoint[i];
1521  }
1522 
1523  AMREX_FORCE_INLINE
1524  int
1525  NumSamplePoints () noexcept
1526  {
1527  return static_cast<int>(samplepoint.size());
1528  }
1529 
1530  amrex::IntVect&
1531  SampleLine (int i)
1532  {
1533  return sampleline[i];
1534  }
1535 
1536  AMREX_FORCE_INLINE
1537  int
1538  NumSampleLines () noexcept
1539  {
1540  return static_cast<int>(sampleline.size());
1541  }
1542 
1543  static amrex::Real startCPUTime;
1544  static amrex::Real previousCPUTimeUsed;
1545 
1546  static amrex::Real
1547  getCPUTime ()
1548  {
1549  int numCores = amrex::ParallelDescriptor::NProcs();
1550 #ifdef _OPENMP
1551  numCores = numCores * omp_get_max_threads();
1552 #endif
1553 
1554  amrex::Real T =
1555  numCores * amrex::Real(amrex::ParallelDescriptor::second() - startCPUTime) +
1556  previousCPUTimeUsed;
1557 
1558  return T;
1559  }
1560 
1561  void setRecordDataInfo (int i, const std::string& filename) // NOLINT
1562  {
1563  if (amrex::ParallelDescriptor::IOProcessor())
1564  {
1565  datalog[i] = std::make_unique<std::fstream>();
1566  datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1567  if (!datalog[i]->good()) {
1568  amrex::FileOpenFailed(filename);
1569  }
1570  }
1571  amrex::ParallelDescriptor::Barrier("ERF::setRecordDataInfo");
1572  }
1573 
1574  void setRecordDerDataInfo (int i, const std::string& filename) // NOLINT
1575  {
1576  if (amrex::ParallelDescriptor::IOProcessor())
1577  {
1578  der_datalog[i] = std::make_unique<std::fstream>();
1579  der_datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1580  if (!der_datalog[i]->good()) {
1581  amrex::FileOpenFailed(filename);
1582  }
1583  }
1584  amrex::ParallelDescriptor::Barrier("ERF::setRecordDerDataInfo");
1585  }
1586 
1587  void setRecordEnergyDataInfo (int i, const std::string& filename) // NOLINT
1588  {
1589  if (amrex::ParallelDescriptor::IOProcessor())
1590  {
1591  tot_e_datalog[i] = std::make_unique<std::fstream>();
1592  tot_e_datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1593  if (!tot_e_datalog[i]->good()) {
1594  amrex::FileOpenFailed(filename);
1595  }
1596  }
1597  amrex::ParallelDescriptor::Barrier("ERF::setRecordEnergyDataInfo");
1598  }
1599 
1600  void setRecordSamplePointInfo (int i, int lev, amrex::IntVect& cell, const std::string& filename) // NOLINT
1601  {
1602  amrex::MultiFab dummy(grids[lev],dmap[lev],1,0);
1603  for (amrex::MFIter mfi(dummy); mfi.isValid(); ++mfi)
1604  {
1605  const amrex::Box& bx = mfi.validbox();
1606  if (bx.contains(cell)) {
1607  sampleptlog[i] = std::make_unique<std::fstream>();
1608  sampleptlog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1609  if (!sampleptlog[i]->good()) {
1610  amrex::FileOpenFailed(filename);
1611  }
1612  }
1613  }
1614  amrex::ParallelDescriptor::Barrier("ERF::setRecordSamplePointInfo");
1615  }
1616 
1617  void setRecordSampleLineInfo (int i, int lev, amrex::IntVect& cell, const std::string& filename) // NOLINT
1618  {
1619  amrex::MultiFab dummy(grids[lev],dmap[lev],1,0);
1620  for (amrex::MFIter mfi(dummy); mfi.isValid(); ++mfi)
1621  {
1622  const amrex::Box& bx = mfi.validbox();
1623  if (bx.contains(cell)) {
1624  samplelinelog[i] = std::make_unique<std::fstream>();
1625  samplelinelog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1626  if (!samplelinelog[i]->good()) {
1627  amrex::FileOpenFailed(filename);
1628  }
1629  }
1630  }
1631  amrex::ParallelDescriptor::Barrier("ERF::setRecordSampleLineInfo");
1632  }
1633 
1634  // Data sampler for line and plane output
1635  int line_sampling_interval = -1;
1636  int plane_sampling_interval = -1;
1637  amrex::Real line_sampling_per = -one;
1638  amrex::Real plane_sampling_per = -one;
1639  std::unique_ptr<LineSampler> line_sampler = nullptr;
1640  std::unique_ptr<PlaneSampler> plane_sampler = nullptr;
1641 
1642  amrex::Vector<std::unique_ptr<std::fstream> > datalog;
1643  amrex::Vector<std::unique_ptr<std::fstream> > der_datalog;
1644  amrex::Vector<std::unique_ptr<std::fstream> > tot_e_datalog;
1645  amrex::Vector<std::string> datalogname;
1646  amrex::Vector<std::string> der_datalogname;
1647  amrex::Vector<std::string> tot_e_datalogname;
1648 
1649  amrex::Vector<std::unique_ptr<std::fstream> > sampleptlog;
1650  amrex::Vector<std::string> sampleptlogname;
1651  amrex::Vector<amrex::IntVect> samplepoint;
1652 
1653  amrex::Vector<std::unique_ptr<std::fstream> > samplelinelog;
1654  amrex::Vector<std::string> samplelinelogname;
1655  amrex::Vector<amrex::IntVect> sampleline;
1656 
1657  //! The filename of the ith datalog file.
1658  [[nodiscard]] std::string DataLogName (int i) const noexcept { return datalogname[i]; }
1659  [[nodiscard]] std::string DerDataLogName (int i) const noexcept { return der_datalogname[i]; }
1660 
1661  //! The filename of the ith sampleptlog file.
1662  [[nodiscard]] std::string SamplePointLogName (int i) const noexcept { return sampleptlogname[i]; }
1663 
1664  //! The filename of the ith samplelinelog file.
1665  [[nodiscard]] std::string SampleLineLogName (int i) const noexcept { return samplelinelogname[i]; }
1666 
1667  // array of EB objects
1668  amrex::Vector<std::unique_ptr<eb_>> eb;
1669 
1670  [[nodiscard]] eb_ const& get_eb (int lev) const noexcept {
1671  AMREX_ASSERT(lev >= 0 && lev < eb.size() && eb[lev] != nullptr);
1672  return *eb[lev];
1673  }
1674 
1675  [[nodiscard]] amrex::EBFArrayBoxFactory const&
1676  EBFactory (int lev) const noexcept {
1677  return *(eb[lev]->get_const_factory());
1678  }
1679 
1680  [[nodiscard]] static int nghost_eb_basic ()
1681  { return 5; }
1682 
1683  // We need 5 for doing StateRedistribution; otherwise 4 would be enough
1684  [[nodiscard]] static int nghost_eb_volume ()
1685  { return 5; }
1686 
1687  [[nodiscard]] static int nghost_eb_full ()
1688  { return 4; }
1689 
1690 #ifdef ERF_USE_FFT
1691  // Vector over levels of Vector over subdomains of solvers
1692  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::FFT::Poisson<amrex::MultiFab>>>> m_3D_poisson;
1693  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::FFT::PoissonHybrid<amrex::MultiFab>>>> m_2D_poisson;
1694 #endif
1695 
1696 public:
1697  void writeJobInfo (const std::string& dir) const;
1698  static void writeBuildInfo (std::ostream& os);
1699 
1700  static void print_banner(MPI_Comm /*comm*/, std::ostream& /*out*/);
1701  static void print_usage(MPI_Comm /*comm*/, std::ostream& /*out*/);
1702  static void print_error(MPI_Comm /*comm*/, const std::string& msg);
1703  static void print_summary(std::ostream&);
1704  static void print_tpls(std::ostream& /*out*/);
1705 };
1706 
1707 #endif
AMREX_ENUM
AMREX_ENUM(StateInterpType, FullState, Perturbational)
one
constexpr amrex::Real one
Definition: ERF_Constants.H:7
zero
constexpr amrex::Real zero
Definition: ERF_Constants.H:6
RayleighDampingType::None
@ None
ERF_DataStruct.H
tau23
@ tau23
Definition: ERF_DataStruct.H:32
tau13
@ tau13
Definition: ERF_DataStruct.H:32
ERF_Derive.H
ERF_EB.H
ERF_EulerianMicrophysics.H
Contains the Eulerian microphysics class.
