ERF
Energy Research and Forecasting: An Atmospheric Modeling Code
ERF.H
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1 #ifndef ERF_H_
2 #define ERF_H_
3 
4 #include <string>
5 #include <limits>
6 #include <memory>
7 
8 #ifdef _OPENMP
9 #include <omp.h>
10 #endif
11 
12 #include <AMReX_AmrCore.H>
13 #include <AMReX_BCRec.H>
14 #include <AMReX_Print.H>
15 
16 #include <AMReX_ParallelDescriptor.H>
17 #include <AMReX_ParmParse.H>
18 #include <AMReX_MultiFabUtil.H>
19 #include <AMReX_FillPatchUtil.H>
20 #include <AMReX_VisMF.H>
21 #include <AMReX_PhysBCFunct.H>
22 #include <AMReX_YAFluxRegister.H>
23 #include <AMReX_ErrorList.H>
24 #include <AMReX_EBFabFactory.H>
25 #include <AMReX_EBMultiFabUtil.H>
26 
27 #include <ERF_EB.H>
28 
29 #ifdef ERF_USE_FFT
30 #include <AMReX_FFT_Poisson.H>
31 #endif
32 
33 #ifdef AMREX_MEM_PROFILING
34 #include <AMReX_MemProfiler.H>
35 #endif
36 
37 #include "ERF_ProbCommon.H"
38 
39 #include <ERF_IndexDefines.H>
40 #include <ERF_DataStruct.H>
41 #include <ERF_TurbPertStruct.H>
42 #include <ERF_InputSoundingData.H>
43 #include <ERF_InputSpongeData.H>
44 #include <ERF_SurfaceLayer.H>
45 #include <ERF_Derive.H>
46 #include <ERF_ReadBndryPlanes.H>
47 #include <ERF_WriteBndryPlanes.H>
48 #include <ERF_MRI.H>
49 #include <ERF_PhysBCFunct.H>
50 #include <ERF_FillPatcher.H>
51 #include <ERF_SampleData.H>
52 #include <ERF_ForestDrag.H>
53 
54 #ifdef ERF_USE_PARTICLES
55 #include "ERF_ParticleData.H"
56 #endif
57 
58 #include "ERF_EulerianMicrophysics.H"
59 #include "ERF_LagrangianMicrophysics.H"
60 #include "ERF_LandSurface.H"
61 
62 #ifdef ERF_USE_WINDFARM
63 #include "ERF_WindFarm.H"
64 #endif
65 
66 #include <ERF_RadiationModels.H>
67 
68 #ifdef ERF_USE_SHOC
69 #include "ERF_ShocInterface.H"
70 #endif
71 
72 #ifdef ERF_USE_P3
73 #include "ERF_P3Interface.H"
74 #endif
75 
76 #include <iostream>
77 
78 #ifdef AMREX_LAZY
79 #include <AMReX_Lazy.H>
80 #endif
81 
82 #ifndef AMREX_USE_MPI
83 using amrex::MPI_COMM_WORLD;
84 using amrex::MPI_Comm;
85 #endif
86 
87 #ifdef ERF_USE_MULTIBLOCK
88 class MultiBlockContainer;
89 #endif
90 
91 /**
92  * Enum of possible interpolation types between coarse/fine
93 */
94 AMREX_ENUM(StateInterpType,
95  FullState, Perturbational
96 );
97 
98 /**
99  * Enum of possible plotfile types
100 */
101 AMREX_ENUM(PlotFileType,
102  None, Amrex, Netcdf
103 );
104 
105 /**
106  * Main class in ERF code, instantiated from main.cpp
107 */
108 
109 class ERF
110  : public amrex::AmrCore
111 {
112 public:
113 
114  ////////////////
115  // public member functions
116 
117  // constructor - reads in parameters from inputs file
118  // - sizes multilevel arrays and data structures
119  ERF ();
120  ~ERF () override;
121 
122  void ERF_shared ();
123 
124  // Declare a default move constructor so we ensure the destructor is
125  // not called when we return an object of this class by value
126  ERF (ERF&&) noexcept = delete;
127 
128  // Declare a default move assignment operator
129  ERF& operator=(ERF&& other) noexcept = delete;
130 
131  // Delete the copy constructor
132  ERF (const ERF& other) = delete;
133  //
134  // Delete the copy assignment operator
135  ERF& operator=(const ERF& other) = delete;
136 
137  // Advance solution to final time
138  void Evolve ();
139 
140  // Tag cells for refinement
141  void ErrorEst (int lev, amrex::TagBoxArray& tags, amrex::Real time, int ngrow) override;
142 
143  // Refinement criteria for hurricanes
144  void HurricaneTracker (int lev,
145  amrex::Real time,
146  const amrex::MultiFab& cc_vel,
147  const amrex::Real velmag_threshold,
148  amrex::TagBoxArray* tags = nullptr);
149 
150  bool FindInitialEye (int lev,
151  const amrex::MultiFab& cc_vel,
152  const amrex::Real velmag_threshold,
153  amrex::Real& eye_x, amrex::Real& eye_y);
154 
155  // Hurricane track line output as VTKPolyline
156  amrex::Vector<std::array<amrex::Real, 2>> hurricane_track_xy;
157  amrex::Vector<std::array<amrex::Real, 2>> hurricane_eye_track_xy,
158  hurricane_eye_track_latlon,
159  hurricane_maxvel_vs_time,
160  hurricane_minpressure_vs_time,
161  hurricane_tracker_circle;
162  amrex::Vector<amrex::MultiFab> weather_forecast_data_1, weather_forecast_data_2;
163  amrex::Vector<amrex::Vector<amrex::MultiFab>> forecast_state_1,
164  forecast_state_2,
165  forecast_state_interp;
166  amrex::Vector<amrex::MultiFab> surface_state_1,
167  surface_state_2,
168  surface_state_interp;
169 
170  std::string MakeVTKFilename(int nstep);
171  std::string MakeVTKFilename_TrackerCircle(int nstep);
172  std::string MakeVTKFilename_EyeTracker_xy(int nstep);
173  std::string MakeFilename_EyeTracker_latlon(int nstep);
174  std::string MakeFilename_EyeTracker_maxvel(int nstep);
175  std::string MakeFilename_EyeTracker_minpressure(int nstep);
176  void WriteVTKPolyline(const std::string& filename,
177  amrex::Vector<std::array<amrex::Real, 2>>& points_xy);
178 
179  void WriteLinePlot(const std::string& filename,
180  amrex::Vector<std::array<amrex::Real, 2>>& points_xy);
181 
182  // Initialize multilevel data
183  void InitData ();
184 
185  // Initialize multilevel data before MultiBlock
186  void InitData_pre ();
187 
188  // Initialize multilevel data after MultiBlock
189  void InitData_post ();
190 
191  // Interpolate 2D arrays lat_m, lon_m, sinPhi, cosPhi
192  void Interp2DArrays (int lev, const amrex::BoxArray& my_ba2d, const amrex::DistributionMapping& my_dm);
193 
194  void WriteMyEBSurface ();
195 
196  // Compute the divergence -- whether EB, no-terrain, flat terrain or general terrain
197  void compute_divergence (int lev, amrex::MultiFab& rhs, amrex::Array<amrex::MultiFab const*,AMREX_SPACEDIM> rho0_u_const,
198  amrex::Geometry const& geom_at_lev);
199 
200  // Project the velocities to be divergence-free -- this is only relevant if anelastic == 1
201  void project_initial_velocity (int lev, amrex::Real time, amrex::Real dt);
202  void project_momenta (int lev, amrex::Real l_time, amrex::Real l_dt, amrex::Vector<amrex::MultiFab >& vars);
203 
204  // Project the velocities to be divergence-free with a thin body
205  void project_velocity_tb (int lev, amrex::Real dt, amrex::Vector<amrex::MultiFab >& vars);
206 
207  // Calculate wall distance by solving a Poisson equation
208  void poisson_wall_dist (int lev);
209 
210  void make_subdomains(const amrex::BoxList& ba, amrex::Vector<amrex::BoxArray>& bins);
211 
212 #ifdef ERF_USE_FFT
213  void solve_with_fft (int lev, const amrex::Box& subdomain,
214  amrex::MultiFab& rhs, amrex::MultiFab& p,
215  amrex::Array<amrex::MultiFab,AMREX_SPACEDIM>& fluxes);
216 #endif
217  void solve_with_gmres (int lev, const amrex::Box& subdomain,
218  amrex::MultiFab& rhs, amrex::MultiFab& p,
219  amrex::Array<amrex::MultiFab,AMREX_SPACEDIM>& fluxes,
220  amrex::MultiFab& ax_sub, amrex::MultiFab& ay_sub,
221  amrex::MultiFab& az_sub,
222  amrex::MultiFab& /*dJ_sub*/, amrex::MultiFab& znd_sub);
223 
224  void ImposeBCsOnPhi (int lev, amrex::MultiFab& phi, const amrex::Box& subdomain);
225 
226  // Init (NOT restart or regrid)
227  void init_only (int lev, amrex::Real time);
228 
229  // Restart
230  void restart ();
231 
232  // Check for NaNs and other bad stuff
233  void check_state_for_nans(amrex::MultiFab const& S);
234  void check_vels_for_nans(amrex::MultiFab const& xvel, amrex::MultiFab const& yvel, amrex::MultiFab const& zvel);
235  void check_for_negative_theta (amrex::MultiFab& S);
236  void check_for_low_temp (amrex::MultiFab& S);
237 
238  // Is it time to write a plotfile or checkpoint?
239  bool writeNow (const amrex::Real cur_time, const int nstep, const int plot_int,
240  const amrex::Real plot_per, const amrex::Real dt_0, amrex::Real& last_file_time);
241 
242  // Called after every level 0 timestep
243  void post_timestep (int nstep, amrex::Real time, amrex::Real dt_lev);
244 
245  // Diagnostics
246  void sum_integrated_quantities (amrex::Real time);
247  void sum_derived_quantities (amrex::Real time);
248  void sum_energy_quantities (amrex::Real time);
249 
250  void write_1D_profiles (amrex::Real time);
251  void write_1D_profiles_stag (amrex::Real time);
252 
253  amrex::Real cloud_fraction (amrex::Real time);
254 
255  // Fill the physical boundary conditions for cell-centered velocity (diagnostic only)
256  void FillBdyCCVels (amrex::MultiFab& mf_cc_vel, amrex::Geometry& lev_geom);
257 
258  void sample_points (int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab& mf);
259  void sample_lines (int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab& mf);
260 
261  void derive_diag_profiles (amrex::Real time,
262  amrex::Gpu::HostVector<amrex::Real>& h_avg_u , amrex::Gpu::HostVector<amrex::Real>& h_avg_v,
263  amrex::Gpu::HostVector<amrex::Real>& h_avg_w , amrex::Gpu::HostVector<amrex::Real>& h_avg_rho,
264  amrex::Gpu::HostVector<amrex::Real>& h_avg_th , amrex::Gpu::HostVector<amrex::Real>& h_avg_ksgs,
265  amrex::Gpu::HostVector<amrex::Real>& h_avg_Kmv , amrex::Gpu::HostVector<amrex::Real>& h_avg_Khv,
266  amrex::Gpu::HostVector<amrex::Real>& h_avg_qv , amrex::Gpu::HostVector<amrex::Real>& h_avg_qc,
267  amrex::Gpu::HostVector<amrex::Real>& h_avg_qr ,
268  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqv , amrex::Gpu::HostVector<amrex::Real>& h_avg_wqc,
269  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqr ,
270  amrex::Gpu::HostVector<amrex::Real>& h_avg_qi , amrex::Gpu::HostVector<amrex::Real>& h_avg_qs,
271  amrex::Gpu::HostVector<amrex::Real>& h_avg_qg ,
272  amrex::Gpu::HostVector<amrex::Real>& h_avg_uu , amrex::Gpu::HostVector<amrex::Real>& h_avg_uv,
273  amrex::Gpu::HostVector<amrex::Real>& h_avg_uw,
274  amrex::Gpu::HostVector<amrex::Real>& h_avg_vv , amrex::Gpu::HostVector<amrex::Real>& h_avg_vw,
275  amrex::Gpu::HostVector<amrex::Real>& h_avg_ww,
276  amrex::Gpu::HostVector<amrex::Real>& h_avg_uth , amrex::Gpu::HostVector<amrex::Real>& h_avg_vth,
277  amrex::Gpu::HostVector<amrex::Real>& h_avg_wth, amrex::Gpu::HostVector<amrex::Real>& h_avg_thth,
278  amrex::Gpu::HostVector<amrex::Real>& h_avg_ku, amrex::Gpu::HostVector<amrex::Real>& h_avg_kv,
279  amrex::Gpu::HostVector<amrex::Real>& h_avg_kw,
280  amrex::Gpu::HostVector<amrex::Real>& h_avg_p,
281  amrex::Gpu::HostVector<amrex::Real>& h_avg_pu, amrex::Gpu::HostVector<amrex::Real>& h_avg_pv,
282  amrex::Gpu::HostVector<amrex::Real>& h_avg_pw, amrex::Gpu::HostVector<amrex::Real>& h_avg_wthv);
283  void derive_diag_profiles_stag (amrex::Real time,
284  amrex::Gpu::HostVector<amrex::Real>& h_avg_u , amrex::Gpu::HostVector<amrex::Real>& h_avg_v,
285  amrex::Gpu::HostVector<amrex::Real>& h_avg_w , amrex::Gpu::HostVector<amrex::Real>& h_avg_rho,
286  amrex::Gpu::HostVector<amrex::Real>& h_avg_th , amrex::Gpu::HostVector<amrex::Real>& h_avg_ksgs,
287  amrex::Gpu::HostVector<amrex::Real>& h_avg_Kmv , amrex::Gpu::HostVector<amrex::Real>& h_avg_Khv,
288  amrex::Gpu::HostVector<amrex::Real>& h_avg_qv , amrex::Gpu::HostVector<amrex::Real>& h_avg_qc,
289  amrex::Gpu::HostVector<amrex::Real>& h_avg_qr ,
290  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqv , amrex::Gpu::HostVector<amrex::Real>& h_avg_wqc,
291  amrex::Gpu::HostVector<amrex::Real>& h_avg_wqr ,
292  amrex::Gpu::HostVector<amrex::Real>& h_avg_qi , amrex::Gpu::HostVector<amrex::Real>& h_avg_qs,
293  amrex::Gpu::HostVector<amrex::Real>& h_avg_qg ,
294  amrex::Gpu::HostVector<amrex::Real>& h_avg_uu , amrex::Gpu::HostVector<amrex::Real>& h_avg_uv,
295  amrex::Gpu::HostVector<amrex::Real>& h_avg_uw,
296  amrex::Gpu::HostVector<amrex::Real>& h_avg_vv , amrex::Gpu::HostVector<amrex::Real>& h_avg_vw,
297  amrex::Gpu::HostVector<amrex::Real>& h_avg_ww,
298  amrex::Gpu::HostVector<amrex::Real>& h_avg_uth , amrex::Gpu::HostVector<amrex::Real>& h_avg_vth,
299  amrex::Gpu::HostVector<amrex::Real>& h_avg_wth, amrex::Gpu::HostVector<amrex::Real>& h_avg_thth,
300  amrex::Gpu::HostVector<amrex::Real>& h_avg_ku, amrex::Gpu::HostVector<amrex::Real>& h_avg_kv,
301  amrex::Gpu::HostVector<amrex::Real>& h_avg_kw,
302  amrex::Gpu::HostVector<amrex::Real>& h_avg_p,
303  amrex::Gpu::HostVector<amrex::Real>& h_avg_pu, amrex::Gpu::HostVector<amrex::Real>& h_avg_pv,
304  amrex::Gpu::HostVector<amrex::Real>& h_avg_pw, amrex::Gpu::HostVector<amrex::Real>& h_avg_wthv);
305 
306  void derive_stress_profiles (amrex::Gpu::HostVector<amrex::Real>& h_avg_tau11, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau12,
307  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau13, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau22,
308  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau23, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau33,
309  amrex::Gpu::HostVector<amrex::Real>& h_avg_hfx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_q1fx3,
310  amrex::Gpu::HostVector<amrex::Real>& h_avg_q2fx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_diss);
311  void derive_stress_profiles_stag (amrex::Gpu::HostVector<amrex::Real>& h_avg_tau11, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau12,
312  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau13, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau22,
313  amrex::Gpu::HostVector<amrex::Real>& h_avg_tau23, amrex::Gpu::HostVector<amrex::Real>& h_avg_tau33,
314  amrex::Gpu::HostVector<amrex::Real>& h_avg_hfx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_q1fx3,
315  amrex::Gpu::HostVector<amrex::Real>& h_avg_q2fx3, amrex::Gpu::HostVector<amrex::Real>& h_avg_diss);
316 
317  // Perform the volume-weighted sum
318  amrex::Real
319  volWgtSumMF (int lev, const amrex::MultiFab& mf, int comp,
320  const amrex::MultiFab& dJ, const amrex::MultiFab& mfx, const amrex::MultiFab& mfy,
321  bool finemask, bool local = true);
322 
323  void
324  volWgtColumnSum (int lev, const amrex::MultiFab& mf, int comp,
325  amrex::MultiFab& mf_2d, const amrex::MultiFab& dJ);
326 
327  // Decide if it is time to take an action
328  static bool is_it_time_for_action (int nstep, amrex::Real time, amrex::Real dt,
329  int action_interval, amrex::Real action_per);
330 
331  // Make a new level using provided BoxArray and DistributionMapping and
332  // fill with interpolated coarse level data.
