REMORA Class Reference

Class that stores all relevant simulation state data with methods for time stepping. More...

#include <REMORA.H>

Inheritance diagram for REMORA:

Collaboration diagram for REMORA:

Public Types
enum class	DriverAtmosForcingMode : int { State = 0 , Flux }

Public Member Functions
	REMORA ()
	REMORA (const amrex::RealBox &rb, int max_level_in, const amrex::Vector< int > &n_cell_in, int coord, const amrex::Vector< amrex::IntVect > &ref_ratio, const amrex::Array< int, AMREX_SPACEDIM > &is_per, std::string prefix)
virtual	~REMORA ()
void	Evolve ()
	Advance solution to final time.
void	WriteAtFinalTime ()
	Write checkpoint and plotfiles at end of simulation.
void	WriteAtIntermediateTime (int step, amrex::Real cur_time)
	Write checkpoint and plotfiles at intermediate point of simulation, if needed.
virtual void	ErrorEst (int lev, amrex::TagBoxArray &tags, amrex::Real time, int ngrow) override
	Tag cells for refinement.
void	InitData ()
	Initialize multilevel data.
amrex::Real	EvolveOneStep (amrex::Real time, amrex::Real dt_request)
void	SetStartTime (amrex::Real time) noexcept
void	ConfigureDriverAtmosToOceanCoupling (bool use_coupling_driver, bool use_two_way_coupling, DriverAtmosForcingMode active_mode)
void	SetDriverAtmosToOceanForcingMode (DriverAtmosForcingMode mode)
void	SetLongwaveFromDriver ()
void	GetDeckConfiguredAtmosStateLanes (std::array< bool, AtmosState::NumTypes > &deck_configured) const
void	GetAtmosToOceanRhoLayout (amrex::BoxArray &ba, amrex::DistributionMapping &dm) const
void	GetAtmosToOceanUFaceLayout (amrex::BoxArray &ba, amrex::DistributionMapping &dm) const
void	GetAtmosToOceanVFaceLayout (amrex::BoxArray &ba, amrex::DistributionMapping &dm) const
void	GetAtmosToOceanPsiCoordinates (const amrex::MultiFab *&x_psi, const amrex::MultiFab *&y_psi) const
void	GetAtmosToOceanPsiLonLat (const amrex::MultiFab *&lon_psi, const amrex::MultiFab *&lat_psi) const
void	GetLandSeaMasks (const amrex::MultiFab *&mskr, const amrex::MultiFab *&msku, const amrex::MultiFab *&mskv) const
void	init_only (int lev, amrex::Real time)
	Init (NOT restart or regrid)
void	restart ()
void	post_timestep (int nstep, amrex::Real time, amrex::Real dt_lev)
	Called after every level 0 timestep.
void	PackSurfaceState (amrex::Vector< amrex::MultiFab * > &state, amrex::Real time, const amrex::MultiFab *weight_o2a_mf, const amrex::iMultiFab *index_o2a_mf, int max_stencil_size, const amrex::iMultiFab *dst_land_mask=nullptr)
	Extracts SST from the 3D conservative state for the atmospheric driver.
void	ApplyAtmosphericStates (const amrex::Vector< amrex::MultiFab * > &states, amrex::Real time)
	Receives atmospheric states from the driver and applies unit conversions.
void	ApplyAtmosphericFluxes (const amrex::Vector< amrex::MultiFab * > &states, amrex::Real time)
	Receives atmospheric flux lanes from the driver and assembles REMORA flux inputs.
void	sum_integrated_quantities (amrex::Real time)
	Integrate conserved quantities for diagnostics.
amrex::Real	volWgtSumMF (int lev, const amrex::MultiFab &mf, int comp, bool local, bool finemask)
	Perform the volume-weighted sum.
bool	is_it_time_for_action (int nstep, amrex::Real time, amrex::Real dt, int action_interval, amrex::Real action_per)
	Decide if it is time to take an action.
virtual void	MakeNewLevelFromCoarse (int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
	Make a new level using provided BoxArray and DistributionMapping and fill with interpolated coarse level data. Overrides the pure virtual function in AmrCore.
virtual void	RemakeLevel (int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
	Remake an existing level using provided BoxArray and DistributionMapping and fill with existing fine and coarse data. Overrides the pure virtual function in AmrCore.
virtual void	ClearLevel (int lev) override
	Delete level data Overrides the pure virtual function in AmrCore.
virtual void	MakeNewLevelFromScratch (int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override
	Make a new level from scratch using provided BoxArray and DistributionMapping. Only used during initialization. Overrides the pure virtual function in AmrCore.
void	set_grid_scale (int lev)
	Set pm and pn arrays and x/y coords on level lev.
void	set_grid_coords_from_grid_scale (int lev)
	Set x/y coords on level lev based on pm and pn.
void	set_curvilinear_terms_from_grid_scale (int lev)
	Set curvilinear derivative terms on level lev based on pm and pn.
void	set_grid_vars_averaged_down (int lev)
	Set pm/pn by averaging down from higher-resolution grid.
void	set_zeta_to_Ztavg (int lev, bool apply_eminusp=true)
	Set zeta components to be equal to time-averaged Zt_avg1.
void	calculate_nodal_masks (int lev)
	Calculate u-, v-, and psi-point masks based on rho-point masks after analytic initialization.
void	fill_3d_masks (int lev)
	Copy maskr to all z levels.
amrex::Real	estTimeStep (int lev) const
	compute dt from CFL considerations
void	remora_advance (int level, amrex::MultiFab &cons_old, amrex::MultiFab &cons_new, amrex::MultiFab &xvel_old, amrex::MultiFab &yvel_old, amrex::MultiFab &zvel_old, amrex::MultiFab &xvel_new, amrex::MultiFab &yvel_new, amrex::MultiFab &zvel_new, amrex::MultiFab &source, const amrex::Geometry fine_geom, const amrex::Real dt, const amrex::Real time)
	Interface for advancing the data at one level by one "slow" timestep.
amrex::MultiFab &	build_fine_mask (int lev)
	Make mask to zero out covered cells (for mesh refinement)
void	WritePlotFile (int istep)
	main driver for writing AMReX plotfiles
void	WriteMultiLevelPlotfileWithBathymetry (const std::string &plotfilename, int nlevels, const amrex::Vector< const amrex::MultiFab * > &mf, const amrex::Vector< const amrex::MultiFab * > &mf_nd, const amrex::Vector< const amrex::MultiFab * > &mf_u, const amrex::Vector< const amrex::MultiFab * > &mf_v, const amrex::Vector< const amrex::MultiFab * > &mf_w, const amrex::Vector< const amrex::MultiFab * > &mf_2d_rho, const amrex::Vector< const amrex::MultiFab * > &mf_2d_u, const amrex::Vector< const amrex::MultiFab * > &mf_2d_v, const amrex::Vector< std::string > &varnames_3d, const amrex::Vector< std::string > &varnames_2d_rho, const amrex::Vector< std::string > &varnames_2d_u, const amrex::Vector< std::string > &varnames_2d_v, const amrex::Vector< amrex::Geometry > &my_geom, amrex::Real time, const amrex::Vector< int > &level_steps, const amrex::Vector< amrex::IntVect > &rr, 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
	write out particular data to an AMReX plotfile
void	WriteGenericPlotfileHeaderWithBathymetry (std::ostream &HeaderFile, int nlevels, const amrex::Vector< amrex::BoxArray > &bArray, const amrex::Vector< std::string > &varnames_3d, const amrex::Vector< std::string > &varnames_2d_rho, const amrex::Vector< std::string > &varnames_2d_u, const amrex::Vector< std::string > &varnames_2d_v, const amrex::Vector< amrex::Geometry > &my_geom, amrex::Real time, const amrex::Vector< int > &level_steps, const amrex::Vector< amrex::IntVect > &rr, const std::string &versionName, const std::string &levelPrefix, const std::string &mfPrefix) const
	write out header data for an AMReX plotfile
void	Advance (int lev, amrex::Real time, amrex::Real dt_lev, int iteration, int ncycle)
	advance a single level for a single time step
void	setup_step (int lev, amrex::Real time, amrex::Real dt_lev)
	Set everything up for a step on a level.
void	advance_3d_ml (int lev, amrex::Real dt_lev)
	3D advance on a single level
void	advance_2d_onestep (int lev, amrex::Real dt_lev, amrex::Real dtfast_lev, int my_iif, int nfast_counter)
	2D advance, one predictor/corrector step
void	advance_2d (int lev, amrex::MultiFab const *mf_rhoS, amrex::MultiFab const *mf_rhoA, amrex::MultiFab *mf_ru2d, amrex::MultiFab *mf_rv2d, amrex::MultiFab *mf_rufrc, amrex::MultiFab *mf_rvfrc, amrex::MultiFab *mf_Zt_avg1, std::unique_ptr< amrex::MultiFab > &mf_DU_avg1, std::unique_ptr< amrex::MultiFab > &mf_DU_avg2, std::unique_ptr< amrex::MultiFab > &mf_DV_avg1, std::unique_ptr< amrex::MultiFab > &mf_DV_avg2, std::unique_ptr< amrex::MultiFab > &mf_rubar, std::unique_ptr< amrex::MultiFab > &mf_rvbar, std::unique_ptr< amrex::MultiFab > &mf_rzeta, std::unique_ptr< amrex::MultiFab > &mf_ubar, std::unique_ptr< amrex::MultiFab > &mf_vbar, amrex::MultiFab *mf_zeta, amrex::MultiFab const *mf_h, amrex::MultiFab const *mf_pm, amrex::MultiFab const *mf_pn, amrex::MultiFab const *mf_fcor, amrex::MultiFab const *mf_visc2_p, amrex::MultiFab const *mf_visc2_r, amrex::MultiFab const *mf_mskr, amrex::MultiFab const *mf_msku, amrex::MultiFab const *mf_mskv, amrex::MultiFab const *mf_mskp, amrex::Real dtfast_lev, bool predictor_2d_step, bool first_2d_step, int my_iif, int &next_indx1)
	Perform a 2D predictor (predictor_2d_step=True) or corrector (predictor_2d_step=False) step.
void	advance_3d (int lev, amrex::MultiFab &mf_cons, amrex::MultiFab &mf_u, amrex::MultiFab &mf_v, amrex::MultiFab *mf_sstore, amrex::MultiFab *mf_ru, amrex::MultiFab *mf_rv, std::unique_ptr< amrex::MultiFab > &mf_DU_avg1, std::unique_ptr< amrex::MultiFab > &mf_DU_avg2, std::unique_ptr< amrex::MultiFab > &mf_DV_avg1, std::unique_ptr< amrex::MultiFab > &mf_DV_avg2, std::unique_ptr< amrex::MultiFab > &mf_ubar, std::unique_ptr< amrex::MultiFab > &mf_vbar, std::unique_ptr< amrex::MultiFab > &mf_Akv, std::unique_ptr< amrex::MultiFab > &mf_Akt, std::unique_ptr< amrex::MultiFab > &mf_Hz, std::unique_ptr< amrex::MultiFab > &mf_Huon, std::unique_ptr< amrex::MultiFab > &mf_Hvom, std::unique_ptr< amrex::MultiFab > &mf_z_w, amrex::MultiFab const *mf_h, amrex::MultiFab const *mf_pm, amrex::MultiFab const *mf_pn, amrex::MultiFab const *mf_mskr, amrex::MultiFab const *mf_msku, amrex::MultiFab const *mf_mskv, const int N, const amrex::Real dt_lev)
	Advance the 3D variables.
void	advance_biology (int lev, amrex::MultiFab const &mf_cons_old, amrex::MultiFab &mf_cons_new, int N, amrex::Real dt_lev)
	Apply biological tracer source/sink terms.
void	bulk_fluxes (int lev, amrex::MultiFab *mf_cons, amrex::MultiFab *mf_uwind, amrex::MultiFab *mf_vwind, amrex::MultiFab *mf_Tair, amrex::MultiFab *mf_qair, amrex::MultiFab *mf_Pair, amrex::MultiFab *mf_srflx, amrex::MultiFab *mf_longwave_down, amrex::MultiFab *mf_evap, amrex::MultiFab *mf_sustr, amrex::MultiFab *mf_svstr, amrex::MultiFab *mf_stflux, amrex::MultiFab *mf_lrflx, amrex::MultiFab *mf_lhflx, amrex::MultiFab *mf_shflx, const int N)
	Calculate bulk temperature, salinity, wind fluxes.
void	prestep (int lev, amrex::MultiFab &mf_uold, amrex::MultiFab &mf_vold, amrex::MultiFab &mf_u, amrex::MultiFab &mf_v, amrex::MultiFab *mf_ru, amrex::MultiFab *mf_rv, amrex::MultiFab &S_old, amrex::MultiFab &S_new, amrex::MultiFab &mf_W, amrex::MultiFab &mf_DC, const amrex::MultiFab *mf_z_r, const amrex::MultiFab *mf_z_w, const amrex::MultiFab *mf_h, const amrex::MultiFab *mf_pm, const amrex::MultiFab *mf_pn, const amrex::MultiFab *mf_sustr, const amrex::MultiFab *mf_svstr, const amrex::MultiFab *mf_bustr, const amrex::MultiFab *mf_bvstr, const amrex::MultiFab *mf_msku, const amrex::MultiFab *mf_mskv, const int iic, const int nfirst, const int nnew, int nstp, int nrhs, int N, const amrex::Real dt_lev)
	Wrapper function for prestep.
void	prestep_t_advection (int lev, const amrex::Box &tbx, const amrex::Box &gbx, const amrex::Array4< amrex::Real > &tempold, const amrex::Array4< amrex::Real > &tempcache, const amrex::Array4< amrex::Real > &Hz, const amrex::Array4< amrex::Real > &Huon, const amrex::Array4< amrex::Real > &Hvom, const amrex::Array4< amrex::Real > &W, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real > &sstore, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &h, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const amrex::Array4< int const > &river_pos, const amrex::Array4< amrex::Real const > &river_source, int iic, int ntfirst, int nrhs, int N, const amrex::Real dt_lev)
	Prestep advection calculations for the tracers.
void	rhs_t_3d (int lev, const amrex::Box &bx, const amrex::Array4< amrex::Real > &t, const amrex::Array4< amrex::Real const > &tempstore, const amrex::Array4< amrex::Real const > &Huon, const amrex::Array4< amrex::Real const > &Hvom, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &W, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &mskr, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const amrex::Array4< int const > &river_pos, const amrex::Array4< amrex::Real const > &river_source, int nrhs, int nnew, int N, const amrex::Real dt_lev)
	RHS terms for tracer.
void	rhs_uv_3d (int lev, const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real > &rufrc, const amrex::Array4< amrex::Real > &rvfrc, const amrex::Array4< amrex::Real const > &sustr, const amrex::Array4< amrex::Real const > &svstr, const amrex::Array4< amrex::Real const > &bustr, const amrex::Array4< amrex::Real const > &bvstr, const amrex::Array4< amrex::Real const > &Huon, const amrex::Array4< amrex::Real const > &Hvom, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &W, const amrex::Array4< amrex::Real > &FC, int nrhs, int N)
	RHS terms for 3D momentum.
void	rhs_uv_2d (int lev, const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &Duon, const amrex::Array4< amrex::Real const > &Dvom, const int nrhs)
	RHS terms for 2D momentum.
void	rho_eos (const amrex::Box &bx, const amrex::Array4< amrex::Real const > &state, const amrex::Array4< amrex::Real > &rho, const amrex::Array4< amrex::Real > &rhoA, const amrex::Array4< amrex::Real > &rhoS, const amrex::Array4< amrex::Real > &bvf, const amrex::Array4< amrex::Real > &alpha, const amrex::Array4< amrex::Real > &beta, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &h, const amrex::Array4< amrex::Real const > &mskr, const int N)
	Wrapper around equation of state calculation.
void	lin_eos (const amrex::Box &bx, const amrex::Array4< amrex::Real const > &state, const amrex::Array4< amrex::Real > &rho, const amrex::Array4< amrex::Real > &rhoA, const amrex::Array4< amrex::Real > &rhoS, const amrex::Array4< amrex::Real > &bvf, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &h, const amrex::Array4< amrex::Real const > &mskr, const int N)
	Calculate density and related quantities from linear equation of state.
void	nonlin_eos (const amrex::Box &bx, const amrex::Array4< amrex::Real const > &state, const amrex::Array4< amrex::Real > &rho, const amrex::Array4< amrex::Real > &rhoA, const amrex::Array4< amrex::Real > &rhoS, const amrex::Array4< amrex::Real > &bvf, const amrex::Array4< amrex::Real > &alpha, const amrex::Array4< amrex::Real > &beta, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &h, const amrex::Array4< amrex::Real const > &mskr, const int N)
	Calculate density and related quantities from nonlinear equation of state.
void	prsgrd (const amrex::Box &bx, const amrex::Box &gbx, const amrex::Box &utbx, const amrex::Box &vtbx, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &rho, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const int nrhs, const int N)
	Calculate pressure gradient.
void	prestep_diffusion (const amrex::Box &bx, const amrex::Box &gbx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &vel, const amrex::Array4< amrex::Real const > &vel_old, const amrex::Array4< amrex::Real > &rvel, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &Akv, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &sstr, const amrex::Array4< amrex::Real const > &bstr, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const int iic, const int ntfirst, const int nnew, int nstp, int nrhs, int N, const amrex::Real lambda, const amrex::Real dt_lev)
	Update velocities or tracers with diffusion/viscosity as the last part of the prestep.
void	vert_visc_3d (const amrex::Box &bx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &phi, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real > &Hzk, const amrex::Array4< amrex::Real > &AK, const amrex::Array4< amrex::Real const > &Akv, const amrex::Array4< amrex::Real > &BC, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real > &CF, const int nnew, const int N, const amrex::Real dt_lev)
	Calculate effects of vertical viscosity or diffusivity.
void	update_massflux_3d (int lev, const amrex::Box &bx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &phi, const amrex::Array4< amrex::Real > &phibar, const amrex::Array4< amrex::Real > &Hphi, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm_or_pn, const amrex::Array4< amrex::Real const > &Dphi1, const amrex::Array4< amrex::Real const > &Dphi2, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &msk, const int nnew)
	Correct mass flux.
void	vert_mean_3d (const amrex::Box &bx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &phi, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &Dphi_avg1, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &CF, const amrex::Array4< amrex::Real const > &pm_or_pn, const amrex::Array4< amrex::Real const > &msk, const int nnew, const int N)
	Adjust 3D momentum variables based on vertical mean momentum.
void	uv3dmix (const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real > &u, const amrex::Array4< amrex::Real > &v, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &rufrc, const amrex::Array4< amrex::Real > &rvfrc, const amrex::Array4< amrex::Real const > &visc2_p, const amrex::Array4< amrex::Real const > &visc2_r, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &mskp, int nrhs, int nnew, const amrex::Real dt_lev)
	Harmonic viscosity.
void	t3dmix2 (const amrex::Box &bx, const amrex::Array4< amrex::Real > &state, const amrex::Array4< amrex::Real > &state_rhs, const amrex::Array4< amrex::Real const > &diff2, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const amrex::Real dt_lev, const int ncomp, const int N)
	Wrapper for harmonic diffusivity for tracers.
void	t3dmix2_s (const amrex::Box &bx, const amrex::Array4< amrex::Real > &state, const amrex::Array4< amrex::Real > &state_rhs, const amrex::Array4< amrex::Real const > &diff2, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const amrex::Real dt_lev, const int ncomp)
	Harmonic diffusivity for tracers along S-coordinate level surfaces.
void	t3dmix2_geo (const amrex::Box &bx, const amrex::Array4< amrex::Real > &state, const amrex::Array4< amrex::Real > &state_rhs, const amrex::Array4< amrex::Real const > &diff2, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const amrex::Real dt_lev, const int ncomp, const int N)
	Harmonic diffusivity for tracers along geopotential surfaces.
void	coriolis (const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &fomn, int nrhs, int nr)
	Calculate Coriolis terms.
void	curvilinear (const amrex::Box &bx, const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &dndx, const amrex::Array4< amrex::Real const > &dmde, int nrhs, int nr)
	Calculate curvilinear advection terms.
void	apply_clim_nudg (const amrex::Box &bx, int ioff, int joff, const amrex::Array4< amrex::Real > &var, const amrex::Array4< amrex::Real const > &var_old, const amrex::Array4< amrex::Real const > &var_clim, const amrex::Array4< amrex::Real const > &clim_coeff, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Real dt_lev=zero)
	Apply climatology nudging.
void	set_2darrays (int lev)
	Set 2D momentum arrays from 3D momentum.
void	set_zeta_average (int lev)
	Set Zt_avg1 to zeta.
void	set_zeta (int lev)
	Initialize zeta from file or analytic.
void	set_zeta_averaged_down (int lev)
	Copy over zeta data that has been averaged down from high res.
void	set_bathymetry (int lev)
	Initialize bathymetry from file or analytic.
void	set_bathymetry_averaged_down (int lev)
	Copy over bathymetry data that has been averaged down from high resolution input netcdf file.
void	set_coriolis (int lev)
	Initialize Coriolis factor from file or analytic.
void	set_masks (int lev)
	Initialize land-sea masks from file or analytic.
void	set_masks_averaged_down (int lev)
	Copy this level's land-sea mask out of the full-domain mask that was coarsened down from hires_grid_level.
void	coarsen_masks_with_grow_cells (int crse_lev)
	Coarsen the full-domain rho-mask from crse_lev+1 onto crse_lev, grow cells included, by the rule that a coarse cell is land only if all its fine cells are land.
void	coarsen_bathymetry_with_grow_cells (int crse_lev)
	Coarsen the full-domain bathymetry from crse_lev+1 onto crse_lev, grow cells included, weighted by the land/sea mask.
void	refine_masks_with_grow_cells (int fine_lev)
	Inject the full-domain rho-mask from fine_lev-1 onto fine_lev, piecewise constant, grow cells included.
void	ensure_full_domain_masks (int top_lev)
	Make sure the full-domain rho-mask exists on levels 0 through top_lev.
void	update_nodal_masks (int lev)
	Rebuild the u-, v- and psi-point masks from vec_mskr and fill their ghosts.
void	update_avgdown_masks (int crse_lev)
	Make sure the coarse masks the average-down kernels read sit on the coarsened layout of level crse_lev+1, rebuilding them if a regrid has moved it.
void	clear_avgdown_masks (int lev)
	Drop the cached average-down masks of every level pair that involves lev.
void	check_mask_consistency ()
	Check every level pair's masks against each other, and every level's mask values, reporting according to remora.mask_consistency.
void	stretch_transform (int lev)
	Calculate vertical stretched coordinates.
void	init_set_vmix (int lev)
	Initialize vertical mixing coefficients from file or analytic.
void	set_analytic_vmix (int lev)
	Set vertical mixing coefficients from analytic.
void	init_gls_vmix (int lev, SolverChoice solver_choice)
	Initialize GLS variables.
void	gls_prestep (int lev, amrex::MultiFab *mf_gls, amrex::MultiFab *mf_tke, amrex::MultiFab &mf_W, amrex::MultiFab *mf_msku, amrex::MultiFab *mf_mskv, const int nstp, const int nnew, const int iic, const int ntfirst, const int N, const amrex::Real dt_lev)
	Prestep for GLS calculation.
void	gls_corrector (int lev, amrex::MultiFab *mf_gls, amrex::MultiFab *mf_tke, amrex::MultiFab &mf_W, amrex::MultiFab *mf_Akv, amrex::MultiFab *mf_Akt, amrex::MultiFab *mf_Akk, amrex::MultiFab *mf_Akp, amrex::MultiFab *mf_mskr, amrex::MultiFab *mf_msku, amrex::MultiFab *mf_mskv, const int nstp, const int nnew, const int N, const amrex::Real dt_lev)
	Corrector step for GLS calculation.
void	scale_rhs_vars ()
	Scale RHS momentum variables by 1/cell area, needed before FillPatch to different levels.
void	scale_rhs_vars_inv ()
	Scale RHS momentum variables by cell area, needed after FillPatch to different levels.
void	set_smflux (int lev)
	Initialize or calculate surface momentum flux from file or analytic.
void	set_surface_state (int lev)
	Initialize or calculate wind speed and other surface state vars from file or analytic.
void	set_hmixcoef (int lev)
	Initialize horizontal mixing coefficients.
void	set_drag (int lev)
	Initialize or calculate bottom drag.
void	set_weights (int lev)
	Set weights for averaging 3D variables to 2D.
void	FillBdyCCVels (int lev, amrex::MultiFab &mf_cc_vel)
	Fill the physical boundary conditions for cell-centered velocity (diagnostic only)
void	FillPatch (int lev, amrex::Real time, amrex::MultiFab &mf_to_be_filled, amrex::Vector< amrex::MultiFab * > const &mfs, const int bccomp, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const bool fill_set=false, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=zero, const amrex::MultiFab &mf_calc=amrex::MultiFab())
	Fill a new MultiFab by copying in phi from valid region and filling ghost cells.
void	FillPatchNoBC (int lev, amrex::Real time, amrex::MultiFab &mf_to_be_filled, amrex::Vector< amrex::MultiFab * > const &mfs, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const bool fill_set=false)
	Fill a new MultiFab by copying in phi from valid region and filling ghost cells without applying boundary conditions.
void	fill_from_bdyfiles (int lev, amrex::MultiFab &mf_to_fill, const amrex::MultiFab &mf_mask, const amrex::Real time, const int bccomp, const int bdy_var_type, const int icomp_to_fill, const int icomp_calc=0, const amrex::MultiFab &mf_calc=amrex::MultiFab(), const amrex::Real=zero)
	Fill boundary data from netcdf file.
void	FillCoarsePatchPC (int lev, amrex::Real time, amrex::MultiFab *mf_fine, amrex::MultiFab *mf_crse, const int bccomp, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=zero, const amrex::MultiFab &mf_calc=amrex::MultiFab())
	fill an entire multifab by interpolating from the coarser level using the piecewise constant interpolater
void	FillCoarsePatch (int lev, amrex::Real time, amrex::MultiFab *mf_fine, amrex::MultiFab *mf_crse, const int bccomp, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=zero, const amrex::MultiFab &mf_calc=amrex::MultiFab())
	fill an entire multifab by interpolating from the coarser level
void	FillCoarsePatchMap (int lev, amrex::Real time, amrex::MultiFab *mf_fine, amrex::MultiFab *mf_crse, const int bccomp, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=zero, const amrex::MultiFab &mf_calc=amrex::MultiFab(), amrex::Interpolater *mapper=nullptr)
	fill an entire multifab by interpolating from the coarser level, explicitly specifying interpolator to use
void	init_stretch_coeffs ()
	initialize and calculate stretch coefficients
void	calc_stretch_coeffs ()
	calculate vertical stretch coefficients
void	init_beta_plane_coriolis (int lev)
	Calculate Coriolis parameters from beta plane parametrization.
void	init_bathymetry_full_domain_from_analytic ()
	Full domain bathymetry data initialization from analytic.
void	init_masks_full_domain_from_analytic ()
	Full domain land-sea mask initialization from analytic.
void	set_init_data_averaged_down (int lev)
	Problem initialization from averaged-down high resolution data.
void	init_data_from_netcdf (int lev)
	Problem initialization from NetCDF file.
void	init_biology_from_netcdf (int lev)
	Biology initialization from NetCDF file.
void	init_scalars_from_netcdf (int lev)
	Passive (dye) scalar initialization from NetCDF file. Called from init_data_from_netcdf: dye follows remora.ic_type rather than having a source flag of its own.
void	init_biology_ic (int lev)
	Initialize biology tracers from whichever source remora.biology_ic_type selects. Call after the physical fields exist: the analytic profiles are functions of temperature.
void	init_biology_ic_full_domain ()
	Full-domain counterpart of init_biology_ic, for the hires_init_level average-down path.
void	init_data_full_domain_from_netcdf ()
	High resolution roblem initialization from NetCDF file.
void	init_biology_full_domain_from_netcdf ()
	Full-domain high-res biology initialization from NetCDF file.
void	init_scalars_full_domain_from_netcdf ()
	Full-domain high-res passive (dye) scalar initialization from NetCDF file.
void	init_bdry_from_netcdf (int lev)
	Boundary data initialization from NetCDF file.
void	init_masks_from_netcdf (int lev)
	Mask data initialization from NetCDF file.
void	init_masks_full_domain_from_netcdf ()
	Full domain high-res mask data initialization from NetCDF file.
void	init_bathymetry_from_netcdf (int lev)
	Bathymetry data initialization from NetCDF file.
void	init_bathymetry_full_domain_from_netcdf ()
	Full domain high-res bathymetry data initialization from NetCDF file.
void	init_grid_vars_from_netcdf (int lev)
	Grid variable initialization from NetCDF file.
void	init_grid_vars_full_domain_from_netcdf ()
	Full domain high-res grid variable initialization from NetCDF file.
void	extrapolate_metric_to_physical_boundaries (amrex::MultiFab &mf, const amrex::Geometry &geom)
	Extrapolate grid metrics to edge of MultiFab.
void	init_zeta_from_netcdf (int lev)
	Sea-surface height data initialization from NetCDF file.
void	init_zeta_full_domain_from_netcdf ()
	Full-domain high res sea-surface height data initialization from NetCDF file.
void	init_coriolis_from_netcdf (int lev)
	Coriolis parameter data initialization from NetCDF file.
void	init_clim_nudg_coeff_from_netcdf (int lev)
	Climatology nudging coefficient initialization from NetCDF file.
void	init_clim_nudg_coeff (int lev)
	Wrapper to initialize climatology nudging coefficient.
void	init_riv_pos_from_netcdf (int lev)
const amrex::DistributionMapping &	full_domain_dmap ()
	The shared full-domain DistributionMapping, built on first use.
void	allocate_bathymetry_grid_vars_full_domain ()
	Allocate multifabs for storing full-domain bathymetry and grid vars data.
void	allocate_init_full_domain ()
	Allocate multifabs for storing full-domain high resolution initial data.
void	convert_inv_days_to_inv_s (amrex::MultiFab *)
	Convert data in a multifab from inverse days to inverse seconds.
void	mask_arrays_for_write (int lev, amrex::Real fill_value, amrex::Real fill_where)
	Mask data arrays before writing output.
void	average_down_with_grow_cells (int lev, amrex::Vector< std::unique_ptr< amrex::MultiFab > > &mf, bool use_mask=false)
	Average down from level lev+1 to lev in mf, including grow cells.
void	average_down_masked (int crse_lev, const amrex::MultiFab &S_fine, amrex::MultiFab &S_crse, const amrex::MultiFab &msk_fine, const amrex::MultiFab &cmsk, int ncomp, int face_dir)
	Average one field down a level, weighted by the land/sea mask.
int	xvel_bc () const noexcept
int	yvel_bc () const noexcept
int	zvel_bc () const noexcept
int	ubar_bc () const noexcept
int	vbar_bc () const noexcept
int	zeta_bc () const noexcept
int	tke_bc () const noexcept
int	foextrap_periodic_bc () const noexcept
int	foextrap_bc () const noexcept
int	u2d_simple_bc () const noexcept
int	v2d_simple_bc () const noexcept
int	num_bc_vars () const noexcept
int	num_passive_scalars () const noexcept
	Number of passive (dye) scalars in the state, not counting biology tracers.
void	writeJobInfo (const std::string &dir) const
	Write job info to stdout.
amrex::Real	get_t_old (int lev) const
	Accessor method for t_old to expose to outside classes.
int	bio_comp_start () const noexcept
	First cons component of the biology block. Problem setups need this to write biology initial conditions, since the passive scalars sit between salinity and the biology tracers.
int	num_bio () const noexcept
	Number of biology tracers carried in the state.
int	num_scalar () const noexcept
	Number of passive (dye) scalars carried in the state.
int	bdy_cons (int icomp) const noexcept
	Accessors for the ncons-dependent entries of BdyVars.
int	bdy_ubar () const noexcept
int	bdy_vbar () const noexcept
int	bdy_zeta () const noexcept
int	num_bdy_vars () const noexcept