ERF_FillPatcher.H
ERF_ForestDrag.H
out
struct @28 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
T
Real T
Definition: ERF_InitCustomPert_Bubble.H:105
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::SurfaceDataInterpolation
void SurfaceDataInterpolation(const int nlevs, const amrex::Real time, amrex::Vector< std::unique_ptr< amrex::MultiFab >> &z_phys_nd, bool regrid_forces_file_read)
Definition: ERF_SurfaceDataInterpolation.cpp:142
ERF::MakeHorizontalAverages
void MakeHorizontalAverages()
Definition: ERF.cpp:2974
ERF::rU_new
amrex::Vector< amrex::MultiFab > rU_new
Definition: ERF.H:882
ERF::last_check_file_step
static int last_check_file_step
Definition: ERF.H:1052
ERF::walldist
amrex::Vector< std::unique_ptr< amrex::MultiFab > > walldist
Definition: ERF.H:992
ERF::h_sponge_ptrs
amrex::Vector< amrex::Vector< amrex::Vector< amrex::Real > > > h_sponge_ptrs
Definition: ERF.H:1353
ERF::start_time
static amrex::Real start_time
Definition: ERF.H:1078
ERF::metgrid_basic_linear
bool metgrid_basic_linear
Definition: ERF.H:1289
ERF::boxes_at_level
amrex::Vector< amrex::Vector< amrex::Box > > boxes_at_level
Definition: ERF.H:833
ERF::samplelinelogname
amrex::Vector< std::string > samplelinelogname
Definition: ERF.H:1654
ERF::MakeEBGeometry
void MakeEBGeometry()
ERF::max_step
int max_step
Definition: ERF.H:1075
ERF::metgrid_debug_msf
bool metgrid_debug_msf
Definition: ERF.H:1287
ERF::DerDataLog
AMREX_FORCE_INLINE std::ostream & DerDataLog(int i)
Definition: ERF.H:1469
ERF::mapfac
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > mapfac
Definition: ERF.H:995
ERF::setRayleighRefFromSounding
void setRayleighRefFromSounding(bool restarting)
Set Rayleigh mean profiles from input sounding.
Definition: ERF_InitRayleigh.cpp:83
ERF::mri_integrator_mem
amrex::Vector< std::unique_ptr< MRISplitIntegrator< amrex::Vector< amrex::MultiFab > > > > mri_integrator_mem
Definition: ERF.H:857
ERF::d_sinesq_stag_ptrs
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_sinesq_stag_ptrs
Definition: ERF.H:1365
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:3243
ERF::Evolve
void Evolve()
Definition: ERF.cpp:610
ERF::avg_xmom
amrex::Vector< amrex::MultiFab > avg_xmom
Definition: ERF.H:864
ERF::pp_inc
amrex::Vector< amrex::MultiFab > pp_inc
Definition: ERF.H:860
ERF::last_plot2d_file_time_2
static amrex::Real last_plot2d_file_time_2
Definition: ERF.H:1057
ERF::make_eb_box
void make_eb_box()
ERF::FPr_u
amrex::Vector< ERFFillPatcher > FPr_u
Definition: ERF.H:932
ERF::sampleline
amrex::Vector< amrex::IntVect > sampleline
Definition: ERF.H:1655
ERF::subvol3d_var_names
amrex::Vector< std::string > subvol3d_var_names
Definition: ERF.H:1140
ERF::SFS_q1fx3_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q1fx3_lev
Definition: ERF.H:955
ERF::Hwave_onegrid
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Hwave_onegrid
Definition: ERF.H:1009
ERF::vars_new
amrex::Vector< amrex::Vector< amrex::MultiFab > > vars_new
Definition: ERF.H:847
ERF::ERF
ERF(ERF &&) noexcept=delete
ERF::project_initial_velocity
void project_initial_velocity(int lev, amrex::Real time, amrex::Real dt)
Definition: ERF_PoissonSolve.cpp:31
ERF::FillBdyCCVels
void FillBdyCCVels(amrex::MultiFab &mf_cc_vel, amrex::Geometry &lev_geom)
Definition: ERF_FillBdyCCVels.cpp:11
ERF::NumSampleLineLogs
AMREX_FORCE_INLINE int NumSampleLineLogs() noexcept
Definition: ERF.H:1512
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:1393
ERF::m_plot2d_per_1
amrex::Real m_plot2d_per_1
Definition: ERF.H:1125
ERF::lagged_delta_rt
amrex::Vector< amrex::MultiFab > lagged_delta_rt
Definition: ERF.H:863
ERF::plane_sampling_per
amrex::Real plane_sampling_per
Definition: ERF.H:1638
ERF::DataLogName
std::string DataLogName(int i) const noexcept
The filename of the ith datalog file.
Definition: ERF.H:1658
ERF::plot2d_file_2
std::string plot2d_file_2
Definition: ERF.H:1112
ERF::remake_zphys
void remake_zphys(int lev, std::unique_ptr< amrex::MultiFab > &temp_zphys_nd)
Definition: ERF_MakeNewArrays.cpp:798
ERF::thin_yforce
amrex::Vector< std::unique_ptr< amrex::MultiFab > > thin_yforce
Definition: ERF.H:1045
ERF::ErrorEst
void ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real time, int ngrow) override
Definition: ERF_Tagging.cpp:26
ERF::SFS_hfx3_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_hfx3_lev
Definition: ERF.H:953
ERF::h_w_subsid
amrex::Vector< amrex::Vector< amrex::Real > > h_w_subsid
Definition: ERF.H:1333
ERF::print_banner
static void print_banner(MPI_Comm, std::ostream &)
Definition: ERF_ConsoleIO.cpp:60
ERF::volWgtColumnSum
void volWgtColumnSum(int lev, const amrex::MultiFab &mf, int comp, amrex::MultiFab &mf_2d, const amrex::MultiFab &dJ)
Definition: ERF_VolWgtSum.cpp:82
ERF::last_plot2d_file_time_1
static amrex::Real last_plot2d_file_time_1
Definition: ERF.H:1056
ERF::datalog
amrex::Vector< std::unique_ptr< std::fstream > > datalog
Definition: ERF.H:1642
ERF::sum_per
static amrex::Real sum_per
Definition: ERF.H:1257
ERF::MakeFilename_EyeTracker_maxvel
std::string MakeFilename_EyeTracker_maxvel(int nstep)
Definition: ERF_TrackerOutput.cpp:66
ERF::FPr_v
amrex::Vector< ERFFillPatcher > FPr_v
Definition: ERF.H:933
ERF::derived_names_2d
const amrex::Vector< std::string > derived_names_2d
Definition: ERF.H:1200
ERF::cf_set_width
int cf_set_width
Definition: ERF.H:930
ERF::wrf_MUB
std::unique_ptr< amrex::MultiFab > wrf_MUB
Definition: ERF.H:1302
ERF::previousCPUTimeUsed
static amrex::Real previousCPUTimeUsed
Definition: ERF.H:1544
ERF::setPlotVariables
void setPlotVariables(const std::string &pp_plot_var_names, amrex::Vector< std::string > &plot_var_names)
Definition: ERF_Plotfile.cpp:28
ERF::d_havg_temperature
amrex::Gpu::DeviceVector< amrex::Real > d_havg_temperature
Definition: ERF.H:1374
ERF::wrf_C1H
std::unique_ptr< amrex::MultiFab > wrf_C1H
Definition: ERF.H:1300
ERF::last_plot2d_file_step_2
static int last_plot2d_file_step_2
Definition: ERF.H:1051