333  // overrides the pure virtual function in AmrCore
334  void MakeNewLevelFromCoarse (int lev, amrex::Real time, const amrex::BoxArray& ba,
335  const amrex::DistributionMapping& dm) override;
336 
337  // Remake an existing level using provided BoxArray and DistributionMapping and
338  // fill with existing fine and coarse data.
339  // overrides the pure virtual function in AmrCore
340  void RemakeLevel (int lev, amrex::Real time, const amrex::BoxArray& ba,
341  const amrex::DistributionMapping& dm) override;
342 
343  // Delete level data
344  // overrides the pure virtual function in AmrCore
345  void ClearLevel (int lev) override;
346 
347  // Make a new level from scratch using provided BoxArray and DistributionMapping.
348  // Only used during initialization.
349  // overrides the pure virtual function in AmrCore
350  void MakeNewLevelFromScratch (int lev, amrex::Real time, const amrex::BoxArray& ba,
351  const amrex::DistributionMapping& dm) override;
352 
353  // compute dt from CFL considerations
354  amrex::Real estTimeStep (int lev, long& dt_fast_ratio) const;
355 
356 #ifdef ERF_USE_WW3_COUPLING
357  //amrex::Print() << " About to call send_to_ww3 from ERF.H" << std::endl;
358  void send_to_ww3(int lev);
359  //amrex::Print() << " About to call read_waves from ERF.H" << std::endl;
360  void read_waves(int lev);
361  //void send_to_ww3 (int lev);
362  //void read_waves (int lev);
363 
364  //void send_to_ww3 (int lev);
365 #endif
366 
367  // Interface for advancing the data at one level by one "slow" timestep
368  void advance_dycore (int level,
369  amrex::Vector<amrex::MultiFab>& state_old,
370  amrex::Vector<amrex::MultiFab>& state_new,
371  amrex::MultiFab& xvel_old, amrex::MultiFab& yvel_old, amrex::MultiFab& zvel_old,
372  amrex::MultiFab& xvel_new, amrex::MultiFab& yvel_new, amrex::MultiFab& zvel_new,
373  amrex::MultiFab& source, amrex::MultiFab& xmom_src,
374  amrex::MultiFab& ymom_src, amrex::MultiFab& zmom_src,
375  amrex::MultiFab& buoyancy, amrex::Geometry fine_geom,
376  amrex::Real dt, amrex::Real time);
377 
378  void advance_microphysics (int lev,
379  amrex::MultiFab& cons_in,
380  const amrex::Real& dt_advance,
381  const int& iteration,
382  const amrex::Real& time);
383 
384  void advance_lsm (int lev,
385  amrex::MultiFab& cons_in,
386  amrex::MultiFab& xvel_in,
387  amrex::MultiFab& yvel_in,
388  const amrex::Real& dt_advance);
389 
390  void advance_radiation (int lev,
391  amrex::MultiFab& cons_in,
392  const amrex::Real& dt_advance);
393 
394 #ifdef ERF_USE_SHOC
395  void compute_shoc_tendencies (int lev,
396  amrex::MultiFab* cons,
397  amrex::MultiFab* xvel,
398  amrex::MultiFab* yvel,
399  amrex::MultiFab* zvel,
400  amrex::Real* w_subsid,
401  amrex::MultiFab* tau13,
402  amrex::MultiFab* tau23,
403  amrex::MultiFab* hfx3,
404  amrex::MultiFab* qfx3,
405  amrex::MultiFab* eddyDiffs,
406  amrex::MultiFab* z_phys_nd,
407  const amrex::Real& dt_advance);
408 #endif
409 
410 #ifdef ERF_USE_P3
411  void compute_p3_tendencies (int lev,
412  amrex::MultiFab& cons_in,
413  amrex::MultiFab& source,
414  const amrex::Real& dt_advance);
415 #endif
416 
417  void build_fine_mask (int lev, amrex::MultiFab& fine_mask);
418 
419  void MakeHorizontalAverages ();
420  void MakeDiagnosticAverage (amrex::Vector<amrex::Real>& h_havg, amrex::MultiFab& S, int n);
421  void derive_upwp (amrex::Vector<amrex::Real>& h_havg);
422 
423  // Write plotfile to disk
424  void Write3DPlotFile (int which, PlotFileType plotfile_type, amrex::Vector<std::string> plot_var_names);
425  void Write2DPlotFile (int which, PlotFileType plotfile_type, amrex::Vector<std::string> plot_var_names);
426 
427  // Write subvolume of data into a different "plotfile"
428  void WriteSubvolume (int isub, amrex::Vector<std::string> subvol_var_names);
429 
430  void WriteMultiLevelPlotfileWithTerrain (const std::string &plotfilename,
431  int nlevels,
432  const amrex::Vector<const amrex::MultiFab*> &mf,
433  const amrex::Vector<const amrex::MultiFab*> &mf_nd,
434  const amrex::Vector<std::string> &varnames,
435  const amrex::Vector<amrex::Geometry>& my_geom,
436  amrex::Real time,
437  const amrex::Vector<int> &level_steps,
438  const amrex::Vector<amrex::IntVect>& my_ref_ratio,
439  const std::string &versionName = "HyperCLaw-V1.1",
440  const std::string &levelPrefix = "Level_",
441  const std::string &mfPrefix = "Cell",
442  const amrex::Vector<std::string>& extra_dirs = amrex::Vector<std::string>()) const;
443 
444 
445  void WriteGenericPlotfileHeaderWithTerrain (std::ostream &HeaderFile,
446  int nlevels,
447  const amrex::Vector<amrex::BoxArray> &bArray,
448  const amrex::Vector<std::string> &varnames,
449  const amrex::Vector<amrex::Geometry>& my_geom,
450  amrex::Real time,
451  const amrex::Vector<int> &level_steps,
452  const amrex::Vector<amrex::IntVect>& my_ref_ratio,
453  const std::string &versionName,
454  const std::string &levelPrefix,
455  const std::string &mfPrefix) const;
456 
457  void erf_enforce_hse (int lev,
458  amrex::MultiFab& dens, amrex::MultiFab& pres, amrex::MultiFab& pi,
459  amrex::MultiFab& th, amrex::MultiFab& qv,
460  std::unique_ptr<amrex::MultiFab>& z_cc);
461 
462 #ifdef ERF_USE_NETCDF
463  //! Write a timestep to 1D vertical column output for coupling
464  void writeToNCColumnFile (int lev,
465  const std::string& colfile_name, amrex::Real xloc, amrex::Real yloc,
466  amrex::Real time);
467 #endif //ERF_USE_NETCDF
468 
469  void init_from_input_sounding (int lev);
470 
471  void init_immersed_forcing (int lev);
472 
473  void input_sponge (int lev);
474 
475  void init_from_hse (int lev);
476 
477  void init_thin_body (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm);
478 
479  void FillForecastStateMultiFabs(const int lev,
480  const std::string& filename,
481  const std::unique_ptr<amrex::MultiFab>& z_phys_nd,
482  amrex::Vector<amrex::Vector<amrex::MultiFab>>& forecast_state);
483 
484  void FillSurfaceStateMultiFabs(const int lev,
485  const std::string& filename,
486  amrex::Vector<amrex::MultiFab>& surface_state);
487 
488 
489  void WeatherDataInterpolation(const int nlevs,
490  const amrex::Real time,
491  amrex::Vector<std::unique_ptr<amrex::MultiFab>>& z_phys_nd,
492  bool regrid_forces_file_read);
493 
494  void SurfaceDataInterpolation(const int nlevs,
495  const amrex::Real time,
496  amrex::Vector<std::unique_ptr<amrex::MultiFab>>& z_phys_nd,
497  bool regrid_forces_file_read);
498 
499  void create_random_perturbations (const int lev,
500  amrex::MultiFab& cons_pert,
501  amrex::MultiFab& xvel_pert,
502  amrex::MultiFab& yvel_pert,
503  amrex::MultiFab& zvel_pert);
504 
505  void apply_gaussian_smoothing_to_perturbations (const int lev,
506  amrex::MultiFab& cons_pert,
507  amrex::MultiFab& xvel_pert,
508  amrex::MultiFab& yvel_pert,
509  amrex::MultiFab& zvel_pert);
510 
511  void init_custom (int lev);
512 
513 #ifdef ERF_USE_MULTIBLOCK
514  // constructor used when ERF is created by a multiblock driver
515  // calls AmrCore constructor -> AmrMesh constructor
516  ERF (const amrex::RealBox& rb, int max_level_in,
517  const amrex::Vector<int>& n_cell_in, int coord,
518  const amrex::Vector<amrex::IntVect>& ref_ratio,
519  const amrex::Array<int,AMREX_SPACEDIM>& is_per,
520  std::string prefix);
521 
522  // Advance a block specified number of time steps
523  void Evolve_MB (int MBstep, int max_block_step);
524 
525  // get the current time values and dt
526  amrex::Real get_t_old (int lev) { return t_old[lev]; }
527  amrex::Real get_t_new (int lev) { return t_new[lev]; }
528  amrex::Real get_dt (int lev) { return dt[lev]; }
529 
530  // Set parmparse prefix for MultiBlock
531  void SetParmParsePrefix (std::string name) { pp_prefix = name; }
532 
533  // Set 'this' from multiblock container
534  void SetMultiBlockPointer (MultiBlockContainer *mbc) { m_mbc = mbc; }
535 
536  // Public data copy for MB
537  std::vector<amrex::Box> domain_p;
538 
539  // Primary solution data data containers
540  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_new;
541  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_old;
542 
543  // Velocity time averaged field
544  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vel_t_avg;
545  amrex::Vector<amrex::Real> t_avg_cnt;
546 #endif
547 
548  std::string pp_prefix {"erf"};
549 
550  void fill_from_bndryregs (const amrex::Vector<amrex::MultiFab*>& mfs,
551  amrex::Real time);
552 
553 #ifdef ERF_USE_NETCDF
554  void init_from_wrfinput (int lev,
555  amrex::MultiFab& mf_C1H,
556  amrex::MultiFab& mf_C2H,
557  amrex::MultiFab& mf_MUB,
558  amrex::MultiFab& mf_PSFC);
559  void init_from_metgrid (int lev);
560  void init_from_ncfile (int lev);
561 #endif // ERF_USE_NETCDF
562 
563 #ifdef ERF_USE_WINDFARM
564  void init_windfarm(int lev);
565  void advance_windfarm (const amrex::Geometry& a_geom,
566  const amrex::Real& dt_advance,
567  amrex::MultiFab& cons_in,
568  amrex::MultiFab& U_old,
569  amrex::MultiFab& V_old,
570  amrex::MultiFab& W_old,
571  amrex::MultiFab& mf_vars_windfarm,
572  const amrex::MultiFab& mf_Nturb,
573  const amrex::MultiFab& mf_SMark,
574  const amrex::Real& time);
575 #endif
576 
577  void MakeEBGeometry ();
578  void make_eb_box ();
579  void make_eb_regular ();
580 
581  // more flexible version of AverageDown() that lets you average down across multiple levels
582  void AverageDownTo (int crse_lev, int scomp, int ncomp); // NOLINT
583 
584  // Write checkpoint file to disk
585  void WriteCheckpointFile () const;
586 
587  // Read checkpoint file from disk
588  void ReadCheckpointFile ();
589 
590  // Read only velocities from checkpoint file
591  void ReadVelsOnlyFromCheckpointFile (int lev_to_fill, std::string& chkfile);
592 
593  // read checkpoint file from disk -- called after instantiating m_SurfaceLayer
594  void ReadCheckpointFileSurfaceLayer ();
595 
596  void init_zphys (int lev, amrex::Real elapsed_time);
597  void remake_zphys (int lev, std::unique_ptr<amrex::MultiFab>& temp_zphys_nd);
598  void update_terrain_arrays (int lev);
599 
600 private:
601 
602  ///////////////////////////
603  // private member functions
604  ///////////////////////////
605 
606  // read in some parameters from inputs file
607  void ReadParameters ();
608  void ParameterSanityChecks ();
609 
610  // set covered coarse cells/faces to be the average of overlying fine cells/faces
611  void AverageDown ();
612 
613  void update_diffusive_arrays (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm);
614 
615  void Construct_ERFFillPatchers (int lev);
616 
617  void Define_ERFFillPatchers (int lev);
618 
619  void init1DArrays ();
620 
621  void init_bcs ();
622  void init_phys_bcs (bool& rho_read, bool& read_prim_theta);
623 
624  void init_stuff (int lev, const amrex::BoxArray& ba, const amrex::DistributionMapping& dm,
625  amrex::Vector<amrex::MultiFab>& lev_new, amrex::Vector<amrex::MultiFab>& lev_old,
626  amrex::MultiFab& tmp_base_state,
627  std::unique_ptr<amrex::MultiFab>& tmp_zphys_nd);
628 
629  // Initialize the Turbulent perturbation
630  void turbPert_update (const int lev, const amrex::Real dt);
631  void turbPert_amplitude (const int lev);
632 
633  // Initialize the integrator object
634  void initialize_integrator (int lev, amrex::MultiFab& cons_mf, amrex::MultiFab& vel_mf);
635 
636  // Create the physbcs objects
637  void make_physbcs (int lev);
638 
639  // Initialize the microphysics object
640  void initializeMicrophysics (const int&);
641 
642 #ifdef ERF_USE_WINDFARM
643  // Initialize the windfarm object
644  void initializeWindFarm (const int&);
645 #endif
646 
647  // Compute a vector of new MultiFabs by copying from valid region and filling ghost cells
648  //
649  // NOTE: FillPatch takes in an empty MF, and returns cell-centered + velocities (not momenta)
650  //
651  // This one works only at level = 0 (base state does not change)
652  void FillPatchCrseLevel (int lev, amrex::Real time,
653  const amrex::Vector<amrex::MultiFab*>& mfs_vel,
654  bool cons_only=false);
655 
656  // This one works only at level > 0 (base state does change)
657  void FillPatchFineLevel (int lev, amrex::Real time,
658  const amrex::Vector<amrex::MultiFab*>& mfs_vel,
659  const amrex::Vector<amrex::MultiFab*>& mfs_mom,
660  const amrex::MultiFab& old_base_state,
661  const amrex::MultiFab& new_base_state,
662  bool fillset=true, bool cons_only=false);
663 
664  // Compute new multifabs by copying data from valid region and filling ghost cells.