Static Public Member Functions
static constexpr bool	DriverUsesStateForcing (DriverAtmosForcingMode mode) noexcept
static amrex::Box	clim_nudg_momentum_box (const amrex::Box &nodal_bx, int dir, const amrex::Box &domain, bool is_periodic)
	Shrink an x- or y-nodal momentum tilebox to the faces ROMS nudges.
static void	writeBuildInfo (std::ostream &os)
	Write build info to os.
static void	print_banner (MPI_Comm, std::ostream &)
static void	print_usage (MPI_Comm, std::ostream &)
static void	print_error (MPI_Comm, const std::string &msg)
static void	print_summary (std::ostream &)
static void	print_tpls (std::ostream &)
AMREX_GPU_HOST_DEVICE static AMREX_FORCE_INLINE amrex::Real	bulk_psiu (amrex::Real ZoL)
	Evaluate stability function psi for wind speed.
AMREX_GPU_HOST_DEVICE static AMREX_FORCE_INLINE amrex::Real	bulk_psit (amrex::Real ZoL)
	Evaluate stability function psi for moisture and heat.

Public Attributes
std::string	pp_prefix {"remora"}
	default prefix for input file parameters
amrex::Vector< amrex::MultiFab * >	cons_old
	multilevel data container for last step's scalar data: temperature, salinity, passive tracer
amrex::Vector< amrex::MultiFab * >	xvel_old
	multilevel data container for last step's x velocities (u in ROMS)
amrex::Vector< amrex::MultiFab * >	yvel_old
	multilevel data container for last step's y velocities (v in ROMS)
amrex::Vector< amrex::MultiFab * >	zvel_old
	multilevel data container for last step's z velocities (largely unused; W stored separately)
amrex::Vector< amrex::MultiFab * >	cons_new
	multilevel data container for current step's scalar data: temperature, salinity, passive tracer
amrex::Vector< amrex::MultiFab * >	xvel_new
	multilevel data container for current step's x velocities (u in ROMS)
amrex::Vector< amrex::MultiFab * >	yvel_new
	multilevel data container for current step's y velocities (v in ROMS)
amrex::Vector< amrex::MultiFab * >	zvel_new
	multilevel data container for current step's z velocities (largely unused; W stored separately)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_cons_full_domain
	multilevel data container for high res initial data: temperature, salinity, passive tracer
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_xvel_full_domain
	multilevel data container for high res initial x velocities (u in ROMS)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_yvel_full_domain
	multilevel data container for high res initial y velocities (v in ROMS)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_h
	multilevel data container for current step's z velocities (largely unused; W stored separately)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_h_full_domain
	Bathymetry data on the whole domain at each potential level.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_mskr_full_domain
	Land/sea mask at cell centers on the whole domain at each potential level. Specified at hires_grid_level and coarsened down from there, so that a refined coastline and the bathymetry it goes with come from the same grid.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Hz
	Width of cells in the vertical (z-) direction (3D, Hz in ROMS)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Huon
	u-volume flux (3D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Hvom
	v-volume flux (3D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_ru
	u velocity RHS (3D, includes horizontal and vertical advection)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rv
	v velocity RHS (3D, includes horizontal and vertical advection)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_ru2d
	u velocity RHS (2D, includes horizontal and vertical advection)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rv2d
	v velocity RHS (2D, includes horizontal and vertical advection)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rufrc
	u velocity RHS, integrated, including advection and bottom/surface stresses (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rvfrc
	v velocity RHS, integrated, including advection and bottom/surface stresses (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Akv
	Vertical viscosity coefficient (3D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Akt
	Vertical diffusion coefficient (3D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_visc2_p
	Harmonic viscosity defined on the psi points (corners of horizontal grid cells)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_visc2_r
	Harmonic viscosity defined on the rho points (centers)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_diff2
	Harmonic diffusivity for temperature / salinity.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_z_r
	z coordinates at rho points (cell centers)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_z_w
	z coordinates at w points (faces between z-cells)
amrex::Gpu::DeviceVector< amrex::Real >	s_r
	Scaled vertical coordinate (range [0,1]) that transforms to z, defined at rho points (cell centers)
amrex::Gpu::DeviceVector< amrex::Real >	s_w
	Scaled vertical coordinate (range [0,1]) that transforms to z, defined at w-points (cell faces)
amrex::Gpu::DeviceVector< amrex::Real >	Cs_r
	Stretching coefficients at rho points.
amrex::Gpu::DeviceVector< amrex::Real >	Cs_w
	Stretching coefficients at w points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_z_phys_nd
	z coordinates at psi points (cell nodes)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Zt_avg1
	Average of the free surface, zeta (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_sustr
	Surface stress in the u direction.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_svstr
	Surface stress in the v direction.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_uwind
	Wind in the u direction, defined at rho-points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_vwind
	Wind in the v direction, defined at rho-points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Tair
	Air temperature [°C], defined at rho-points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_qair
	Specific humidity [kg/kg], defined at rho-points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Pair
	Air pressure [mb], defined at rho-points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_srflx
	Shortwave radiation flux [W/m²], defined at rho-points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_lrflx
	longwave radiation
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_longwave_down
	Downward longwave radiation.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_lhflx
	latent heat flux
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_shflx
	sensible heat flux
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_stflx
	Surface tracer flux; working arrays.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_stflux
	Surface tracer flux; input arrays.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_btflx
	Bottom tracer flux; working arrays.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_btflux
	Bottom tracer flux; input arrays.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rain
	precipitation rate [kg/m^2/s]
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_evap
	evaporation rate [kg/m^2/s]
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_cloud
	cloud cover fraction [0-1], defined at rho-points
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_EminusP
	evaporation minus precipitation [kg/m^2/s], defined at rho-points
std::array< bool, AtmosState::NumTypes >	driver_atmos_state_from_driver {}
	provenance flags for driver-supplied atmospheric forcing lanes
bool	running_with_coupling_driver = false
	True once REMORA has received forcing through the coupling driver.
bool	driver_uses_two_way_coupling = false
	Driver-level direction flag copied in before InitData.
DriverAtmosForcingMode	driver_atmos_forcing_mode = DriverAtmosForcingMode::State
	Active atmosphere-to-ocean forcing contract on the most recent driver apply.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rdrag
	Linear drag coefficient [m/s], defined at rho points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rdrag2
	Quadratic drag coefficient [unitless], defined at rho points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_ZoBot
	Bottom roughness length [m], defined at rho points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_bustr
	Bottom stress in the u direction.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_bvstr
	Bottom stress in the v direction.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_DU_avg1
	time average of barotropic x velocity flux (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_DU_avg2
	correct time average of barotropic x velocity flux for coupling (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_DV_avg1
	time average of barotropic y velocity flux
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_DV_avg2
	correct time average of barotropic y velocity flux for coupling (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rubar
	barotropic x velocity for the RHS (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rvbar
	barotropic y velocity for the RHS (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rzeta
	free surface height for the RHS (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_ubar
	barotropic x velocity (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_vbar
	barotropic y velocity (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_zeta
	free surface height (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_zeta_full_domain
	high resolution initial free surface height (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_mskr
	land/sea mask at cell centers (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_msku
	land/sea mask at x-faces (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_mskv
	land/sea mask at y-faces (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_mskp
	land/sea mask at cell corners (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_mskr3d
	land/sea mask at cell centers, copied to all z levels (3D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_mskr_crse_on_fine
	the level's rho-, u- and v-masks copied onto the layout of the level above it coarsened, which is the layout the two-way average-down computes on. Indexed by the coarse level of the pair. Built on demand and reused until a regrid, since the masks are a function of position alone and so do not change between them.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_msku_crse_on_fine
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_mskv_crse_on_fine
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_pm
	horizontal scaling factor: 1 / dx (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_pn
	horizontal scaling factor: 1 / dy (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_pm_full_domain
	horizontal scaling factor: 1 / dx (2D) on whole domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_pn_full_domain
	horizontal scaling factor: 1 / dy (2D) on whole domain
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_fcor
	coriolis factor (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_xr
	x_grid on rho points (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_yr
	y_grid on rho points (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_xu
	x_grid on u-points (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_yu
	y_grid on u-points (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_xv
	x_grid on v-points (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_yv
	y_grid on v-points (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_xp
	x_grid on psi-points (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_yp
	y_grid on psi-points (2D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_lonp
	longitude on psi-points (2D, degrees east); only filled when the grid NetCDF file carries lon_psi
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_latp
	latitude on psi-points (2D, degrees north); only filled when the grid NetCDF file carries lat_psi
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_dndx
	d(1/n)/d(xi)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_dmde
	d(1/m)/d(eta)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_sstore
	additional scratch space for calculations on temp, salt, etc
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rhoS
	density perturbation
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_rhoA
	vertically-averaged density
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_bvf
	Brunt-Vaisala frequency (3D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_alpha
	Thermal expansion coefficient (3D)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_beta
	Saline contraction coefficient (3D)
amrex::Vector< amrex::Real >	vec_weight1
	Weights for calculating avg1 in 2D advance.
amrex::Vector< amrex::Real >	vec_weight2
	Weights for calculating avg2 in 2D advance.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_tke
	Turbulent kinetic energy.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_gls
	Turbulent generic length scale.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Lscale
	Vertical mixing turbulent length scale.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Akk
	Turbulent kinetic energy vertical diffusion coefficient.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Akp
	Turbulent length scale vertical diffusion coefficient.
amrex::Vector< amrex::Vector< std::unique_ptr< amrex::MultiFab > > >	vec_nudg_coeff
	Climatology nudging coefficients.
amrex::DistributionMapping	dm_full_domain
	the DistributionMapping every full-domain multifab is built on. Each of those covers the domain in a single box, so the map holds one entry, and which rank it names is whichever holds the least fab memory when it is built. Building one per allocator therefore put the mask and the data it weights on different ranks under MPI. Empty until full_domain_dmap first needs it.

Static Public Attributes
static int	total_nc_plot_file_step = 1

Private Member Functions
void	ReadParameters ()
	read in some parameters from inputs file
void	init_scalar_metadata ()
	Build runtime scalar names after nscalar is known.
void	AverageDown ()
	set covered coarse cells to be the average of overlying fine cells
void	init_bcs ()
	Read in boundary parameters from input file and set up data structures.
void	init_analytic (int lev)
	Initialize initial problem data from analytic functions.
void	init_full_domain_from_analytic ()
	Initialize high resolution initial problem data from analytic functions.
void	init_full_domain_zeta_from_analytic ()
	Initialize high resolution initial sea surface height from analytic functions.
void	init_stuff (int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)
	Allocate MultiFabs for state and evolution variables.
void	init_masks (int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)
	Allocate MultiFabs for masks.
void	resize_stuff (int lev)
	Resize variable containers to accommodate data on levels 0 to max_lev.
void	AverageDownTo (int crse_lev)
	more flexible version of AverageDown() that lets you average down across multiple levels
void	Construct_REMORAFillPatchers (int lev)
	Construct FillPatchers.
void	Define_REMORAFillPatchers (int lev)
	Define FillPatchers.
TimeInterpolatedData	GetDataAtTime (int lev, amrex::Real time)
	utility to copy in data from old and/or new state into another multifab
void	timeStep (int lev, amrex::Real time, int iteration)
	advance a level by dt, includes a recursive call for finer levels
void	timeStepML (amrex::Real time, int iteration)
	advance all levels by dt, loops over finer levels
void	ComputeDt ()
	a wrapper for estTimeStep()
std::string	PlotFileName (int lev) const
	get plotfile name
void	set2DPlotVariables (const std::string &pp_plot_var_names_2d)
void	set3DPlotVariables (const std::string &pp_plot_var_names_3d)
void	append2DPlotVariables (const std::string &pp_plot_var_names_2d)
void	append3DPlotVariables (const std::string &pp_plot_var_names_3d)
void	WriteNCPlotFile (int istep, amrex::MultiFab const *plotMF)
	Write plotfile using NetCDF (wrapper)
void	WriteNCPlotFile_which (int lev, int which_subdomain, amrex::MultiFab const *plotMF, bool write_header, ncutils::NCFile &ncf, bool is_history)
	Write a particular NetCDF plotfile.
void	WriteNCMultiFab (const amrex::FabArray< amrex::FArrayBox > &fab, const std::string &name, bool set_ghost=false) const
	Write MultiFab in NetCDF format.
void	ReadNCMultiFab (amrex::FabArray< amrex::FArrayBox > &fab, const std::string &name, int coordinatorProc=amrex::ParallelDescriptor::IOProcessorNumber(), int allow_empty_mf=0)
	Read MultiFab in NetCDF format.
void	WriteCheckpointFile ()
	write checkpoint file to disk
void	ReadCheckpointFile ()
	read checkpoint file from disk
void	InitializeFromFile ()
	Read the file passed to remora.restart and use it as an initial condition for the current simulation.
void	InitializeLevelFromData (int lev, const amrex::MultiFab &initial_data)
	Initialize the new-time data at a level from the initial_data MultiFab.
void	refinement_criteria_setup ()
	Set refinement criteria.
void	init_ref_ratios ()
	Reject vertical refinement and accumulate the refinement ratios.
AMREX_FORCE_INLINE int	ComputeGhostCells (const int &spatial_order)
	Helper function to determine number of ghost cells.
AMREX_FORCE_INLINE std::ostream &	DataLog (int i)
	Helper function for IO stream.
AMREX_FORCE_INLINE int	NumDataLogs () noexcept
amrex::Real	getCPUTime () const
	Get CPU time used.
void	setRecordDataInfo (int i, const std::string &filename)
const std::string	DataLogName (int i) const noexcept
	The filename of the ith datalog file.