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:1068
ERF::setRecordDataInfo
void setRecordDataInfo(int i, const std::string &filename)
Definition: ERF.H:1561
ERF::SFS_hfx1_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_hfx1_lev
Definition: ERF.H:953
ERF::hurricane_eye_track_xy
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_eye_track_xy
Definition: ERF.H:161
ERF::ba2d
amrex::Vector< amrex::BoxArray > ba2d
Definition: ERF.H:1298
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:1026
ERF::init_from_input_sounding
void init_from_input_sounding(int lev)
Definition: ERF_InitFromInputSounding.cpp:53
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:210
ERF::gradp
amrex::Vector< amrex::Vector< amrex::MultiFab > > gradp
Definition: ERF.H:851
ERF::plot3d_file_1
std::string plot3d_file_1
Definition: ERF.H:1109
ERF::get_eb
eb_ const & get_eb(int lev) const noexcept
Definition: ERF.H:1670
ERF::d_havg_qv
amrex::Gpu::DeviceVector< amrex::Real > d_havg_qv
Definition: ERF.H:1376
ERF::qfx3_EB
amrex::Vector< std::unique_ptr< amrex::MultiFab > > qfx3_EB
Definition: ERF.H:962
ERF::column_loc_y
static amrex::Real column_loc_y
Definition: ERF.H:1314
ERF::plot_file_on_restart
static bool plot_file_on_restart
Definition: ERF.H:1063
ERF::bckgnd_state
amrex::Vector< amrex::Vector< amrex::MultiFab > > bckgnd_state
Definition: ERF.H:174
ERF::mg_verbose
static int mg_verbose
Definition: ERF.H:1249
ERF::ReadParameters
void ReadParameters()
Definition: ERF.cpp:2383
ERF::PlotFileVarNames
static amrex::Vector< std::string > PlotFileVarNames(amrex::Vector< std::string > plot_var_names)
Definition: ERF_Plotfile.cpp:309
ERF::forecast_state_interp
amrex::Vector< amrex::Vector< amrex::MultiFab > > forecast_state_interp
Definition: ERF.H:169
ERF::FindInitialEye
bool FindInitialEye(int lev, const amrex::MultiFab &cc_vel, const amrex::Real velmag_threshold, amrex::Real &eye_x, amrex::Real &eye_y)
Definition: ERF_Tagging.cpp:880
ERF::InitializeFromFile
void InitializeFromFile()
ERF::physbcs_cons
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_cons > > physbcs_cons
Definition: ERF.H:869
ERF::project_velocity_tb
void project_velocity_tb(int lev, amrex::Real dt, amrex::Vector< amrex::MultiFab > &vars)
Definition: ERF_PoissonSolve_tb.cpp:22
ERF::mf_PSFC
amrex::Vector< std::unique_ptr< amrex::MultiFab > > mf_PSFC
Definition: ERF.H:1307
ERF::ERF
ERF()
Definition: ERF.cpp:142
ERF::init_Dirichlet_bc_data
void init_Dirichlet_bc_data(const std::string input_file)
Definition: ERF_InitBCs.cpp:692
ERF::~ERF
~ERF() override
ERF::z_phys_nd_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_nd_src
Definition: ERF.H:976
ERF::detJ_cc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > detJ_cc
Definition: ERF.H:971
ERF::lsm_flux_name
amrex::Vector< std::string > lsm_flux_name
Definition: ERF.H:911
ERF::WriteMyEBSurface
void WriteMyEBSurface()
ERF::z_phys_cc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_cc
Definition: ERF.H:969
ERF::eb
amrex::Vector< std::unique_ptr< eb_ > > eb
Definition: ERF.H:1668
ERF::eddyDiffs_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > eddyDiffs_lev
Definition: ERF.H:939
ERF::solverChoice
static SolverChoice solverChoice
Definition: ERF.H:1213
ERF::hfx3_EB
amrex::Vector< std::unique_ptr< amrex::MultiFab > > hfx3_EB
Definition: ERF.H:961
ERF::FPr_c
amrex::Vector< ERFFillPatcher > FPr_c
Definition: ERF.H:931
ERF::plot_rad
bool plot_rad
Definition: ERF.H:925
ERF::hurricane_tracker_circle
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_tracker_circle
Definition: ERF.H:165
ERF::use_fft
static bool use_fft
Definition: ERF.H:1250
ERF::m_plot_face_vels
bool m_plot_face_vels
Definition: ERF.H:1127
ERF::hurricane_maxvel_vs_time
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_maxvel_vs_time
Definition: ERF.H:163
ERF::sum_derived_quantities
void sum_derived_quantities(double time)
Definition: ERF_WriteScalarProfiles.cpp:177
ERF::base_state_new
amrex::Vector< amrex::MultiFab > base_state_new
Definition: ERF.H:1004
ERF::plot3d_file_2
std::string plot3d_file_2
Definition: ERF.H:1110
ERF::az
amrex::Vector< std::unique_ptr< amrex::MultiFab > > az
Definition: ERF.H:974
ERF::regrid_int
int regrid_int
Definition: ERF.H:1102
ERF::fixed_dt
amrex::Vector< amrex::Real > fixed_dt
Definition: ERF.H:1096
ERF::derive_diag_profiles
void derive_diag_profiles(double 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::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:1944
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:1361
ERF::dt_mri_ratio
amrex::Vector< long > dt_mri_ratio
Definition: ERF.H:842
ERF::Tau
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > Tau
Definition: ERF.H:937
ERF::vel_t_avg
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vel_t_avg
Definition: ERF.H:854
ERF::SFS_q2fx3_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q2fx3_lev
Definition: ERF.H:956
ERF::dt_max
static amrex::Real dt_max
Definition: ERF.H:1093
ERF::lmask_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::iMultiFab > > > lmask_lev
Definition: ERF.H:945
ERF::NumSamplePointLogs
AMREX_FORCE_INLINE int NumSamplePointLogs() noexcept
Definition: ERF.H:1498
ERF::h_havg_pressure
amrex::Vector< amrex::Real > h_havg_pressure
Definition: ERF.H:1369
ERF::update_diffusive_arrays
void update_diffusive_arrays(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)
Definition: ERF_MakeNewArrays.cpp:527
ERF::wrf_PHB
std::unique_ptr< amrex::MultiFab > wrf_PHB
Definition: ERF.H:1305
ERF::verbose
static int verbose
Definition: ERF.H:1248
ERF::h_havg_qc
amrex::Vector< amrex::Real > h_havg_qc
Definition: ERF.H:1371
ERF::physbcs_w
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_w > > physbcs_w
Definition: ERF.H:872
ERF::nghost_eb_basic
static int nghost_eb_basic()
Definition: ERF.H:1680
ERF::AverageDownMoistStateTo
void AverageDownMoistStateTo(int crse_lev)
Conservation-preserving fine→coarse average of moist state components (RhoTheta and the contiguous mo...