665  // Unlike FillPatch, FillIntermediatePatch will use the supplied multifabs instead of fine level data.
666  // This is to support filling boundary cells at an intermediate time between old/new times
667  // on the fine level when valid data at a specific time is already available (such as
668  // at each RK stage when integrating between initial and final times at a given level).
669  //
670  // NOTE: FillIntermediatePatch takes in updated momenta, and returns both updated velocity and momenta
671  //
672  void FillIntermediatePatch (int lev, amrex::Real time,
673  const amrex::Vector<amrex::MultiFab*>& mfs_vel,
674  const amrex::Vector<amrex::MultiFab*>& mfs_mom,
675  int ng_cons, int ng_vel, bool cons_only, int icomp_cons, int ncomp_cons);
676 
677  // Fill all multifabs (and all components) in a vector of multifabs corresponding to the
678  // grid variables defined in vars_old and vars_new just as FillCoarsePatch.
679  void FillCoarsePatch (int lev, amrex::Real time);
680 
681  // advance a level by dt
682  // includes a recursive call for finer levels
683  void timeStep (int lev, amrex::Real time, int iteration);
684 
685  // advance a single level for a single time step
686  void Advance (int lev, amrex::Real time, amrex::Real dt_lev, int iteration, int ncycle);
687 
688  //! Initialize HSE
689  void initHSE ();
690  void initHSE (int lev);
691 
692  //! Initialize Rayleigh damping profiles at a level
693  void initRayleigh_at_level (const int& lev);
694 
695  //! Initialize sponge profiles
696  void initSponge ();
697 
698  //! Set Rayleigh mean profiles from input sounding
699  void setRayleighRefFromSounding (bool restarting);
700 
701  //! Set sponge mean profiles from input sounding
702  void setSpongeRefFromSounding (bool restarting);
703 
704  // a wrapper for estTimeStep()
705  void ComputeDt (int step = -1);
706 
707  // get plotfile name
708  [[nodiscard]] std::string PlotFileName (int lev) const;
709 
710  // set plotfile variable names
711  static amrex::Vector<std::string> PlotFileVarNames (amrex::Vector<std::string> plot_var_names);
712 
713  // set which variables and derived quantities go into plotfiles
714  void setPlotVariables (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
715  void setPlotVariables2D (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
716  // append variables to plot
717  void appendPlotVariables (const std::string& pp_plot_var_names, amrex::Vector<std::string>& plot_var_names);
718 
719  void setSubVolVariables (const std::string& pp_subvol_var_names, amrex::Vector<std::string>& subvol_var_names);
720 
721 #ifdef ERF_USE_NETCDF
722  //! Create 1D vertical column output for coupling
723  void createNCColumnFile (int lev,
724  const std::string& colfile_name, amrex::Real xloc, amrex::Real yloc);
725 
726  // Copy from the NC*fabs into the MultiFabs holding the boundary data
727  void init_from_wrfbdy (amrex::Vector<amrex::FArrayBox*> x_vel_lateral,
728  amrex::Vector<amrex::FArrayBox*> y_vel_lateral,
729  amrex::Vector<amrex::FArrayBox*> z_vel_lateral,
730  amrex::Vector<amrex::FArrayBox*> T_lateral);
731 
732  static amrex::Real start_bdy_time;
733  static amrex::Real final_bdy_time;
734 
735  static amrex::Real start_low_time;
736  static amrex::Real final_low_time;
737 
738  static amrex::Real bdy_time_interval;
739  static amrex::Real low_time_interval;
740 
741  // *** *** FArrayBox's for holding the SURFACE data
742  // amrex::IArrayBox NC_IVGTYP_fab; // Vegetation type (IVGTYP); Discrete numbers;
743  // amrex::FArrayBox NC_z0_fab; // Surface Roughness, z0 = z0 (IVGTYP)
744  // amrex::FArrayBox NC_PSFC_fab; // Surface pressure
745 
746  // TODO: Clarify the relation between SST and TSK
747  // amrex::FArrayBox NC_SST_fab; // Sea Surface Temperature; Defined even for land area
748  // amrex::FArrayBox NC_TSK_fab; // Surface Skin Temperature; Appears to be same as SST...
749 
750  // Vectors (over time) of Vector (over variables) of FArrayBoxs for holding the data read from the wrfbdy NetCDF file
751  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_xlo;
752  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_xhi;
753  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_ylo;
754  amrex::Vector<amrex::Vector<amrex::FArrayBox>> bdy_data_yhi;
755 
756  amrex::Vector<amrex::Vector<amrex::FArrayBox>> low_data_zlo;
757 
758  // Maximum value of terrain read in from wrfinput at level 0
759  amrex::Real z_top = zero;
760 
761 #endif // ERF_USE_NETCDF
762 
763  amrex::Vector<std::unique_ptr<amrex::MultiFab>> lat_m, lon_m; // Latitude and Longitude on the grid
764 
765  amrex::Vector<std::unique_ptr<amrex::MultiFab>> sinPhi_m, cosPhi_m; // Coriolis factors on the grid
766 
767  // Struct for working with the sounding data we take as an input
768  InputSoundingData input_sounding_data;
769 
770  // Struct for working with the sponge data we take as an input
771  InputSpongeData input_sponge_data;
772 
773  // Vector (6 planes) of DeviceVectors (ncell in plane) for Dirichlet BC data
774  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> xvel_bc_data;
775  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> yvel_bc_data;
776  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> zvel_bc_data;
777  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> th_bc_data;
778 
779  // Function to read and populate above vectors (if input file exists)
780  void init_Dirichlet_bc_data (const std::string input_file);
781 
782  // Read the file passed to amr.restart and use it as an initial condition for
783  // the current simulation. Supports a different number of components and
784  // ghost cells.
785  void InitializeFromFile ();
786 
787  // Initialize the new-time data at a level from the initial_data MultiFab
788  void InitializeLevelFromData (int lev, const amrex::MultiFab& initial_data);
789 
790  // utility to skip to next line in Header
791  static void GotoNextLine (std::istream& is);
792 
793  // Single level functions called by advance()
794  void post_update (amrex::MultiFab& state_mf, amrex::Real time, const amrex::Geometry& geom);
795  void fill_rhs (amrex::MultiFab& rhs_mf, const amrex::MultiFab& state_mf, amrex::Real time, const amrex::Geometry& geom);
796 
797  ////////////////
798  // private data members
799 
800  std::unique_ptr<ProblemBase> prob = nullptr; // problem-specific functions
801 
802  amrex::Vector<int> num_boxes_at_level; // how many boxes specified at each level by tagging criteria
803  amrex::Vector<int> num_files_at_level; // how many wrfinput files specified at each level
804  amrex::Vector<amrex::Vector<amrex::Box>> boxes_at_level; // the boxes specified at each level by tagging criteria
805 
806  amrex::Vector<int> istep; // which step?
807  amrex::Vector<int> nsubsteps; // how many substeps on each level?
808 
809  // keep track of old time, new time, and time step at each level
810  amrex::Vector<amrex::Real> t_new;
811  amrex::Vector<amrex::Real> t_old;
812  amrex::Vector<amrex::Real> dt;
813  amrex::Vector<long> dt_mri_ratio;
814 
815 #ifndef ERF_USE_MULTIBLOCK
816  // Array of multifabs to store the solution at each level of refinement;
817  // after advancing a level we use "swap".
818  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_new;
819  amrex::Vector<amrex::Vector<amrex::MultiFab> > vars_old;
820 
821  // Pressure gradient at each level
822  amrex::Vector<amrex::Vector<amrex::MultiFab> > gradp;
823 
824  // Velocity time averaged field
825  amrex::Vector<std::unique_ptr<amrex::MultiFab>> vel_t_avg;
826  amrex::Vector<amrex::Real> t_avg_cnt;
827 #endif
828  amrex::Vector<std::unique_ptr<MRISplitIntegrator<amrex::Vector<amrex::MultiFab> > > > mri_integrator_mem;
829 
830  // Used for anelastic or when we impose an initial projection
831  amrex::Vector<amrex::MultiFab> pp_inc;
832 
833  // Used only for fast substepping
834  amrex::Vector<amrex::MultiFab> lagged_delta_rt;
835  amrex::Vector<amrex::MultiFab> avg_xmom;
836  amrex::Vector<amrex::MultiFab> avg_ymom;
837  amrex::Vector<amrex::MultiFab> avg_zmom;
838 
839  // Vector over levels of routines to impose physical boundary conditions
840  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_cons>> physbcs_cons;
841  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_u>> physbcs_u;
842  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_v>> physbcs_v;
843  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_w>> physbcs_w;
844  amrex::Vector<std::unique_ptr<ERFPhysBCFunct_base>> physbcs_base;
845 
846  // Store primitive variable for MOST BC
847  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Theta_prim;
848  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Qv_prim;
849  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Qr_prim;
850 
851  // Scratch space for time integrator
852  amrex::Vector<amrex::MultiFab> rU_old;
853  amrex::Vector<amrex::MultiFab> rU_new;
854  amrex::Vector<amrex::MultiFab> rV_old;
855  amrex::Vector<amrex::MultiFab> rV_new;
856  amrex::Vector<amrex::MultiFab> rW_old;
857  amrex::Vector<amrex::MultiFab> rW_new;
858 
859  // amrex::Vector<amrex::MultiFab> xmom_crse_rhs;
860  // amrex::Vector<amrex::MultiFab> ymom_crse_rhs;
861  amrex::Vector<amrex::MultiFab> zmom_crse_rhs;
862 
863  std::unique_ptr<Microphysics> micro;
864  amrex::Vector<amrex::Vector<amrex::MultiFab*>> qmoist; // (lev,ncomp) rain_accum, snow_accum, graup_accum
865 
866  // Variables for wind farm parametrization models
867 
868 #ifdef ERF_USE_WINDFARM
869  std::unique_ptr<WindFarm> windfarm;
870  amrex::Vector<amrex::MultiFab> Nturb;
871  amrex::Vector<amrex::MultiFab> vars_windfarm; // Fitch: Vabs, Vabsdt, dudt, dvdt, dTKEdt
872  // EWP: dudt, dvdt, dTKEdt
873 
874  amrex::Vector<amrex::MultiFab> SMark; // A multifab that holds an integer corresponding
875  // to the number of the wind turbine to sample
876  // velocity upstream of the turbine
877 #endif
878 
879  LandSurface lsm;
880  amrex::Vector<std::string> lsm_data_name; // (ncomp) -- e.g., sw_dn_dir/dif_vis/nir, lw_dn, cos_zen
881  amrex::Vector<amrex::Vector<amrex::MultiFab*>> lsm_data; // (lev,ncomp) Data for LSM coupling
882  amrex::Vector<std::string> lsm_flux_name; // (ncomp) -- e.g., hfx3, q1fx3, tau13, tau23
883  amrex::Vector<amrex::Vector<amrex::MultiFab*>> lsm_flux; // (lev,ncomp) Fluxes from LSM needed by DYCORE
884 
885  amrex::Vector<std::unique_ptr<IRadiation>> rad; // Radiation model at each level
886  amrex::Vector<std::unique_ptr<amrex::MultiFab>> qheating_rates; // radiation heating rate source terms (SW, LW) (DYCORE)
887  amrex::Vector<std::unique_ptr<amrex::MultiFab>> rad_fluxes; // radiation fluxes (SW up/dn, LW up/dn) (OUTPUT ONLY)
888 #ifdef ERF_USE_SHOC
889  amrex::Vector<std::unique_ptr<SHOCInterface>> shoc_interface; // SHOC model at each level
890 #endif
891 
892 #ifdef ERF_USE_P3
893  amrex::Vector<std::unique_ptr<P3Interface>> p3_interface; // P3 model at each level
894 #endif
895 
896  bool plot_rad = false;
897  int rad_datalog_int = -1;
898 
899  // Fillpatcher classes for coarse-fine boundaries
900  int cf_width{0};
901  int cf_set_width{0};
902  amrex::Vector<ERFFillPatcher> FPr_c;
903  amrex::Vector<ERFFillPatcher> FPr_u;
904  amrex::Vector<ERFFillPatcher> FPr_v;
905  amrex::Vector<ERFFillPatcher> FPr_w;
906 
907  // Diffusive stresses and Smag
908  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> Tau;
909  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> Tau_corr; // correction to tau for implicit
910  amrex::Vector<std::unique_ptr<amrex::MultiFab>> eddyDiffs_lev;
911  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SmnSmn_lev;
912 
913  // Sea Surface Temps, Skin Temperature and Land Masks (lev, ntimes)
914  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> sst_lev;
915  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> tsk_lev;
916  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::iMultiFab>>> lmask_lev;
917 
918  // Land grid types and urban fraction
919  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::iMultiFab>>> land_type_lev;
920  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::iMultiFab>>> soil_type_lev;
921  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> urb_frac_lev;
922 
923  // Other SFS terms
924  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_hfx1_lev, SFS_hfx2_lev, SFS_hfx3_lev;
925  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_diss_lev;
926  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_q1fx1_lev, SFS_q1fx2_lev, SFS_q1fx3_lev;
927  amrex::Vector<std::unique_ptr<amrex::MultiFab>> SFS_q2fx3_lev;
928 
929  // Diffusive fluxes for EB
930  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> Tau_EB;
931  amrex::Vector<std::unique_ptr<amrex::MultiFab>> hfx3_EB;
932  amrex::Vector<std::unique_ptr<amrex::MultiFab>> qfx3_EB;
933 
934  // Grid stretching
935  amrex::Vector<amrex::Vector<amrex::Real>> zlevels_stag; // nominal height levels
936 
937  // Data structures for terrain-fitted coordinates
938  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_nd;
939  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_cc;
940 
941  amrex::Vector<std::unique_ptr<amrex::MultiFab>> detJ_cc;
942  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ax;
943  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ay;
944  amrex::Vector<std::unique_ptr<amrex::MultiFab>> az;
945 
946  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_nd_src;
947  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_cc_src;
948  amrex::Vector<std::unique_ptr<amrex::MultiFab>> detJ_cc_src;
949  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ax_src;
950  amrex::Vector<std::unique_ptr<amrex::MultiFab>> ay_src;
951  amrex::Vector<std::unique_ptr<amrex::MultiFab>> az_src;
952 
953  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_phys_nd_new;
954  amrex::Vector<std::unique_ptr<amrex::MultiFab>> detJ_cc_new;
955 
956  amrex::Vector<std::unique_ptr<amrex::MultiFab>> z_t_rk;
957 
958  // Data structures for terrain immersed forcing
959  amrex::Vector<std::unique_ptr<amrex::MultiFab>> terrain_blanking;
960 
961  // Wall distance function
962  amrex::Vector<std::unique_ptr<amrex::MultiFab>> walldist;
963 
964  // Map scale factors -- vector across levels of vector across types
965  amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab>>> mapfac;
966 
967  // Mask to be used to identify cells covered by finer level (if level > 0)
968  amrex::Vector<std::unique_ptr<amrex::MultiFab>> fine_mask;
969 
970  amrex::Vector<amrex::Vector<amrex::Real>> stretched_dz_h;
971  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real>> stretched_dz_d;
972 
973  amrex::Vector<amrex::MultiFab> base_state;
974  amrex::Vector<amrex::MultiFab> base_state_new;
975 
976  // Wave coupling data
977  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Hwave;
978  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Lwave;
979  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Hwave_onegrid;
980  amrex::Vector<std::unique_ptr<amrex::MultiFab>> Lwave_onegrid;
981  bool finished_wave = false;
982 
983  // array of flux registers
984  amrex::Vector<amrex::YAFluxRegister*> advflux_reg;
985 
986  // A BCRec is essentially a 2*DIM integer array storing the boundary
987  // condition type at each lo/hi walls in each direction. We have one BCRec
988  // for each component of the cell-centered variables and each velocity component.