Static Private Member Functions
static void	GotoNextLine (std::istream &is)
	utility to skip to next line in Header

Private Attributes
std::unique_ptr< NCTimeSeries >	sustr_data_from_file
	Data container for u-component surface momentum flux read from file.
std::unique_ptr< NCTimeSeries >	svstr_data_from_file
	Data container for v-component surface momentum flux read from file.
std::unique_ptr< NCTimeSeries >	Uwind_data_from_file
	Data container for u-direction wind read from file.
std::unique_ptr< NCTimeSeries >	Vwind_data_from_file
	Data container for v-direction wind read from file.
std::unique_ptr< NCTimeSeries >	Tair_data_from_file
	Data container for air temperature read from file.
std::unique_ptr< NCTimeSeries >	qair_data_from_file
	Data container for specific humidity read from file.
std::unique_ptr< NCTimeSeries >	Pair_data_from_file
	Data container for air pressure read from file.
std::unique_ptr< NCTimeSeries >	srflx_data_from_file
	Data container for shortwave radiation flux read from file.
std::unique_ptr< NCTimeSeries >	longwave_down_data_from_file
	Data container for downward longwave radiation flux read from file.
std::unique_ptr< NCTimeSeries >	rain_data_from_file
	Data container for precipitation rate read from file.
std::unique_ptr< NCTimeSeries >	cloud_data_from_file
	Data container for cloud cover fraction read from file.
std::unique_ptr< NCTimeSeries >	EminusP_data_from_file
	Data container for evaporation minus precipitation read from file.
std::unique_ptr< NCTimeSeries >	ubar_clim_data_from_file
	Data container for ubar climatology data read from file.
std::unique_ptr< NCTimeSeries >	vbar_clim_data_from_file
	Data container for vbar climatology data read from file.
std::unique_ptr< NCTimeSeries >	u_clim_data_from_file
	Data container for u-velocity climatology data read from file.
std::unique_ptr< NCTimeSeries >	v_clim_data_from_file
	Data container for v-velocity climatology data read from file.
amrex::Vector< std::unique_ptr< NCTimeSeries > >	cons_clim_data_from_file
	Vector over cons components of climatology data read from file.
amrex::Vector< std::unique_ptr< NCTimeSeriesRiver > >	river_source_cons
	Vector of data containers for scalar data in rivers.
std::unique_ptr< NCTimeSeriesRiver >	river_source_transport
	Data container for momentum transport in rivers.
std::unique_ptr< NCTimeSeriesRiver >	river_source_transportbar
	Data container for vertically integrated momentum transport in rivers.
amrex::Vector< amrex::Vector< std::unique_ptr< NCTimeSeriesBoundary > > >	boundary_series
	Vector over BdyVars of boundary series data containers.
amrex::Vector< std::unique_ptr< amrex::iMultiFab > >	vec_river_position
	iMultiFab for river positions; contents are indices of rivers
amrex::Gpu::DeviceVector< int >	river_direction
	Vector over rivers of river direction: 0: u-face; 1: v-face; 2: w-face.
int	cf_width {0}
	Nudging width at coarse-fine interface.
int	cf_set_width {0}
	Width for fixing values at coarse-fine interface.
amrex::Vector< REMORAFillPatcher >	FPr_c
	Vector over levels of FillPatchers for scalars.
amrex::Vector< REMORAFillPatcher >	FPr_u
	Vector over levels of FillPatchers for u (3D)
amrex::Vector< REMORAFillPatcher >	FPr_v
	Vector over levels of FillPatchers for v (3D)
amrex::Vector< REMORAFillPatcher >	FPr_w
	Vector over levels of FillPatchers for w.
amrex::Vector< REMORAFillPatcher >	FPr_ubar
	Vector over levels of FillPatchers for ubar (2D)
amrex::Vector< REMORAFillPatcher >	FPr_vbar
	Vector over levels of FillPatchers for vbar (2D)
std::unique_ptr< ProblemBase >	prob = nullptr
	Pointer to container of analytical functions for problem definition.
amrex::Vector< int >	num_boxes_at_level
	how many boxes specified at each level by tagging criteria
amrex::Vector< int >	num_files_at_level
	how many netcdf input files specified at each level
amrex::Vector< amrex::Vector< amrex::Box > >	boxes_at_level
	the boxes specified at each level by tagging criteria
amrex::Vector< int >	istep
	which step?
amrex::Vector< int >	nsubsteps
	How many substeps on each level?
amrex::Vector< amrex::Real >	t_new
	new time at each level
amrex::Vector< amrex::Real >	t_old
	old time at each level
amrex::Vector< amrex::Real >	dt
	time step at each level
bool	set_bcs_by_var
	whether to set boundary conditions by variable rather than just by side
amrex::Vector< std::unique_ptr< REMORAPhysBCFunct > >	physbcs
	Vector (over level) of functors to apply physical boundary conditions.
amrex::Vector< std::unique_ptr< amrex::YAFluxRegister > >	advflux_reg
	array of flux registers for refluxing in multilevel
amrex::Vector< amrex::BCRec >	domain_bcs_type
	vector (over BCVars) of BCRecs
amrex::Gpu::DeviceVector< amrex::BCRec >	domain_bcs_type_d
	GPU vector (over BCVars) of BCRecs.
amrex::Array< std::string, 2 *AMREX_SPACEDIM >	domain_bc_type
	Array of strings describing domain boundary conditions.
amrex::Vector< amrex::GpuArray< amrex::Real, AMREX_SPACEDIM *2 > >	m_bc_extdir_vals
	Array holding the Dirichlet values at walls which need them.
amrex::Vector< amrex::GpuArray< REMORA_BC, AMREX_SPACEDIM *2 > >	phys_bc_type
	Array holding the "physical" boundary condition types (e.g. "inflow")
amrex::Vector< amrex::GpuArray< bool, AMREX_SPACEDIM *2 > >	phys_bc_need_data
	These are flags that indicate whether we need to read in boundary data from file.
amrex::Vector< int >	bdy_index
	Container to connect boundary data being read in boundary condition containers.
int	last_plot_file_step
	Step when we last output a plotfile.
amrex::Real	last_plot_file_time
	Simulation time when we last output a plotfile.
int	last_check_file_step
	Step when we last output a checkpoint file.
amrex::Real	last_check_file_time
	Simulation time when we last output a checkpoint file.
int	plot_file_on_restart = 1
	Whether to output a plotfile on restart from checkpoint.
int	max_step = std::numeric_limits<int>::max()
	maximum number of steps
amrex::Real	stop_time = std::numeric_limits<amrex::Real>::max()
	Whether max_step was set in the inputs; the default above is not a distinguishable sentinel.
amrex::Real	start_time = zero
	Time of the start of the simulation, in seconds.
std::string	restart_chkfile = ""
	If set, restart from this checkpoint file.
int	nscalar = 0
	Number of passive (dye) scalars carried in the state, beyond temperature and salinity. Does not count biology tracers. Dye is opt-in: a run carries one only when remora.nscalar asks for it.
int	nbio = 0
	Number of biology tracers, set by the active biology model. Zero when no biology model is active.
int	Bio_comp = Tracer_comp
	First cons component of the biology block, i.e. Tracer_comp + nscalar. The state is laid out as temp, salt, the passive scalars, then biology.
int	ncons = Tracer_comp + 1
	Number of conserved scalars in the state (temperature + salt + passive scalars + biology tracers)
REMORABiology::BiologyModel	biology_model = REMORABiology::BiologyModel::none
	Active biology package.
REMORABiology::FennelParameters	fennel_params
	Runtime parameters for the Fennel biology package.
REMORABiology::BiologyICType	biology_ic_type = REMORABiology::BiologyICType::follow_ic_type
	Source of the biology tracer initial condition, independent of remora.ic_type. Default follows ic_type.
int	use_biology_cpp_answer = 1
	Select the native C++ biology kernel (1) or the ROMS Fortran bridge oracle (0). Only meaningful when built with USE_FENNEL_FORT=TRUE; ignored otherwise. Runtime-controlled so the two paths can be compared without a rebuild.
int	biology_debug = 0
	Biology diagnostic verbosity: 0 off, 1 target column, 2 all columns. See Source/Biology/Fortran/tag_map.md.
int	biology_debug_i = 2
	Target column i index for biology_debug = 1.
int	biology_debug_j = 2
	Target column j index for biology_debug = 1.
int	nfast
	Number of fast steps to take.
int	do_substep = 0
	Whether to substep fine levels in time.
int	regrid_int = 2
	how often each level regrids the higher levels of refinement (after a level advances that many time steps)
std::string	plot_file_name {"plt_"}
	Plotfile prefix.
int	plot_int = -1
	Plotfile output interval in iterations.
amrex::Real	plot_int_time = amrex::Real(-one)
	Plotfile output interval in seconds.
std::string	check_file {"chk"}
	Checkpoint file prefix.
int	check_int = -1
	Checkpoint output interval in iterations.
amrex::Real	check_int_time = amrex::Real(-one)
	Checkpoint output interval in seconds.
bool	chunk_history_file = false
	Whether to split the netcdf history file into fixed-length chunks.
int	steps_per_history_file = -1
	Time steps per netcdf history file. Must be > 0 if chunk_history_file.
int	history_count = 0
	Counter for which time index we are writing to in the netcdf history file.
amrex::Vector< std::string >	plot_var_names_3d
	Names of 3D variables to output to AMReX plotfile.
amrex::Vector< std::string >	plot_var_names_2d
	Names of 2D variables to output to AMReX plotfile.
amrex::Vector< std::string >	cons_names {"temp", "salt", "tracer"}
	Names of scalars for plotfile output.
const amrex::Vector< std::string >	derived_names_3d {"vorticity"}
	Names of derived fields for 3d plotfile fields.
const amrex::Vector< std::string >	derived_names_2d {}
	Names of derived fields for 2d plotfile fields.
bool	expand_plotvars_to_unif_rr = false
	whether plotfile variables should be expanded to a uniform refinement ratio
amrex::Real	plotfile_fill_value = zero
	fill value for masked arrays in amrex plotfiles
amrex::Real	netcdf_fill_value = amrex::Real(1.0e37)
	fill value for masked arrays in netcdf output
int	hires_grid_level = -1
	Which level the high resolution bathymetry is at.
std::string	nc_grid_file_hires
	Grid file for high resolution bathymetry.
amrex::Box	nc_hires_grid_box
	Box for the full domain at nc_hires_grid_level.
int	hires_init_level = -1
	Which level the high resolution initialization data is at.
std::string	nc_init_file_hires
	Init file for high resolution.
amrex::Box	nc_hires_init_box
	Box for the full domain at nc_hires_init_level.
amrex::Vector< amrex::IntVect >	cum_ref_ratios
	Cumulative refinement ratio between level 0 and level i.
amrex::Vector< std::string >	nc_frc_file
	NetCDF forcing file(s)
amrex::Vector< std::string >	nc_riv_file
	NetCDF river file(s)
amrex::Vector< std::string >	nc_clim_his_file
	NetCDF climatology history file(s)
std::string	nc_clim_coeff_file
	NetCDF climatology coefficient file.
std::string	bdry_time_varname = "ocean_time"
	Default name of time field for boundary data.
amrex::Vector< std::string >	bdry_time_name_byvar
	Name of time fields for boundary data.
std::string	clim_ubar_time_varname = "ocean_time"
	Name of time field for ubar climatology data.
std::string	clim_vbar_time_varname = "ocean_time"
	Name of time field for vbar climatology data.
std::string	clim_u_time_varname = "ocean_time"
	Name of time field for u climatology data.
std::string	clim_v_time_varname = "ocean_time"
	Name of time field for v climatology data.
amrex::Vector< std::string >	clim_cons_time_varname
	Vector over cons components of the name of the time field for that tracer's climatology data.
std::string	riv_time_varname = "river_time"
	Name of time field for river time.
std::string	frc_time_varname = ""
	Name of time field for forcing data.
amrex::MultiFab	fine_mask
	Mask that zeroes out values on a coarse level underlying grids on the next finest level.
amrex::Vector< std::unique_ptr< std::fstream > >	datalog
amrex::Vector< std::string >	datalogname

Static Private Attributes
static bool	write_history_file = true
	Whether to output NetCDF files as a single history file with several time steps.
static amrex::Real	cfl = Real(0.8)
	CFL condition.
static amrex::Real	change_max = Real(1.1)
	Fraction maximum change in subsequent time steps.
static amrex::Real	fixed_dt = -one
	User specified fixed baroclinic time step.
static int	ndtfast = 0
	User specified, number of barotropic steps per baroclinic step.
static SolverChoice	solverChoice
	Container for algorithmic choices.
static int	verbose = 0
	Verbosity level of output.
static int	sum_interval = -1
	Diagnostic sum output interval in number of steps.
static amrex::Real	sum_per = -one
	Diagnostic sum output interval in time.
static int	file_min_digits = 5
	Minimum number of digits in plotfile name or chunked history file.
static bool	plot_staggered_vels = false
	Whether to write the staggered velocities (not averaged to cell centers)
static bool	plot_nodal_data = true
	Whether to write nodal data (Nu_nd) to plotfiles.
static PlotfileType	plotfile_type = PlotfileType::amrex
	Native or NetCDF plotfile output.
static amrex::Vector< amrex::Vector< std::string > >	nc_init_file = {{""}}
	NetCDF initialization file.
static amrex::Vector< amrex::Vector< std::string > >	nc_grid_file = {{""}}
	NetCDF grid file.
static amrex::Vector< std::string >	nc_bdry_file = {""}
	NetCDF boundary data.
static amrex::Vector< amrex::AMRErrorTag >	ref_tags
	Holds info for dynamically generated tagging criteria.
static amrex::Real	startCPUTime = zero
	Variable for CPU timing.
static amrex::Real	previousCPUTimeUsed = zero
	Accumulator variable for CPU time used thusfar.

Detailed Description

Class that stores all relevant simulation state data with methods for time stepping.

Definition at line 89 of file REMORA.H.

Member Enumeration Documentation

DriverAtmosForcingMode

enum class REMORA::DriverAtmosForcingMode : int

strong

Enumerator
State
Flux

Definition at line 93 of file REMORA.H.

Constructor & Destructor Documentation

REMORA() [1/2]

REMORA::REMORA

(

)

constructor:

• reads in parameters from inputs file
• sizes multilevel arrays and data structures
• initializes BCRec boundary condition object

Definition at line 69 of file REMORA.cpp.

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REMORA() [2/2]

REMORA::REMORA	(	const amrex::RealBox &	rb,
		int	max_level_in,
		const amrex::Vector< int > &	n_cell_in,
		int	coord,
		const amrex::Vector< amrex::IntVect > &	ref_ratio,
		const amrex::Array< int, AMREX_SPACEDIM > &	is_per,
		std::string	prefix
	)

Definition at line 148 of file REMORA.cpp.

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~REMORA()

REMORA::~REMORA ( )

virtual

Definition at line 211 of file REMORA.cpp.

Member Function Documentation

Advance()

void REMORA::Advance	(	int	lev,
		amrex::Real	time,
		amrex::Real	dt_lev,
		int	iteration,
		int	ncycle
	)

advance a single level for a single time step

Parameters

[in]	lev	level of refinement
[in]	time	simulation time at start of step
[in]	dt_lev	baroclinic time step at level
[in]	iteration	iteration in subcycling, if using
[in]	ncycle	total number of subcycles, if using

Definition at line 17 of file REMORA_Advance.cpp.

Referenced by timeStep().

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advance_2d()

void REMORA::advance_2d	(	int	lev,
		amrex::MultiFab const *	mf_rhoS,
		amrex::MultiFab const *	mf_rhoA,
		amrex::MultiFab *	mf_ru2d,
		amrex::MultiFab *	mf_rv2d,
		amrex::MultiFab *	mf_rufrc,
		amrex::MultiFab *	mf_rvfrc,
		amrex::MultiFab *	mf_Zt_avg1,
		std::unique_ptr< amrex::MultiFab > &	mf_DU_avg1,
		std::unique_ptr< amrex::MultiFab > &	mf_DU_avg2,
		std::unique_ptr< amrex::MultiFab > &	mf_DV_avg1,
		std::unique_ptr< amrex::MultiFab > &	mf_DV_avg2,
		std::unique_ptr< amrex::MultiFab > &	mf_rubar,
		std::unique_ptr< amrex::MultiFab > &	mf_rvbar,
		std::unique_ptr< amrex::MultiFab > &	mf_rzeta,
		std::unique_ptr< amrex::MultiFab > &	mf_ubar,
		std::unique_ptr< amrex::MultiFab > &	mf_vbar,
		amrex::MultiFab *	mf_zeta,
		amrex::MultiFab const *	mf_h,
		amrex::MultiFab const *	mf_pm,
		amrex::MultiFab const *	mf_pn,
		amrex::MultiFab const *	mf_fcor,
		amrex::MultiFab const *	mf_visc2_p,
		amrex::MultiFab const *	mf_visc2_r,
		amrex::MultiFab const *	mf_mskr,
		amrex::MultiFab const *	mf_msku,
		amrex::MultiFab const *	mf_mskv,
		amrex::MultiFab const *	mf_mskp,
		amrex::Real	dtfast_lev,
		bool	predictor_2d_step,
		bool	first_2d_step,
		int	my_iif,
		int &	next_indx1
	)

Perform a 2D predictor (predictor_2d_step=True) or corrector (predictor_2d_step=False) step.

Nonlinear shallow-water rpimitive equations predictor (Leap-frog) and corrector (Adams-Moulton) time-stepping engine. Corresponds to Nonlinear/step2d_LF_AM3.h in ROMS.

Parameters

[in]	lev	level of refinement (coarsest level is 0)
[in]	mf_rhoS	density perturbation
[in]	mf_rhoA	vertically-averaged density
[in,out]	mf_ru2d	RHS contributions to 2D u-momentum
[in,out]	mf_rv2d	RHS contribtuions to 2D v-momentum
[in,out]	mf_rufrc	before first predictor, vertical integral of 3D RHS for uvel, converted to forcing terms
[in,out]	mf_rvfrc	before first predictor, vertical integral of 3D RHS for vvel, converted to forcing term
[in,out]	mf_Zt_avg1	average of sea surface height over all fast steps
[in,out]	mf_DU_avg1	time-averaged u-flux for 2D equations
[in,out]	mf_DU_avg2	time-averaged u-flux for 3D equation coupling
[in,out]	mf_DV_avg1	time-averaged v-flux for 2D equations
[in,out]	mf_DV_avg2	time-averaged v-flux for 3D equation coupling
[in,out]	mf_rubar	RHS of vertically integrated u-momentum
[in,out]	mf_rvbar	RHS of vertically integrated v-momentum
[in,out]	mf_rzeta	RHS of sea surface height
[in,out]	mf_ubar	vertically integrated u-momentum
[in,out]	mf_vbar	vertically integrated v-momentum
[in,out]	mf_zeta	Sea-surface height
[in]	mf_h	Bathymetry
[in]	mf_pm	1 / dx
[in]	mf_pn	1 / dy
[in]	mf_fcor	Coriolis factor
[in,out]	mf_visc2_p	Harmonic viscosity at psi points
[in,out]	mf_visc2_r	Harmoic viscosity at rho points
[in]	mf_mskr	Land-sea mask at rho-points
[in]	mf_msku	Land-sea mask at u-points
[in]	mf_mskv	Land-sea mask at v-points
[in]	mf_mskp	Land-sea mask at psi-points
[in]	dtfast_lev	Length of current barotropic step
[in]	predictor_2d_step	Is this a predictor step?
[in]	first_2d_step	Is this the first barotropic step?
[in]	my_iif	Which barotropic predictor-corrector pair?
[in,out]	next_indx1	Cached index for

Definition at line 44 of file REMORA_advance_2d.cpp.

Referenced by advance_2d_onestep().

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advance_2d_onestep()

void REMORA::advance_2d_onestep	(	int	lev,
		amrex::Real	dt_lev,
		amrex::Real	dtfast_lev,
		int	my_iif,
		int	nfast_counter
	)

2D advance, one predictor/corrector step

Parameters

[in]	lev	level of refinement
[in]	dt_lev	baroclinic time step at level
[in]	dtfast_lev	barotropic time step at level
[in]	my_iif	current barotropic time step
[in]	nfast_counter	how many bartropicc time steps to do per baroclinic step

Definition at line 12 of file REMORA_advance_2d_onestep.cpp.

Referenced by Advance(), and timeStepML().

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advance_3d()

void REMORA::advance_3d	(	int	lev,
		amrex::MultiFab &	mf_cons,
		amrex::MultiFab &	mf_u,
		amrex::MultiFab &	mf_v,
		amrex::MultiFab *	mf_sstore,
		amrex::MultiFab *	mf_ru,
		amrex::MultiFab *	mf_rv,
		std::unique_ptr< amrex::MultiFab > &	mf_DU_avg1,
		std::unique_ptr< amrex::MultiFab > &	mf_DU_avg2,
		std::unique_ptr< amrex::MultiFab > &	mf_DV_avg1,
		std::unique_ptr< amrex::MultiFab > &	mf_DV_avg2,
		std::unique_ptr< amrex::MultiFab > &	mf_ubar,
		std::unique_ptr< amrex::MultiFab > &	mf_vbar,
		std::unique_ptr< amrex::MultiFab > &	mf_Akv,
		std::unique_ptr< amrex::MultiFab > &	mf_Akt,
		std::unique_ptr< amrex::MultiFab > &	mf_Hz,
		std::unique_ptr< amrex::MultiFab > &	mf_Huon,
		std::unique_ptr< amrex::MultiFab > &	mf_Hvom,
		std::unique_ptr< amrex::MultiFab > &	mf_z_w,
		amrex::MultiFab const *	mf_h,
		amrex::MultiFab const *	mf_pm,
		amrex::MultiFab const *	mf_pn,
		amrex::MultiFab const *	mf_mskr,
		amrex::MultiFab const *	mf_msku,
		amrex::MultiFab const *	mf_mskv,
		const int	N,
		const amrex::Real	dt_lev
	)

Advance the 3D variables.

Corresponds to step3d_uv.F and step3d_t.F in ROMS

Parameters

[in]	lev	level of refinement (coarsest level is 0)
[in,out]	mf_cons	scalar variables (temp, salt, scalar, etc)
[in,out]	mf_u	u-velocity
[in,out]	mf_v	v-velocity
[in,out]	mf_sstore	intermediate-step scalar variables
[in,out]	mf_ru	RHS of total u-velocity
[in,out]	mf_rv	RHS of total v-velocity
[in]	mf_DU_avg1	time-averaged u-flux for 2D equations
[in]	mf_DU_avg2	time-averaged u-flux for 3D equation coupling
[in]	mf_DV_avg1	time-averaged v-flux for 2D equations
[in]	mf_DV_avg2	time-averaged v-flux for 3D equation coupling
[in,out]	mf_ubar	vertically integrated u-momentum
[in,out]	mf_vbar	vertically integrated v-momentum
[in,out]	mf_Akv	vertical viscosity coefficient
[in,out]	mf_Akt	vertical diffusivity coefficient
[in,out]	mf_Hz	vertical height of cells
[in,out]	mf_Huon	u-volume flux
[in,out]	mf_Huon	v-volume flux
[in,out]	mf_z_w	vertical coordinates on w points
[in]	mf_h	bathymetry
[in]	mf_pm	1 / dx
[in]	mf_pn	1 / dy
[in]	mf_msku	land-sea mask at u-points
[in]	mf_mskv	land-sea mask at v-points
[in]	N	number of vertical levels
[in]	dt_lev	time step at this refinement level

Definition at line 35 of file REMORA_advance_3d.cpp.

Referenced by advance_3d_ml().

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advance_3d_ml()

void REMORA::advance_3d_ml	(	int	lev,
		amrex::Real	dt_lev
	)

3D advance on a single level

Parameters

[in]	lev	refinement level
[in]	dt_lev	time step at refinement level

Definition at line 9 of file REMORA_advance_3d_ml.cpp.

Referenced by Advance(), and timeStepML().

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advance_biology()

void REMORA::advance_biology	(	int	lev,
		amrex::MultiFab const &	mf_cons_old,
		amrex::MultiFab &	mf_cons_new,
		int	N,
		amrex::Real	dt_lev
	)

Apply biological tracer source/sink terms.

Definition at line 494 of file REMORA_Biology.cpp.

Referenced by advance_3d().

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allocate_bathymetry_grid_vars_full_domain()

void REMORA::allocate_bathymetry_grid_vars_full_domain

(

)

Allocate multifabs for storing full-domain bathymetry and grid vars data.

Definition at line 330 of file REMORA_init.cpp.

Referenced by init_only().

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allocate_init_full_domain()

void REMORA::allocate_init_full_domain

(

)

Allocate multifabs for storing full-domain high resolution initial data.

Definition at line 399 of file REMORA_init.cpp.

Referenced by init_only().

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append2DPlotVariables()

void REMORA::append2DPlotVariables ( const std::string &  pp_plot_var_names_2d )

private

Parameters

pp_plot_var_names_2d

variables to add to plot list

Definition at line 254 of file REMORA_SetPlotVars.cpp.