Definition: ERF_AverageDown.cpp:243
ERF::Advance
void Advance(int lev, amrex::Real time, amrex::Real dt_lev, int iteration, int ncycle)
Definition: ERF_Advance.cpp:20
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 >> &forecast_state)
Definition: ERF_WeatherDataInterpolation.cpp:64
ERF::column_file_name
static std::string column_file_name
Definition: ERF.H:1315
ERF::samplelinelog
amrex::Vector< std::unique_ptr< std::fstream > > samplelinelog
Definition: ERF.H:1653
ERF::last_plot3d_file_time_2
static amrex::Real last_plot3d_file_time_2
Definition: ERF.H:1055
ERF::terrain_blanking
amrex::Vector< std::unique_ptr< amrex::MultiFab > > terrain_blanking
Definition: ERF.H:989
ERF::micro
std::unique_ptr< Microphysics > micro
Definition: ERF.H:892
ERF::m_plot2d_int_2
int m_plot2d_int_2
Definition: ERF.H:1118
ERF::base_state
amrex::Vector< amrex::MultiFab > base_state
Definition: ERF.H:1003
ERF::getAdvFluxReg
AMREX_FORCE_INLINE amrex::YAFluxRegister * getAdvFluxReg(int lev)
Definition: ERF.H:1455
ERF::m_plot3d_int_1
int m_plot3d_int_1
Definition: ERF.H:1115
ERF::h_havg_density
amrex::Vector< amrex::Real > h_havg_density
Definition: ERF.H:1367
ERF::z_phys_nd_new
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_nd_new
Definition: ERF.H:983
ERF::fixed_fast_dt
amrex::Vector< amrex::Real > fixed_fast_dt
Definition: ERF.H:1097
ERF::derive_diag_profiles_stag
void derive_diag_profiles_stag(double 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::create_background_state_for_ensemble
void create_background_state_for_ensemble(int lev, amrex::MultiFab &mf_cc_pert, amrex::MultiFab &cons_pert, amrex::MultiFab &xvel_pert, amrex::MultiFab &yvel_pert, amrex::MultiFab &zvel_pert)
Definition: ERF_InitForEnsemble.cpp:515
ERF::project_momenta
void project_momenta(int lev, amrex::Real l_time, amrex::Real l_dt, amrex::Vector< amrex::MultiFab > &vars)
Definition: ERF_PoissonSolve.cpp:102
ERF::derived_subvol_names
const amrex::Vector< std::string > derived_subvol_names
Definition: ERF.H:1210
ERF::hurricane_minpressure_vs_time
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_minpressure_vs_time
Definition: ERF.H:164
ERF::metgrid_retain_sfc
bool metgrid_retain_sfc
Definition: ERF.H:1292
ERF::Qv_prim
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Qv_prim
Definition: ERF.H:877
ERF::sum_interval
static int sum_interval
Definition: ERF.H:1255
ERF::pert_interval
static int pert_interval
Definition: ERF.H:1256
ERF::line_sampling_per
amrex::Real line_sampling_per
Definition: ERF.H:1637
ERF::restart
void restart()
Definition: ERF.cpp:2193
ERF::last_plot3d_file_step_2
static int last_plot3d_file_step_2
Definition: ERF.H:1049
ERF::SFS_q1fx2_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q1fx2_lev
Definition: ERF.H:955
ERF::SampleLine
amrex::IntVect & SampleLine(int i)
Definition: ERF.H:1531
ERF::build_fine_mask
void build_fine_mask(int lev, amrex::MultiFab &fine_mask)
Definition: ERF_VolWgtSum.cpp:125
ERF::file_name_digits
int file_name_digits
Definition: ERF.H:1265
ERF::rV_new
amrex::Vector< amrex::MultiFab > rV_new
Definition: ERF.H:884
ERF::PlotFileName
std::string PlotFileName(int lev) const
ERF::initialize_integrator
void initialize_integrator(int lev, amrex::MultiFab &cons_mf, amrex::MultiFab &vel_mf)
Definition: ERF_MakeNewArrays.cpp:875
ERF::thin_zforce
amrex::Vector< std::unique_ptr< amrex::MultiFab > > thin_zforce
Definition: ERF.H:1046
ERF::plot3d_var_names_2
amrex::Vector< std::string > plot3d_var_names_2
Definition: ERF.H:1143
ERF::domain_bcs_type
amrex::Vector< amrex::BCRec > domain_bcs_type
Definition: ERF.H:1019
ERF::Qr_prim
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Qr_prim
Definition: ERF.H:878
ERF::apply_gaussian_smoothing_to_perturbations
void apply_gaussian_smoothing_to_perturbations(const int lev, amrex::MultiFab &mf_cc_pert)
Definition: ERF_InitForEnsemble.cpp:86
ERF::pp_prefix
std::string pp_prefix
Definition: ERF.H:562
ERF::SampleLineLogName
std::string SampleLineLogName(int i) const noexcept
The filename of the ith samplelinelog file.
Definition: ERF.H:1665
ERF::sst_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > sst_lev
Definition: ERF.H:943
ERF::plot2d_var_names_1
amrex::Vector< std::string > plot2d_var_names_1
Definition: ERF.H:1144
ERF::thin_xforce
amrex::Vector< std::unique_ptr< amrex::MultiFab > > thin_xforce
Definition: ERF.H:1044
ERF::NumSamplePoints
AMREX_FORCE_INLINE int NumSamplePoints() noexcept
Definition: ERF.H:1525
ERF::metgrid_use_sfc
bool metgrid_use_sfc
Definition: ERF.H:1291
ERF::m_plot2d_per_2
amrex::Real m_plot2d_per_2
Definition: ERF.H:1126
ERF::writeNow
bool writeNow(double 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:3203
ERF::bndry_output_planes_per
static amrex::Real bndry_output_planes_per
Definition: ERF.H:1320
ERF::setPlotVariables2D
void setPlotVariables2D(const std::string &pp_plot_var_names, amrex::Vector< std::string > &plot_var_names)
Definition: ERF_Plotfile.cpp:190
ERF::m_check_per
amrex::Real m_check_per
Definition: ERF.H:1138
ERF::init_custom
void init_custom(int lev)
Definition: ERF_InitCustomPertState.cpp:26
ERF::rad
amrex::Vector< std::unique_ptr< IRadiation > > rad
Definition: ERF.H:914
ERF::ComputeAndWriteEnsemblePerturbations
void ComputeAndWriteEnsemblePerturbations()
ERF::prob
std::unique_ptr< ProblemBase > prob
Definition: ERF.H:829
ERF::num_files_at_level
amrex::Vector< int > num_files_at_level
Definition: ERF.H:832
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:1857
ERF::init_bcs
void init_bcs()
Definition: ERF_InitBCs.cpp:295
ERF::EvolveOneStep
amrex::Real EvolveOneStep(amrex::Real time, amrex::Real dt_request)
Definition: ERF_Coupling.cpp:15
ERF::profile_int
int profile_int
Definition: ERF.H:1132
ERF::metgrid_debug_quiescent
bool metgrid_debug_quiescent
Definition: ERF.H:1283
ERF::physbcs_u
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_u > > physbcs_u
Definition: ERF.H:870
ERF::t_new
amrex::Vector< amrex::Real > t_new
Definition: ERF.H:839
ERF::destag_profiles
bool destag_profiles
Definition: ERF.H:1133
ERF::stretched_dz_d
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > stretched_dz_d
Definition: ERF.H:1001
ERF::th_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > th_bc_data
Definition: ERF.H:806
ERF::t_avg_cnt
amrex::Vector< amrex::Real > t_avg_cnt
Definition: ERF.H:855
ERF::DerDataLogName
std::string DerDataLogName(int i) const noexcept
Definition: ERF.H:1659
ERF::compute_max_pressure_gradient_diagnostic
void compute_max_pressure_gradient_diagnostic(int lev)
Definition: ERF_Diagnostics.cpp:12
ERF::m_check_int
int m_check_int
Definition: ERF.H:1137
ERF::ReadVelsOnlyFromCheckpointFile
void ReadVelsOnlyFromCheckpointFile(int lev_to_fill, std::string &chkfile)
Definition: ERF_Checkpoint.cpp:1073
ERF::estTimeStep
amrex::Real estTimeStep(int lev, long &dt_fast_ratio) const
Definition: ERF_ComputeTimestep.cpp:60
ERF::startCPUTime
static amrex::Real startCPUTime
Definition: ERF.H:1543
ERF::surface_state_1
amrex::Vector< amrex::MultiFab > surface_state_1
Definition: ERF.H:170
ERF::SFS_diss_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_diss_lev
Definition: ERF.H:954
ERF::d_sinesq_ptrs
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_sinesq_ptrs
Definition: ERF.H:1364
ERF::rU_old
amrex::Vector< amrex::MultiFab > rU_old
Definition: ERF.H:881
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:840
ERF::NumSampleLines
AMREX_FORCE_INLINE int NumSampleLines() noexcept
Definition: ERF.H:1538
ERF::m_bc_nonreflecting
amrex::Array< bool, AMREX_SPACEDIM *2 > m_bc_nonreflecting
Definition: ERF.H:1032
ERF::Theta_prim
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Theta_prim
Definition: ERF.H:876
ERF::write_1D_profiles
void write_1D_profiles(double time)
Definition: ERF_Write1DProfiles.cpp:17
ERF::init1DArrays
void init1DArrays()
ERF::z_t_rk
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_t_rk
Definition: ERF.H:986
ERF::HurricaneTracker
void HurricaneTracker(int lev, amrex::Real time, const amrex::MultiFab &cc_vel, const amrex::Real velmag_threshold, amrex::TagBoxArray *tags=nullptr)
Definition: ERF_Tagging.cpp:980
ERF::check_for_nans
static int check_for_nans
Definition: ERF.H:1252
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_TrackerOutput.cpp:11
ERF::initRayleigh_at_level
void initRayleigh_at_level(const int &lev)
Initialize Rayleigh damping profiles at a level.