989  amrex::Vector <amrex::BCRec> domain_bcs_type;
990  amrex::Gpu::DeviceVector<amrex::BCRec> domain_bcs_type_d;
991 
992  // We store these so that we can print them out in the job_info file
993  amrex::Array<std::string,2*AMREX_SPACEDIM> domain_bc_type;
994 
995  // These hold the Dirichlet values at walls which need them ...
996  amrex::Array<amrex::Array<amrex::Real, AMREX_SPACEDIM*2>, AMREX_SPACEDIM+NBCVAR_max> m_bc_extdir_vals;
997 
998  // These hold the Neumann values at walls which need them ...
999  amrex::Array<amrex::Array<amrex::Real, AMREX_SPACEDIM*2>, AMREX_SPACEDIM+NBCVAR_max> m_bc_neumann_vals;
1000 
1001  // Per-face flag: non-reflecting inflow (extrapolate RhoTheta instead of prescribing)
1002  amrex::Array<bool, AMREX_SPACEDIM*2> m_bc_nonreflecting = {{false}};
1003 
1004  // These are the "physical" boundary condition types (e.g. "inflow")
1005  amrex::GpuArray<ERF_BC, AMREX_SPACEDIM*2> phys_bc_type;
1006 
1007  // These are the masks for the thin immersed body
1008  amrex::Vector<std::unique_ptr<amrex::iMultiFab>> xflux_imask;
1009  amrex::Vector<std::unique_ptr<amrex::iMultiFab>> yflux_imask;
1010  amrex::Vector<std::unique_ptr<amrex::iMultiFab>> zflux_imask;
1011  //amrex::Vector<std::unique_ptr<amrex::iMultiFab>> overset_imask;
1012 
1013  // These are the body forces that result from the thin immersed body
1014  amrex::Vector<std::unique_ptr<amrex::MultiFab>> thin_xforce;
1015  amrex::Vector<std::unique_ptr<amrex::MultiFab>> thin_yforce;
1016  amrex::Vector<std::unique_ptr<amrex::MultiFab>> thin_zforce;
1017 
1018  static int last_plot3d_file_step_1;
1019  static int last_plot3d_file_step_2;
1020  static int last_plot2d_file_step_1;
1021  static int last_plot2d_file_step_2;
1022  static int last_check_file_step;
1023 
1024  static amrex::Real last_plot3d_file_time_1;
1025  static amrex::Real last_plot3d_file_time_2;
1026  static amrex::Real last_plot2d_file_time_1;
1027  static amrex::Real last_plot2d_file_time_2;
1028  static amrex::Real last_check_file_time;
1029 
1030  amrex::Vector<int> last_subvol_step;
1031  amrex::Vector<amrex::Real> last_subvol_time;
1032 
1033  static bool plot_file_on_restart;
1034 
1035  // Output control
1036  const int datwidth = 14;
1037  const int datprecision = 6;
1038  const int timeprecision = 13; // e.g., 1-yr LES: 31,536,000 s with dt ~ amrex::Real(0.01) ==> min prec = 10
1039  // epoch time for 2030-01-01 00:00:00 is 1,893,456,000 s with dt ~ amrex::Real(0.01) ==> min prec = 12
1040 
1041  ////////////////
1042  // runtime parameters
1043 
1044  // Maximum number of steps
1045  int max_step = -1;
1046 
1047  // Start and stop times
1048  static amrex::Real start_time;
1049  static amrex::Real stop_time;
1050 
1051  bool use_datetime = false;
1052  const std::string datetime_format = "%Y-%m-%d %H:%M:%S"; // ISO 8601 standard
1053 
1054  // if >= 0 we restart from a checkpoint
1055  std::string restart_chkfile = "";
1056 
1057  // Time step controls
1058  static amrex::Real cfl;
1059  static amrex::Real sub_cfl;
1060  static amrex::Real init_shrink;
1061  static amrex::Real change_max;
1062  static amrex::Real dt_max_initial;
1063  static amrex::Real dt_max;
1064 
1065  // Fixed dt at each level (only used if positive)
1066  amrex::Vector<amrex::Real> fixed_dt;
1067  amrex::Vector<amrex::Real> fixed_fast_dt;
1068  static int fixed_mri_dt_ratio;
1069 
1070  // how often each level regrids the higher levels of refinement
1071  // (after a level advances that many time steps)
1072  int regrid_int = -1;
1073 
1074  // Should we regrid level 0 after restart if Ngrids < Nprocs or
1075  // max_grid_size has changed?
1076  bool regrid_level_0_on_restart = false;
1077 
1078  // plotfile prefix and frequency
1079  std::string plot3d_file_1 {"plt_1_"};
1080  std::string plot3d_file_2 {"plt_2_"};
1081  std::string plot2d_file_1 {"plt2d_1_"};
1082  std::string plot2d_file_2 {"plt2d_2_"};
1083  std::string subvol_file {"subvol"};
1084  bool m_expand_plotvars_to_unif_rr = false;
1085  int m_plot3d_int_1 = -1;
1086  int m_plot3d_int_2 = -1;
1087  int m_plot2d_int_1 = -1;
1088  int m_plot2d_int_2 = -1;
1089 
1090  amrex::Vector<int> m_subvol_int;
1091  amrex::Vector<amrex::Real> m_subvol_per;
1092 
1093  amrex::Real m_plot3d_per_1 = -one;
1094  amrex::Real m_plot3d_per_2 = -one;
1095  amrex::Real m_plot2d_per_1 = -one;
1096  amrex::Real m_plot2d_per_2 = -one;
1097  bool m_plot_face_vels = false;
1098 
1099  bool plot_lsm = false;
1100 
1101  // other sampling output control
1102  int profile_int = -1;
1103  bool destag_profiles = true;
1104 
1105  // Checkpoint type, prefix and frequency
1106  std::string check_file {"chk"};
1107  int m_check_int = -1;
1108  amrex::Real m_check_per = -one;
1109 
1110  amrex::Vector<std::string> subvol3d_var_names;
1111 
1112  amrex::Vector<std::string> plot3d_var_names_1;
1113  amrex::Vector<std::string> plot3d_var_names_2;
1114  amrex::Vector<std::string> plot2d_var_names_1;
1115  amrex::Vector<std::string> plot2d_var_names_2;
1116  const amrex::Vector<std::string> cons_names {"density", "rhotheta", "rhoKE", "rhoadv_0",
1117  "rhoQ1", "rhoQ2", "rhoQ3",
1118  "rhoQ4", "rhoQ5", "rhoQ6"};
1119 
1120  // **************************************************************************************
1121  // NOTE: The order of variable names here **MUST MATCH THE ORDER** in IO/ERF_Plotfile.cpp
1122  // **************************************************************************************
1123  const amrex::Vector<std::string> derived_names {"temp", "theta", "KE", "scalar", "soundspeed",
1124  "reflectivity","max_reflectivity", "precipitable", "mucape",
1125  "vorticity_x","vorticity_y","vorticity_z",
1126  "helicity", "local_helicity",
1127  "magvel", "divU",
1128  "pres_hse", "dens_hse", "theta_hse", "pressure", "pert_pres", "pert_dens",
1129  "eq_pot_temp", "VPD",
1130 #ifdef ERF_USE_WINDFARM
1131  "num_turb", "SMark0", "SMark1",
1132 #endif
1133  "dpdx", "dpdy", "dpdz", "pres_hse_x", "pres_hse_y",
1134  "z_phys", "detJ", "mapfac", "lat_m", "lon_m",
1135  // Time averaged velocity
1136  "u_t_avg", "v_t_avg", "w_t_avg", "umag_t_avg",
1137  // eddy viscosity
1138  "nut",
1139  // eddy diffusivity of momentum
1140  "Kmv","Kmh",
1141  // eddy diffusivity of heat
1142  "Khv","Khh",
1143  // turbulence lengthscale
1144  "Lturb",
1145  // wall distance
1146  "walldist",
1147  // dissipation
1148  "diss",
1149  // moisture vars
1150  "moist_density", "qv", "qc", "qi", "qrain", "qsnow", "qgraup", "qt", "qn", "qp", "qsat",
1151  "rain_accum", "snow_accum", "graup_accum",
1152  "rel_humidity", "condensation_rate",
1153  // Terrain IB mask
1154  "terrain_IB_mask",
1155  // EB variables
1156  "volfrac"
1157 #ifdef ERF_COMPUTE_ERROR
1158  // error vars
1159  ,"xvel_err", "yvel_err", "zvel_err", "pp_err"
1160 #endif
1161  ,"qsrc_sw", "qsrc_lw"
1162  };
1163 
1164  // **************************************************************************************
1165  // NOTE: The order of variable names here **MUST MATCH THE ORDER** in IO/ERF_Plotfile.cpp
1166  // **************************************************************************************
1167  const amrex::Vector<std::string> derived_names_2d {
1168  "z_surf", "landmask", "mapfac", "lat_m", "lon_m",
1169  "u_star", "w_star", "t_star", "q_star", "Olen", "pblh",
1170  "t_surf", "q_surf", "z0", "OLR", "sens_flux", "laten_flux",
1171  "surf_pres", "integrated_qv"
1172  };
1173 
1174  // **************************************************************************************
1175  // NOTE: The order of variable names here **MUST MATCH THE ORDER** in IO/ERF_WriteSubVolume.cpp
1176  // **************************************************************************************
1177  const amrex::Vector<std::string> derived_subvol_names {"soundspeed", "temp", "theta", "KE", "scalar"};
1178 
1179  // algorithm choices
1180  static SolverChoice solverChoice;
1181 
1182  // Turbulent perturbation structure
1183  TurbulentPerturbation turbPert;
1184 
1185 #ifdef ERF_USE_PARTICLES
1186  // Particle container with all particle species
1187  ParticleData particleData;
1188 
1189  // variables and functions for tracers particles
1190  bool m_use_tracer_particles; /*!< tracer particles that advect with flow with optional sedimentation */
1191 
1192  /*! Read tracer and hydro particles parameters */
1193  void readTracersParams();
1194 
1195  /*! Initialize tracer and hydro particles */
1196  void initializeTracers ( amrex::ParGDBBase*,
1197  const amrex::Vector<std::unique_ptr<amrex::MultiFab>>&,
1198  const amrex::Real time);
1199 
1200  /*! Restart tracer and hydro particles */
1201  void restartTracers ( amrex::ParGDBBase*, const std::string& );
1202 
1203  /*! Evolve tracers and hydro particles */
1204  void evolveTracers( int,
1205  amrex::Real,
1206  amrex::Vector<amrex::Vector<amrex::MultiFab>>&,
1207  const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& );
1208 
1209 #endif
1210 
1211 #ifdef ERF_USE_MULTIBLOCK
1212  MultiBlockContainer *m_mbc = nullptr;
1213 #endif
1214 
1215  static int verbose;
1216  static int mg_verbose;
1217  static bool use_fft;
1218 
1219  static int check_for_nans;
1220 
1221  // Diagnostic output interval
1222  static int sum_interval;
1223  static int pert_interval;
1224  static amrex::Real sum_per;
1225 
1226  // Write in native AMReX or NetCDF format for each plotfile
1227  static PlotFileType plotfile3d_type_1;
1228  static PlotFileType plotfile3d_type_2;
1229  static PlotFileType plotfile2d_type_1;
1230  static PlotFileType plotfile2d_type_2;
1231 
1232  int file_name_digits = 5;
1233  bool use_real_time_in_pltname = false;
1234 
1235  static StateInterpType interpolation_type;
1236 
1237  // sponge_type: "input_sponge"
1238  static std::string sponge_type;
1239 
1240  // NetCDF initialization (wrfinput) file
1241  static amrex::Vector<amrex::Vector<std::string>> nc_init_file;
1242  static amrex::Vector<amrex::Vector<int>> have_read_nc_init_file;
1243 
1244  // NetCDF initialization (wrfbdy/met_em) file
1245  static std::string nc_bdy_file;
1246  int real_width{0};
1247  bool real_extrap_w{true};
1248 
1249  // NetCDF initialization of zlo boundary values
1250  static std::string nc_low_file;
1251 
1252  // Options for vertical interpolation of met_em*.nc data.