Referenced by InitData().

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append3DPlotVariables()

void REMORA::append3DPlotVariables ( const std::string &  pp_plot_var_names_3d )

private

Parameters

pp_plot_var_names

variables to add to plot list

Definition at line 216 of file REMORA_SetPlotVars.cpp.

Referenced by InitData().

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apply_clim_nudg()

void REMORA::apply_clim_nudg	(	const amrex::Box &	bx,
		int	ioff,
		int	joff,
		const amrex::Array4< amrex::Real > &	var,
		const amrex::Array4< amrex::Real const > &	var_old,
		const amrex::Array4< amrex::Real const > &	var_clim,
		const amrex::Array4< amrex::Real const > &	clim_coeff,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		const amrex::Real	dt_lev = zero
	)

Apply climatology nudging.

Parameters

[in]	bx	box to apply climatology on
[in]	ioff	offset in x-direction
[in]	joff	offset in y-direction
[in,out]	var	variable to update
[in]	var_old	variable to compare against for nudging
[in]	var_clim	climatology value to nudge towards
[in]	clim_coeff	nudging time scale (1/s)
[in]	Hz	vertical cell height
[in]	pm	1/dx
[in]	pn	1/dy
[in]	dt_lev	time step

Definition at line 19 of file REMORA_apply_clim_nudg.cpp.

Referenced by advance_2d(), advance_3d(), and setup_step().

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ApplyAtmosphericFluxes()

void REMORA::ApplyAtmosphericFluxes	(	const amrex::Vector< amrex::MultiFab * > &	states,
		amrex::Real	time
	)

Receives atmospheric flux lanes from the driver and assembles REMORA flux inputs.

Expected active-lane order matches the driver FluxPassing contract: tau_x, tau_y, SHflux, LHflux, SWrad, LWrad, rain, evap.

This routine copies imported forcing lanes into REMORA's existing flux arrays and assembles vec_stflux directly from those imported values. It intentionally leaves the downstream salt_old multiplication to setup_step().

Definition at line 511 of file REMORA_Coupling.cpp.

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ApplyAtmosphericStates()

void REMORA::ApplyAtmosphericStates	(	const amrex::Vector< amrex::MultiFab * > &	states,
		amrex::Real	time
	)

Receives atmospheric states from the driver and applies unit conversions.

Fills REMORA's internal forcing MultiFabs from states and records which lanes were successfully updated in driver_atmos_state_from_driver. Unit conversions applied: Pair Pa to mb; Tair K to Celsius.

Parameters

[in]	states	ATM2OCN forcing slab buffer from the driver (Warner et al. 2010, Block B state-passing contract), indexed by AtmosState. Expected units per lane: Uwind/Vwind: 10-m winds [m/s]; Pair: mean sea-level pressure [Pa, converted to mb]; Qair: near-surface specific humidity [kg/kg]; Tair: 2-m air temperature [K, converted to degC]; Cloud: cloud fraction [0-1]; Rain: precipitation rate [kg/m^2/s]; SWrad/LWrad: downwelling shortwave/longwave radiation [W/m^2]. Missing lanes (null pointer or index out of range) are skipped; driver_atmos_state_from_driver tracks populated lanes for the bulk-flux parameterization fallback logic.
[in]	time	Current ocean model time (unused; retained for driver interface conformance).

Definition at line 426 of file REMORA_Coupling.cpp.

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average_down_masked()

void REMORA::average_down_masked	(	int	crse_lev,
		const amrex::MultiFab &	S_fine,
		amrex::MultiFab &	S_crse,
		const amrex::MultiFab &	msk_fine,
		const amrex::MultiFab &	cmsk,
		int	ncomp,
		int	face_dir
	)

Average one field down a level, weighted by the land/sea mask.

Average one field from crse_lev+1 onto crse_lev, weighting by the land/sea mask.

Follows amrex::average_down's non-MFIter-safe branch, since coarsen(grids[flev]) does not match grids[crse_lev] in general: compute onto a temporary on the coarsened-fine layout, then ParallelCopy that onto the coarse level.

Parameters

[in]	crse_lev	level to average down to
[in]	S_fine	fine-level field
[out]	S_crse	coarse-level field
[in]	msk_fine	fine-level mask, on S_fine's layout and nodality
[in]	cmsk	coarse-level mask, already on the coarsened-fine layout
[in]	ncomp	number of components to average
[in]	face_dir	face direction, or -1 for a cell-centered field

Definition at line 2551 of file REMORA.cpp.

Referenced by AverageDownTo().

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average_down_with_grow_cells()

void REMORA::average_down_with_grow_cells	(	int	lev,
		amrex::Vector< std::unique_ptr< amrex::MultiFab > > &	mf,
		bool	use_mask = false
	)

Average down from level lev+1 to lev in mf, including grow cells.

Average a full-domain field from crse_lev+1 onto crse_lev, grow cells included.

With use_mask this takes REMORAMaskedAvgDown's mask-weighted mean instead of the plain one, so the initial state on a coarse cell only partly covered by water comes from that water. It is the formula AverageDownTo applies every step, so the initial and the running state agree on what a land point holds. Leave use_mask off for grid metrics: a cell size is well defined under land, and masking pm/pn would corrupt it.

Parameters

[in]	crse_lev	level to average data down to
[in,out]	vec_mf	vector over levels of multifabs containing data to average
[in]	use_mask	weight by the land/sea mask rather than averaging every fine cell

Definition at line 2711 of file REMORA.cpp.

Referenced by init_biology_ic_full_domain(), init_data_full_domain_from_netcdf(), init_full_domain_from_analytic(), init_full_domain_zeta_from_analytic(), init_grid_vars_full_domain_from_netcdf(), and init_zeta_full_domain_from_netcdf().

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AverageDown()

void REMORA::AverageDown ( )

private

set covered coarse cells to be the average of overlying fine cells

Definition at line 2431 of file REMORA.cpp.

Referenced by InitData().

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AverageDownTo()

void REMORA::AverageDownTo ( int  crse_lev )

private

more flexible version of AverageDown() that lets you average down across multiple levels

Parameters

[in]

crse_lev

level to average down to

Definition at line 2506 of file REMORA.cpp.

Referenced by AverageDown(), post_timestep(), timeStep(), and timeStepML().

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bdy_cons()

int REMORA::bdy_cons ( int  icomp ) const

inlinenoexcept

Accessors for the ncons-dependent entries of BdyVars.

Definition at line 1392 of file REMORA.H.

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bdy_ubar()

int REMORA::bdy_ubar ( ) const

inlinenoexcept

Definition at line 1393 of file REMORA.H.

Referenced by advance_2d(), advance_3d_ml(), init_bcs(), init_bdry_from_netcdf(), init_clim_nudg_coeff(), init_clim_nudg_coeff_from_netcdf(), init_stuff(), MakeNewLevelFromCoarse(), RemakeLevel(), resize_stuff(), and set_2darrays().

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bdy_vbar()

int REMORA::bdy_vbar ( ) const

inlinenoexcept

Definition at line 1394 of file REMORA.H.

Referenced by advance_2d(), advance_3d_ml(), init_bcs(), init_bdry_from_netcdf(), init_clim_nudg_coeff(), init_clim_nudg_coeff_from_netcdf(), init_stuff(), MakeNewLevelFromCoarse(), RemakeLevel(), resize_stuff(), and set_2darrays().

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bdy_zeta()

int REMORA::bdy_zeta ( ) const

inlinenoexcept

Definition at line 1395 of file REMORA.H.

Referenced by advance_2d(), fill_from_bdyfiles(), init_bcs(), init_bdry_from_netcdf(), init_clim_nudg_coeff(), init_stuff(), init_zeta_from_netcdf(), resize_stuff(), and set_zeta_averaged_down().

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bio_comp_start()

int REMORA::bio_comp_start ( ) const

inlinenoexcept

First cons component of the biology block. Problem setups need this to write biology initial conditions, since the passive scalars sit between salinity and the biology tracers.

Definition at line 1999 of file REMORA.H.

build_fine_mask()

MultiFab & REMORA::build_fine_mask

(

int

level

)

Make mask to zero out covered cells (for mesh refinement)

Parameters

[in]

lev

level to calculate on

Definition at line 245 of file REMORA_SumIQ.cpp.

Referenced by volWgtSumMF().

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bulk_fluxes()

void REMORA::bulk_fluxes	(	int	lev,
		amrex::MultiFab *	mf_cons,
		amrex::MultiFab *	mf_uwind,
		amrex::MultiFab *	mf_vwind,
		amrex::MultiFab *	mf_Tair,
		amrex::MultiFab *	mf_qair,
		amrex::MultiFab *	mf_Pair,
		amrex::MultiFab *	mf_srflx,
		amrex::MultiFab *	mf_longwave_down,
		amrex::MultiFab *	mf_evap,
		amrex::MultiFab *	mf_sustr,
		amrex::MultiFab *	mf_svstr,
		amrex::MultiFab *	mf_stflux,
		amrex::MultiFab *	mf_lrflx,
		amrex::MultiFab *	mf_lhflx,
		amrex::MultiFab *	mf_shflx,
		const int	N
	)

Calculate bulk temperature, salinity, wind fluxes.

Parameters

[in]	lev	level to operate on
[in]	mf_cons	scalar data: temperature, salinity, passsive scalar, etc
[in]	mf_uwind	u-direction wind dvelocity
[in]	mf_vwind	v-direction wind dvelocity
[in]	mf_Tair	air temperature [°C]
[in]	mf_qair	specific humidity [kg/kg]
[in]	mf_Pair	air pressure [mb]
[in]	mf_srflx	shortwave radiation flux [W/m²]
[in]	mf_longwave_down	external longwave radiation flux [W/m²]
[in,out]	mf_evap	evaporation rate
[out]	mf_sustr	u-direction surface momentum stress
[out]	mf_svstr	v-direction surface momentum stress
[out]	mf_stflux	surface scalar flux (temperature, salinity)
[out]	mf_lrflx	longwave radiation flux
[in,out]	mf_lhflx	latent heat flux
[in,out]	mf_shflx	sensible heat flux
[in]	N	number of vertical levels

Spec Hum (kg/kg)

Definition at line 25 of file REMORA_bulk_flux.cpp.

Referenced by setup_step().

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bulk_psit()

AMREX_GPU_HOST_DEVICE static AMREX_FORCE_INLINE amrex::Real REMORA::bulk_psit ( amrex::Real  ZoL )

inlinestatic

Evaluate stability function psi for moisture and heat.

Definition at line 2039 of file REMORA.H.

Referenced by bulk_fluxes().

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bulk_psiu()

AMREX_GPU_HOST_DEVICE static AMREX_FORCE_INLINE amrex::Real REMORA::bulk_psiu ( amrex::Real  ZoL )

inlinestatic

Evaluate stability function psi for wind speed.

Definition at line 2007 of file REMORA.H.

Referenced by bulk_fluxes().

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calc_stretch_coeffs()

void REMORA::calc_stretch_coeffs

(

)

calculate vertical stretch coefficients

Definition at line 12 of file REMORA_DepthStretchTransform.H.

Referenced by init_stretch_coeffs().

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calculate_nodal_masks()

void REMORA::calculate_nodal_masks

(

int

lev

)

Calculate u-, v-, and psi-point masks based on rho-point masks after analytic initialization.

Parameters

[in]

lev

level to operate on

Definition at line 987 of file REMORA_make_new_level.cpp.

Referenced by update_nodal_masks().

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check_mask_consistency()

void REMORA::check_mask_consistency

(

)

Check every level pair's masks against each other, and every level's mask values, reporting according to remora.mask_consistency.

Check the land-sea masks for what the rest of the code relies on. Only runs when remora.check_mask_consistency is set; remora.mask_consistency picks abort or warn.

Per level, that the masks hold only the values they are meant to and that no water cell has a non-positive depth. Per level pair, over the region the finer level covers, that no coarse water point sits over fine points that are all land.

Definition at line 977 of file REMORA.cpp.

Referenced by InitData(), timeStep(), and timeStepML().

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clear_avgdown_masks()

void REMORA::clear_avgdown_masks

(

int

lev

)

Drop the cached average-down masks of every level pair that involves lev.

Drop the cached average-down masks of every level pair that involves lev, so the next AverageDownTo rebuilds them.

Called from set_masks, which is the one place a level's mask is written, so a regrid cannot leave a cached copy of a mask that no longer exists behind.

Parameters

[in]

lev

level whose mask has just been rebuilt

Definition at line 2450 of file REMORA.cpp.

Referenced by set_masks().

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ClearLevel()

void REMORA::ClearLevel ( int  lev )

overridevirtual

Delete level data Overrides the pure virtual function in AmrCore.

Delete level data. Overrides the pure virtual function in AmrCore

Parameters

[in]

lev

level to operate on

Definition at line 802 of file REMORA_make_new_level.cpp.

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clim_nudg_momentum_box()

Box REMORA::clim_nudg_momentum_box ( const amrex::Box &  nodal_bx, int  dir, const amrex::Box &  domain, bool  is_periodic  )

static

Shrink an x- or y-nodal momentum tilebox to the faces ROMS nudges.

ROMS nudges momentum toward climatology over i=IstrU..Iend (j=JstrV..Jend), which excludes the u-face on the western and eastern domain edges (v-face on the southern and northern edges). This returns the part of nodal_bx that survives that exclusion. Under EW_PERIODIC (NS_PERIODIC) ROMS sets IstrU=Istr (JstrV=Jstr) and nudges every face, so a periodic direction is left alone.

Parameters

[in]	nodal_bx	box from MFIter::nodaltilebox(dir)
[in]	dir	direction the box is nodal in (0 for u, 1 for v)
[in]	domain	cell-centered problem domain at this level
[in]	is_periodic	whether dir is periodic
[in]	nodal_bx	box from MFIter::nodaltilebox(dir)
[in]	dir	direction the box is nodal in (0 for u, 1 for v)
[in]	domain	cell-centered problem domain at this level
[in]	is_periodic	whether dir is periodic

Definition at line 52 of file REMORA_apply_clim_nudg.cpp.

Referenced by advance_2d(), and setup_step().

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coarsen_bathymetry_with_grow_cells()

void REMORA::coarsen_bathymetry_with_grow_cells

(

int

crse_lev

)

Coarsen the full-domain bathymetry from crse_lev+1 onto crse_lev, grow cells included, weighted by the land/sea mask.

Coarsen the full-domain bathymetry from crse_lev+1 onto crse_lev, grow cells included, weighted by the land/sea mask.

Averaging every fine cell would mix in whatever the grid file holds under land, which on a ROMS grid is a fill value with no physical meaning. A wet coarse cell should take the depth of the water under it. See REMORA_MaskedAverageDown.H for why the arithmetic is written the way it is.

Parameters

[in]

crse_lev

level to coarsen onto

Definition at line 1202 of file REMORA.cpp.

Referenced by init_bathymetry_full_domain_from_analytic(), and init_bathymetry_full_domain_from_netcdf().

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coarsen_masks_with_grow_cells()

void REMORA::coarsen_masks_with_grow_cells

(

int

crse_lev

)

Coarsen the full-domain rho-mask from crse_lev+1 onto crse_lev, grow cells included, by the rule that a coarse cell is land only if all its fine cells are land.

Coarsen the full-domain rho-mask from crse_lev+1 onto crse_lev, grow cells included, so a coarse cell is land only if every one of its fine cells is land.

average_down_with_grow_cells cannot be used: an arithmetic mean over a partly wet group of fine cells gives a fractional value, and the mask has to stay exactly 0 or 1. Taking the cell as wet also means the coarse level never declares land where the fine grid found water.

Parameters

[in]

crse_lev

level to coarsen onto

Definition at line 944 of file REMORA.cpp.

Referenced by init_masks_full_domain_from_analytic(), and init_masks_full_domain_from_netcdf().

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ComputeDt()

void REMORA::ComputeDt ( )

private

a wrapper for estTimeStep()

Definition at line 8 of file REMORA_ComputeTimestep.cpp.

Referenced by Evolve(), EvolveOneStep(), and InitData().

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ComputeGhostCells()

AMREX_FORCE_INLINE int REMORA::ComputeGhostCells ( const int &  spatial_order )

inlineprivate

Helper function to determine number of ghost cells.

Definition at line 1901 of file REMORA.H.

Referenced by MakeNewLevelFromScratch(), and RemakeLevel().

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ConfigureDriverAtmosToOceanCoupling()

void REMORA::ConfigureDriverAtmosToOceanCoupling	(	bool	use_coupling_driver,
		bool	use_two_way_coupling,
		DriverAtmosForcingMode	active_mode
	)

Definition at line 248 of file REMORA_Coupling.cpp.

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Construct_REMORAFillPatchers()

void REMORA::Construct_REMORAFillPatchers ( int  lev )

private

Construct FillPatchers.

Parameters

[in]

lev

level to operate on

Definition at line 529 of file REMORA.cpp.

Referenced by init_stuff(), InitData(), and MakeNewLevelFromCoarse().

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convert_inv_days_to_inv_s()

void REMORA::convert_inv_days_to_inv_s

(

amrex::MultiFab *

)

Convert data in a multifab from inverse days to inverse seconds.

Parameters

[in,out]

mf

multifab of data to convert

Definition at line 1100 of file REMORA_init_from_netcdf.cpp.

Referenced by init_clim_nudg_coeff_from_netcdf().

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coriolis()

void REMORA::coriolis	(	const amrex::Box &	xbx,
		const amrex::Box &	ybx,
		const amrex::Array4< amrex::Real const > &	uold,
		const amrex::Array4< amrex::Real const > &	vold,
		const amrex::Array4< amrex::Real > &	ru,
		const amrex::Array4< amrex::Real > &	rv,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	fomn,
		int	nrhs,
		int	nr
	)

Calculate Coriolis terms.

Parameters

[in]	xbx	nodal box in x-direction
[in]	ybx	nodal box in y-direction
[in]	uold	u-direction velocity
[in]	vold	v-direction velocity
[in,out]	ru	u-direction velocity RHS
[in,out]	rv	v-direction velocity RHS
[in]	Hz	vertical cell height
[in]	fomn	scaled coriolis factor
[in]	nrhs	which velocity component to use
[in]	nr	which RHS component to update

Definition at line 19 of file REMORA_coriolis.cpp.

Referenced by advance_2d(), and setup_step().

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curvilinear()

void REMORA::curvilinear	(	const amrex::Box &	bx,
		const amrex::Box &	xbx,
		const amrex::Box &	ybx,
		const amrex::Array4< amrex::Real const > &	uold,
		const amrex::Array4< amrex::Real const > &	vold,
		const amrex::Array4< amrex::Real > &	ru,
		const amrex::Array4< amrex::Real > &	rv,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	dndx,
		const amrex::Array4< amrex::Real const > &	dmde,
		int	nrhs,
		int	nr
	)

Calculate curvilinear advection terms.

Parameters

[in]	bx	box to update on
[in]	xbx	nodal-x box to update on
[in]	ybx	nodal-y box to update on
[in]	uold	u-direction velocity
[in]	vold	v-direction velocity
[in,out]	ru	u-direction velocity RHS
[in,out]	rv	v-direction velocity RHS
[in]	Hz	vertical cell height
[in]	dndx	d(1/n)/d(xi)
[in]	dmde	d(1/m)/d(eta)
[in]	nrhs	which velocity component to use
[in]	nr	which RHS component to update

Definition at line 21 of file REMORA_curvilinear.cpp.

Referenced by advance_2d(), and setup_step().

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DataLog()

AMREX_FORCE_INLINE std::ostream & REMORA::DataLog ( int  i )

inlineprivate

Helper function for IO stream.

Definition at line 1929 of file REMORA.H.

Referenced by sum_integrated_quantities().

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DataLogName()

const std::string REMORA::DataLogName ( int  i ) const

inlineprivatenoexcept

The filename of the ith datalog file.

Definition at line 1979 of file REMORA.H.

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Define_REMORAFillPatchers()

void REMORA::Define_REMORAFillPatchers ( int  lev )

private

Define FillPatchers.

Parameters

[in]

lev

level to operate on

Definition at line 578 of file REMORA.cpp.

Referenced by init_stuff(), MakeNewLevelFromCoarse(), and RemakeLevel().

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DriverUsesStateForcing()

static constexpr bool REMORA::DriverUsesStateForcing ( DriverAtmosForcingMode  mode )

inlinestaticconstexprnoexcept

Definition at line 98 of file REMORA.H.

Referenced by InitData(), and setup_step().

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ensure_full_domain_masks()

void REMORA::ensure_full_domain_masks

(

int

top_lev

)

Make sure the full-domain rho-mask exists on levels 0 through top_lev.

Make sure the full-domain rho-mask exists on levels 0 through top_lev.

Only fills what the hires_grid_level coarsening has not: levels above it, by injection, and level 0 itself when there is no high-resolution grid and the mask was given per level.

Parameters

[in]

top_lev

highest level that needs a mask

Definition at line 2635 of file REMORA.cpp.

Referenced by init_only().

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ErrorEst()

void REMORA::ErrorEst ( int  lev, amrex::TagBoxArray &  tags, amrex::Real  time, int  ngrow  )

overridevirtual

Tag cells for refinement.

Function to tag cells for refinement – this overrides the pure virtual function in AmrCore

Parameters

[in]	levc	level of refinement (0 is coarsest level)
[out]	tags	array of tagged cells
[in]	time	current time
[in]	ngrow	number of grow cells

Definition at line 97 of file REMORA_Tagging.cpp.

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estTimeStep()

Real REMORA::estTimeStep

(

int

level

)

const

compute dt from CFL considerations

Estimate the largest stable slow (baroclinic) timestep on a level.

The estimate is the smaller of an advective limit and an external gravity wave limit, each a maximum over the wet cells of the level:

dt_adv  = cfl / max( |u|*pm, |v|*pn, |w|/Hz )
dt_grav = cfl * ndtfast / max( sqrt(g*|h|) * sqrt(pm^2 + pn^2) )

The second is the Courant quantity ROMS forms as Cg_max in metrics.F. It is what keeps the estimate finite for a run started from rest, where every velocity is zero and the advective limit alone is undefined.

pm and pn are the per-cell 1/dx and 1/dy metric terms rather than the geometry's uniform cell size, so stretched and curvilinear grids give the right answer.

Parameters

[in]

level

level of refinement

Definition at line 69 of file REMORA_ComputeTimestep.cpp.

Referenced by ComputeDt().

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Evolve()

void REMORA::Evolve

(

)

Advance solution to final time.

Definition at line 279 of file REMORA.cpp.

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EvolveOneStep()

amrex::Real REMORA::EvolveOneStep	(	amrex::Real	time,
		amrex::Real	dt_request
	)

Definition at line 219 of file REMORA_Coupling.cpp.

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extrapolate_metric_to_physical_boundaries()

void REMORA::extrapolate_metric_to_physical_boundaries	(	amrex::MultiFab &	mf,
		const amrex::Geometry &	geom
	)

Extrapolate grid metrics to edge of MultiFab.

Parameters

[in,out]	mf	multifab of data to extrapolate on
[in]	geom	geometry

Definition at line 1227 of file REMORA_init_from_netcdf.cpp.

Referenced by init_grid_vars_from_netcdf(), and init_grid_vars_full_domain_from_netcdf().

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fill_3d_masks()

void REMORA::fill_3d_masks

(

int

lev

)

Copy maskr to all z levels.

Parameters

[in]

lev

level to operate on

Definition at line 1050 of file REMORA_make_new_level.cpp.