Definition: ERF_InitRayleigh.cpp:14
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:232
ERF::physbcs_v
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_v > > physbcs_v
Definition: ERF.H:871
ERF::column_per
static amrex::Real column_per
Definition: ERF.H:1312
ERF::tot_e_datalogname
amrex::Vector< std::string > tot_e_datalogname
Definition: ERF.H:1647
ERF::stop_time
static amrex::Real stop_time
Definition: ERF.H:1079
ERF::output_bndry_planes
static int output_bndry_planes
Definition: ERF.H:1318
ERF::d_v_geos
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_v_geos
Definition: ERF.H:1340
ERF::update_terrain_arrays
void update_terrain_arrays(int lev)
Definition: ERF_MakeNewArrays.cpp:858
ERF::nc_bdy_file
static std::string nc_bdy_file
Definition: ERF.H:1275
ERF::metgrid_interp_theta
bool metgrid_interp_theta
Definition: ERF.H:1288
ERF::nc_init_file
static amrex::Vector< amrex::Vector< std::string > > nc_init_file
Definition: ERF.H:1271
ERF::init_only
void init_only(int lev, amrex::Real time)
Definition: ERF.cpp:2255
ERF::input_bndry_planes
static int input_bndry_planes
Definition: ERF.H:1324
ERF::interpolation_type
static StateInterpType interpolation_type
Definition: ERF.H:1268
ERF::d_havg_qc
amrex::Gpu::DeviceVector< amrex::Real > d_havg_qc
Definition: ERF.H:1377
ERF::cloud_fraction
amrex::Real cloud_fraction(double time)
Definition: ERF_WriteScalarProfiles.cpp:452
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:1339
ERF::regrid_level_0_on_restart
bool regrid_level_0_on_restart
Definition: ERF.H:1106
ERF::Lwave_onegrid
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Lwave_onegrid
Definition: ERF.H:1010
ERF::input_sounding_data
InputSoundingData input_sounding_data
Definition: ERF.H:797
ERF::write_1D_profiles_stag
void write_1D_profiles_stag(double time)
Definition: ERF_Write1DProfiles_stag.cpp:25
ERF::h_sinesq_ptrs
amrex::Vector< amrex::Vector< amrex::Real > > h_sinesq_ptrs
Definition: ERF.H:1356
ERF::create_random_perturbations
void create_random_perturbations(const int lev, amrex::MultiFab &mf_cc_pert)
Definition: ERF_InitForEnsemble.cpp:14
ERF::Write2DPlotFile
void Write2DPlotFile(int which, PlotFileType plotfile_type, amrex::Vector< std::string > plot_var_names)
Definition: ERF_Plotfile.cpp:2033
ERF::d_havg_density
amrex::Gpu::DeviceVector< amrex::Real > d_havg_density
Definition: ERF.H:1373
ERF::rhotheta_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > rhotheta_src
Definition: ERF.H:1330
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:1082
ERF::advflux_reg
amrex::Vector< amrex::YAFluxRegister * > advflux_reg
Definition: ERF.H:1014
ERF::metgrid_force_sfc_k
int metgrid_force_sfc_k
Definition: ERF.H:1295
ERF::setSubVolVariables
void setSubVolVariables(const std::string &pp_subvol_var_names, amrex::Vector< std::string > &subvol_var_names)
Definition: ERF_WriteSubvolume.cpp:9
ERF::ng_pres_hse
static int ng_pres_hse
Definition: ERF.H:1327
ERF::bndry_output_planes_start_time
static amrex::Real bndry_output_planes_start_time
Definition: ERF.H:1321
ERF::real_extrap_w
bool real_extrap_w
Definition: ERF.H:1277
ERF::cfl
static amrex::Real cfl
Definition: ERF.H:1088
ERF::fine_mask
amrex::Vector< std::unique_ptr< amrex::MultiFab > > fine_mask
Definition: ERF.H:998
ERF::domain_bcs_type_d
amrex::Gpu::DeviceVector< amrex::BCRec > domain_bcs_type_d
Definition: ERF.H:1020
ERF::m_forest_drag
amrex::Vector< std::unique_ptr< ForestDrag > > m_forest_drag
Definition: ERF.H:1384
ERF::datwidth
const int datwidth
Definition: ERF.H:1066
ERF::ba1d
amrex::Vector< amrex::BoxArray > ba1d
Definition: ERF.H:1297
ERF::input_sponge_data
InputSpongeData input_sponge_data
Definition: ERF.H:800
ERF::subdomains
amrex::Vector< amrex::Vector< amrex::BoxArray > > subdomains
Definition: ERF.H:1391
ERF::check_state_for_nans
void check_state_for_nans(amrex::MultiFab const &S)
Definition: ERF.cpp:3224
ERF::restart_chkfile
std::string restart_chkfile
Definition: ERF.H:1085
ERF::metgrid_use_below_sfc
bool metgrid_use_below_sfc
Definition: ERF.H:1290
ERF::sampleptlogname
amrex::Vector< std::string > sampleptlogname
Definition: ERF.H:1650
ERF::xvel_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > xvel_bc_data
Definition: ERF.H:803
ERF::init_zphys
void init_zphys(int lev, amrex::Real elapsed_time)
Definition: ERF_MakeNewArrays.cpp:693
ERF::InitData_pre
void InitData_pre()
Definition: ERF.cpp:994
ERF::SamplePoint
amrex::IntVect & SamplePoint(int i)
Definition: ERF.H:1518
ERF::use_datetime
bool use_datetime
Definition: ERF.H:1081
ERF::hurricane_track_xy
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_track_xy
Definition: ERF.H:160
ERF::h_u_geos
amrex::Vector< amrex::Vector< amrex::Real > > h_u_geos
Definition: ERF.H:1336
ERF::InitializeLevelFromData
void InitializeLevelFromData(int lev, const amrex::MultiFab &initial_data)
ERF::subvol_file
std::string subvol_file
Definition: ERF.H:1113
ERF::m_subvol_per
amrex::Vector< amrex::Real > m_subvol_per
Definition: ERF.H:1121
ERF::rad_datalog_int
int rad_datalog_int
Definition: ERF.H:926
ERF::datalogname
amrex::Vector< std::string > datalogname
Definition: ERF.H:1645
ERF::post_timestep
void post_timestep(int nstep, double time, amrex::Real dt_lev)
Definition: ERF.cpp:774
ERF::initHSE
void initHSE()
Initialize HSE.