1253  bool metgrid_debug_quiescent{false};
1254  bool metgrid_debug_isothermal{false};
1255  bool metgrid_debug_dry{false};
1256  bool metgrid_debug_psfc{false};
1257  bool metgrid_debug_msf{false};
1258  bool metgrid_interp_theta{false};
1259  bool metgrid_basic_linear{false};
1260  bool metgrid_use_below_sfc{true};
1261  bool metgrid_use_sfc{true};
1262  bool metgrid_retain_sfc{false};
1263  amrex::Real metgrid_proximity{amrex::Real(500.0)};
1264  int metgrid_order{2};
1265  int metgrid_force_sfc_k{6};
1266 
1267  amrex::Vector<amrex::BoxArray> ba1d;
1268  amrex::Vector<amrex::BoxArray> ba2d;
1269  std::unique_ptr<amrex::MultiFab> mf_C1H;
1270  std::unique_ptr<amrex::MultiFab> mf_C2H;
1271  std::unique_ptr<amrex::MultiFab> mf_MUB;
1272 
1273  amrex::Vector<std::unique_ptr<amrex::MultiFab>> mf_PSFC;
1274 
1275  // 1D CDF output (for ingestion in AMR-Wind)
1276  static int output_1d_column;
1277  static int column_interval;
1278  static amrex::Real column_per;
1279  static amrex::Real column_loc_x;
1280  static amrex::Real column_loc_y;
1281  static std::string column_file_name;
1282 
1283  // 2D BndryRegister output (for ingestion in AMR-Wind)
1284  static int output_bndry_planes;
1285  static int bndry_output_planes_interval;
1286  static amrex::Real bndry_output_planes_per;
1287  static amrex::Real bndry_output_planes_start_time;
1288 
1289  // 2D BndryRegister input
1290  static int input_bndry_planes;
1291 
1292  static int ng_dens_hse;
1293  static int ng_pres_hse;
1294 
1295  // Custom source terms
1296  amrex::Vector<std::unique_ptr<amrex::MultiFab>> rhotheta_src;
1297  amrex::Vector<std::unique_ptr<amrex::MultiFab>> rhoqt_src;
1298 
1299  amrex::Vector< amrex::Vector<amrex::Real> > h_w_subsid;
1300  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_w_subsid;
1301 
1302  amrex::Vector< amrex::Vector<amrex::Real> > h_u_geos;
1303  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_u_geos;
1304 
1305  amrex::Vector< amrex::Vector<amrex::Real> > h_v_geos;
1306  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_v_geos;
1307 
1308  // Function to read and populate above host vectors (if input file exists)
1309  void init_geo_wind_profile (const std::string input_file,
1310  amrex::Vector<amrex::Real>& u_geos,
1311  amrex::Gpu::DeviceVector<amrex::Real>& u_geos_d,
1312  amrex::Vector<amrex::Real>& v_geos,
1313  amrex::Gpu::DeviceVector<amrex::Real>& v_geos_d,
1314  const amrex::Geometry& lgeom,
1315  const amrex::Vector<amrex::Real>& zlev_stag);
1316 
1317  // This is a vector over levels of vectors across quantities of Vectors
1318  amrex::Vector<amrex::Vector<amrex::Vector<amrex::Real> > > h_rayleigh_ptrs;
1319  amrex::Vector<amrex::Vector<amrex::Vector<amrex::Real> > > h_sponge_ptrs;
1320 
1321  // These are vectors over levels of Vectors
1322  amrex::Vector<amrex::Vector<amrex::Real> > h_sinesq_ptrs;
1323  amrex::Vector<amrex::Vector<amrex::Real> > h_sinesq_stag_ptrs;
1324 
1325  // This is a vector over levels of vectors across quantities of DeviceVectors
1326  amrex::Vector<amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > > d_rayleigh_ptrs;
1327  amrex::Vector<amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > > d_sponge_ptrs;
1328 
1329  // These are vectors over levels of DeviceVectors
1330  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_sinesq_ptrs;
1331  amrex::Vector<amrex::Gpu::DeviceVector<amrex::Real> > d_sinesq_stag_ptrs;
1332 
1333  amrex::Vector<amrex::Real> h_havg_density;
1334  amrex::Vector<amrex::Real> h_havg_temperature;
1335  amrex::Vector<amrex::Real> h_havg_pressure;
1336  amrex::Vector<amrex::Real> h_havg_qv;
1337  amrex::Vector<amrex::Real> h_havg_qc;
1338 
1339  amrex::Gpu::DeviceVector<amrex::Real> d_havg_density;
1340  amrex::Gpu::DeviceVector<amrex::Real> d_havg_temperature;
1341  amrex::Gpu::DeviceVector<amrex::Real> d_havg_pressure;
1342  amrex::Gpu::DeviceVector<amrex::Real> d_havg_qv;
1343  amrex::Gpu::DeviceVector<amrex::Real> d_havg_qc;
1344 
1345  void refinement_criteria_setup ();
1346 
1347  std::unique_ptr<WriteBndryPlanes> m_w2d = nullptr;
1348  std::unique_ptr<ReadBndryPlanes> m_r2d = nullptr;
1349  std::unique_ptr<SurfaceLayer> m_SurfaceLayer = nullptr;
1350  amrex::Vector<std::unique_ptr<ForestDrag>> m_forest_drag;
1351 
1352  //
1353  // Holds info for dynamically generated tagging criteria
1354  //
1355  static amrex::Vector<amrex::AMRErrorTag> ref_tags;
1356 
1357  amrex::Vector<amrex::Vector<amrex::BoxArray>> subdomains;
1358 
1359  amrex::Vector<amrex::Real> dz_min;
1360 
1361  static AMREX_FORCE_INLINE
1362  int
1363  ComputeGhostCells (const SolverChoice& sc)
1364  {
1365  int ngrow = 0;
1366 
1367  if (sc.use_num_diff)
1368  {
1369  ngrow = 3;
1370  } else {
1371  if (
1372  (sc.advChoice.dycore_horiz_adv_type == AdvType::Centered_6th)
1373  || (sc.advChoice.dycore_vert_adv_type == AdvType::Centered_6th)
1374  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Centered_6th)
1375  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Centered_6th)
1376  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Centered_6th)
1377  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Centered_6th) )
1378  { ngrow = 3; }
1379  else if (
1380  (sc.advChoice.dycore_horiz_adv_type == AdvType::Upwind_5th)
1381  || (sc.advChoice.dycore_vert_adv_type == AdvType::Upwind_5th)
1382  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Upwind_5th)
1383  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Upwind_5th)
1384  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Upwind_5th)
1385  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Upwind_5th) )
1386  { ngrow = 3; }
1387  else if (
1388  (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_5)
1389  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_5)
1390  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_5)
1391  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_5)
1392  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_5Z)
1393  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_5Z)
1394  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_5Z)
1395  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_5Z) )
1396  { ngrow = 3; }
1397  else if (
1398  (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_7)
1399  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_7)
1400  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_7)
1401  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_7)
1402  || (sc.advChoice.moistscal_horiz_adv_type == AdvType::Weno_7Z)
1403  || (sc.advChoice.moistscal_vert_adv_type == AdvType::Weno_7Z)
1404  || (sc.advChoice.dryscal_horiz_adv_type == AdvType::Weno_7Z)
1405  || (sc.advChoice.dryscal_vert_adv_type == AdvType::Weno_7Z) )
1406  { ngrow = 4; }
1407  else
1408  {
1409  if (sc.terrain_type == TerrainType::EB){
1410  ngrow = 4;
1411  } else {
1412  ngrow = 2;
1413  }
1414  }
1415  }
1416 
1417  return ngrow;
1418  }
1419 
1420  AMREX_FORCE_INLINE
1421  amrex::YAFluxRegister* getAdvFluxReg (int lev)
1422  {
1423  return advflux_reg[lev];
1424  }
1425 
1426  AMREX_FORCE_INLINE
1427  std::ostream&
1428  DataLog (int i)
1429  {
1430  return *datalog[i];
1431  }
1432 
1433  AMREX_FORCE_INLINE
1434  std::ostream&
1435  DerDataLog (int i)
1436  {
1437  return *der_datalog[i];
1438  }
1439 
1440  AMREX_FORCE_INLINE
1441  int
1442  NumDataLogs () noexcept
1443  {
1444  return datalog.size();
1445  }
1446 
1447  AMREX_FORCE_INLINE
1448  int
1449  NumDerDataLogs () noexcept
1450  {
1451  return der_datalog.size();
1452  }
1453 
1454 
1455  AMREX_FORCE_INLINE
1456  std::ostream&
1457  SamplePointLog (int i)
1458  {
1459  return *sampleptlog[i];
1460  }
1461 
1462  AMREX_FORCE_INLINE
1463  int
1464  NumSamplePointLogs () noexcept
1465  {
1466  return sampleptlog.size();
1467  }
1468 
1469  AMREX_FORCE_INLINE
1470  std::ostream&
1471  SampleLineLog (int i)
1472  {
1473  return *samplelinelog[i];
1474  }
1475 
1476  AMREX_FORCE_INLINE
1477  int
1478  NumSampleLineLogs () noexcept
1479  {
1480  return samplelinelog.size();
1481  }
1482 
1483  amrex::IntVect&
1484  SamplePoint (int i)
1485  {
1486  return samplepoint[i];
1487  }
1488 
1489  AMREX_FORCE_INLINE
1490  int
1491  NumSamplePoints () noexcept
1492  {
1493  return samplepoint.size();
1494  }
1495 
1496  amrex::IntVect&
1497  SampleLine (int i)
1498  {
1499  return sampleline[i];
1500  }
1501 
1502  AMREX_FORCE_INLINE
1503  int
1504  NumSampleLines () noexcept
1505  {
1506  return sampleline.size();
1507  }
1508 
1509  static amrex::Real startCPUTime;
1510  static amrex::Real previousCPUTimeUsed;
1511 
1512  static amrex::Real
1513  getCPUTime ()
1514  {
1515  int numCores = amrex::ParallelDescriptor::NProcs();
1516 #ifdef _OPENMP
1517  numCores = numCores * omp_get_max_threads();
1518 #endif
1519 
1520  amrex::Real T =
1521  numCores * (amrex::ParallelDescriptor::second() - startCPUTime) +
1522  previousCPUTimeUsed;
1523 
1524  return T;
1525  }
1526 
1527  void setRecordDataInfo (int i, const std::string& filename) // NOLINT
1528  {
1529  if (amrex::ParallelDescriptor::IOProcessor())
1530  {
1531  datalog[i] = std::make_unique<std::fstream>();
1532  datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1533  if (!datalog[i]->good()) {
1534  amrex::FileOpenFailed(filename);
1535  }
1536  }
1537  amrex::ParallelDescriptor::Barrier("ERF::setRecordDataInfo");
1538  }
1539 
1540  void setRecordDerDataInfo (int i, const std::string& filename) // NOLINT
1541  {
1542  if (amrex::ParallelDescriptor::IOProcessor())
1543  {
1544  der_datalog[i] = std::make_unique<std::fstream>();
1545  der_datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1546  if (!der_datalog[i]->good()) {
1547  amrex::FileOpenFailed(filename);
1548  }
1549  }
1550  amrex::ParallelDescriptor::Barrier("ERF::setRecordDerDataInfo");
1551  }
1552 
1553  void setRecordEnergyDataInfo (int i, const std::string& filename) // NOLINT
1554  {
1555  if (amrex::ParallelDescriptor::IOProcessor())
1556  {
1557  tot_e_datalog[i] = std::make_unique<std::fstream>();
1558  tot_e_datalog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1559  if (!tot_e_datalog[i]->good()) {
1560  amrex::FileOpenFailed(filename);
1561  }
1562  }
1563  amrex::ParallelDescriptor::Barrier("ERF::setRecordEnergyDataInfo");
1564  }
1565 
1566  void setRecordSamplePointInfo (int i, int lev, amrex::IntVect& cell, const std::string& filename) // NOLINT
1567  {
1568  amrex::MultiFab dummy(grids[lev],dmap[lev],1,0);
1569  for (amrex::MFIter mfi(dummy); mfi.isValid(); ++mfi)
1570  {
1571  const amrex::Box& bx = mfi.validbox();
1572  if (bx.contains(cell)) {
1573  sampleptlog[i] = std::make_unique<std::fstream>();
1574  sampleptlog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1575  if (!sampleptlog[i]->good()) {
1576  amrex::FileOpenFailed(filename);
1577  }
1578  }
1579  }
1580  amrex::ParallelDescriptor::Barrier("ERF::setRecordSamplePointInfo");
1581  }
1582 
1583  void setRecordSampleLineInfo (int i, int lev, amrex::IntVect& cell, const std::string& filename) // NOLINT
1584  {
1585  amrex::MultiFab dummy(grids[lev],dmap[lev],1,0);
1586  for (amrex::MFIter mfi(dummy); mfi.isValid(); ++mfi)
1587  {
1588  const amrex::Box& bx = mfi.validbox();
1589  if (bx.contains(cell)) {
1590  samplelinelog[i] = std::make_unique<std::fstream>();
1591  samplelinelog[i]->open(filename.c_str(),std::ios::out|std::ios::app);
1592  if (!samplelinelog[i]->good()) {
1593  amrex::FileOpenFailed(filename);
1594  }
1595  }
1596  }
1597  amrex::ParallelDescriptor::Barrier("ERF::setRecordSampleLineInfo");
1598  }
1599 
1600  // Data sampler for line and plane output
1601  int line_sampling_interval = -1;
1602  int plane_sampling_interval = -1;
1603  amrex::Real line_sampling_per = -one;
1604  amrex::Real plane_sampling_per = -one;
1605  std::unique_ptr<LineSampler> line_sampler = nullptr;
1606  std::unique_ptr<PlaneSampler> plane_sampler = nullptr;
1607 
1608  amrex::Vector<std::unique_ptr<std::fstream> > datalog;
1609  amrex::Vector<std::unique_ptr<std::fstream> > der_datalog;
1610  amrex::Vector<std::unique_ptr<std::fstream> > tot_e_datalog;
1611  amrex::Vector<std::string> datalogname;
1612  amrex::Vector<std::string> der_datalogname;
1613  amrex::Vector<std::string> tot_e_datalogname;
1614 
1615  amrex::Vector<std::unique_ptr<std::fstream> > sampleptlog;
1616  amrex::Vector<std::string> sampleptlogname;
1617  amrex::Vector<amrex::IntVect> samplepoint;
1618 
1619  amrex::Vector<std::unique_ptr<std::fstream> > samplelinelog;
1620  amrex::Vector<std::string> samplelinelogname;
1621  amrex::Vector<amrex::IntVect> sampleline;
1622 
1623  //! The filename of the ith datalog file.
1624  [[nodiscard]] std::string DataLogName (int i) const noexcept { return datalogname[i]; }
1625  [[nodiscard]] std::string DerDataLogName (int i) const noexcept { return der_datalogname[i]; }
1626 
1627  //! The filename of the ith sampleptlog file.
1628  [[nodiscard]] std::string SamplePointLogName (int i) const noexcept { return sampleptlogname[i]; }
1629 
1630  //! The filename of the ith samplelinelog file.
1631  [[nodiscard]] std::string SampleLineLogName (int i) const noexcept { return samplelinelogname[i]; }
1632 
1633  // array of EB objects
1634  amrex::Vector<std::unique_ptr<eb_>> eb;
1635 
1636  [[nodiscard]] eb_ const& get_eb (int lev) const noexcept {
1637  AMREX_ASSERT(lev >= 0 && lev < eb.size() && eb[lev] != nullptr);
1638  return *eb[lev];
1639  }
1640 
1641  [[nodiscard]] amrex::EBFArrayBoxFactory const&
1642  EBFactory (int lev) const noexcept {
1643  return *(eb[lev]->get_const_factory());
1644  }
1645 
1646  [[nodiscard]] static int nghost_eb_basic ()
1647  { return 5; }
1648 
1649  // We need 5 for doing StateRedistribution; otherwise 4 would be enough
1650  [[nodiscard]] static int nghost_eb_volume ()
1651  { return 5; }
1652 
1653  [[nodiscard]] static int nghost_eb_full ()
1654  { return 4; }
1655 
1656 #ifdef ERF_USE_FFT
1657  amrex::Vector<std::unique_ptr<amrex::FFT::Poisson<amrex::MultiFab>>> m_3D_poisson;
1658  amrex::Vector<std::unique_ptr<amrex::FFT::PoissonHybrid<amrex::MultiFab>>> m_2D_poisson;
1659 #endif
1660 
1661 public:
1662  void writeJobInfo (const std::string& dir) const;
1663  static void writeBuildInfo (std::ostream& os);
1664 
1665  static void print_banner(MPI_Comm /*comm*/, std::ostream& /*out*/);
1666  static void print_usage(MPI_Comm /*comm*/, std::ostream& /*out*/);
1667  static void print_error(MPI_Comm /*comm*/, const std::string& msg);
1668  static void print_summary(std::ostream&);
1669  static void print_tpls(std::ostream& /*out*/);
1670 };
1671 
1672 #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 @22 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
p
Real * p
Definition: ERF_InitCustomPert_SquallLine.H:61
ERF_InputSoundingData.H
ERF_InputSpongeData.H
ERF_LagrangianMicrophysics.H
Contains the Lagrangian microphysics class.