Referenced by set_masks().

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fill_from_bdyfiles()

void REMORA::fill_from_bdyfiles	(	int	lev,
		amrex::MultiFab &	mf_to_fill,
		const amrex::MultiFab &	mf_mask,
		const amrex::Real	time,
		const int	bccomp,
		const int	bdy_var_type,
		const int	icomp_to_fill,
		const int	icomp_calc = 0,
		const amrex::MultiFab &	mf_calc = amrex::MultiFab(),
		const amrex::Real	= zero
	)

Fill boundary data from netcdf file.

Definition at line 20 of file REMORA_BoundaryConditions_netcdf.cpp.

Referenced by advance_3d(), FillCoarsePatchMap(), FillPatch(), and init_zeta_from_netcdf().

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FillBdyCCVels()

void REMORA::FillBdyCCVels	(	int	lev,
		amrex::MultiFab &	mf_cc_vel
	)

Fill the physical boundary conditions for cell-centered velocity (diagnostic only)

Fill boundary ghost cells for cell-centered velocities. Each component takes the sign implied by its own BC, which with remora.boundary_per_variable can differ between u, v and w on one face.

Parameters

[in]	lev	level to fill at
[in,out]	mf_cc_vel	MultiFab of cell-centered velocities

Definition at line 597 of file REMORA_FillPatch.cpp.

Referenced by ErrorEst(), and WritePlotFile().

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FillCoarsePatch()

void REMORA::FillCoarsePatch	(	int	lev,
		amrex::Real	time,
		amrex::MultiFab *	mf_fine,
		amrex::MultiFab *	mf_crse,
		const int	bccomp,
		const int	bdy_var_type = BdyVars::null,
		const int	icomp = 0,
		const bool	fill_all = true,
		const int	n_not_fill = 0,
		const int	icomp_calc = 0,
		const amrex::Real	dt = zero,
		const amrex::MultiFab &	mf_calc = amrex::MultiFab()
	)

fill an entire multifab by interpolating from the coarser level

Fill an entire multifab by interpolating from the coarser level – this is used only when a new level of refinement is being created during a run (i.e not at initialization) This will never be used with static refinement.

Parameters

[in]	lev	level to FillPatch on
[in]	time	current time
[in,out]	mf_to_fill	MultiFab to fill
[in,out]	mf_crse	MultiFab of coarse data
[in]	bccomp	index into domain_bcs_type
[in]	bdy_var_type	when filling from NetCDF, which boundary data
[in]	icomp	component to fill
[in]	fill_all	whether to fill all components
[in]	icomp_calc	component to use in RHS boundary calculation
[in]	dt_lev	time step at this level
[in]	mf_calc	data to use in RHS boundary calculation

Definition at line 411 of file REMORA_FillPatch.cpp.

Referenced by FillCoarsePatchMap(), init_only(), MakeNewLevelFromCoarse(), set_bathymetry(), set_coriolis(), set_grid_scale(), and set_zeta().

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FillCoarsePatchMap()

void REMORA::FillCoarsePatchMap	(	int	lev,
		amrex::Real	time,
		amrex::MultiFab *	mf_fine,
		amrex::MultiFab *	mf_crse,
		const int	bccomp,
		const int	bdy_var_type = BdyVars::null,
		const int	icomp = 0,
		const bool	fill_all = true,
		const int	n_not_fill = 0,
		const int	icomp_calc = 0,
		const amrex::Real	dt = zero,
		const amrex::MultiFab &	mf_calc = amrex::MultiFab(),
		amrex::Interpolater *	mapper = nullptr
	)

fill an entire multifab by interpolating from the coarser level, explicitly specifying interpolator to use

Fill an entire multifab by interpolating from the coarser level – this is used only when a new level of refinement is being created during a run (i.e not at initialization) This will never be used with static refinement.

Parameters

[in]	lev	level to FillPatch on
[in]	time	current time
[in,out]	mf_to_fill	MultiFab to fill
[in,out]	mf_crse	MultiFab of coarse data
[in]	bccomp	index into domain_bcs_type
[in]	bdy_var_type	when filling from NetCDF, which boundary data
[in]	icomp	component to fill
[in]	fill_all	whether to fill all components
[in]	icomp_calc	component to use in RHS boundary calculation
[in]	dt_lev	time step at this level
[in]	mf_calc	data to use in RHS boundary calculation

Definition at line 445 of file REMORA_FillPatch.cpp.

Referenced by FillCoarsePatch(), and FillCoarsePatchPC().

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FillCoarsePatchPC()

void REMORA::FillCoarsePatchPC	(	int	lev,
		amrex::Real	time,
		amrex::MultiFab *	mf_fine,
		amrex::MultiFab *	mf_crse,
		const int	bccomp,
		const int	bdy_var_type = BdyVars::null,
		const int	icomp = 0,
		const bool	fill_all = true,
		const int	n_not_fill = 0,
		const int	icomp_calc = 0,
		const amrex::Real	dt = zero,
		const amrex::MultiFab &	mf_calc = amrex::MultiFab()
	)

fill an entire multifab by interpolating from the coarser level using the piecewise constant interpolater

Like FillCoarsePatch but uses piecewise constant interpolater

Parameters

[in]	lev	level to FillPatch on
[in]	time	current time
[in,out]	mf_to_fill	MultiFab to fill
[in,out]	mf_crse	MultiFab of coarse data
[in]	bccomp	index into domain_bcs_type
[in]	bdy_var_type	when filling from NetCDF, which boundary data
[in]	icomp	component to fill
[in]	fill_all	whether to fill all components
[in]	icomp_calc	component to use in RHS boundary calculation
[in]	dt_lev	time step at this level
[in]	mf_calc	data to use in RHS boundary calculation

Definition at line 377 of file REMORA_FillPatch.cpp.

Referenced by set_masks().

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FillPatch()

void REMORA::FillPatch	(	int	lev,
		amrex::Real	time,
		amrex::MultiFab &	mf_to_be_filled,
		amrex::Vector< amrex::MultiFab * > const &	mfs,
		const int	bccomp,
		const int	bdy_var_type = BdyVars::null,
		const int	icomp = 0,
		const bool	fill_all = true,
		const bool	fill_set = false,
		const int	n_not_fill = 0,
		const int	icomp_calc = 0,
		const amrex::Real	dt = zero,
		const amrex::MultiFab &	mf_calc = amrex::MultiFab()
	)

Fill a new MultiFab by copying in phi from valid region and filling ghost cells.

Fill valid and ghost data in the MultiFab "mf" This version fills the MultiFab mf_to_fill in valid regions with the "state data" at the given time; values in mf when it is passed in are not used.

Parameters

[in]	lev	level to FillPatch on
[in]	time	current time
[in,out]	mf_to_fill	MultiFab to fill
[in]	mfs	vector over levels of multifabs associated with mf_to_fill
[in]	bccomp	index into domain_bcs_type
[in]	bdy_var_type	when filling from NetCDF, which boundary data
[in]	icomp	component to fill
[in]	fill_all	whether to fill all components
[in]	fill_set	whether to use FillPatchers
[in]	icomp_calc	component to use in RHS boundary calculation
[in]	dt_lev	time step at this level
[in]	mf_calc	data to use in RHS boundary calculation

Definition at line 30 of file REMORA_FillPatch.cpp.

Referenced by advance_2d(), advance_3d(), advance_3d_ml(), ErrorEst(), gls_corrector(), gls_prestep(), init_bathymetry_from_netcdf(), init_grid_vars_from_netcdf(), init_zeta_from_netcdf(), InitData(), RemakeLevel(), set_2darrays(), set_analytic_vmix(), set_bathymetry_averaged_down(), set_coriolis(), set_grid_vars_averaged_down(), set_hmixcoef(), set_init_data_averaged_down(), set_smflux(), set_surface_state(), set_zeta_averaged_down(), setup_step(), and timeStepML().

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FillPatchNoBC()

void REMORA::FillPatchNoBC	(	int	lev,
		amrex::Real	time,
		amrex::MultiFab &	mf_to_be_filled,
		amrex::Vector< amrex::MultiFab * > const &	mfs,
		const int	bdy_var_type = BdyVars::null,
		const int	icomp = 0,
		const bool	fill_all = true,
		const bool	fill_set = false
	)

Fill a new MultiFab by copying in phi from valid region and filling ghost cells without applying boundary conditions.

Fill valid and ghost data in the MultiFab "mf" This version fills the MultiFab mf_to_fill in valid regions with the "state data" at the given time; values in mf when it is passed in are not used. Unlike FillPatch, FillPatchNoBC does not apply boundary conditions

Parameters

[in]	lev	level to FillPatch on
[in]	time	current time
[in,out]	mf_to_fill	MultiFab to fill
[in]	mfs	vector over levels of multifabs associated with mf_to_fill
[in]	bdy_var_type	when filling from NetCDF, which boundary data
[in]	icomp	component to fill
[in]	fill_all	whether to fill all components
[in]	fill_set	whether to use FillPatchers

Definition at line 199 of file REMORA_FillPatch.cpp.

Referenced by advance_2d(), advance_3d_ml(), gls_corrector(), setup_step(), timeStepML(), and WritePlotFile().

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foextrap_bc()

int REMORA::foextrap_bc ( ) const

inlinenoexcept

Definition at line 1385 of file REMORA.H.

Referenced by gls_corrector(), init_bcs(), init_only(), set_coriolis(), set_grid_scale(), set_masks(), and WritePlotFile().

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foextrap_periodic_bc()

int REMORA::foextrap_periodic_bc ( ) const

inlinenoexcept

Definition at line 1384 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_bcs(), init_grid_vars_from_netcdf(), MakeNewLevelFromCoarse(), RemakeLevel(), set_bathymetry(), set_bathymetry_averaged_down(), set_grid_vars_averaged_down(), set_hmixcoef(), set_smflux(), and set_surface_state().

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full_domain_dmap()

const DistributionMapping & REMORA::full_domain_dmap

(

)

The shared full-domain DistributionMapping, built on first use.

Definition at line 321 of file REMORA_init.cpp.

Referenced by allocate_bathymetry_grid_vars_full_domain(), allocate_init_full_domain(), and ensure_full_domain_masks().

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get_t_old()

amrex::Real REMORA::get_t_old

(

int

lev

)

const

Accessor method for t_old to expose to outside classes.

Parameters

[in]

lev

level at which to get time

Definition at line 2782 of file REMORA.cpp.

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GetAtmosToOceanPsiCoordinates()

void REMORA::GetAtmosToOceanPsiCoordinates	(	const amrex::MultiFab *&	x_psi,
		const amrex::MultiFab *&	y_psi
	)		const

Definition at line 336 of file REMORA_Coupling.cpp.

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GetAtmosToOceanPsiLonLat()

void REMORA::GetAtmosToOceanPsiLonLat	(	const amrex::MultiFab *&	lon_psi,
		const amrex::MultiFab *&	lat_psi
	)		const

Definition at line 350 of file REMORA_Coupling.cpp.

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GetAtmosToOceanRhoLayout()

void REMORA::GetAtmosToOceanRhoLayout	(	amrex::BoxArray &	ba,
		amrex::DistributionMapping &	dm
	)		const

Definition at line 303 of file REMORA_Coupling.cpp.

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GetAtmosToOceanUFaceLayout()

void REMORA::GetAtmosToOceanUFaceLayout	(	amrex::BoxArray &	ba,
		amrex::DistributionMapping &	dm
	)		const

Definition at line 314 of file REMORA_Coupling.cpp.

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GetAtmosToOceanVFaceLayout()

void REMORA::GetAtmosToOceanVFaceLayout	(	amrex::BoxArray &	ba,
		amrex::DistributionMapping &	dm
	)		const

Definition at line 325 of file REMORA_Coupling.cpp.

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getCPUTime()

amrex::Real REMORA::getCPUTime ( ) const

inlineprivate

Get CPU time used.

Definition at line 1948 of file REMORA.H.

Referenced by writeJobInfo().

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GetDataAtTime()

TimeInterpolatedData REMORA::GetDataAtTime ( int  lev, amrex::Real  time  )

private

utility to copy in data from old and/or new state into another multifab

Definition at line 303 of file REMORA_FillPatch.cpp.

Referenced by GetDataAtTime().

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GetDeckConfiguredAtmosStateLanes()

void REMORA::GetDeckConfiguredAtmosStateLanes

(

std::array< bool, AtmosState::NumTypes > &

deck_configured

)

const

Definition at line 269 of file REMORA_Coupling.cpp.

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GetLandSeaMasks()

void REMORA::GetLandSeaMasks	(	const amrex::MultiFab *&	mskr,
		const amrex::MultiFab *&	msku,
		const amrex::MultiFab *&	mskv
	)		const

Definition at line 364 of file REMORA_Coupling.cpp.

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gls_corrector()

void REMORA::gls_corrector	(	int	lev,
		amrex::MultiFab *	mf_gls,
		amrex::MultiFab *	mf_tke,
		amrex::MultiFab &	mf_W,
		amrex::MultiFab *	mf_Akv,
		amrex::MultiFab *	mf_Akt,
		amrex::MultiFab *	mf_Akk,
		amrex::MultiFab *	mf_Akp,
		amrex::MultiFab *	mf_mskr,
		amrex::MultiFab *	mf_msku,
		amrex::MultiFab *	mf_mskv,
		const int	nstp,
		const int	nnew,
		const int	N,
		const amrex::Real	dt_lev
	)

Corrector step for GLS calculation.

Parameters

[in]	lev	level to operate on
[in,out]	mf_gls	turbulent generic length scale
[in,out]	mf_tke	turbulent kinetic energy
[in]	mf_W	vertical velocity
[in,out]	mf_Akv	vertical viscosity coefficient
[in,out]	mf_Akt	vertical diffusivity coefficients
[in,out]	mf_Akk	turbulent kinetic energy vertical diffusion coefficient
[in,out]	mf_Akp	turbulent length scale vertical diffusion coefficient
[in]	mf_mskr	land-sea mask on rho points
[in]	mf_msku	land-sea mask on u points
[in]	mf_mskv	land-sea mask on v points
[in]	nstp	index of last time step in gls and tke MultiFabs
[in]	nnew	index of time step to update in gls and tke MultiFabs
[in]	N	number of vertical levels
[in]	dt_lev	time step at this level

Definition at line 247 of file REMORA_gls.cpp.

Referenced by advance_3d().

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gls_prestep()

void REMORA::gls_prestep	(	int	lev,
		amrex::MultiFab *	mf_gls,
		amrex::MultiFab *	mf_tke,
		amrex::MultiFab &	mf_W,
		amrex::MultiFab *	mf_msku,
		amrex::MultiFab *	mf_mskv,
		const int	nstp,
		const int	nnew,
		const int	iic,
		const int	ntfirst,
		const int	N,
		const amrex::Real	dt_lev
	)

Prestep for GLS calculation.

Parameters

[in]	lev	level to operate on
[in,out]	mf_gls	turbulent generic length scale
[in,out]	mf_tke	turbulent kinetic energy
[in]	mf_W	vertical velocity
[in]	mf_msku	land-sea mask on u points
[in]	mf_mskv	land-sea mask on v points
[in]	nstp	index of last time step in gls and tke MultiFabs
[in]	nnew	index of time step to update in gls and tke MultiFabs
[in]	iic	which time step we're on
[in]	ntfirst	what is the first time step?
[in]	N	number of vertical levels
[in]	dt_lev	time step at this level

Definition at line 20 of file REMORA_gls.cpp.

Referenced by setup_step().

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GotoNextLine()

void REMORA::GotoNextLine ( std::istream &  is )

staticprivate

utility to skip to next line in Header

Definition at line 8 of file REMORA_Checkpoint.cpp.

Referenced by ReadCheckpointFile().

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init_analytic()

void REMORA::init_analytic ( int  lev )

private

Initialize initial problem data from analytic functions.

Parameters

[in]

lev

level to initialize on

Definition at line 15 of file REMORA_init.cpp.

Referenced by init_only().

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init_bathymetry_from_netcdf()

void REMORA::init_bathymetry_from_netcdf

(

int

lev

)

Bathymetry data initialization from NetCDF file.

Parameters

lev	Integer specifying the current level

Definition at line 669 of file REMORA_init_from_netcdf.cpp.

Referenced by set_bathymetry().

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init_bathymetry_full_domain_from_analytic()

void REMORA::init_bathymetry_full_domain_from_analytic

(

)

Full domain bathymetry data initialization from analytic.

Definition at line 373 of file REMORA_init.cpp.

Referenced by init_only().

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init_bathymetry_full_domain_from_netcdf()

void REMORA::init_bathymetry_full_domain_from_netcdf

(

)

Full domain high-res bathymetry data initialization from NetCDF file.

Definition at line 1115 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only().

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init_bcs()

void REMORA::init_bcs ( )

private

Read in boundary parameters from input file and set up data structures.

Definition at line 9 of file REMORA_init_bcs.cpp.

Referenced by InitData().

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init_bdry_from_netcdf()

void REMORA::init_bdry_from_netcdf

(

int

lev

)

Boundary data initialization from NetCDF file.

Parameters

lev	Integer specifying the current level

Definition at line 789 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only().

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init_beta_plane_coriolis()

void REMORA::init_beta_plane_coriolis

(

int

lev

)

Calculate Coriolis parameters from beta plane parametrization.

Parameters

[in]

lev

level to initialize on

Definition at line 112 of file REMORA_init.cpp.

Referenced by set_coriolis().

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init_biology_from_netcdf()

void REMORA::init_biology_from_netcdf

(

int

lev

)

Biology initialization from NetCDF file.

Initialize the biological tracers from the initial NetCDF file.

Called from init_biology_ic, which chooses between this and the analytic profile on remora.biology_ic_type rather than on remora.ic_type.

Parameters

lev	Integer specifying the current level

Definition at line 261 of file REMORA_init_from_netcdf.cpp.

Referenced by init_biology_ic().

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init_biology_full_domain_from_netcdf()

void REMORA::init_biology_full_domain_from_netcdf

(

)

Full-domain high-res biology initialization from NetCDF file.

Biology initialization from full-domain NetCDF file.

Definition at line 399 of file REMORA_init_from_netcdf.cpp.

Referenced by init_biology_ic_full_domain().

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init_biology_ic()

void REMORA::init_biology_ic

(

int

lev

)

Initialize biology tracers from whichever source remora.biology_ic_type selects. Call after the physical fields exist: the analytic profiles are functions of temperature.

Initialize the biology tracers from whichever source remora.biology_ic_type selects.

Deliberately decoupled from remora.ic_type. A NetCDF initial file supplies only the tracers it happens to contain – the BioToy file has oxygen but no PO4 or ODU – so validating an option set the file does not cover would otherwise mean regenerating binary input that no fresh clone can reproduce. With biology_ic_type = analytic the physical fields still come from NetCDF while biology comes from the problem's analytic profile.

Must be called after the physical fields are initialized: the analytic biology profiles are functions of temperature.

Parameters

[in]

lev

level to initialize on

Definition at line 39 of file REMORA_init.cpp.

Referenced by init_only().

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init_biology_ic_full_domain()

void REMORA::init_biology_ic_full_domain

(

)

Full-domain counterpart of init_biology_ic, for the hires_init_level average-down path.

Full-domain counterpart of init_biology_ic, for the hires_init_level path where initial data is specified on a high-resolution level and averaged down.

Fills the biology components of vec_cons_full_domain[hires_init_level]. Must be called after the physical fields on that level are set (the analytic profiles are functions of temperature) and before whatever averages vec_cons_full_domain down.

Definition at line 76 of file REMORA_init.cpp.

Referenced by init_full_domain_from_analytic(), and init_only().

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init_clim_nudg_coeff()

void REMORA::init_clim_nudg_coeff

(

int

lev

)

Wrapper to initialize climatology nudging coefficient.

Parameters

[in]

lev

level to operate on

Definition at line 280 of file REMORA_init.cpp.

Referenced by init_only().

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init_clim_nudg_coeff_from_netcdf()

void REMORA::init_clim_nudg_coeff_from_netcdf

(

int

lev

)

Climatology nudging coefficient initialization from NetCDF file.

Parameters

lev	Integer specifying the current level

Definition at line 922 of file REMORA_init_from_netcdf.cpp.

Referenced by init_clim_nudg_coeff().

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init_coriolis_from_netcdf()

void REMORA::init_coriolis_from_netcdf

(

int

lev

)

Coriolis parameter data initialization from NetCDF file.

Parameters

lev	Integer specifying the current level

Definition at line 716 of file REMORA_init_from_netcdf.cpp.

Referenced by set_coriolis().

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init_data_from_netcdf()

void REMORA::init_data_from_netcdf

(

int

lev

)

Problem initialization from NetCDF file.

Parameters

lev	Integer specifying the current level

Definition at line 152 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only().

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init_data_full_domain_from_netcdf()

void REMORA::init_data_full_domain_from_netcdf

(

)

High resolution roblem initialization from NetCDF file.

Definition at line 298 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only().

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init_full_domain_from_analytic()

void REMORA::init_full_domain_from_analytic ( )

private

Initialize high resolution initial problem data from analytic functions.

Definition at line 442 of file REMORA_init.cpp.

Referenced by init_only().

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init_full_domain_zeta_from_analytic()

void REMORA::init_full_domain_zeta_from_analytic ( )

private

Initialize high resolution initial sea surface height from analytic functions.

Definition at line 459 of file REMORA_init.cpp.

Referenced by init_only().

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init_gls_vmix()

void REMORA::init_gls_vmix	(	int	lev,
		SolverChoice	solver_choice
	)

Initialize GLS variables.

Parameters

[in]	lev	level to operate on
[in]	solver_choice	algorithmic choices

Definition at line 235 of file REMORA_init.cpp.

Referenced by init_set_vmix().

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init_grid_vars_from_netcdf()

void REMORA::init_grid_vars_from_netcdf

(

int

lev

)

Grid variable initialization from NetCDF file.

Parameters

lev	Integer specifying the current level

Definition at line 530 of file REMORA_init_from_netcdf.cpp.

Referenced by set_bathymetry(), and set_grid_scale().

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init_grid_vars_full_domain_from_netcdf()

void REMORA::init_grid_vars_full_domain_from_netcdf

(

)

Full domain high-res grid variable initialization from NetCDF file.

Definition at line 1168 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only().

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init_masks()

void REMORA::init_masks ( int  lev, const amrex::BoxArray &  ba, const amrex::DistributionMapping &  dm  )

private

Allocate MultiFabs for masks.

Parameters

[in]	lev	level to operate on
[in]	ba	BoxArray for the level
[in]	dm	DistributionMapping for the level

Definition at line 545 of file REMORA_make_new_level.cpp.

Referenced by MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), and RemakeLevel().

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init_masks_from_netcdf()

void REMORA::init_masks_from_netcdf

(

int

lev

)

Mask data initialization from NetCDF file.

Parameters

lev	Integer specifying the current level

Definition at line 751 of file REMORA_init_from_netcdf.cpp.

Referenced by set_masks().

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init_masks_full_domain_from_analytic()

void REMORA::init_masks_full_domain_from_analytic

(

)

Full domain land-sea mask initialization from analytic.

Definition at line 385 of file REMORA_init.cpp.

Referenced by init_only().

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init_masks_full_domain_from_netcdf()

void REMORA::init_masks_full_domain_from_netcdf

(

)

Full domain high-res mask data initialization from NetCDF file.

Definition at line 1141 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only().

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init_only()

void REMORA::init_only	(	int	lev,
		amrex::Real	time
	)

Init (NOT restart or regrid)

Parameters

[in]	lev	level to operate on
[in]	time	current time for initialization

Definition at line 1681 of file REMORA.cpp.