Definition: ERF_Init1D.cpp:192
ERF::AverageDownTo
void AverageDownTo(int crse_lev, int scomp, int ncomp, bool do_perturbational_and_momenta=true)
Definition: ERF_AverageDown.cpp:36
ERF::column_loc_x
static amrex::Real column_loc_x
Definition: ERF.H:1313
ERF::surface_state_2
amrex::Vector< amrex::MultiFab > surface_state_2
Definition: ERF.H:171
ERF::ax
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ax
Definition: ERF.H:972
ERF::z_phys_nd
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_nd
Definition: ERF.H:968
ERF::MakeDiagnosticAverage
void MakeDiagnosticAverage(amrex::Vector< amrex::Real > &h_havg, amrex::MultiFab &S, int n)
Definition: ERF.cpp:3080
ERF::metgrid_proximity
amrex::Real metgrid_proximity
Definition: ERF.H:1293
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:1574
ERF::h_havg_temperature
amrex::Vector< amrex::Real > h_havg_temperature
Definition: ERF.H:1368
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:1649
ERF::poisson_wall_dist
void poisson_wall_dist(int lev)
Definition: ERF_PoissonWallDist.cpp:22
ERF::hurricane_eye_track_latlon
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_eye_track_latlon
Definition: ERF.H:162
ERF::detJ_cc_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > detJ_cc_src
Definition: ERF.H:978
ERF::d_havg_pressure
amrex::Gpu::DeviceVector< amrex::Real > d_havg_pressure
Definition: ERF.H:1375
ERF::PackAtmosphericStates
void PackAtmosphericStates(amrex::Vector< amrex::MultiFab * > &states, amrex::Real time)
Definition: ERF_Coupling.cpp:91
ERF::plot2d_file_1
std::string plot2d_file_1
Definition: ERF.H:1111
ERF::der_datalogname
amrex::Vector< std::string > der_datalogname
Definition: ERF.H:1646
ERF::SmnSmn_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SmnSmn_lev
Definition: ERF.H:940
ERF::derived_names
const amrex::Vector< std::string > derived_names
Definition: ERF.H:1155
ERF::sum_integrated_quantities
void sum_integrated_quantities(double time)
Definition: ERF_WriteScalarProfiles.cpp:15
ERF::MakeVTKFilename_TrackerCircle
std::string MakeVTKFilename_TrackerCircle(int nstep)
Definition: ERF_TrackerOutput.cpp:24
ERF::ay_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ay_src
Definition: ERF.H:980
ERF::sample_points
void sample_points(int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab &mf)
Definition: ERF_WriteScalarProfiles.cpp:528
ERF::ComputeDt
void ComputeDt(int step=-1, double cur_time_d=0.0)
Definition: ERF_ComputeTimestep.cpp:11
ERF::DataLog
AMREX_FORCE_INLINE std::ostream & DataLog(int i)
Definition: ERF.H:1462
ERF::writeJobInfo
void writeJobInfo(const std::string &dir) const
Definition: ERF_WriteJobInfo.cpp:9
ERF::MakeVTKFilename_EyeTracker_xy
std::string MakeVTKFilename_EyeTracker_xy(int nstep)
Definition: ERF_TrackerOutput.cpp:38
ERF::nsubsteps
amrex::Vector< int > nsubsteps
Definition: ERF.H:836
ERF::yflux_imask
amrex::Vector< std::unique_ptr< amrex::iMultiFab > > yflux_imask
Definition: ERF.H:1039
ERF::rW_new
amrex::Vector< amrex::MultiFab > rW_new
Definition: ERF.H:886
ERF::weather_forecast_data_2
amrex::Vector< amrex::MultiFab > weather_forecast_data_2
Definition: ERF.H:166
ERF::lon_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > lon_m
Definition: ERF.H:792
ERF::m_w2d
std::unique_ptr< WriteBndryPlanes > m_w2d
Definition: ERF.H:1381
ERF::SampleLineLog
AMREX_FORCE_INLINE std::ostream & SampleLineLog(int i)
Definition: ERF.H:1505
ERF::lsm_flux
amrex::Vector< amrex::Vector< amrex::MultiFab * > > lsm_flux
Definition: ERF.H:912
ERF::plot3d_var_names_1
amrex::Vector< std::string > plot3d_var_names_1
Definition: ERF.H:1142
ERF::ApplyOceanSurfaceState
void ApplyOceanSurfaceState(const amrex::Vector< amrex::MultiFab * > &state, amrex::Real time)
Definition: ERF_Coupling.cpp:288
ERF::SamplePointLogName
std::string SamplePointLogName(int i) const noexcept
The filename of the ith sampleptlog file.
Definition: ERF.H:1662
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:1018
ERF::refinement_criteria_setup
void refinement_criteria_setup()
Definition: ERF_Tagging.cpp:464
ERF::nghost_eb_volume
static int nghost_eb_volume()
Definition: ERF.H:1684
ERF::metgrid_debug_dry
bool metgrid_debug_dry
Definition: ERF.H:1285
ERF::ComputeGhostCells
static AMREX_FORCE_INLINE int ComputeGhostCells(const SolverChoice &sc)
Definition: ERF.H:1397
ERF::bndry_output_planes_interval
static int bndry_output_planes_interval
Definition: ERF.H:1319
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:157
ERF::plot2d_var_names_2
amrex::Vector< std::string > plot2d_var_names_2
Definition: ERF.H:1145
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:938
ERF::FillPatchCrseLevel
void FillPatchCrseLevel(int lev, double time, const amrex::Vector< amrex::MultiFab * > &mfs_vel, bool cons_only=false)
Definition: ERF_FillPatch.cpp:290
ERF::WriteSubvolume
void WriteSubvolume(int isub, amrex::Vector< std::string > subvol_var_names)
Definition: ERF_WriteSubvolume.cpp:145
ERF::sum_energy_quantities
void sum_energy_quantities(double time)
Definition: ERF_WriteScalarProfiles.cpp:313
ERF::nghost_eb_full
static int nghost_eb_full()
Definition: ERF.H:1687
ERF::RemakeLevel
void RemakeLevel(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: ERF_MakeNewLevel.cpp:534
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:890
ERF::metgrid_debug_isothermal
bool metgrid_debug_isothermal
Definition: ERF.H:1284
ERF::PerformDataAssimilation
void PerformDataAssimilation(int da_iter)
ERF::lsm_data_name
amrex::Vector< std::string > lsm_data_name
Definition: ERF.H:909
ERF::rhoqt_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > rhoqt_src
Definition: ERF.H:1331
ERF::initSponge
void initSponge()
Initialize sponge profiles.