ERF_LandSurface.H
ERF_MRI.H
ERF_ParticleData.H
ERF_PhysBCFunct.H
ERF_ProbCommon.H
ERF_RadiationModels.H
ERF_ReadBndryPlanes.H
ERF_SampleData.H
ERF_ShocInterface.H
Real
amrex::Real Real
Definition: ERF_ShocInterface.H:19
ERF_SurfaceLayer.H
ERF_TurbPertStruct.H
ERF_WindFarm.H
ERF_WriteBndryPlanes.H
ERF
Definition: ERF.H:111
ERF::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:2889
ERF::rU_new
amrex::Vector< amrex::MultiFab > rU_new
Definition: ERF.H:853
ERF::last_check_file_step
static int last_check_file_step
Definition: ERF.H:1022
ERF::walldist
amrex::Vector< std::unique_ptr< amrex::MultiFab > > walldist
Definition: ERF.H:962
ERF::h_sponge_ptrs
amrex::Vector< amrex::Vector< amrex::Vector< amrex::Real > > > h_sponge_ptrs
Definition: ERF.H:1319
ERF::start_time
static amrex::Real start_time
Definition: ERF.H:1048
ERF::metgrid_basic_linear
bool metgrid_basic_linear
Definition: ERF.H:1259
ERF::boxes_at_level
amrex::Vector< amrex::Vector< amrex::Box > > boxes_at_level
Definition: ERF.H:804
ERF::samplelinelogname
amrex::Vector< std::string > samplelinelogname
Definition: ERF.H:1620
ERF::MakeEBGeometry
void MakeEBGeometry()
ERF::max_step
int max_step
Definition: ERF.H:1045
ERF::metgrid_debug_msf
bool metgrid_debug_msf
Definition: ERF.H:1257
ERF::DerDataLog
AMREX_FORCE_INLINE std::ostream & DerDataLog(int i)
Definition: ERF.H:1435
ERF::mapfac
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > mapfac
Definition: ERF.H:965
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:828
ERF::d_sinesq_stag_ptrs
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_sinesq_stag_ptrs
Definition: ERF.H:1331
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:3158
ERF::Evolve
void Evolve()
Definition: ERF.cpp:605
ERF::avg_xmom
amrex::Vector< amrex::MultiFab > avg_xmom
Definition: ERF.H:835
ERF::pp_inc
amrex::Vector< amrex::MultiFab > pp_inc
Definition: ERF.H:831
ERF::last_plot2d_file_time_2
static amrex::Real last_plot2d_file_time_2
Definition: ERF.H:1027
ERF::make_eb_box
void make_eb_box()
ERF::FPr_u
amrex::Vector< ERFFillPatcher > FPr_u
Definition: ERF.H:903
ERF::cloud_fraction
amrex::Real cloud_fraction(amrex::Real time)
Definition: ERF_WriteScalarProfiles.cpp:452
ERF::sampleline
amrex::Vector< amrex::IntVect > sampleline
Definition: ERF.H:1621
ERF::subvol3d_var_names
amrex::Vector< std::string > subvol3d_var_names
Definition: ERF.H:1110
ERF::SFS_q1fx3_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q1fx3_lev
Definition: ERF.H:926
ERF::Hwave_onegrid
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Hwave_onegrid
Definition: ERF.H:979
ERF::vars_new
amrex::Vector< amrex::Vector< amrex::MultiFab > > vars_new
Definition: ERF.H:818
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:1478
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:1359
ERF::m_plot2d_per_1
amrex::Real m_plot2d_per_1
Definition: ERF.H:1095
ERF::lagged_delta_rt
amrex::Vector< amrex::MultiFab > lagged_delta_rt
Definition: ERF.H:834
ERF::plane_sampling_per
amrex::Real plane_sampling_per
Definition: ERF.H:1604
ERF::DataLogName
std::string DataLogName(int i) const noexcept
The filename of the ith datalog file.
Definition: ERF.H:1624
ERF::plot2d_file_2
std::string plot2d_file_2
Definition: ERF.H:1082
ERF::remake_zphys
void remake_zphys(int lev, std::unique_ptr< amrex::MultiFab > &temp_zphys_nd)
Definition: ERF_MakeNewArrays.cpp:775
ERF::thin_yforce
amrex::Vector< std::unique_ptr< amrex::MultiFab > > thin_yforce
Definition: ERF.H:1015
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:924
ERF::h_w_subsid
amrex::Vector< amrex::Vector< amrex::Real > > h_w_subsid
Definition: ERF.H:1299
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:1026
ERF::datalog
amrex::Vector< std::unique_ptr< std::fstream > > datalog
Definition: ERF.H:1608
ERF::sum_per
static amrex::Real sum_per
Definition: ERF.H:1224
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:904
ERF::derived_names_2d
const amrex::Vector< std::string > derived_names_2d
Definition: ERF.H:1167
ERF::cf_set_width
int cf_set_width
Definition: ERF.H:901
ERF::previousCPUTimeUsed
static amrex::Real previousCPUTimeUsed
Definition: ERF.H:1510
ERF::setPlotVariables
void setPlotVariables(const std::string &pp_plot_var_names, amrex::Vector< std::string > &plot_var_names)
Definition: ERF_Plotfile.cpp:25
ERF::d_havg_temperature
amrex::Gpu::DeviceVector< amrex::Real > d_havg_temperature
Definition: ERF.H:1340
ERF::last_plot2d_file_step_2
static int last_plot2d_file_step_2
Definition: ERF.H:1021
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:1038
ERF::setRecordDataInfo
void setRecordDataInfo(int i, const std::string &filename)
Definition: ERF.H:1527
ERF::SFS_hfx1_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_hfx1_lev
Definition: ERF.H:924
ERF::hurricane_eye_track_xy
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_eye_track_xy
Definition: ERF.H:157
ERF::ba2d
amrex::Vector< amrex::BoxArray > ba2d
Definition: ERF.H:1268
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:996
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:204
ERF::gradp
amrex::Vector< amrex::Vector< amrex::MultiFab > > gradp
Definition: ERF.H:822
ERF::plot3d_file_1
std::string plot3d_file_1
Definition: ERF.H:1079
ERF::FillPatchCrseLevel
void FillPatchCrseLevel(int lev, amrex::Real time, const amrex::Vector< amrex::MultiFab * > &mfs_vel, bool cons_only=false)
Definition: ERF_FillPatch.cpp:288
ERF::get_eb
eb_ const & get_eb(int lev) const noexcept
Definition: ERF.H:1636
ERF::d_havg_qv
amrex::Gpu::DeviceVector< amrex::Real > d_havg_qv
Definition: ERF.H:1342
ERF::qfx3_EB
amrex::Vector< std::unique_ptr< amrex::MultiFab > > qfx3_EB
Definition: ERF.H:932
ERF::column_loc_y
static amrex::Real column_loc_y
Definition: ERF.H:1280
ERF::plot_file_on_restart
static bool plot_file_on_restart
Definition: ERF.H:1033
ERF::mg_verbose
static int mg_verbose
Definition: ERF.H:1216
ERF::ReadParameters
void ReadParameters()
Definition: ERF.cpp:2306
ERF::PlotFileVarNames
static amrex::Vector< std::string > PlotFileVarNames(amrex::Vector< std::string > plot_var_names)
Definition: ERF_Plotfile.cpp:306
ERF::forecast_state_interp
amrex::Vector< amrex::Vector< amrex::MultiFab > > forecast_state_interp
Definition: ERF.H:165
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:760
ERF::InitializeFromFile
void InitializeFromFile()
ERF::physbcs_cons
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_cons > > physbcs_cons
Definition: ERF.H:840
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:1273
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:946
ERF::detJ_cc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > detJ_cc
Definition: ERF.H:941
ERF::lsm_flux_name
amrex::Vector< std::string > lsm_flux_name
Definition: ERF.H:882
ERF::WriteMyEBSurface
void WriteMyEBSurface()
ERF::z_phys_cc
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_cc
Definition: ERF.H:939
ERF::eb
amrex::Vector< std::unique_ptr< eb_ > > eb
Definition: ERF.H:1634
ERF::eddyDiffs_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > eddyDiffs_lev
Definition: ERF.H:910
ERF::solverChoice
static SolverChoice solverChoice
Definition: ERF.H:1180
ERF::hfx3_EB
amrex::Vector< std::unique_ptr< amrex::MultiFab > > hfx3_EB
Definition: ERF.H:931
ERF::FPr_c
amrex::Vector< ERFFillPatcher > FPr_c
Definition: ERF.H:902
ERF::plot_rad
bool plot_rad
Definition: ERF.H:896
ERF::hurricane_tracker_circle
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_tracker_circle
Definition: ERF.H:161
ERF::use_fft
static bool use_fft
Definition: ERF.H:1217
ERF::m_plot_face_vels
bool m_plot_face_vels
Definition: ERF.H:1097
ERF::hurricane_maxvel_vs_time
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_maxvel_vs_time
Definition: ERF.H:159
ERF::base_state_new
amrex::Vector< amrex::MultiFab > base_state_new
Definition: ERF.H:974
ERF::plot3d_file_2
std::string plot3d_file_2
Definition: ERF.H:1080
ERF::az
amrex::Vector< std::unique_ptr< amrex::MultiFab > > az
Definition: ERF.H:944
ERF::regrid_int
int regrid_int
Definition: ERF.H:1072
ERF::fixed_dt
amrex::Vector< amrex::Real > fixed_dt
Definition: ERF.H:1066
ERF::write_1D_profiles_stag
void write_1D_profiles_stag(amrex::Real time)
Definition: ERF_Write1DProfiles_stag.cpp:25
ERF::WriteGenericPlotfileHeaderWithTerrain
void WriteGenericPlotfileHeaderWithTerrain(std::ostream &HeaderFile, int nlevels, const amrex::Vector< amrex::BoxArray > &bArray, const amrex::Vector< std::string > &varnames, const amrex::Vector< amrex::Geometry > &my_geom, amrex::Real time, const amrex::Vector< int > &level_steps, const amrex::Vector< amrex::IntVect > &my_ref_ratio, const std::string &versionName, const std::string &levelPrefix, const std::string &mfPrefix) const
Definition: ERF_Plotfile.cpp:1854
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:1327
ERF::dt_mri_ratio
amrex::Vector< long > dt_mri_ratio
Definition: ERF.H:813
ERF::Tau
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > Tau
Definition: ERF.H:908
ERF::vel_t_avg
amrex::Vector< std::unique_ptr< amrex::MultiFab > > vel_t_avg
Definition: ERF.H:825
ERF::sum_energy_quantities
void sum_energy_quantities(amrex::Real time)
Definition: ERF_WriteScalarProfiles.cpp:313
ERF::SFS_q2fx3_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q2fx3_lev
Definition: ERF.H:927
ERF::dt_max
static amrex::Real dt_max
Definition: ERF.H:1063
ERF::lmask_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::iMultiFab > > > lmask_lev
Definition: ERF.H:916
ERF::NumSamplePointLogs
AMREX_FORCE_INLINE int NumSamplePointLogs() noexcept
Definition: ERF.H:1464
ERF::h_havg_pressure
amrex::Vector< amrex::Real > h_havg_pressure
Definition: ERF.H:1335
ERF::update_diffusive_arrays
void update_diffusive_arrays(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)
Definition: ERF_MakeNewArrays.cpp:523
ERF::verbose
static int verbose
Definition: ERF.H:1215
ERF::h_havg_qc
amrex::Vector< amrex::Real > h_havg_qc
Definition: ERF.H:1337
ERF::physbcs_w
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_w > > physbcs_w
Definition: ERF.H:843
ERF::nghost_eb_basic
static int nghost_eb_basic()
Definition: ERF.H:1646
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:1281
ERF::samplelinelog
amrex::Vector< std::unique_ptr< std::fstream > > samplelinelog
Definition: ERF.H:1619
ERF::last_plot3d_file_time_2
static amrex::Real last_plot3d_file_time_2
Definition: ERF.H:1025
ERF::terrain_blanking
amrex::Vector< std::unique_ptr< amrex::MultiFab > > terrain_blanking
Definition: ERF.H:959
ERF::micro
std::unique_ptr< Microphysics > micro
Definition: ERF.H:863
ERF::m_plot2d_int_2
int m_plot2d_int_2
Definition: ERF.H:1088
ERF::base_state
amrex::Vector< amrex::MultiFab > base_state
Definition: ERF.H:973
ERF::getAdvFluxReg
AMREX_FORCE_INLINE amrex::YAFluxRegister * getAdvFluxReg(int lev)
Definition: ERF.H:1421
ERF::m_plot3d_int_1
int m_plot3d_int_1
Definition: ERF.H:1085
ERF::h_havg_density
amrex::Vector< amrex::Real > h_havg_density
Definition: ERF.H:1333
ERF::z_phys_nd_new
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_nd_new
Definition: ERF.H:953
ERF::fixed_fast_dt
amrex::Vector< amrex::Real > fixed_fast_dt
Definition: ERF.H:1067
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:1177
ERF::hurricane_minpressure_vs_time
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_minpressure_vs_time
Definition: ERF.H:160
ERF::metgrid_retain_sfc
bool metgrid_retain_sfc
Definition: ERF.H:1262
ERF::Qv_prim
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Qv_prim
Definition: ERF.H:848
ERF::sum_interval
static int sum_interval
Definition: ERF.H:1222
ERF::pert_interval
static int pert_interval
Definition: ERF.H:1223
ERF::line_sampling_per
amrex::Real line_sampling_per
Definition: ERF.H:1603
ERF::restart
void restart()
Definition: ERF.cpp:2114
ERF::last_plot3d_file_step_2
static int last_plot3d_file_step_2
Definition: ERF.H:1019
ERF::SFS_q1fx2_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q1fx2_lev
Definition: ERF.H:926
ERF::SampleLine
amrex::IntVect & SampleLine(int i)
Definition: ERF.H:1497
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:1232
ERF::rV_new
amrex::Vector< amrex::MultiFab > rV_new
Definition: ERF.H:855
ERF::PlotFileName
std::string PlotFileName(int lev) const
ERF::write_1D_profiles
void write_1D_profiles(amrex::Real time)
Definition: ERF_Write1DProfiles.cpp:17
ERF::initialize_integrator
void initialize_integrator(int lev, amrex::MultiFab &cons_mf, amrex::MultiFab &vel_mf)
Definition: ERF_MakeNewArrays.cpp:852
ERF::thin_zforce
amrex::Vector< std::unique_ptr< amrex::MultiFab > > thin_zforce
Definition: ERF.H:1016
ERF::plot3d_var_names_2
amrex::Vector< std::string > plot3d_var_names_2
Definition: ERF.H:1113
ERF::domain_bcs_type
amrex::Vector< amrex::BCRec > domain_bcs_type
Definition: ERF.H:989
ERF::Qr_prim
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Qr_prim
Definition: ERF.H:849
ERF::post_timestep
void post_timestep(int nstep, amrex::Real time, amrex::Real dt_lev)
Definition: ERF.cpp:767
ERF::mf_MUB
std::unique_ptr< amrex::MultiFab > mf_MUB
Definition: ERF.H:1271
ERF::pp_prefix
std::string pp_prefix
Definition: ERF.H:548
ERF::SampleLineLogName
std::string SampleLineLogName(int i) const noexcept
The filename of the ith samplelinelog file.