Referenced by MakeNewLevelFromScratch().

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init_ref_ratios()

void REMORA::init_ref_ratios ( )

private

Reject vertical refinement and accumulate the refinement ratios.

Reject refinement in the vertical, and accumulate the refinement ratios.

Shared by both constructors. It used to be written out in each of them, and the explicit one had been left without the cum_ref_ratios half – so the vector stayed empty, and every full-domain hires array and every mask coarsening that indexes it read out of bounds.

Definition at line 223 of file REMORA.cpp.

Referenced by REMORA(), and REMORA().

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init_riv_pos_from_netcdf()

void REMORA::init_riv_pos_from_netcdf

(

int

lev

)

Parameters

[in]

lev

level to read in river data

Definition at line 1006 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only(), MakeNewLevelFromCoarse(), and RemakeLevel().

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init_scalar_metadata()

void REMORA::init_scalar_metadata ( )

private

Build runtime scalar names after nscalar is known.

Definition at line 252 of file REMORA.cpp.

Referenced by ReadParameters().

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init_scalars_from_netcdf()

void REMORA::init_scalars_from_netcdf

(

int

lev

)

Passive (dye) scalar initialization from NetCDF file. Called from init_data_from_netcdf: dye follows remora.ic_type rather than having a source flag of its own.

Initialize the passive (dye) scalars from the initial NetCDF file.

Unlike biology, dye has no initialization-source flag of its own: it follows remora.ic_type along with temperature, salinity, and velocity, so this is called from init_data_from_netcdf rather than from a dispatcher. Each dye whose variable the file carries is read into its own component; the rest keep the zero written just before the call.

Parameters

lev	Integer specifying the current level

Definition at line 215 of file REMORA_init_from_netcdf.cpp.

Referenced by init_data_from_netcdf().

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init_scalars_full_domain_from_netcdf()

void REMORA::init_scalars_full_domain_from_netcdf

(

)

Full-domain high-res passive (dye) scalar initialization from NetCDF file.

Full-domain counterpart of init_scalars_from_netcdf, for the hires_init_level average-down path. Called from init_data_full_domain_from_netcdf before that routine averages vec_cons_full_domain down, so no average down is needed here.

Definition at line 362 of file REMORA_init_from_netcdf.cpp.

Referenced by init_data_full_domain_from_netcdf().

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init_set_vmix()

void REMORA::init_set_vmix

(

int

lev

)

Initialize vertical mixing coefficients from file or analytic.

Definition at line 832 of file REMORA.cpp.

Referenced by init_only(), MakeNewLevelFromCoarse(), and RemakeLevel().

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init_stretch_coeffs()

void REMORA::init_stretch_coeffs

(

)

initialize and calculate stretch coefficients

Definition at line 310 of file REMORA_init.cpp.

Referenced by InitData().

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init_stuff()

void REMORA::init_stuff ( int  lev, const amrex::BoxArray &  ba, const amrex::DistributionMapping &  dm  )

private

Allocate MultiFabs for state and evolution variables.

Parameters

[in]	lev	level to operate on
[in]	ba	BoxArray for the level
[in]	dm	DistributionMapping for the level

Definition at line 573 of file REMORA_make_new_level.cpp.

Referenced by MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), and RemakeLevel().

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init_zeta_from_netcdf()

void REMORA::init_zeta_from_netcdf

(

int

lev

)

Sea-surface height data initialization from NetCDF file.

Parameters

lev	Integer specifying the current level

Definition at line 440 of file REMORA_init_from_netcdf.cpp.

Referenced by set_zeta().

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init_zeta_full_domain_from_netcdf()

void REMORA::init_zeta_full_domain_from_netcdf

(

)

Full-domain high res sea-surface height data initialization from NetCDF file.

Definition at line 486 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only().

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InitData()

void REMORA::InitData

(

)

Initialize multilevel data.

This is called from main.cpp and handles all initialization, whether from start or restart

Definition at line 408 of file REMORA.cpp.

Referenced by main().

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InitializeFromFile()

void REMORA::InitializeFromFile ( )

private

Read the file passed to remora.restart and use it as an initial condition for the current simulation.

InitializeLevelFromData()

void REMORA::InitializeLevelFromData ( int  lev, const amrex::MultiFab &  initial_data  )

private

Initialize the new-time data at a level from the initial_data MultiFab.

is_it_time_for_action()

bool REMORA::is_it_time_for_action	(	int	nstep,
		amrex::Real	time,
		amrex::Real	dt,
		int	action_interval,
		amrex::Real	action_per
	)

Decide if it is time to take an action.

Parameters

[in]	nstep	what step we're on
[in]	lev	level to calculate on
[in]	dtlev	time step for this level
[in]	action_interval	number of time steps between actions
[in]	action_per	time interval between actions

Definition at line 280 of file REMORA_SumIQ.cpp.

Referenced by InitData(), and post_timestep().

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lin_eos()

void REMORA::lin_eos	(	const amrex::Box &	bx,
		const amrex::Array4< amrex::Real const > &	state,
		const amrex::Array4< amrex::Real > &	rho,
		const amrex::Array4< amrex::Real > &	rhoA,
		const amrex::Array4< amrex::Real > &	rhoS,
		const amrex::Array4< amrex::Real > &	bvf,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	z_w,
		const amrex::Array4< amrex::Real const > &	z_r,
		const amrex::Array4< amrex::Real const > &	h,
		const amrex::Array4< amrex::Real const > &	mskr,
		const int	N
	)

Calculate density and related quantities from linear equation of state.

Parameters

[in]	bx	box for calculation
[in]	state	state holds temp, salt
[out]	rho	density
[out]	rhoA	vertically-averaged density
[out]	rhoS	density perturbation
[out]	bvf	Brunt-Vaisala frequency
[in]	Hz	vertical cell height
[in]	z_r	z coordinates at rho points
[in]	z_w	z coordinates at w points
[in]	h	bathymetry
[in]	mskr	land-sea mask on rho points
[in]	N	number of vertical levels

Definition at line 61 of file REMORA_rho_eos.cpp.

Referenced by rho_eos().

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MakeNewLevelFromCoarse()

void REMORA::MakeNewLevelFromCoarse ( int  lev, amrex::Real  time, const amrex::BoxArray &  ba, const amrex::DistributionMapping &  dm  )

overridevirtual

Make a new level using provided BoxArray and DistributionMapping and fill with interpolated coarse level data. Overrides the pure virtual function in AmrCore.

Make a new level using provided BoxArray and DistributionMapping and fill with interpolated coarse level data (overrides the pure virtual function in AmrCore) regrid --> RemakeLevel (if level already existed) regrid --> MakeNewLevelFromCoarse (if adding new level)

Parameters

[in]	lev	level to make
[in]	time	current time
[in]	ba	BoxArray for the level
[in]	dm	DistributionMapping for the level

Definition at line 24 of file REMORA_make_new_level.cpp.

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MakeNewLevelFromScratch()

void REMORA::MakeNewLevelFromScratch ( int  lev, amrex::Real  time, const amrex::BoxArray &  ba, const amrex::DistributionMapping &  dm  )

overridevirtual

Make a new level from scratch using provided BoxArray and DistributionMapping. Only used during initialization. Overrides the pure virtual function in AmrCore.

Make a new level from scratch using provided BoxArray and DistributionMapping. This is called both for initialization and for restart (overrides the pure virtual function in AmrCore) main.cpp --> REMORA::InitData --> InitFromScratch --> MakeNewGrids --> MakeNewLevelFromScratch restart --> MakeNewGrids --> MakeNewLevelFromScratch

Parameters

[in]	lev	level to make
[in]	time	current time
[in]	ba	BoxArray for the level
[in]	dm	DistributionMapping for the level

Definition at line 344 of file REMORA_make_new_level.cpp.

Referenced by ReadCheckpointFile().

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mask_arrays_for_write()

void REMORA::mask_arrays_for_write	(	int	lev,
		amrex::Real	fill_value,
		amrex::Real	fill_where
	)

Mask data arrays before writing output.

Parameters

lev	level to mask
fill_value	fill value to mask with
fill_where	value at cells where we will apply the mask. This is necessary because rivers

Definition at line 992 of file REMORA_Plotfile.cpp.

Referenced by WritePlotFile().

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nonlin_eos()

void REMORA::nonlin_eos	(	const amrex::Box &	bx,
		const amrex::Array4< amrex::Real const > &	state,
		const amrex::Array4< amrex::Real > &	rho,
		const amrex::Array4< amrex::Real > &	rhoA,
		const amrex::Array4< amrex::Real > &	rhoS,
		const amrex::Array4< amrex::Real > &	bvf,
		const amrex::Array4< amrex::Real > &	alpha,
		const amrex::Array4< amrex::Real > &	beta,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	z_w,
		const amrex::Array4< amrex::Real const > &	z_r,
		const amrex::Array4< amrex::Real const > &	h,
		const amrex::Array4< amrex::Real const > &	mskr,
		const int	N
	)

Calculate density and related quantities from nonlinear equation of state.

Parameters

[in]	bx	box for calculation
[in]	state	state holds temp, salt
[out]	rho	density
[out]	rhoA	vertically-averaged density
[out]	rhoS	density perturbation
[out]	bvf	Brunt-Vaisala frequency
[out]	alpha	thermal expansion coefficient
[out]	beta	saline contraction coefficient
[in]	Hz	vertical cell height
[in]	z_r	z coordinates at rho points
[in]	z_w	z coordinates at w points
[in]	h	bathymetry
[in]	mskr	land-sea mask on rho points
[in]	N	number of vertical levels

Definition at line 158 of file REMORA_rho_eos.cpp.

Referenced by rho_eos().

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num_bc_vars()

int REMORA::num_bc_vars ( ) const

inlinenoexcept

Definition at line 1388 of file REMORA.H.

Referenced by init_bcs().

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num_bdy_vars()

int REMORA::num_bdy_vars ( ) const

inlinenoexcept

Definition at line 1396 of file REMORA.H.

Referenced by init_bcs(), init_bdry_from_netcdf(), and resize_stuff().

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num_bio()

int REMORA::num_bio ( ) const

inlinenoexcept

Number of biology tracers carried in the state.

Definition at line 2001 of file REMORA.H.

num_passive_scalars()

int REMORA::num_passive_scalars ( ) const

inlinenoexcept

Number of passive (dye) scalars in the state, not counting biology tracers.

Zero means the state has no dye component at all, so Tracer_comp is either the first biology tracer or one past the end of cons. Problem setups that initialize a dye have to test this rather than nComp(), which cannot tell a dye apart from a biology tracer.

Definition at line 1405 of file REMORA.H.

num_scalar()

int REMORA::num_scalar ( ) const

inlinenoexcept

Number of passive (dye) scalars carried in the state.

Definition at line 2003 of file REMORA.H.

NumDataLogs()

AMREX_FORCE_INLINE int REMORA::NumDataLogs ( )

inlineprivatenoexcept

Definition at line 1936 of file REMORA.H.

Referenced by sum_integrated_quantities().

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PackSurfaceState()

void REMORA::PackSurfaceState	(	amrex::Vector< amrex::MultiFab * > &	state,
		amrex::Real	time,
		const amrex::MultiFab *	weight_o2a_mf,
		const amrex::iMultiFab *	index_o2a_mf,
		int	max_stencil_size,
		const amrex::iMultiFab *	dst_land_mask = nullptr
	)

Extracts SST from the 3D conservative state for the atmospheric driver.

Reads Temp_comp at the top water-column cell (k_sfc), converts from Celsius to Kelvin, and copies the result into state[SSTIndex].

Parameters

[in,out]	state	OCN2ATM slab buffer sized by the driver (one MultiFab per ocean-to-atmosphere export layer). state[SSTIndex] (index 0) is overwritten with sea-surface temperature (SST) sampled from the Temp_comp tracer at the uppermost sigma level (k = Nz) and converted from degrees Celsius to Kelvin for the atmospheric driver. An empty vector or null state[0] is treated as a no-op.
[in]	time	Current ocean model time (unused; retained for driver interface conformance).

Definition at line 380 of file REMORA_Coupling.cpp.

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PlotFileName()

std::string REMORA::PlotFileName ( int  lev ) const

private

get plotfile name

post_timestep()

void REMORA::post_timestep	(	int	nstep,
		amrex::Real	time,
		amrex::Real	dt_lev
	)

Called after every level 0 timestep.

Parameters

[in]	nstep	which step we're on
[in]	time	current time
[in]	dt_lev0	time step on level 0

Definition at line 376 of file REMORA.cpp.

Referenced by Evolve(), and EvolveOneStep().

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prestep()

void REMORA::prestep	(	int	lev,
		amrex::MultiFab &	mf_uold,
		amrex::MultiFab &	mf_vold,
		amrex::MultiFab &	mf_u,
		amrex::MultiFab &	mf_v,
		amrex::MultiFab *	mf_ru,
		amrex::MultiFab *	mf_rv,
		amrex::MultiFab &	S_old,
		amrex::MultiFab &	S_new,
		amrex::MultiFab &	mf_W,
		amrex::MultiFab &	mf_DC,
		const amrex::MultiFab *	mf_z_r,
		const amrex::MultiFab *	mf_z_w,
		const amrex::MultiFab *	mf_h,
		const amrex::MultiFab *	mf_pm,
		const amrex::MultiFab *	mf_pn,
		const amrex::MultiFab *	mf_sustr,
		const amrex::MultiFab *	mf_svstr,
		const amrex::MultiFab *	mf_bustr,
		const amrex::MultiFab *	mf_bvstr,
		const amrex::MultiFab *	mf_msku,
		const amrex::MultiFab *	mf_mskv,
		const int	iic,
		const int	nfirst,
		const int	nnew,
		int	nstp,
		int	nrhs,
		int	N,
		const amrex::Real	dt_lev
	)

Wrapper function for prestep.

Parameters

[in]	lev	level to operate on
[in]	mf_uold	u-velocity from last time step
[in]	mf_vold	v-velocity from last time step
[out]	mf_u	u-velocity at current time step
[out]	mf_v	v-velocity at current time step
[in,out]	mf_ru	u-velocity RHS at current time step
[in,out]	mf_rv	v-velocity RHS at current time step
[in]	S_old	scalar variables at last time step
[in,out]	S_new	scalar variables at current time step
[in]	mf_W	vertical velocity
	mf_DC	temporary variable container
[in]	mf_z_r	z coordinates at rho points (cell centers)
[in]	mf_z_w	z coordinates at w points
[in]	mf_h	bathymetry
[in]	mf_pm	1/dx
[in]	mf_pn	1/dy
[in]	mf_sustr	u-direction surface momentum flux
[in]	mf_svstr	v-direction surface momentum flux
[in]	mf_bustr	u-direction bottom stress
[in]	mf_bvstr	v-direction bottom stress
[in]	mf_msku	land-sea mask on u-points
[in]	mf_mskv	land-sea mask on v-points
[in]	iic	which time step we're on
[in]	ntfirst	what is the first time step?
[in]	nnew	index of time step to update
[in]	nstp	index of last time step
[in]	nrhs	index of RHS component
[in]	N	number of vertical levels
[in]	dt_lev	time step at this level

Definition at line 38 of file REMORA_prestep.cpp.

Referenced by setup_step().

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prestep_diffusion()

void REMORA::prestep_diffusion	(	const amrex::Box &	bx,
		const amrex::Box &	gbx,
		const int	ioff,
		const int	joff,
		const amrex::Array4< amrex::Real > &	vel,
		const amrex::Array4< amrex::Real const > &	vel_old,
		const amrex::Array4< amrex::Real > &	rvel,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	Akv,
		const amrex::Array4< amrex::Real > &	FC,
		const amrex::Array4< amrex::Real const > &	sstr,
		const amrex::Array4< amrex::Real const > &	bstr,
		const amrex::Array4< amrex::Real const > &	z_r,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		const int	iic,
		const int	ntfirst,
		const int	nnew,
		int	nstp,
		int	nrhs,
		int	N,
		const amrex::Real	lambda,
		const amrex::Real	dt_lev
	)

Update velocities or tracers with diffusion/viscosity as the last part of the prestep.

Called from prestep. The tracer update is a bit different from the u,v updates so we test for it, but checking if ioff=0 and joff=0. In some cases, though, we can recover the tracer update from the generic one by setting those indices. Setting icc and ntfirst identically for the tracers should be equivalent to setting ioff=0 and joff=0

Parameters

[in]	vel_bx	tile box
[in]	gbx	grown tile box
[in]	ioff	offset in x direction
[in]	joff	offset in y direction
[out]	vel	velocity or scalar to update
[in]	vel_old	velocity or scalar at last time
[in,out]	rvel	velocity or scalar RHS
[in]	Hz	vertical cell height
[in]	Akv	vertical viscosity coefficient
	FC	temporary
[in]	sstr	surface flux
[in]	bstr	bottom flux
[in]	z_r	z coordinates at rho points
[in]	pm	1/dx
[in]	pn	1/dy
[in]	iic	which time step we're on
[in]	ntfirst	what is the first time step?
[in]	nnew	index of time step to update
[in]	nstp	index of last time step
[in]	nrhs	index of RHS component
[in]	N	number of vertical levels
[in]	lambda	weighting coefficient for the newest (implicit) time step derivatives
[in]	dt_lev	time step at this level

Definition at line 38 of file REMORA_prestep_diffusion.cpp.

Referenced by prestep().

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prestep_t_advection()

void REMORA::prestep_t_advection	(	int	lev,
		const amrex::Box &	tbx,
		const amrex::Box &	gbx,
		const amrex::Array4< amrex::Real > &	tempold,
		const amrex::Array4< amrex::Real > &	tempcache,
		const amrex::Array4< amrex::Real > &	Hz,
		const amrex::Array4< amrex::Real > &	Huon,
		const amrex::Array4< amrex::Real > &	Hvom,
		const amrex::Array4< amrex::Real > &	W,
		const amrex::Array4< amrex::Real > &	DC,
		const amrex::Array4< amrex::Real > &	FC,
		const amrex::Array4< amrex::Real > &	sstore,
		const amrex::Array4< amrex::Real const > &	z_w,
		const amrex::Array4< amrex::Real const > &	h,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		const amrex::Array4< amrex::Real const > &	msku,
		const amrex::Array4< amrex::Real const > &	mskv,
		const amrex::Array4< int const > &	river_pos,
		const amrex::Array4< amrex::Real const > &	river_source,
		int	iic,
		int	ntfirst,
		int	nrhs,
		int	N,
		const amrex::Real	dt_lev
	)

Prestep advection calculations for the tracers.

Parameters

[in]	lev	level to operate on
[in]	tbx	tile box
[in]	gbx	grown tile box
[in]	tempold	scalar at last time
[in]	tempcache	cached current time step's scalar value
[in]	Hz	vertical cell height
[in]	Huon	u-volume flux
[in]	Hvom	v-volume flux
[in]	Akv	vertical viscosity coefficient
[in,out]	W	vertical velocity
	DC	temporary
	FC	temporary
[out]	tempstore	scratch space for calculations on scalars
[in]	z_w	z coordinates at w points
[in]	h	bathymetry
[in]	pm	1/dx
[in]	pn	1/dy
[in]	msku	land-sea mask on u-points
[in]	mskv	land-sea mask on v-points
[in]	river_pos	river positions
[in]	river_source	river source data to add, if using
[in]	iic	which time step we're on
[in]	ntfirst	what is the first time step?
[in]	nrhs	index of RHS component
[in]	N	number of vertical levels
[in]	dt_lev	time step at this level

Definition at line 35 of file REMORA_prestep_t_advection.cpp.

Referenced by prestep().

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print_banner()

void REMORA::print_banner ( MPI_Comm  comm, std::ostream &  out  )

static

Definition at line 60 of file REMORA_console_io.cpp.

Referenced by main().

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print_error()

void REMORA::print_error ( MPI_Comm  comm, const std::string &  msg  )

static

Definition at line 43 of file REMORA_console_io.cpp.

Referenced by main().

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print_summary()

static void REMORA::print_summary ( std::ostream &  )

static

print_tpls()

void REMORA::print_tpls ( std::ostream &  out )

static

Definition at line 137 of file REMORA_console_io.cpp.

print_usage()

void REMORA::print_usage ( MPI_Comm  comm, std::ostream &  out  )

static

Definition at line 26 of file REMORA_console_io.cpp.

Referenced by main().

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prsgrd()

void REMORA::prsgrd	(	const amrex::Box &	bx,
		const amrex::Box &	gbx,
		const amrex::Box &	utbx,
		const amrex::Box &	vtbx,
		const amrex::Array4< amrex::Real > &	ru,
		const amrex::Array4< amrex::Real > &	rv,
		const amrex::Array4< amrex::Real const > &	pn,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	rho,
		const amrex::Array4< amrex::Real > &	FC,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	z_r,
		const amrex::Array4< amrex::Real const > &	z_w,
		const amrex::Array4< amrex::Real const > &	msku,
		const amrex::Array4< amrex::Real const > &	mskv,
		const int	nrhs,
		const int	N
	)

Calculate pressure gradient.

Parameters

[in]	phi_bx	tilebox
[in]	phi_gbx	grownbox
[in]	utbx	u-nodal tilebox
[in]	vtbx	v-nodal tilebox
[out]	ru	u-velocity RHS
[out]	rv	v-velocity RHS
[in]	pm	1/dx
[in]	pn	1/dy
[in]	rho	density
	FC	temporary
[in]	Hz	vertical cell height
[in]	z_r	z coordinates at rho points
[in]	z_w	z coordinates at w points
[in]	msku	land-sea mask on u-points
[in]	mskv	land-sea mask on v-points
[in]	nrhs	index of RHS component
[in]	N	number of vertical levels

Definition at line 25 of file REMORA_prsgrd.cpp.

Referenced by setup_step().

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ReadCheckpointFile()

void REMORA::ReadCheckpointFile ( )

private

read checkpoint file from disk

Definition at line 220 of file REMORA_Checkpoint.cpp.

Referenced by restart().

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ReadNCMultiFab()

void REMORA::ReadNCMultiFab ( amrex::FabArray< amrex::FArrayBox > &  fab, const std::string &  name, int  coordinatorProc = amrex::ParallelDescriptor::IOProcessorNumber(), int  allow_empty_mf = 0  )

private

Read MultiFab in NetCDF format.

ReadParameters()

void REMORA::ReadParameters ( )

private

read in some parameters from inputs file

Definition at line 2047 of file REMORA.cpp.

Referenced by REMORA(), and REMORA().

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refine_masks_with_grow_cells()

void REMORA::refine_masks_with_grow_cells

(

int

fine_lev

)

Inject the full-domain rho-mask from fine_lev-1 onto fine_lev, piecewise constant, grow cells included.

Inject the full-domain rho-mask from fine_lev-1 up onto fine_lev, grow cells included.

Piecewise constant, which is the rule set_masks already uses for a level above the one the mask was specified on. Nothing finer is known there, so refining cannot add coastline.

Parameters

[in]

fine_lev

level to inject onto

Definition at line 2609 of file REMORA.cpp.

Referenced by ensure_full_domain_masks().

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refinement_criteria_setup()

void REMORA::refinement_criteria_setup ( )

private

Set refinement criteria.

Function to define the refinement criteria based on user input

Definition at line 277 of file REMORA_Tagging.cpp.

Referenced by REMORA(), and REMORA().