Definition: ERF_InitSponge.cpp:35
ERF::plane_sampler
std::unique_ptr< PlaneSampler > plane_sampler
Definition: ERF.H:1640
ERF::check_for_low_temp
void check_for_low_temp(amrex::MultiFab &S)
Definition: ERF.cpp:3270
ERF::der_datalog
amrex::Vector< std::unique_ptr< std::fstream > > der_datalog
Definition: ERF.H:1643
ERF::have_read_nc_init_file
static amrex::Vector< amrex::Vector< int > > have_read_nc_init_file
Definition: ERF.H:1272
ERF::m_plot3d_per_2
amrex::Real m_plot3d_per_2
Definition: ERF.H:1124
ERF::tot_e_datalog
amrex::Vector< std::unique_ptr< std::fstream > > tot_e_datalog
Definition: ERF.H:1644
ERF::sinPhi_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > sinPhi_m
Definition: ERF.H:794
ERF::real_width
int real_width
Definition: ERF.H:1276
ERF::MakeNewLevelFromCoarse
void MakeNewLevelFromCoarse(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: ERF_MakeNewLevel.cpp:274
ERF::last_subvol_step
amrex::Vector< int > last_subvol_step
Definition: ERF.H:1060
ERF::ax_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ax_src
Definition: ERF.H:979
ERF::urb_frac_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > urb_frac_lev
Definition: ERF.H:950
ERF::z_phys_cc_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_cc_src
Definition: ERF.H:977
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:1337
ERF::Define_ERFFillPatchers
void Define_ERFFillPatchers(int lev)
Definition: ERF.cpp:3152
ERF::NumDataLogs
AMREX_FORCE_INLINE int NumDataLogs() noexcept
Definition: ERF.H:1476
ERF::plotfile3d_type_2
static PlotFileType plotfile3d_type_2
Definition: ERF.H:1261
ERF::setRecordEnergyDataInfo
void setRecordEnergyDataInfo(int i, const std::string &filename)
Definition: ERF.H:1587
ERF::turbPert
TurbulentPerturbation turbPert
Definition: ERF.H:1216
ERF::rW_old
amrex::Vector< amrex::MultiFab > rW_old
Definition: ERF.H:885
ERF::forecast_state_2
amrex::Vector< amrex::Vector< amrex::MultiFab > > forecast_state_2
Definition: ERF.H:168
ERF::check_for_negative_theta
void check_for_negative_theta(amrex::MultiFab &S)
Definition: ERF.cpp:3305
ERF::ImposeBCsOnPhi
void ImposeBCsOnPhi(int lev, amrex::MultiFab &phi, const amrex::Box &subdomain)
Definition: ERF_ImposeBCsOnPhi.cpp:12
ERF::Interp2DArrays
void Interp2DArrays(int lev, const amrex::BoxArray &my_ba2d, const amrex::DistributionMapping &my_dm)
Definition: ERF.cpp:1961
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:810
ERF::MakeFilename_EyeTracker_minpressure
std::string MakeFilename_EyeTracker_minpressure(int nstep)
Definition: ERF_TrackerOutput.cpp:80
ERF::m_SurfaceLayer
std::unique_ptr< SurfaceLayer > m_SurfaceLayer
Definition: ERF.H:1383
ERF::plotfile2d_type_2
static PlotFileType plotfile2d_type_2
Definition: ERF.H:1263
ERF::plane_sampling_interval
int plane_sampling_interval
Definition: ERF.H:1636
ERF::ref_tags
static amrex::Vector< amrex::AMRErrorTag > ref_tags
Definition: ERF.H:1389
ERF::make_physbcs
void make_physbcs(int lev)
Definition: ERF_MakeNewArrays.cpp:897
ERF::d_w_subsid
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_w_subsid
Definition: ERF.H:1334
ERF::FPr_w
amrex::Vector< ERFFillPatcher > FPr_w
Definition: ERF.H:934
ERF::SFS_hfx2_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_hfx2_lev
Definition: ERF.H:953
ERF::WriteLinePlot
void WriteLinePlot(const std::string &filename, amrex::Vector< std::array< amrex::Real, 2 >> &points_xy)
Definition: ERF_Write1DProfiles.cpp:574
ERF::soil_type_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::iMultiFab > > > soil_type_lev
Definition: ERF.H:949
ERF::zlevels_stag
amrex::Vector< amrex::Vector< amrex::Real > > zlevels_stag
Definition: ERF.H:965
ERF::NumDerDataLogs
AMREX_FORCE_INLINE int NumDerDataLogs() noexcept
Definition: ERF.H:1483
ERF::EBFactory
amrex::EBFArrayBoxFactory const & EBFactory(int lev) const noexcept
Definition: ERF.H:1676
ERF::lsm_data
amrex::Vector< amrex::Vector< amrex::MultiFab * > > lsm_data
Definition: ERF.H:910
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:1000
ERF::use_real_time_in_pltname
bool use_real_time_in_pltname
Definition: ERF.H:1266
ERF::m_plot2d_int_1
int m_plot2d_int_1
Definition: ERF.H:1117
ERF::WriteCheckpointFile
void WriteCheckpointFile() const
Definition: ERF_Checkpoint.cpp:26
ERF::output_1d_column
static int output_1d_column
Definition: ERF.H:1310
ERF::metgrid_debug_psfc
bool metgrid_debug_psfc
Definition: ERF.H:1286
ERF::az_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > az_src
Definition: ERF.H:981
ERF::fixed_mri_dt_ratio
static int fixed_mri_dt_ratio
Definition: ERF.H:1098
ERF::dt
amrex::Vector< amrex::Real > dt
Definition: ERF.H:841
ERF::init_shrink
static amrex::Real init_shrink
Definition: ERF.H:1090
ERF::WriteVTKPolyline
void WriteVTKPolyline(const std::string &filename, amrex::Vector< std::array< amrex::Real, 2 >> &points_xy)
Definition: ERF_TrackerOutput.cpp:94
ERF::Write3DPlotFile
void Write3DPlotFile(int which, PlotFileType plotfile_type, amrex::Vector< std::string > plot_var_names)
Definition: ERF_Plotfile.cpp:321
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:1092
ERF::nc_low_file
static std::string nc_low_file
Definition: ERF.H:1280
ERF::d_rayleigh_ptrs
amrex::Vector< amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > > d_rayleigh_ptrs
Definition: ERF.H:1360
ERF::InitData
void InitData()
Definition: ERF.cpp:985
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:1008
ERF::cosPhi_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > cosPhi_m
Definition: ERF.H:794
ERF::ParameterSanityChecks
void ParameterSanityChecks()
Definition: ERF.cpp:2906
ERF::land_type_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::iMultiFab > > > land_type_lev
Definition: ERF.H:948
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:167
ERF::cf_width
int cf_width
Definition: ERF.H:929
ERF::last_plot2d_file_step_1
static int last_plot2d_file_step_1
Definition: ERF.H:1050
ERF::zflux_imask
amrex::Vector< std::unique_ptr< amrex::iMultiFab > > zflux_imask
Definition: ERF.H:1040
ERF::m_expand_plotvars_to_unif_rr
bool m_expand_plotvars_to_unif_rr
Definition: ERF.H:1114
ERF::m_plot3d_per_1
amrex::Real m_plot3d_per_1
Definition: ERF.H:1123
ERF::Construct_ERFFillPatchers
void Construct_ERFFillPatchers(int lev)
Definition: ERF.cpp:3126
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:831
ERF::init_phys_bcs
void init_phys_bcs(bool &rho_read, bool &read_prim_theta)
Definition: ERF_InitBCs.cpp:20
ERF::FillSurfaceStateMultiFabs
void FillSurfaceStateMultiFabs(const int lev, const std::string &filename, amrex::Vector< amrex::MultiFab > &surface_state)
Definition: ERF_SurfaceDataInterpolation.cpp:19
ERF::sub_cfl
static amrex::Real sub_cfl
Definition: ERF.H:1089
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:1326
ERF::m_r2d
std::unique_ptr< ReadBndryPlanes > m_r2d
Definition: ERF.H:1382
ERF::ay
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ay
Definition: ERF.H:973
ERF::qmoist
amrex::Vector< amrex::Vector< amrex::MultiFab * > > qmoist
Definition: ERF.H:893
ERF::SFS_q1fx1_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q1fx1_lev
Definition: ERF.H:955
ERF::getCPUTime
static amrex::Real getCPUTime()
Definition: ERF.H:1547
ERF::zvel_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > zvel_bc_data
Definition: ERF.H:805
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:908
ERF::change_max