Definition: ERF.H:1631
ERF::sst_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > sst_lev
Definition: ERF.H:914
ERF::plot2d_var_names_1
amrex::Vector< std::string > plot2d_var_names_1
Definition: ERF.H:1114
ERF::thin_xforce
amrex::Vector< std::unique_ptr< amrex::MultiFab > > thin_xforce
Definition: ERF.H:1014
ERF::NumSamplePoints
AMREX_FORCE_INLINE int NumSamplePoints() noexcept
Definition: ERF.H:1491
ERF::mf_C2H
std::unique_ptr< amrex::MultiFab > mf_C2H
Definition: ERF.H:1270
ERF::metgrid_use_sfc
bool metgrid_use_sfc
Definition: ERF.H:1261
ERF::m_plot2d_per_2
amrex::Real m_plot2d_per_2
Definition: ERF.H:1096
ERF::bndry_output_planes_per
static amrex::Real bndry_output_planes_per
Definition: ERF.H:1286
ERF::setPlotVariables2D
void setPlotVariables2D(const std::string &pp_plot_var_names, amrex::Vector< std::string > &plot_var_names)
Definition: ERF_Plotfile.cpp:187
ERF::m_check_per
amrex::Real m_check_per
Definition: ERF.H:1108
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:885
ERF::prob
std::unique_ptr< ProblemBase > prob
Definition: ERF.H:800
ERF::num_files_at_level
amrex::Vector< int > num_files_at_level
Definition: ERF.H:803
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:1767
ERF::init_bcs
void init_bcs()
Definition: ERF_InitBCs.cpp:295
ERF::profile_int
int profile_int
Definition: ERF.H:1102
ERF::metgrid_debug_quiescent
bool metgrid_debug_quiescent
Definition: ERF.H:1253
ERF::physbcs_u
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_u > > physbcs_u
Definition: ERF.H:841
ERF::t_new
amrex::Vector< amrex::Real > t_new
Definition: ERF.H:810
ERF::destag_profiles
bool destag_profiles
Definition: ERF.H:1103
ERF::stretched_dz_d
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > stretched_dz_d
Definition: ERF.H:971
ERF::th_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > th_bc_data
Definition: ERF.H:777
ERF::t_avg_cnt
amrex::Vector< amrex::Real > t_avg_cnt
Definition: ERF.H:826
ERF::FillPatchFineLevel
void FillPatchFineLevel(int lev, amrex::Real time, const amrex::Vector< amrex::MultiFab * > &mfs_vel, const amrex::Vector< amrex::MultiFab * > &mfs_mom, const amrex::MultiFab &old_base_state, const amrex::MultiFab &new_base_state, bool fillset=true, bool cons_only=false)
Definition: ERF_FillPatch.cpp:20
ERF::DerDataLogName
std::string DerDataLogName(int i) const noexcept
Definition: ERF.H:1625
ERF::m_check_int
int m_check_int
Definition: ERF.H:1107
ERF::ReadVelsOnlyFromCheckpointFile
void ReadVelsOnlyFromCheckpointFile(int lev_to_fill, std::string &chkfile)
Definition: ERF_Checkpoint.cpp:1076
ERF::estTimeStep
amrex::Real estTimeStep(int lev, long &dt_fast_ratio) const
Definition: ERF_ComputeTimestep.cpp:60
ERF::sponge_type
static std::string sponge_type
Definition: ERF.H:1238
ERF::startCPUTime
static amrex::Real startCPUTime
Definition: ERF.H:1509
ERF::surface_state_1
amrex::Vector< amrex::MultiFab > surface_state_1
Definition: ERF.H:166
ERF::SFS_diss_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_diss_lev
Definition: ERF.H:925
ERF::d_sinesq_ptrs
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_sinesq_ptrs
Definition: ERF.H:1330
ERF::rU_old
amrex::Vector< amrex::MultiFab > rU_old
Definition: ERF.H:852
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:811
ERF::NumSampleLines
AMREX_FORCE_INLINE int NumSampleLines() noexcept
Definition: ERF.H:1504
ERF::m_bc_nonreflecting
amrex::Array< bool, AMREX_SPACEDIM *2 > m_bc_nonreflecting
Definition: ERF.H:1002
ERF::Theta_prim
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Theta_prim
Definition: ERF.H:847
ERF::init1DArrays
void init1DArrays()
ERF::z_t_rk
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_t_rk
Definition: ERF.H:956
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:860
ERF::check_for_nans
static int check_for_nans
Definition: ERF.H:1219
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:229
ERF::physbcs_v
amrex::Vector< std::unique_ptr< ERFPhysBCFunct_v > > physbcs_v
Definition: ERF.H:842
ERF::column_per
static amrex::Real column_per
Definition: ERF.H:1278
ERF::tot_e_datalogname
amrex::Vector< std::string > tot_e_datalogname
Definition: ERF.H:1613
ERF::stop_time
static amrex::Real stop_time
Definition: ERF.H:1049
ERF::output_bndry_planes
static int output_bndry_planes
Definition: ERF.H:1284
ERF::d_v_geos
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_v_geos
Definition: ERF.H:1306
ERF::update_terrain_arrays
void update_terrain_arrays(int lev)
Definition: ERF_MakeNewArrays.cpp:835
ERF::nc_bdy_file
static std::string nc_bdy_file
Definition: ERF.H:1245
ERF::metgrid_interp_theta
bool metgrid_interp_theta
Definition: ERF.H:1258
ERF::nc_init_file
static amrex::Vector< amrex::Vector< std::string > > nc_init_file
Definition: ERF.H:1241
ERF::init_only
void init_only(int lev, amrex::Real time)
Definition: ERF.cpp:2176
ERF::input_bndry_planes
static int input_bndry_planes
Definition: ERF.H:1290
ERF::interpolation_type
static StateInterpType interpolation_type
Definition: ERF.H:1235
ERF::d_havg_qc
amrex::Gpu::DeviceVector< amrex::Real > d_havg_qc
Definition: ERF.H:1343
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:1305
ERF::regrid_level_0_on_restart
bool regrid_level_0_on_restart
Definition: ERF.H:1076
ERF::Lwave_onegrid
amrex::Vector< std::unique_ptr< amrex::MultiFab > > Lwave_onegrid
Definition: ERF.H:980
ERF::input_sounding_data
InputSoundingData input_sounding_data
Definition: ERF.H:768
ERF::h_sinesq_ptrs
amrex::Vector< amrex::Vector< amrex::Real > > h_sinesq_ptrs
Definition: ERF.H:1322
ERF::Write2DPlotFile
void Write2DPlotFile(int which, PlotFileType plotfile_type, amrex::Vector< std::string > plot_var_names)
Definition: ERF_Plotfile.cpp:1943
ERF::d_havg_density
amrex::Gpu::DeviceVector< amrex::Real > d_havg_density
Definition: ERF.H:1339
ERF::rhotheta_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > rhotheta_src
Definition: ERF.H:1296
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:1052
ERF::advflux_reg
amrex::Vector< amrex::YAFluxRegister * > advflux_reg
Definition: ERF.H:984
ERF::metgrid_force_sfc_k
int metgrid_force_sfc_k
Definition: ERF.H:1265
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:1293
ERF::bndry_output_planes_start_time
static amrex::Real bndry_output_planes_start_time
Definition: ERF.H:1287
ERF::real_extrap_w
bool real_extrap_w
Definition: ERF.H:1247
ERF::cfl
static amrex::Real cfl
Definition: ERF.H:1058
ERF::fine_mask
amrex::Vector< std::unique_ptr< amrex::MultiFab > > fine_mask
Definition: ERF.H:968
ERF::domain_bcs_type_d
amrex::Gpu::DeviceVector< amrex::BCRec > domain_bcs_type_d
Definition: ERF.H:990
ERF::m_forest_drag
amrex::Vector< std::unique_ptr< ForestDrag > > m_forest_drag
Definition: ERF.H:1350
ERF::datwidth
const int datwidth
Definition: ERF.H:1036
ERF::derive_diag_profiles_stag
void derive_diag_profiles_stag(amrex::Real time, amrex::Gpu::HostVector< amrex::Real > &h_avg_u, amrex::Gpu::HostVector< amrex::Real > &h_avg_v, amrex::Gpu::HostVector< amrex::Real > &h_avg_w, amrex::Gpu::HostVector< amrex::Real > &h_avg_rho, amrex::Gpu::HostVector< amrex::Real > &h_avg_th, amrex::Gpu::HostVector< amrex::Real > &h_avg_ksgs, amrex::Gpu::HostVector< amrex::Real > &h_avg_Kmv, amrex::Gpu::HostVector< amrex::Real > &h_avg_Khv, amrex::Gpu::HostVector< amrex::Real > &h_avg_qv, amrex::Gpu::HostVector< amrex::Real > &h_avg_qc, amrex::Gpu::HostVector< amrex::Real > &h_avg_qr, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqv, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqc, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqr, amrex::Gpu::HostVector< amrex::Real > &h_avg_qi, amrex::Gpu::HostVector< amrex::Real > &h_avg_qs, amrex::Gpu::HostVector< amrex::Real > &h_avg_qg, amrex::Gpu::HostVector< amrex::Real > &h_avg_uu, amrex::Gpu::HostVector< amrex::Real > &h_avg_uv, amrex::Gpu::HostVector< amrex::Real > &h_avg_uw, amrex::Gpu::HostVector< amrex::Real > &h_avg_vv, amrex::Gpu::HostVector< amrex::Real > &h_avg_vw, amrex::Gpu::HostVector< amrex::Real > &h_avg_ww, amrex::Gpu::HostVector< amrex::Real > &h_avg_uth, amrex::Gpu::HostVector< amrex::Real > &h_avg_vth, amrex::Gpu::HostVector< amrex::Real > &h_avg_wth, amrex::Gpu::HostVector< amrex::Real > &h_avg_thth, amrex::Gpu::HostVector< amrex::Real > &h_avg_ku, amrex::Gpu::HostVector< amrex::Real > &h_avg_kv, amrex::Gpu::HostVector< amrex::Real > &h_avg_kw, amrex::Gpu::HostVector< amrex::Real > &h_avg_p, amrex::Gpu::HostVector< amrex::Real > &h_avg_pu, amrex::Gpu::HostVector< amrex::Real > &h_avg_pv, amrex::Gpu::HostVector< amrex::Real > &h_avg_pw, amrex::Gpu::HostVector< amrex::Real > &h_avg_wthv)
Definition: ERF_Write1DProfiles_stag.cpp:296
ERF::ba1d
amrex::Vector< amrex::BoxArray > ba1d
Definition: ERF.H:1267
ERF::input_sponge_data
InputSpongeData input_sponge_data
Definition: ERF.H:771
ERF::subdomains
amrex::Vector< amrex::Vector< amrex::BoxArray > > subdomains
Definition: ERF.H:1357
ERF::check_state_for_nans
void check_state_for_nans(amrex::MultiFab const &S)
Definition: ERF.cpp:3139
ERF::restart_chkfile
std::string restart_chkfile
Definition: ERF.H:1055
ERF::metgrid_use_below_sfc
bool metgrid_use_below_sfc
Definition: ERF.H:1260
ERF::sampleptlogname
amrex::Vector< std::string > sampleptlogname
Definition: ERF.H:1616
ERF::xvel_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > xvel_bc_data
Definition: ERF.H:774
ERF::init_zphys
void init_zphys(int lev, amrex::Real elapsed_time)
Definition: ERF_MakeNewArrays.cpp:670
ERF::InitData_pre
void InitData_pre()
Definition: ERF.cpp:989
ERF::SamplePoint
amrex::IntVect & SamplePoint(int i)
Definition: ERF.H:1484
ERF::use_datetime
bool use_datetime
Definition: ERF.H:1051
ERF::hurricane_track_xy
amrex::Vector< std::array< amrex::Real, 2 > > hurricane_track_xy
Definition: ERF.H:156
ERF::h_u_geos
amrex::Vector< amrex::Vector< amrex::Real > > h_u_geos
Definition: ERF.H:1302
ERF::InitializeLevelFromData
void InitializeLevelFromData(int lev, const amrex::MultiFab &initial_data)
ERF::subvol_file
std::string subvol_file
Definition: ERF.H:1083
ERF::m_subvol_per
amrex::Vector< amrex::Real > m_subvol_per
Definition: ERF.H:1091
ERF::rad_datalog_int
int rad_datalog_int
Definition: ERF.H:897
ERF::sum_derived_quantities
void sum_derived_quantities(amrex::Real time)
Definition: ERF_WriteScalarProfiles.cpp:177
ERF::sum_integrated_quantities
void sum_integrated_quantities(amrex::Real time)
Definition: ERF_WriteScalarProfiles.cpp:15
ERF::datalogname
amrex::Vector< std::string > datalogname
Definition: ERF.H:1611
ERF::initHSE
void initHSE()
Initialize HSE.
Definition: ERF_Init1D.cpp:186
ERF::column_loc_x
static amrex::Real column_loc_x
Definition: ERF.H:1279
ERF::surface_state_2
amrex::Vector< amrex::MultiFab > surface_state_2
Definition: ERF.H:167
ERF::ax
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ax
Definition: ERF.H:942
ERF::z_phys_nd
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_nd
Definition: ERF.H:938
ERF::MakeDiagnosticAverage
void MakeDiagnosticAverage(amrex::Vector< amrex::Real > &h_havg, amrex::MultiFab &S, int n)
Definition: ERF.cpp:2995
ERF::metgrid_proximity
amrex::Real metgrid_proximity
Definition: ERF.H:1263
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:1540
ERF::h_havg_temperature
amrex::Vector< amrex::Real > h_havg_temperature
Definition: ERF.H:1334
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:1615
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:158
ERF::detJ_cc_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > detJ_cc_src
Definition: ERF.H:948
ERF::d_havg_pressure
amrex::Gpu::DeviceVector< amrex::Real > d_havg_pressure
Definition: ERF.H:1341
ERF::plot2d_file_1
std::string plot2d_file_1
Definition: ERF.H:1081
ERF::der_datalogname
amrex::Vector< std::string > der_datalogname
Definition: ERF.H:1612
ERF::SmnSmn_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SmnSmn_lev
Definition: ERF.H:911
ERF::derived_names
const amrex::Vector< std::string > derived_names
Definition: ERF.H:1123
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:950
ERF::sample_points
void sample_points(int lev, amrex::Real time, amrex::IntVect cell, amrex::MultiFab &mf)
Definition: ERF_WriteScalarProfiles.cpp:528
ERF::DataLog
AMREX_FORCE_INLINE std::ostream & DataLog(int i)
Definition: ERF.H:1428
ERF::writeJobInfo
void writeJobInfo(const std::string &dir) const
Definition: ERF_WriteJobInfo.cpp:10
ERF::MakeVTKFilename_EyeTracker_xy
std::string MakeVTKFilename_EyeTracker_xy(int nstep)
Definition: ERF_TrackerOutput.cpp:38
ERF::ComputeDt
void ComputeDt(int step=-1)
Definition: ERF_ComputeTimestep.cpp:11
ERF::nsubsteps
amrex::Vector< int > nsubsteps
Definition: ERF.H:807
ERF::yflux_imask
amrex::Vector< std::unique_ptr< amrex::iMultiFab > > yflux_imask
Definition: ERF.H:1009
ERF::rW_new
amrex::Vector< amrex::MultiFab > rW_new
Definition: ERF.H:857
ERF::weather_forecast_data_2
amrex::Vector< amrex::MultiFab > weather_forecast_data_2
Definition: ERF.H:162
ERF::lon_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > lon_m
Definition: ERF.H:763
ERF::m_w2d
std::unique_ptr< WriteBndryPlanes > m_w2d
Definition: ERF.H:1347
ERF::SampleLineLog
AMREX_FORCE_INLINE std::ostream & SampleLineLog(int i)
Definition: ERF.H:1471
ERF::lsm_flux
amrex::Vector< amrex::Vector< amrex::MultiFab * > > lsm_flux
Definition: ERF.H:883
ERF::plot3d_var_names_1
amrex::Vector< std::string > plot3d_var_names_1
Definition: ERF.H:1112
ERF::SamplePointLogName
std::string SamplePointLogName(int i) const noexcept
The filename of the ith sampleptlog file.
Definition: ERF.H:1628
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:1013
ERF::refinement_criteria_setup
void refinement_criteria_setup()
Definition: ERF_Tagging.cpp:375
ERF::apply_gaussian_smoothing_to_perturbations
void apply_gaussian_smoothing_to_perturbations(const int lev, amrex::MultiFab &cons_pert, amrex::MultiFab &xvel_pert, amrex::MultiFab &yvel_pert, amrex::MultiFab &zvel_pert)
Definition: ERF_InitCustomPertState.cpp:178
ERF::nghost_eb_volume
static int nghost_eb_volume()
Definition: ERF.H:1650
ERF::metgrid_debug_dry
bool metgrid_debug_dry
Definition: ERF.H:1255
ERF::ComputeGhostCells
static AMREX_FORCE_INLINE int ComputeGhostCells(const SolverChoice &sc)
Definition: ERF.H:1363
ERF::bndry_output_planes_interval
static int bndry_output_planes_interval
Definition: ERF.H:1285
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:1115
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:909
ERF::WriteSubvolume
void WriteSubvolume(int isub, amrex::Vector< std::string > subvol_var_names)
Definition: ERF_WriteSubvolume.cpp:145
ERF::nghost_eb_full
static int nghost_eb_full()
Definition: ERF.H:1653
ERF::RemakeLevel
void RemakeLevel(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: ERF_MakeNewLevel.cpp:539
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:861
ERF::metgrid_debug_isothermal
bool metgrid_debug_isothermal
Definition: ERF.H:1254
ERF::lsm_data_name
amrex::Vector< std::string > lsm_data_name
Definition: ERF.H:880
ERF::rhoqt_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > rhoqt_src
Definition: ERF.H:1297
ERF::initSponge
void initSponge()
Initialize sponge profiles.