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RemakeLevel()

void REMORA::RemakeLevel ( int  lev, amrex::Real  time, const amrex::BoxArray &  ba, const amrex::DistributionMapping &  dm  )

overridevirtual

Remake an existing level using provided BoxArray and DistributionMapping and fill with existing fine and coarse data. Overrides the pure virtual function in AmrCore.

Remake an existing level using provided BoxArray and DistributionMapping and fill with existing fine and coarse data. overrides the pure virtual function in AmrCore

Parameters

[in]	lev	level to make
[in]	time	current time
[in]	ba	BoxArray for the level
[in]	dm	DistributionMapping for the level

Definition at line 164 of file REMORA_make_new_level.cpp.

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remora_advance()

void REMORA::remora_advance	(	int	level,
		amrex::MultiFab &	cons_old,
		amrex::MultiFab &	cons_new,
		amrex::MultiFab &	xvel_old,
		amrex::MultiFab &	yvel_old,
		amrex::MultiFab &	zvel_old,
		amrex::MultiFab &	xvel_new,
		amrex::MultiFab &	yvel_new,
		amrex::MultiFab &	zvel_new,
		amrex::MultiFab &	source,
		const amrex::Geometry	fine_geom,
		const amrex::Real	dt,
		const amrex::Real	time
	)

Interface for advancing the data at one level by one "slow" timestep.

resize_stuff()

void REMORA::resize_stuff ( int  lev )

private

Resize variable containers to accommodate data on levels 0 to max_lev.

Parameters

[in]

lev

level do operate on

Definition at line 414 of file REMORA_make_new_level.cpp.

Referenced by MakeNewLevelFromCoarse(), and MakeNewLevelFromScratch().

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restart()

void REMORA::restart

(

)

\briefRestart

Definition at line 625 of file REMORA.cpp.

Referenced by InitData().

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rho_eos()

void REMORA::rho_eos	(	const amrex::Box &	bx,
		const amrex::Array4< amrex::Real const > &	state,
		const amrex::Array4< amrex::Real > &	rho,
		const amrex::Array4< amrex::Real > &	rhoA,
		const amrex::Array4< amrex::Real > &	rhoS,
		const amrex::Array4< amrex::Real > &	bvf,
		const amrex::Array4< amrex::Real > &	alpha,
		const amrex::Array4< amrex::Real > &	beta,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	z_w,
		const amrex::Array4< amrex::Real const > &	z_r,
		const amrex::Array4< amrex::Real const > &	h,
		const amrex::Array4< amrex::Real const > &	mskr,
		const int	N
	)

Wrapper around equation of state calculation.

Parameters

[in]	bx	box for calculation
[in]	state	state holds temp, salt
[out]	rho	density
[out]	rhoA	vertically-averaged density
[out]	rhoS	density perturbation
[out]	bvf	Brunt-Vaisala frequency
[out]	alpha	thermal expansion coefficient
[out]	beta	saline contraction coefficient
[in]	Hz	vertical cell height
[in]	z_r	z coordinates at rho points
[in]	z_w	z coordinates at w points
[in]	h	bathymetry
[in]	mskr	land-sea mask on rho points
[in]	N	number of vertical levels

Definition at line 22 of file REMORA_rho_eos.cpp.

Referenced by setup_step().

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rhs_t_3d()

void REMORA::rhs_t_3d	(	int	lev,
		const amrex::Box &	bx,
		const amrex::Array4< amrex::Real > &	t,
		const amrex::Array4< amrex::Real const > &	tempstore,
		const amrex::Array4< amrex::Real const > &	Huon,
		const amrex::Array4< amrex::Real const > &	Hvom,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	pn,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	W,
		const amrex::Array4< amrex::Real > &	FC,
		const amrex::Array4< amrex::Real const > &	mskr,
		const amrex::Array4< amrex::Real const > &	msku,
		const amrex::Array4< amrex::Real const > &	mskv,
		const amrex::Array4< int const > &	river_pos,
		const amrex::Array4< amrex::Real const > &	river_source,
		int	nrhs,
		int	nnew,
		int	N,
		const amrex::Real	dt_lev
	)

RHS terms for tracer.

Parameters

[in]	lev	level to operate on
[in]	bx	tilebox
[in,out]	t	tracer data
[in]	sstore	scratch space for tracer calculations
[in]	Huon	u-volume flux
[in]	Hvom	v-volume flux
[in]	Hz	vertical cell height
[in]	pn	1/dx
[in]	pm	1/dy
[in]	W	vertical velocity
	FC	temporary
[in]	mskr	land-sea mask on rho-points
[in]	msku	land-sea mask on u-points
[in]	mskv	land-sea mask on v-points
[in]	river_pos	river positions
[in]	river_source	river source data to add, if using
[in]	nrhs	index of RHS component
[in]	nnew	index of current time step
[in]	N	number of vertical levels
[in]	dt_lev	time step at this level

Definition at line 28 of file REMORA_rhs_t_3d.cpp.

Referenced by advance_3d().

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rhs_uv_2d()

void REMORA::rhs_uv_2d	(	int	lev,
		const amrex::Box &	xbx,
		const amrex::Box &	ybx,
		const amrex::Array4< amrex::Real const > &	uold,
		const amrex::Array4< amrex::Real const > &	vold,
		const amrex::Array4< amrex::Real > &	ru,
		const amrex::Array4< amrex::Real > &	rv,
		const amrex::Array4< amrex::Real const > &	Duon,
		const amrex::Array4< amrex::Real const > &	Dvom,
		const int	nrhs
	)

RHS terms for 2D momentum.

Parameters

[in]	lev	level to operate on
[in]	xbx	Box for operations on x-velocity
[in]	ybx	Box for operations on y-velocity
[in]	ubar	barotropic x-velocity
[in]	vbar	barotropic y-velocity
[in,out]	rhs_ubar	RHS for barotropic x-velocity
[in,out]	rhs_vbar	RHS for barotropic y-velocity
[in]	DUon	u-volume flux (barotropic)
[in]	DVom	v-volume flux (barotropic)
[in]	krhs	index of rhs component

Definition at line 18 of file REMORA_rhs_uv_2d.cpp.

Referenced by advance_2d().

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rhs_uv_3d()

void REMORA::rhs_uv_3d	(	int	lev,
		const amrex::Box &	xbx,
		const amrex::Box &	ybx,
		const amrex::Array4< amrex::Real const > &	uold,
		const amrex::Array4< amrex::Real const > &	vold,
		const amrex::Array4< amrex::Real > &	ru,
		const amrex::Array4< amrex::Real > &	rv,
		const amrex::Array4< amrex::Real > &	rufrc,
		const amrex::Array4< amrex::Real > &	rvfrc,
		const amrex::Array4< amrex::Real const > &	sustr,
		const amrex::Array4< amrex::Real const > &	svstr,
		const amrex::Array4< amrex::Real const > &	bustr,
		const amrex::Array4< amrex::Real const > &	bvstr,
		const amrex::Array4< amrex::Real const > &	Huon,
		const amrex::Array4< amrex::Real const > &	Hvom,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		const amrex::Array4< amrex::Real const > &	W,
		const amrex::Array4< amrex::Real > &	FC,
		int	nrhs,
		int	N
	)

RHS terms for 3D momentum.

Parameters

[in]	lev	level to operate on
[in]	xbx	Box for operations on x-velocity
[in]	ybx	Box for operations on y-velocity
[in]	uold	u-velocity at last time step
[in]	vold	v-velocity at last time step
[in,out]	ru	u-velocity RHS
[in,out]	rv	v-velocity RHS
[in,out]	rufrc	forcing for u-velocity RHS
[in,out]	rvfrc	forcing for v-velocity RHS
[in]	sustr	u-direction surface momentum flux
[in]	svstr	v-direction surface momentum flux
[in]	bustr	u-direction bottom stress
[in]	bvstr	v-direction bottom stress
[in]	Huon	u-volume flux
[in]	Hvom	v-volume flux
[in]	pm	1/dx
[in]	pn	1/dy
[in]	W	vertical velocity
	FC	temporary
[in]	nrhs	index of component for RHS
[in]	N	number of vertical levels

Definition at line 29 of file REMORA_rhs_uv_3d.cpp.

Referenced by setup_step().

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scale_rhs_vars()

void REMORA::scale_rhs_vars

(

)

Scale RHS momentum variables by 1/cell area, needed before FillPatch to different levels.

Definition at line 6 of file REMORA_scale_rhs_vars.cpp.

Referenced by timeStep(), and timeStepML().

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scale_rhs_vars_inv()

void REMORA::scale_rhs_vars_inv

(

)

Scale RHS momentum variables by cell area, needed after FillPatch to different levels.

Definition at line 55 of file REMORA_scale_rhs_vars.cpp.

Referenced by timeStep(), and timeStepML().

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set2DPlotVariables()

void REMORA::set2DPlotVariables ( const std::string &  pp_plot_var_names_2d )

private

Parameters

pp_plot_var_names_2d

list of variable names to plot read in from parameter file

Definition at line 118 of file REMORA_SetPlotVars.cpp.

Referenced by REMORA(), and REMORA().

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set3DPlotVariables()

void REMORA::set3DPlotVariables ( const std::string &  pp_plot_var_names_3d )

private

Parameters

pp_plot_var_names_3d

list of variable names to plot read in from parameter file

Definition at line 16 of file REMORA_SetPlotVars.cpp.

Referenced by REMORA(), and REMORA().

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set_2darrays()

void REMORA::set_2darrays

(

int

lev

)

Set 2D momentum arrays from 3D momentum.

Parameters

[in]

lev

level to operate on

Definition at line 172 of file REMORA_init.cpp.

Referenced by init_only().

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set_analytic_vmix()

void REMORA::set_analytic_vmix

(

int

lev

)

Set vertical mixing coefficients from analytic.

Parameters

[in]

lev

level to operate on

Definition at line 849 of file REMORA.cpp.

Referenced by init_set_vmix(), and setup_step().

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set_bathymetry()

void REMORA::set_bathymetry

(

int

lev

)

Initialize bathymetry from file or analytic.

Parameters

[in]

lev

level to operate on

Definition at line 681 of file REMORA.cpp.

Referenced by init_only().

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set_bathymetry_averaged_down()

void REMORA::set_bathymetry_averaged_down

(

int

lev

)

Copy over bathymetry data that has been averaged down from high resolution input netcdf file.

Parameters

[in]

lev

level to operate on

Definition at line 740 of file REMORA.cpp.

Referenced by MakeNewLevelFromCoarse(), RemakeLevel(), and set_bathymetry().

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set_coriolis()

void REMORA::set_coriolis

(

int

lev

)

Initialize Coriolis factor from file or analytic.

Parameters

[in]

lev

level to operate on

Definition at line 803 of file REMORA.cpp.

Referenced by init_only(), MakeNewLevelFromCoarse(), and RemakeLevel().

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set_curvilinear_terms_from_grid_scale()

void REMORA::set_curvilinear_terms_from_grid_scale

(

int

lev

)

Set curvilinear derivative terms on level lev based on pm and pn.

Parameters

[in]

level to operate on

Definition at line 912 of file REMORA_make_new_level.cpp.

Referenced by set_grid_scale().

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set_drag()

void REMORA::set_drag

(

int

lev

)

Initialize or calculate bottom drag.

set_grid_coords_from_grid_scale()

void REMORA::set_grid_coords_from_grid_scale

(

int

lev

)

Set x/y coords on level lev based on pm and pn.

Parameters

[in]

level to operate on

Definition at line 867 of file REMORA_make_new_level.cpp.

Referenced by set_grid_scale().

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set_grid_scale()

void REMORA::set_grid_scale

(

int

lev

)

Set pm and pn arrays and x/y coords on level lev.

Parameters

[in]

lev

level to operate on

Definition at line 812 of file REMORA_make_new_level.cpp.

Referenced by init_analytic(), init_only(), MakeNewLevelFromCoarse(), RemakeLevel(), and set_bathymetry().

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set_grid_vars_averaged_down()

void REMORA::set_grid_vars_averaged_down

(

int

lev

)

Set pm/pn by averaging down from higher-resolution grid.

Parameters

[in]

lev

level to operate on

Definition at line 757 of file REMORA.cpp.

Referenced by set_bathymetry(), and set_grid_scale().

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set_hmixcoef()

void REMORA::set_hmixcoef

(

int

lev

)

Initialize horizontal mixing coefficients.

Parameters

[in]

lev

level to operate on

Definition at line 1247 of file REMORA.cpp.

Referenced by init_only(), MakeNewLevelFromCoarse(), and RemakeLevel().

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set_init_data_averaged_down()

void REMORA::set_init_data_averaged_down

(

int

lev

)

Problem initialization from averaged-down high resolution data.

Parameters

[in]

lev

level to operate on

Definition at line 786 of file REMORA.cpp.

Referenced by init_only().

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set_masks()

void REMORA::set_masks

(

int

lev

)

Initialize land-sea masks from file or analytic.

Initialize the land-sea mask on this level.

Mirrors set_bathymetry: the mask is specified once, on level 0 or at hires_grid_level, and every other level derived from it, so the levels cannot disagree about the coastline.

Parameters

[in]

lev

level to operate on

Definition at line 872 of file REMORA.cpp.

Referenced by init_only(), MakeNewLevelFromCoarse(), and RemakeLevel().

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set_masks_averaged_down()

void REMORA::set_masks_averaged_down

(

int

lev

)

Copy this level's land-sea mask out of the full-domain mask that was coarsened down from hires_grid_level.

Parameters

[in]

lev

level to operate on

Definition at line 923 of file REMORA.cpp.

Referenced by set_masks().

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set_smflux()

void REMORA::set_smflux

(

int

lev

)

Initialize or calculate surface momentum flux from file or analytic.

Parameters

[in]

lev

level to operate on

Definition at line 1532 of file REMORA.cpp.

Referenced by setup_step().

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set_surface_state()

void REMORA::set_surface_state

(

int

lev

)

Initialize or calculate wind speed and other surface state vars from file or analytic.

Parameters

[in]

lev

level to operate on

Definition at line 1551 of file REMORA.cpp.

Referenced by setup_step().

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set_weights()

void REMORA::set_weights

(

int

lev

)

Set weights for averaging 3D variables to 2D.

Parameters

[in]

lev

level to operate on

Definition at line 11 of file REMORA_set_weights.cpp.

Referenced by init_stuff().

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set_zeta()

void REMORA::set_zeta

(

int

lev

)

Initialize zeta from file or analytic.

Parameters

[in]

lev

level to operate on

Definition at line 642 of file REMORA.cpp.

Referenced by init_only().

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set_zeta_average()

void REMORA::set_zeta_average

(

int

lev

)

Set Zt_avg1 to zeta.

Parameters

[in]

lev

level to operate on

Definition at line 148 of file REMORA_init.cpp.

Referenced by set_zeta().

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set_zeta_averaged_down()

void REMORA::set_zeta_averaged_down

(

int

lev

)

Copy over zeta data that has been averaged down from high res.

Parameters

[in]

lev

level to operate on

Definition at line 775 of file REMORA.cpp.

Referenced by set_zeta().

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set_zeta_to_Ztavg()

void REMORA::set_zeta_to_Ztavg	(	int	lev,
		bool	apply_eminusp = true
	)

Set zeta components to be equal to time-averaged Zt_avg1.

Parameters

[in]	lev	level to operate on
[in]	apply_eminusp	whether to apply the evaporation-minus-precipitation correction to Zt_avg1

Definition at line 934 of file REMORA_make_new_level.cpp.

Referenced by init_only(), MakeNewLevelFromCoarse(), RemakeLevel(), and setup_step().

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SetDriverAtmosToOceanForcingMode()

void REMORA::SetDriverAtmosToOceanForcingMode

(

DriverAtmosForcingMode

mode

)

Definition at line 297 of file REMORA_Coupling.cpp.

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SetLongwaveFromDriver()

void REMORA::SetLongwaveFromDriver

(

)

Definition at line 258 of file REMORA_Coupling.cpp.

setRecordDataInfo()

void REMORA::setRecordDataInfo ( int  i, const std::string &  filename  )

inlineprivate

Definition at line 1962 of file REMORA.H.

Referenced by ReadParameters().

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SetStartTime()

void REMORA::SetStartTime ( amrex::Real  time )

inlinenoexcept

Definition at line 122 of file REMORA.H.

setup_step()

void REMORA::setup_step	(	int	lev,
		amrex::Real	time,
		amrex::Real	dt_lev
	)

Set everything up for a step on a level.

Parameters

[in]	lev	level to operate on
[in]	time	time at start of step
[in]	dt_lev	time step at level

Definition at line 11 of file REMORA_setup_step.cpp.

Referenced by Advance(), and timeStepML().

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stretch_transform()

void REMORA::stretch_transform

(

int

lev

)

Calculate vertical stretched coordinates.

Parameters

[in]

lev

level to operate on

Definition at line 78 of file REMORA_DepthStretchTransform.H.

Referenced by advance_3d(), AverageDownTo(), init_only(), MakeNewLevelFromCoarse(), ReadCheckpointFile(), and RemakeLevel().

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sum_integrated_quantities()

void REMORA::sum_integrated_quantities

(

amrex::Real

time

)

Integrate conserved quantities for diagnostics.

Parameters

[in]

time

current time

Definition at line 11 of file REMORA_SumIQ.cpp.

Referenced by InitData(), and post_timestep().

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t3dmix2()

void REMORA::t3dmix2	(	const amrex::Box &	bx,
		const amrex::Array4< amrex::Real > &	state,
		const amrex::Array4< amrex::Real > &	state_rhs,
		const amrex::Array4< amrex::Real const > &	diff2,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	z_r,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		const amrex::Array4< amrex::Real const > &	msku,
		const amrex::Array4< amrex::Real const > &	mskv,
		const amrex::Real	dt_lev,
		const int	ncomp,
		const int	N
	)

Wrapper for harmonic diffusivity for tracers.

Parameters

[in]	bx	box to operate on
[in,out]	state	scalar data
[out]	state_rhs	scalar data RHS
[in]	diff2	diffusivity
[in]	Hz	vertical cell height
[in]	z_r	rho-point z coordinate
[in]	pm	1/dx
[in]	pn	1/dy
[in]	msku	land-sea mask on u-points
[in]	mskv	land-sea mask on v-points
[in]	dt_lev	time step at level
[in]	ncomp	number of components to do this calculation on
[in]	N	number of vertical levels

Definition at line 21 of file REMORA_t3dmix.cpp.

Referenced by setup_step().

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t3dmix2_geo()

void REMORA::t3dmix2_geo	(	const amrex::Box &	bx,
		const amrex::Array4< amrex::Real > &	state,
		const amrex::Array4< amrex::Real > &	state_rhs,
		const amrex::Array4< amrex::Real const > &	diff2,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	z_r,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		const amrex::Array4< amrex::Real const > &	msku,
		const amrex::Array4< amrex::Real const > &	mskv,
		const amrex::Real	dt_lev,
		const int	ncomp,
		const int	N
	)

Harmonic diffusivity for tracers along geopotential surfaces.

Parameters

[in]	bx	box to operate on
[in,out]	state	scalar data
[out]	state_rhs	scalar data RHS
[in]	diff2	diffusivity
[in]	Hz	vertical cell height
[in]	z_r	rho-point z coordinates
[in]	pm	1/dx
[in]	pn	1/dy
[in]	msku	land-sea mask on u-points
[in]	mskv	land-sea mask on v-points
[in]	dt_lev	time step at level
[in]	ncomp	number of components to do this calculation on
[in]	N	number of vertical levels

Definition at line 126 of file REMORA_t3dmix.cpp.

Referenced by t3dmix2().

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t3dmix2_s()

void REMORA::t3dmix2_s	(	const amrex::Box &	bx,
		const amrex::Array4< amrex::Real > &	state,
		const amrex::Array4< amrex::Real > &	state_rhs,
		const amrex::Array4< amrex::Real const > &	diff2,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		const amrex::Array4< amrex::Real const > &	msku,
		const amrex::Array4< amrex::Real const > &	mskv,
		const amrex::Real	dt_lev,
		const int	ncomp
	)

Harmonic diffusivity for tracers along S-coordinate level surfaces.

Parameters

[in]	bx	box to operate on
[in,out]	state	scalar data
[out]	state_rhs	scalar data RHS
[in]	diff2	diffusivity
[in]	Hz	vertical cell height
[in]	pm	1/dx
[in]	pn	1/dy
[in]	msku	land-sea mask on u-points
[in]	mskv	land-sea mask on v-points
[in]	dt_lev	time step at level
[in]	ncomp	number of components to do this calculation on

Definition at line 55 of file REMORA_t3dmix.cpp.

Referenced by t3dmix2().

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timeStep()

void REMORA::timeStep ( int  lev, amrex::Real  time, int  iteration  )

private

advance a level by dt, includes a recursive call for finer levels

Parameters

[in]	lev	level of refinement
[in]	time	simulation time at start of step
[in]	iteration	iteration in subcycling, if using

Definition at line 11 of file REMORA_TimeStep.cpp.

Referenced by Evolve(), EvolveOneStep(), and timeStep().

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timeStepML()

void REMORA::timeStepML ( amrex::Real  time, int  iteration  )

private

advance all levels by dt, loops over finer levels

Parameters

[in]	time	simulation time at start of step
[in]	iteration	iteration in subcycling, if using

Definition at line 10 of file REMORA_TimeStepML.cpp.

Referenced by Evolve(), and EvolveOneStep().

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tke_bc()

int REMORA::tke_bc ( ) const

inlinenoexcept

Definition at line 1383 of file REMORA.H.

Referenced by init_bcs().

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u2d_simple_bc()

int REMORA::u2d_simple_bc ( ) const

inlinenoexcept

Definition at line 1386 of file REMORA.H.

Referenced by init_bcs(), and setup_step().

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ubar_bc()

int REMORA::ubar_bc ( ) const

inlinenoexcept

Definition at line 1380 of file REMORA.H.

Referenced by advance_2d(), fill_from_bdyfiles(), init_bcs(), MakeNewLevelFromCoarse(), RemakeLevel(), and set_2darrays().

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update_avgdown_masks()

void REMORA::update_avgdown_masks

(

int

crse_lev

)

Make sure the coarse masks the average-down kernels read sit on the coarsened layout of level crse_lev+1, rebuilding them if a regrid has moved it.

Make sure the coarse rho-, u- and v-masks are defined on the layout average_down_masked computes on: level crse_lev+1's grids coarsened, rather than level crse_lev's own grids.

The masks are a function of position alone, so between regrids this is the same answer every step; building it once turns three allocations and three ParallelCopy calls per step into three per regrid.

Parameters

[in]

crse_lev

coarse level of the pair

Definition at line 2474 of file REMORA.cpp.

Referenced by AverageDownTo().

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update_massflux_3d()

void REMORA::update_massflux_3d	(	int	lev,
		const amrex::Box &	bx,
		const int	ioff,
		const int	joff,
		const amrex::Array4< amrex::Real > &	phi,
		const amrex::Array4< amrex::Real > &	phibar,
		const amrex::Array4< amrex::Real > &	Hphi,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	pm_or_pn,
		const amrex::Array4< amrex::Real const > &	Dphi1,
		const amrex::Array4< amrex::Real const > &	Dphi2,
		const amrex::Array4< amrex::Real > &	DC,
		const amrex::Array4< amrex::Real > &	FC,
		const amrex::Array4< amrex::Real const > &	msk,
		const int	nnew
	)

Correct mass flux.