static amrex::Real change_max
Definition: ERF.H:1091
ERF::setRecordSampleLineInfo
void setRecordSampleLineInfo(int i, int lev, amrex::IntVect &cell, const std::string &filename)
Definition: ERF.H:1617
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:865
ERF::line_sampling_interval
int line_sampling_interval
Definition: ERF.H:1635
ERF::h_sinesq_stag_ptrs
amrex::Vector< amrex::Vector< amrex::Real > > h_sinesq_stag_ptrs
Definition: ERF.H:1357
ERF::detJ_cc_new
amrex::Vector< std::unique_ptr< amrex::MultiFab > > detJ_cc_new
Definition: ERF.H:984
ERF::domain_bc_type
amrex::Array< std::string, 2 *AMREX_SPACEDIM > domain_bc_type
Definition: ERF.H:1023
ERF::yvel_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > yvel_bc_data
Definition: ERF.H:804
ERF::writeBuildInfo
static void writeBuildInfo(std::ostream &os)
Definition: ERF_WriteJobInfo.cpp:143
ERF::phys_bc_type
amrex::GpuArray< ERF_BC, AMREX_SPACEDIM *2 > phys_bc_type
Definition: ERF.H:1035
ERF::check_file
std::string check_file
Definition: ERF.H:1136
ERF::samplepoint
amrex::Vector< amrex::IntVect > samplepoint
Definition: ERF.H:1651
ERF::surface_state_interp
amrex::Vector< amrex::MultiFab > surface_state_interp
Definition: ERF.H:172
ERF::h_havg_qv
amrex::Vector< amrex::Real > h_havg_qv
Definition: ERF.H:1370
ERF::last_subvol_time
amrex::Vector< amrex::Real > last_subvol_time
Definition: ERF.H:1061
ERF::weather_forecast_data_1
amrex::Vector< amrex::MultiFab > weather_forecast_data_1
Definition: ERF.H:166
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:883
ERF::lat_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > lat_m
Definition: ERF.H:792
ERF::timeStep
void timeStep(int lev, double time, int iteration)
Definition: ERF_TimeStep.cpp:17
ERF::h_rayleigh_ptrs
amrex::Vector< amrex::Vector< amrex::Vector< amrex::Real > > > h_rayleigh_ptrs
Definition: ERF.H:1352
ERF::make_eb_regular
void make_eb_regular()
ERF::last_check_file_time
static amrex::Real last_check_file_time
Definition: ERF.H:1058
ERF::last_plot3d_file_step_1
static int last_plot3d_file_step_1
Definition: ERF.H:1048
ERF::last_plot3d_file_time_1
static amrex::Real last_plot3d_file_time_1
Definition: ERF.H:1054
ERF::FillPatchFineLevel
void FillPatchFineLevel(int lev, double 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::line_sampler
std::unique_ptr< LineSampler > line_sampler
Definition: ERF.H:1639
ERF::Hwave
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Hwave
Definition: ERF.H:1007
ERF::Tau_EB
amrex::Vector< amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > > Tau_EB
Definition: ERF.H:960
ERF::istep
amrex::Vector< int > istep
Definition: ERF.H:835
ERF::datprecision
const int datprecision
Definition: ERF.H:1067
ERF::xflux_imask
amrex::Vector< std::unique_ptr< amrex::iMultiFab > > xflux_imask
Definition: ERF.H:1038
ERF::advance_lsm
void advance_lsm(int lev, amrex::MultiFab &cons_in, amrex::MultiFab &xvel_in, amrex::MultiFab &yvel_in, const amrex::Real &time, const amrex::Real &dt_advance)
Definition: ERF_AdvanceLSM.cpp:5
ERF::derive_upwp
void derive_upwp(amrex::Vector< amrex::Real > &h_havg)
ERF::plotfile2d_type_1
static PlotFileType plotfile2d_type_1
Definition: ERF.H:1262
ERF::metgrid_order
int metgrid_order
Definition: ERF.H:1294
ERF::finished_wave
bool finished_wave
Definition: ERF.H:1011
ERF::ReadCheckpointFile
void ReadCheckpointFile()
Definition: ERF_Checkpoint.cpp:471
ERF::vars_old
amrex::Vector< amrex::Vector< amrex::MultiFab > > vars_old
Definition: ERF.H:848
ERF::physbcs_base
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_base > > physbcs_base
Definition: ERF.H:873
ERF::init_thin_body
void init_thin_body(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)
Definition: ERF_MakeNewLevel.cpp:895
ERF::plotfile3d_type_1
static PlotFileType plotfile3d_type_1
Definition: ERF.H:1260
ERF::m_subvol_int
amrex::Vector< int > m_subvol_int
Definition: ERF.H:1120
ERF::is_it_time_for_action
static bool is_it_time_for_action(int nstep, double time, amrex::Real dt, int action_interval, amrex::Real action_per)
Definition: ERF_WriteScalarProfiles.cpp:654
ERF::SamplePointLog
AMREX_FORCE_INLINE std::ostream & SamplePointLog(int i)
Definition: ERF.H:1491
ERF::MakeFilename_EyeTracker_latlon
std::string MakeFilename_EyeTracker_latlon(int nstep)
Definition: ERF_TrackerOutput.cpp:52
ERF::m_bc_neumann_vals
amrex::Array< amrex::Array< amrex::Real, AMREX_SPACEDIM *2 >, AMREX_SPACEDIM+NBCVAR_max > m_bc_neumann_vals
Definition: ERF.H:1029
ERF::tsk_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > tsk_lev
Definition: ERF.H:944
ERF::setRecordSamplePointInfo
void setRecordSamplePointInfo(int i, int lev, amrex::IntVect &cell, const std::string &filename)
Definition: ERF.H:1600
ERF::column_interval
static int column_interval
Definition: ERF.H:1311
ERF::print_summary
static void print_summary(std::ostream &)
ERF::m_plot3d_int_2
int m_plot3d_int_2
Definition: ERF.H:1116
ERF::qheating_rates
amrex::Vector< std::unique_ptr< amrex::MultiFab > > qheating_rates
Definition: ERF.H:915
ERF::turbPert_amplitude
void turbPert_amplitude(const int lev)
Definition: ERF_InitTurbPert.cpp:33
ERF::sample_lines
void sample_lines(int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab &mf)
Definition: ERF_WriteScalarProfiles.cpp:564
ERF::rad_fluxes
amrex::Vector< std::unique_ptr< amrex::MultiFab > > rad_fluxes
Definition: ERF.H:916
ERF::initializeMicrophysics
void initializeMicrophysics(const int &)
Definition: ERF.cpp:2159
ERF::wrf_C2H
std::unique_ptr< amrex::MultiFab > wrf_C2H
Definition: ERF.H:1301
ERF::plot_lsm
bool plot_lsm
Definition: ERF.H:1129
ERF::avg_zmom
amrex::Vector< amrex::MultiFab > avg_zmom
Definition: ERF.H:866
ERF::cons_names
const amrex::Vector< std::string > cons_names
Definition: ERF.H:1146
ERF::ReadCheckpointFileSurfaceLayer
void ReadCheckpointFileSurfaceLayer()
Definition: ERF_Checkpoint.cpp:1113
LandSurface
Definition: ERF_LandSurface.H:16
eb_
Definition: ERF_EB.H:13
ERF
Definition: ERF_InterpolationUtils.H:16
MicVar_Kess::pres
@ pres
Definition: ERF_Kessler.H:26
MicVar_Kess::qv
@ qv
Definition: ERF_Kessler.H:29
Vars::xvel
@ xvel
Definition: ERF_IndexDefines.H:175
Vars::cons
@ cons
Definition: ERF_IndexDefines.H:174
Vars::zvel
@ zvel
Definition: ERF_IndexDefines.H:177
Vars::yvel
@ yvel
Definition: ERF_IndexDefines.H:176
WSM6Ind::p
@ p
Definition: ERF_WSM6.H:176
amrex
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
mp_wsm6::dens
real(kind=kind_phys), parameter, private dens
Definition: ERF_module_mp_wsm6.F90:39
AdvChoice::moistscal_horiz_adv_type
AdvType moistscal_horiz_adv_type
Definition: ERF_AdvStruct.H:423
AdvChoice::dycore_vert_adv_type
AdvType dycore_vert_adv_type
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
AdvType dycore_horiz_adv_type
Definition: ERF_AdvStruct.H:419
AdvChoice::dryscal_vert_adv_type
AdvType dryscal_vert_adv_type
Definition: ERF_AdvStruct.H:422
InputSoundingData
Definition: ERF_InputSoundingData.H:22
InputSpongeData
Definition: ERF_InputSpongeData.H:19
SolverChoice
Definition: ERF_DataStruct.H:141
SolverChoice::use_num_diff
bool use_num_diff
Definition: ERF_DataStruct.H:1295
SolverChoice::advChoice
AdvChoice advChoice
Definition: ERF_DataStruct.H:1142
SolverChoice::terrain_type
static TerrainType terrain_type
Definition: ERF_DataStruct.H:1125
TurbulentPerturbation
Definition: ERF_TurbPertStruct.H:22