Definition: ERF_InitSponge.cpp:35
ERF::plane_sampler
std::unique_ptr< PlaneSampler > plane_sampler
Definition: ERF.H:1606
ERF::check_for_low_temp
void check_for_low_temp(amrex::MultiFab &S)
Definition: ERF.cpp:3185
ERF::der_datalog
amrex::Vector< std::unique_ptr< std::fstream > > der_datalog
Definition: ERF.H:1609
ERF::have_read_nc_init_file
static amrex::Vector< amrex::Vector< int > > have_read_nc_init_file
Definition: ERF.H:1242
ERF::m_plot3d_per_2
amrex::Real m_plot3d_per_2
Definition: ERF.H:1094
ERF::advance_lsm
void advance_lsm(int lev, amrex::MultiFab &cons_in, amrex::MultiFab &xvel_in, amrex::MultiFab &yvel_in, const amrex::Real &dt_advance)
Definition: ERF_AdvanceLSM.cpp:5
ERF::tot_e_datalog
amrex::Vector< std::unique_ptr< std::fstream > > tot_e_datalog
Definition: ERF.H:1610
ERF::sinPhi_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > sinPhi_m
Definition: ERF.H:765
ERF::derive_diag_profiles
void derive_diag_profiles(amrex::Real time, amrex::Gpu::HostVector< amrex::Real > &h_avg_u, amrex::Gpu::HostVector< amrex::Real > &h_avg_v, amrex::Gpu::HostVector< amrex::Real > &h_avg_w, amrex::Gpu::HostVector< amrex::Real > &h_avg_rho, amrex::Gpu::HostVector< amrex::Real > &h_avg_th, amrex::Gpu::HostVector< amrex::Real > &h_avg_ksgs, amrex::Gpu::HostVector< amrex::Real > &h_avg_Kmv, amrex::Gpu::HostVector< amrex::Real > &h_avg_Khv, amrex::Gpu::HostVector< amrex::Real > &h_avg_qv, amrex::Gpu::HostVector< amrex::Real > &h_avg_qc, amrex::Gpu::HostVector< amrex::Real > &h_avg_qr, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqv, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqc, amrex::Gpu::HostVector< amrex::Real > &h_avg_wqr, amrex::Gpu::HostVector< amrex::Real > &h_avg_qi, amrex::Gpu::HostVector< amrex::Real > &h_avg_qs, amrex::Gpu::HostVector< amrex::Real > &h_avg_qg, amrex::Gpu::HostVector< amrex::Real > &h_avg_uu, amrex::Gpu::HostVector< amrex::Real > &h_avg_uv, amrex::Gpu::HostVector< amrex::Real > &h_avg_uw, amrex::Gpu::HostVector< amrex::Real > &h_avg_vv, amrex::Gpu::HostVector< amrex::Real > &h_avg_vw, amrex::Gpu::HostVector< amrex::Real > &h_avg_ww, amrex::Gpu::HostVector< amrex::Real > &h_avg_uth, amrex::Gpu::HostVector< amrex::Real > &h_avg_vth, amrex::Gpu::HostVector< amrex::Real > &h_avg_wth, amrex::Gpu::HostVector< amrex::Real > &h_avg_thth, amrex::Gpu::HostVector< amrex::Real > &h_avg_ku, amrex::Gpu::HostVector< amrex::Real > &h_avg_kv, amrex::Gpu::HostVector< amrex::Real > &h_avg_kw, amrex::Gpu::HostVector< amrex::Real > &h_avg_p, amrex::Gpu::HostVector< amrex::Real > &h_avg_pu, amrex::Gpu::HostVector< amrex::Real > &h_avg_pv, amrex::Gpu::HostVector< amrex::Real > &h_avg_pw, amrex::Gpu::HostVector< amrex::Real > &h_avg_wthv)
Definition: ERF_Write1DProfiles.cpp:190
ERF::real_width
int real_width
Definition: ERF.H:1246
ERF::MakeNewLevelFromCoarse
void MakeNewLevelFromCoarse(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
Definition: ERF_MakeNewLevel.cpp:281
ERF::last_subvol_step
amrex::Vector< int > last_subvol_step
Definition: ERF.H:1030
ERF::ax_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ax_src
Definition: ERF.H:949
ERF::urb_frac_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > urb_frac_lev
Definition: ERF.H:921
ERF::z_phys_cc_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > z_phys_cc_src
Definition: ERF.H:947
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:1303
ERF::Define_ERFFillPatchers
void Define_ERFFillPatchers(int lev)
Definition: ERF.cpp:3067
ERF::NumDataLogs
AMREX_FORCE_INLINE int NumDataLogs() noexcept
Definition: ERF.H:1442
ERF::plotfile3d_type_2
static PlotFileType plotfile3d_type_2
Definition: ERF.H:1228
ERF::setRecordEnergyDataInfo
void setRecordEnergyDataInfo(int i, const std::string &filename)
Definition: ERF.H:1553
ERF::turbPert
TurbulentPerturbation turbPert
Definition: ERF.H:1183
ERF::rW_old
amrex::Vector< amrex::MultiFab > rW_old
Definition: ERF.H:856
ERF::forecast_state_2
amrex::Vector< amrex::Vector< amrex::MultiFab > > forecast_state_2
Definition: ERF.H:164
ERF::check_for_negative_theta
void check_for_negative_theta(amrex::MultiFab &S)
Definition: ERF.cpp:3220
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:1882
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:816
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:1349
ERF::plotfile2d_type_2
static PlotFileType plotfile2d_type_2
Definition: ERF.H:1230
ERF::plane_sampling_interval
int plane_sampling_interval
Definition: ERF.H:1602
ERF::ref_tags
static amrex::Vector< amrex::AMRErrorTag > ref_tags
Definition: ERF.H:1355
ERF::make_physbcs
void make_physbcs(int lev)
Definition: ERF_MakeNewArrays.cpp:874
ERF::d_w_subsid
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > d_w_subsid
Definition: ERF.H:1300
ERF::FPr_w
amrex::Vector< ERFFillPatcher > FPr_w
Definition: ERF.H:905
ERF::SFS_hfx2_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_hfx2_lev
Definition: ERF.H:924
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:920
ERF::writeNow
bool writeNow(const amrex::Real cur_time, const int nstep, const int plot_int, const amrex::Real plot_per, const amrex::Real dt_0, amrex::Real &last_file_time)
Definition: ERF.cpp:3118
ERF::zlevels_stag
amrex::Vector< amrex::Vector< amrex::Real > > zlevels_stag
Definition: ERF.H:935
ERF::NumDerDataLogs
AMREX_FORCE_INLINE int NumDerDataLogs() noexcept
Definition: ERF.H:1449
ERF::EBFactory
amrex::EBFArrayBoxFactory const & EBFactory(int lev) const noexcept
Definition: ERF.H:1642
ERF::lsm_data
amrex::Vector< amrex::Vector< amrex::MultiFab * > > lsm_data
Definition: ERF.H:881
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:970
ERF::use_real_time_in_pltname
bool use_real_time_in_pltname
Definition: ERF.H:1233
ERF::m_plot2d_int_1
int m_plot2d_int_1
Definition: ERF.H:1087
ERF::WriteCheckpointFile
void WriteCheckpointFile() const
Definition: ERF_Checkpoint.cpp:26
ERF::output_1d_column
static int output_1d_column
Definition: ERF.H:1276
ERF::metgrid_debug_psfc
bool metgrid_debug_psfc
Definition: ERF.H:1256
ERF::az_src
amrex::Vector< std::unique_ptr< amrex::MultiFab > > az_src
Definition: ERF.H:951
ERF::fixed_mri_dt_ratio
static int fixed_mri_dt_ratio
Definition: ERF.H:1068
ERF::create_random_perturbations
void create_random_perturbations(const int lev, amrex::MultiFab &cons_pert, amrex::MultiFab &xvel_pert, amrex::MultiFab &yvel_pert, amrex::MultiFab &zvel_pert)
Definition: ERF_InitCustomPertState.cpp:156
ERF::dt
amrex::Vector< amrex::Real > dt
Definition: ERF.H:812
ERF::init_shrink
static amrex::Real init_shrink
Definition: ERF.H:1060
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:318
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:1062
ERF::is_it_time_for_action
static bool is_it_time_for_action(int nstep, amrex::Real time, amrex::Real dt, int action_interval, amrex::Real action_per)
Definition: ERF_WriteScalarProfiles.cpp:654
ERF::nc_low_file
static std::string nc_low_file
Definition: ERF.H:1250
ERF::d_rayleigh_ptrs
amrex::Vector< amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > > d_rayleigh_ptrs
Definition: ERF.H:1326
ERF::InitData
void InitData()
Definition: ERF.cpp:980
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:978
ERF::cosPhi_m
amrex::Vector< std::unique_ptr< amrex::MultiFab > > cosPhi_m
Definition: ERF.H:765
ERF::ParameterSanityChecks
void ParameterSanityChecks()
Definition: ERF.cpp:2824
ERF::land_type_lev
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::iMultiFab > > > land_type_lev
Definition: ERF.H:919
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:163
ERF::cf_width
int cf_width
Definition: ERF.H:900
ERF::last_plot2d_file_step_1
static int last_plot2d_file_step_1
Definition: ERF.H:1020
ERF::zflux_imask
amrex::Vector< std::unique_ptr< amrex::iMultiFab > > zflux_imask
Definition: ERF.H:1010
ERF::m_expand_plotvars_to_unif_rr
bool m_expand_plotvars_to_unif_rr
Definition: ERF.H:1084
ERF::m_plot3d_per_1
amrex::Real m_plot3d_per_1
Definition: ERF.H:1093
ERF::Construct_ERFFillPatchers
void Construct_ERFFillPatchers(int lev)
Definition: ERF.cpp:3041
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:802
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:1059
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:1292
ERF::m_r2d
std::unique_ptr< ReadBndryPlanes > m_r2d
Definition: ERF.H:1348
ERF::ay
amrex::Vector< std::unique_ptr< amrex::MultiFab > > ay
Definition: ERF.H:943
ERF::qmoist
amrex::Vector< amrex::Vector< amrex::MultiFab * > > qmoist
Definition: ERF.H:864
ERF::SFS_q1fx1_lev
amrex::Vector< std::unique_ptr< amrex::MultiFab > > SFS_q1fx1_lev
Definition: ERF.H:926
ERF::getCPUTime
static amrex::Real getCPUTime()
Definition: ERF.H:1513
ERF::zvel_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > zvel_bc_data
Definition: ERF.H:776
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:879
ERF::change_max
static amrex::Real change_max
Definition: ERF.H:1061
ERF::AverageDownTo
void AverageDownTo(int crse_lev, int scomp, int ncomp)
Definition: ERF_AverageDown.cpp:36
ERF::setRecordSampleLineInfo
void setRecordSampleLineInfo(int i, int lev, amrex::IntVect &cell, const std::string &filename)
Definition: ERF.H:1583
ERF::Tau_EB
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > > Tau_EB
Definition: ERF.H:930
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:836
ERF::line_sampling_interval
int line_sampling_interval
Definition: ERF.H:1601
ERF::h_sinesq_stag_ptrs
amrex::Vector< amrex::Vector< amrex::Real > > h_sinesq_stag_ptrs
Definition: ERF.H:1323
ERF::detJ_cc_new
amrex::Vector< std::unique_ptr< amrex::MultiFab > > detJ_cc_new
Definition: ERF.H:954
ERF::domain_bc_type
amrex::Array< std::string, 2 *AMREX_SPACEDIM > domain_bc_type
Definition: ERF.H:993
ERF::yvel_bc_data
amrex::Vector< amrex::Gpu::DeviceVector< amrex::Real > > yvel_bc_data
Definition: ERF.H:775
ERF::writeBuildInfo
static void writeBuildInfo(std::ostream &os)
Definition: ERF_WriteJobInfo.cpp:144
ERF::phys_bc_type
amrex::GpuArray< ERF_BC, AMREX_SPACEDIM *2 > phys_bc_type
Definition: ERF.H:1005
ERF::check_file
std::string check_file
Definition: ERF.H:1106
ERF::samplepoint
amrex::Vector< amrex::IntVect > samplepoint
Definition: ERF.H:1617
ERF::surface_state_interp
amrex::Vector< amrex::MultiFab > surface_state_interp
Definition: ERF.H:168
ERF::h_havg_qv
amrex::Vector< amrex::Real > h_havg_qv
Definition: ERF.H:1336
ERF::last_subvol_time
amrex::Vector< amrex::Real > last_subvol_time
Definition: ERF.H:1031
ERF::weather_forecast_data_1
amrex::Vector< amrex::MultiFab > weather_forecast_data_1
Definition: ERF.H:162
ERF::print_usage
static void print_usage(MPI_Comm, std::ostream &)
Definition: ERF_ConsoleIO.cpp:26
ERF::rV_old
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Definition: ERF.H:854
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Definition: ERF.H:763
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Definition: ERF.H:1318
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Definition: ERF.H:1028
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Definition: ERF.H:1269
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Definition: ERF.H:1018
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Definition: ERF.H:1024
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Definition: ERF.H:1605
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Definition: ERF.H:977
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Definition: ERF.H:806
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Definition: ERF.H:1037
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Definition: ERF.H:1008
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Definition: ERF.H:1229
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Definition: ERF.H:1264
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Definition: ERF.H:981
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Definition: ERF_Checkpoint.cpp:466
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Definition: ERF.H:819
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Definition: ERF.H:844
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Definition: ERF_MakeNewLevel.cpp:885
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Definition: ERF.H:1227
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Definition: ERF.H:1090
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AMREX_FORCE_INLINE std::ostream & SamplePointLog(int i)
Definition: ERF.H:1457
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Definition: ERF_TrackerOutput.cpp:52
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Definition: ERF.H:999
ERF::tsk_lev
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Definition: ERF.H:915
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Definition: ERF.H:1566
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Definition: ERF.H:1277
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Definition: ERF.H:1086
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Definition: ERF.H:886
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Definition: ERF_InitTurbPert.cpp:32
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Definition: ERF_WriteScalarProfiles.cpp:564
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Definition: ERF.H:887
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Definition: ERF.cpp:2080
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Definition: ERF.H:1099
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Definition: ERF.H:837
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Definition: ERF.H:1116
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Definition: ERF_Checkpoint.cpp:1116
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Definition: ERF_TimeStep.cpp:17
LandSurface
Definition: ERF_LandSurface.H:15
eb_
Definition: ERF_EB.H:13
MicVar_Kess::pres
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Definition: ERF_Kessler.H:25
MicVar_Kess::qv
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Definition: ERF_Kessler.H:28
Vars::xvel
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Definition: ERF_IndexDefines.H:159
Vars::cons
@ cons
Definition: ERF_IndexDefines.H:158
Vars::zvel
@ zvel
Definition: ERF_IndexDefines.H:161
Vars::yvel
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Definition: ERF_IndexDefines.H:160
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:130
SolverChoice::use_num_diff
bool use_num_diff
Definition: ERF_DataStruct.H:1199
SolverChoice::advChoice
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Definition: ERF_DataStruct.H:1087
SolverChoice::terrain_type
static TerrainType terrain_type
Definition: ERF_DataStruct.H:1067
TurbulentPerturbation
Definition: ERF_TurbPertStruct.H:22