Parameters

[in]	lev	level of refinement (coarsest level is 0)
[in]	bx	box on which to update
[in]	ioff	offset in x-direction
[in]	joff	offset in y-direction
[in,out]	phi	u or v
[in,out]	phibar	ubar or vbar
[in,out]	Hphi	phi-volume flux
[in]	Hz	vertical cell height
[in]	pm_or_pn	pm or pn
[in]	Dphi_avg1	DU_avg1 or DV_avg1
[in]	Dphi_avg2	DU_avg2 or DV_avg2
	DC	temporary
	FC	temporary
[in]	msk	land-sea mask
[in]	nnew	component of velocity

Definition at line 23 of file REMORA_update_massflux_3d.cpp.

Referenced by advance_3d().

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update_nodal_masks()

void REMORA::update_nodal_masks

(

int

lev

)

Rebuild the u-, v- and psi-point masks from vec_mskr and fill their ghosts.

Rebuild the u-, v- and psi-point masks from vec_mskr and fill their ghost cells.

Every path goes through here, so the levels cannot end up with different definitions.

Parameters

[in]

lev

level to operate on

Definition at line 1037 of file REMORA_make_new_level.cpp.

Referenced by init_masks_from_netcdf(), set_masks(), and set_masks_averaged_down().

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uv3dmix()

void REMORA::uv3dmix	(	const amrex::Box &	xbx,
		const amrex::Box &	ybx,
		const amrex::Array4< amrex::Real > &	u,
		const amrex::Array4< amrex::Real > &	v,
		const amrex::Array4< amrex::Real const > &	uold,
		const amrex::Array4< amrex::Real const > &	vold,
		const amrex::Array4< amrex::Real > &	rufrc,
		const amrex::Array4< amrex::Real > &	rvfrc,
		const amrex::Array4< amrex::Real const > &	visc2_p,
		const amrex::Array4< amrex::Real const > &	visc2_r,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		const amrex::Array4< amrex::Real const > &	mskp,
		int	nrhs,
		int	nnew,
		const amrex::Real	dt_lev
	)

Harmonic viscosity.

Parameters

[in]	xbx	x-nodal tile box
[in]	ybx	y-nodal tile box
[in,out]	u	u-direction velocity
[in,out]	v	v-direction velocity
[in]	uold	u-direction velocity at last step
[in]	vold	v-direction velocity at last step
[in,out]	rufrc	forcing term for u-velocity RHS
[in,out]	rvfrc	forcing term for v-velocity RHS
[in]	visc2_p	harmonic viscosity on psi points
[in]	visc2_r	harmonic viscosity on rho points
[in]	Hz	vertical cell height
[in]	pm	1/dx
[in]	pn	1/dy
[in]	mskp	land-sea mask on psi-points
[in]	nrhs	index of RHS component
[in]	nnew	index of time step to update
[in]	dt_lev	time step at this level

Definition at line 25 of file REMORA_uv3dmix.cpp.

Referenced by advance_2d(), and setup_step().

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v2d_simple_bc()

int REMORA::v2d_simple_bc ( ) const

inlinenoexcept

Definition at line 1387 of file REMORA.H.

Referenced by init_bcs(), and setup_step().

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vbar_bc()

int REMORA::vbar_bc ( ) const

inlinenoexcept

Definition at line 1381 of file REMORA.H.

Referenced by advance_2d(), fill_from_bdyfiles(), init_bcs(), MakeNewLevelFromCoarse(), RemakeLevel(), and set_2darrays().

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vert_mean_3d()

void REMORA::vert_mean_3d	(	const amrex::Box &	bx,
		const int	ioff,
		const int	joff,
		const amrex::Array4< amrex::Real > &	phi,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real const > &	Dphi_avg1,
		const amrex::Array4< amrex::Real > &	DC,
		const amrex::Array4< amrex::Real > &	CF,
		const amrex::Array4< amrex::Real const > &	pm_or_pn,
		const amrex::Array4< amrex::Real const > &	msk,
		const int	nnew,
		const int	N
	)

Adjust 3D momentum variables based on vertical mean momentum.

Parameters

[in]	phi_bx	box to update on
[in]	ioff	x-direction offset
[in]	joff	y-direction offset
[in,out]	phi	velocity (u or v)
[in]	Dphi_avg1	time average of barotropic velocity
	DC	temporary
	CF	temporary
[in]	pm_or_pn	1/dx or 1/dy
[in]	msk	land-sea mask
[in]	nnew	index of time step to update
[in]	N	number of vertical levels

Definition at line 19 of file REMORA_vert_mean_3d.cpp.

Referenced by advance_3d().

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vert_visc_3d()

void REMORA::vert_visc_3d	(	const amrex::Box &	bx,
		const int	ioff,
		const int	joff,
		const amrex::Array4< amrex::Real > &	phi,
		const amrex::Array4< amrex::Real const > &	Hz,
		const amrex::Array4< amrex::Real > &	Hzk,
		const amrex::Array4< amrex::Real > &	AK,
		const amrex::Array4< amrex::Real const > &	Akv,
		const amrex::Array4< amrex::Real > &	BC,
		const amrex::Array4< amrex::Real > &	DC,
		const amrex::Array4< amrex::Real > &	FC,
		const amrex::Array4< amrex::Real > &	CF,
		const int	nnew,
		const int	N,
		const amrex::Real	dt_lev
	)

Calculate effects of vertical viscosity or diffusivity.

Parameters

[in]	phi_bx	box to update on
[in]	ioff	x-direction offset
[in]	joff	y-direction offset
[in,out]	phi	velocity (u or v)
[in]	Hz	vertical height of cells
	Hzk	temporary
	AK	temporary
[in]	Akv	vertical viscosity coefficient
	BC	temporary
	DC	temporary
	FC	temporary
	CF	temporary
[in]	nnew	index of time step to update
[in]	N	number of vertical levels
[in]	dt_lev	time step at this refinement level

Definition at line 23 of file REMORA_vert_visc_3d.cpp.

Referenced by advance_3d().

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volWgtSumMF()

Real REMORA::volWgtSumMF	(	int	lev,
		const amrex::MultiFab &	mf,
		int	comp,
		bool	local,
		bool	finemask
	)

Perform the volume-weighted sum.

Parameters

[in]	lev	level to calculate on
[in]	mf	data to sum over
[in]	comp	component on which to calculate sum
[in]	local	whether to do the sum locally
[in]	finemask	whether to mask fine level

Definition at line 204 of file REMORA_SumIQ.cpp.

Referenced by sum_integrated_quantities().

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WriteAtFinalTime()

void REMORA::WriteAtFinalTime

(

)

Write checkpoint and plotfiles at end of simulation.

Definition at line 336 of file REMORA.cpp.

Referenced by Evolve().

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WriteAtIntermediateTime()

void REMORA::WriteAtIntermediateTime	(	int	step,
		amrex::Real	cur_time
	)

Write checkpoint and plotfiles at intermediate point of simulation, if needed.

Definition at line 351 of file REMORA.cpp.

Referenced by Evolve(), and EvolveOneStep().

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writeBuildInfo()

void REMORA::writeBuildInfo ( std::ostream &  os )

static

Write build info to os.

Definition at line 135 of file REMORA_writeJobInfo.cpp.

Referenced by main().

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WriteCheckpointFile()

void REMORA::WriteCheckpointFile ( )

private

write checkpoint file to disk

Definition at line 15 of file REMORA_Checkpoint.cpp.

Referenced by InitData(), WriteAtFinalTime(), and WriteAtIntermediateTime().

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WriteGenericPlotfileHeaderWithBathymetry()

void REMORA::WriteGenericPlotfileHeaderWithBathymetry	(	std::ostream &	HeaderFile,
		int	nlevels,
		const amrex::Vector< amrex::BoxArray > &	bArray,
		const amrex::Vector< std::string > &	varnames_3d,
		const amrex::Vector< std::string > &	varnames_2d_rho,
		const amrex::Vector< std::string > &	varnames_2d_u,
		const amrex::Vector< std::string > &	varnames_2d_v,
		const amrex::Vector< amrex::Geometry > &	my_geom,
		amrex::Real	time,
		const amrex::Vector< int > &	level_steps,
		const amrex::Vector< amrex::IntVect > &	rr,
		const std::string &	versionName,
		const std::string &	levelPrefix,
		const std::string &	mfPrefix
	)		const

write out header data for an AMReX plotfile

Parameters

HeaderFile	output stream for header
nlevels	number of levels to write out
bArray	vector over levels of BoxArrays
varnames_3d	3D variable names to write out
varnames_2d	2D variable names to write out
my_geom	geometry to use for writing plotfile
time	time at which to output
level_steps	vector over level of iterations
my_ref_ratio	refinement ratio to use for writing plotfile
versionName	version string for VisIt
levelPrefix	string to prepend to level number
mfPrefix	subdirectory for multifab data

Definition at line 835 of file REMORA_Plotfile.cpp.

Referenced by WriteMultiLevelPlotfileWithBathymetry().

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writeJobInfo()

void REMORA::writeJobInfo

(

const std::string &

dir

)

const

Write job info to stdout.

Definition at line 7 of file REMORA_writeJobInfo.cpp.

Referenced by WritePlotFile().

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WriteMultiLevelPlotfileWithBathymetry()

void REMORA::WriteMultiLevelPlotfileWithBathymetry	(	const std::string &	plotfilename,
		int	nlevels,
		const amrex::Vector< const amrex::MultiFab * > &	mf,
		const amrex::Vector< const amrex::MultiFab * > &	mf_nd,
		const amrex::Vector< const amrex::MultiFab * > &	mf_u,
		const amrex::Vector< const amrex::MultiFab * > &	mf_v,
		const amrex::Vector< const amrex::MultiFab * > &	mf_w,
		const amrex::Vector< const amrex::MultiFab * > &	mf_2d_rho,
		const amrex::Vector< const amrex::MultiFab * > &	mf_2d_u,
		const amrex::Vector< const amrex::MultiFab * > &	mf_2d_v,
		const amrex::Vector< std::string > &	varnames_3d,
		const amrex::Vector< std::string > &	varnames_2d_rho,
		const amrex::Vector< std::string > &	varnames_2d_u,
		const amrex::Vector< std::string > &	varnames_2d_v,
		const amrex::Vector< amrex::Geometry > &	my_geom,
		amrex::Real	time,
		const amrex::Vector< int > &	level_steps,
		const amrex::Vector< amrex::IntVect > &	rr,
		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

write out particular data to an AMReX plotfile

Parameters

plotfilename	name of plotfile to write to
nlevels	number of levels to write out
mf	MultiFab of data to write out
mf_nd	Multifab of nodal data to write out
varnames_3d	3D variable names to write out
varnames_2d_rho	2D cell-centered variable names to write out
varnames_2d_u	2D x-face-based variable names to write out
varnames_2d_v	2D y-face-based variable names to write out
my_geom	geometry to use for writing plotfile
time	time at which to output
level_steps	vector over level of iterations
rr	refinement ratio to use for writing plotfile
versionName	version string for VisIt
levelPrefix	string to prepend to level number
mfPrefix	subdirectory for multifab data
extra_dirs	additional subdirectories within plotfile

Definition at line 670 of file REMORA_Plotfile.cpp.

Referenced by WritePlotFile().

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WriteNCMultiFab()

void REMORA::WriteNCMultiFab ( const amrex::FabArray< amrex::FArrayBox > &  fab, const std::string &  name, bool  set_ghost = false  ) const

private

Write MultiFab in NetCDF format.

WriteNCPlotFile()

void REMORA::WriteNCPlotFile ( int  istep, amrex::MultiFab const *  plotMF  )

private

Write plotfile using NetCDF (wrapper)

Parameters

which_step

current step for output

Definition at line 171 of file REMORA_NCPlotFile.cpp.

Referenced by WritePlotFile().

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WriteNCPlotFile_which()

void REMORA::WriteNCPlotFile_which ( int  lev, int  which_subdomain, amrex::MultiFab const *  plotMF, bool  write_header, ncutils::NCFile &  ncf, bool  is_history  )

private

Write a particular NetCDF plotfile.

Parameters

lev	level of data to output
which_subdomain	index of subdomain if lev != 0
write_header	whether to write a header
ncf	netcdf file object
is_history	whether the file being written is a history file

Definition at line 256 of file REMORA_NCPlotFile.cpp.

Referenced by WriteNCPlotFile().

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WritePlotFile()

void REMORA::WritePlotFile

(

int

istep

)

main driver for writing AMReX plotfiles

Definition at line 16 of file REMORA_Plotfile.cpp.

Referenced by InitData(), timeStepML(), WriteAtFinalTime(), and WriteAtIntermediateTime().

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xvel_bc()

int REMORA::xvel_bc ( ) const

inlinenoexcept

Definition at line 1377 of file REMORA.H.

Referenced by advance_3d(), ErrorEst(), FillBdyCCVels(), FillPatchNoBC(), gls_corrector(), gls_prestep(), init_bcs(), init_only(), InitData(), MakeNewLevelFromCoarse(), RemakeLevel(), rhs_uv_2d(), set_init_data_averaged_down(), timeStepML(), and update_massflux_3d().

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yvel_bc()

int REMORA::yvel_bc ( ) const

inlinenoexcept

Definition at line 1378 of file REMORA.H.

Referenced by advance_3d(), ErrorEst(), FillPatchNoBC(), gls_corrector(), gls_prestep(), init_bcs(), init_only(), InitData(), MakeNewLevelFromCoarse(), RemakeLevel(), rhs_uv_2d(), set_init_data_averaged_down(), timeStepML(), and update_massflux_3d().

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zeta_bc()

int REMORA::zeta_bc ( ) const

inlinenoexcept

Definition at line 1382 of file REMORA.H.

Referenced by advance_2d(), fill_from_bdyfiles(), init_bcs(), init_zeta_from_netcdf(), RemakeLevel(), and set_zeta_averaged_down().

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zvel_bc()

int REMORA::zvel_bc ( ) const

inlinenoexcept

Definition at line 1379 of file REMORA.H.

Referenced by advance_3d_ml(), ErrorEst(), FillPatchNoBC(), gls_corrector(), gls_prestep(), init_bcs(), init_only(), InitData(), MakeNewLevelFromCoarse(), RemakeLevel(), set_analytic_vmix(), setup_step(), and timeStepML().

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Member Data Documentation

advflux_reg

amrex::Vector<std::unique_ptr<amrex::YAFluxRegister> > REMORA::advflux_reg

private

array of flux registers for refluxing in multilevel

Definition at line 1628 of file REMORA.H.

Referenced by InitData(), REMORA(), and REMORA().

bdry_time_name_byvar

amrex::Vector<std::string> REMORA::bdry_time_name_byvar

private

Name of time fields for boundary data.

Definition at line 1868 of file REMORA.H.

Referenced by init_bdry_from_netcdf(), and ReadParameters().

bdry_time_varname

std::string REMORA::bdry_time_varname = "ocean_time"

private

Default name of time field for boundary data.

Definition at line 1866 of file REMORA.H.

Referenced by ReadParameters().

bdy_index

amrex::Vector<int> REMORA::bdy_index

private

Container to connect boundary data being read in boundary condition containers.

Needed for phys_bc_need_data to work correctly

Definition at line 1661 of file REMORA.H.

Referenced by init_bcs().

Bio_comp

int REMORA::Bio_comp = Tracer_comp

private

First cons component of the biology block, i.e. Tracer_comp + nscalar. The state is laid out as temp, salt, the passive scalars, then biology.

Definition at line 1700 of file REMORA.H.

Referenced by advance_biology(), bio_comp_start(), init_biology_from_netcdf(), init_biology_full_domain_from_netcdf(), init_scalars_from_netcdf(), init_scalars_full_domain_from_netcdf(), ReadParameters(), and set3DPlotVariables().

biology_debug

int REMORA::biology_debug = 0

private

Biology diagnostic verbosity: 0 off, 1 target column, 2 all columns. See Source/Biology/Fortran/tag_map.md.

Definition at line 1718 of file REMORA.H.

Referenced by advance_biology(), and ReadParameters().

biology_debug_i

int REMORA::biology_debug_i = 2

private

Target column i index for biology_debug = 1.

Definition at line 1720 of file REMORA.H.

Referenced by advance_biology(), and ReadParameters().

biology_debug_j

int REMORA::biology_debug_j = 2

private

Target column j index for biology_debug = 1.

Definition at line 1722 of file REMORA.H.

Referenced by advance_biology(), and ReadParameters().

biology_ic_type

REMORABiology::BiologyICType REMORA::biology_ic_type = REMORABiology::BiologyICType::follow_ic_type

private

Source of the biology tracer initial condition, independent of remora.ic_type. Default follows ic_type.

Definition at line 1710 of file REMORA.H.

Referenced by init_biology_ic(), init_biology_ic_full_domain(), and ReadParameters().

biology_model

REMORABiology::BiologyModel REMORA::biology_model = REMORABiology::BiologyModel::none

private

Active biology package.

Definition at line 1705 of file REMORA.H.

Referenced by advance_biology(), init_biology_from_netcdf(), init_biology_full_domain_from_netcdf(), init_biology_ic(), init_biology_ic_full_domain(), init_scalar_metadata(), ReadParameters(), and set3DPlotVariables().

boundary_series

amrex::Vector<amrex::Vector<std::unique_ptr<NCTimeSeriesBoundary> > > REMORA::boundary_series

private

Vector over BdyVars of boundary series data containers.

Definition at line 1549 of file REMORA.H.

Referenced by fill_from_bdyfiles(), init_bdry_from_netcdf(), and ReadParameters().

boxes_at_level

amrex::Vector<amrex::Vector<amrex::Box> > REMORA::boxes_at_level

private

the boxes specified at each level by tagging criteria

Definition at line 1608 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_biology_from_netcdf(), init_clim_nudg_coeff_from_netcdf(), init_coriolis_from_netcdf(), init_data_from_netcdf(), init_grid_vars_from_netcdf(), init_masks_from_netcdf(), init_scalars_from_netcdf(), init_zeta_from_netcdf(), ReadParameters(), refinement_criteria_setup(), and WriteNCPlotFile_which().

cf_set_width

int REMORA::cf_set_width {0}

private

Width for fixing values at coarse-fine interface.

Definition at line 1565 of file REMORA.H.

Referenced by Construct_REMORAFillPatchers(), Define_REMORAFillPatchers(), FillPatch(), and FillPatchNoBC().

cf_width

int REMORA::cf_width {0}

private

Nudging width at coarse-fine interface.

Definition at line 1563 of file REMORA.H.

Referenced by Construct_REMORAFillPatchers(), Define_REMORAFillPatchers(), init_stuff(), InitData(), MakeNewLevelFromCoarse(), RemakeLevel(), and timeStepML().

cfl

amrex::Real REMORA::cfl = Real(0.8)

staticprivate

CFL condition.

Definition at line 1726 of file REMORA.H.

Referenced by estTimeStep(), and ReadParameters().

change_max

amrex::Real REMORA::change_max = Real(1.1)

staticprivate

Fraction maximum change in subsequent time steps.

Definition at line 1728 of file REMORA.H.

Referenced by ComputeDt(), and ReadParameters().

check_file

std::string REMORA::check_file {"chk"}

private

Checkpoint file prefix.

Definition at line 1750 of file REMORA.H.

Referenced by ReadParameters(), and WriteCheckpointFile().

check_int

int REMORA::check_int = -1

private

Checkpoint output interval in iterations.

Definition at line 1752 of file REMORA.H.

Referenced by InitData(), ReadParameters(), WriteAtFinalTime(), and WriteAtIntermediateTime().

check_int_time

amrex::Real REMORA::check_int_time = amrex::Real(-one)

private

Checkpoint output interval in seconds.

Definition at line 1754 of file REMORA.H.

Referenced by InitData(), ReadParameters(), WriteAtFinalTime(), and WriteAtIntermediateTime().

chunk_history_file

bool REMORA::chunk_history_file = false

private

Whether to split the netcdf history file into fixed-length chunks.

Definition at line 1757 of file REMORA.H.

Referenced by ReadParameters(), WriteNCPlotFile(), and WriteNCPlotFile_which().

clim_cons_time_varname

amrex::Vector<std::string> REMORA::clim_cons_time_varname

private

Vector over cons components of the name of the time field for that tracer's climatology data.

Definition at line 1880 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

clim_u_time_varname

std::string REMORA::clim_u_time_varname = "ocean_time"

private

Name of time field for u climatology data.

Definition at line 1875 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

clim_ubar_time_varname

std::string REMORA::clim_ubar_time_varname = "ocean_time"

private

Name of time field for ubar climatology data.

Definition at line 1871 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

clim_v_time_varname

std::string REMORA::clim_v_time_varname = "ocean_time"

private

Name of time field for v climatology data.

Definition at line 1877 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

clim_vbar_time_varname

std::string REMORA::clim_vbar_time_varname = "ocean_time"

private

Name of time field for vbar climatology data.

Definition at line 1873 of file REMORA.H.

Referenced by ReadParameters().

cloud_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::cloud_data_from_file

private

Data container for cloud cover fraction read from file.

Definition at line 1524 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

cons_clim_data_from_file

amrex::Vector<std::unique_ptr<NCTimeSeries> > REMORA::cons_clim_data_from_file

private

Vector over cons components of climatology data read from file.

Entry icomp is null unless solverChoice.do_cons_clim_nudg[icomp] is set.

Definition at line 1539 of file REMORA.H.

Referenced by advance_3d(), and init_only().

cons_names

amrex::Vector<std::string> REMORA::cons_names {"temp", "salt", "tracer"}

private

Names of scalars for plotfile output.

Definition at line 1768 of file REMORA.H.

Referenced by ErrorEst(), init_bcs(), init_bdry_from_netcdf(), init_biology_from_netcdf(), init_biology_full_domain_from_netcdf(), init_clim_nudg_coeff_from_netcdf(), init_only(), init_scalar_metadata(), init_scalars_from_netcdf(), init_scalars_full_domain_from_netcdf(), ReadParameters(), set2DPlotVariables(), set3DPlotVariables(), sum_integrated_quantities(), WriteNCPlotFile_which(), and WritePlotFile().

cons_new

amrex::Vector<amrex::MultiFab*> REMORA::cons_new

multilevel data container for current step's scalar data: temperature, salinity, passive tracer

Definition at line 383 of file REMORA.H.

Referenced by advance_3d(), advance_3d_ml(), allocate_init_full_domain(), AverageDownTo(), ClearLevel(), Construct_REMORAFillPatchers(), Define_REMORAFillPatchers(), ErrorEst(), init_analytic(), init_bathymetry_from_netcdf(), init_beta_plane_coriolis(), init_biology_from_netcdf(), init_biology_ic(), init_clim_nudg_coeff_from_netcdf(), init_coriolis_from_netcdf(), init_data_from_netcdf(), init_grid_vars_from_netcdf(), init_masks_from_netcdf(), init_only(), init_scalars_from_netcdf(), init_zeta_from_netcdf(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), mask_arrays_for_write(), PackSurfaceState(), ReadCheckpointFile(), RemakeLevel(), REMORA(), REMORA(), scale_rhs_vars(), scale_rhs_vars_inv(), set_2darrays(), set_init_data_averaged_down(), set_zeta_average(), setup_step(), stretch_transform(), sum_integrated_quantities(), timeStep(), timeStepML(), volWgtSumMF(), WriteCheckpointFile(), and WritePlotFile().

cons_old

amrex::Vector<amrex::MultiFab*> REMORA::cons_old

multilevel data container for last step's scalar data: temperature, salinity, passive tracer

Definition at line 374 of file REMORA.H.

Referenced by advance_3d(), ClearLevel(), gls_corrector(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), REMORA(), REMORA(), setup_step(), timeStep(), timeStepML(), and WriteCheckpointFile().

Cs_r

amrex::Gpu::DeviceVector<amrex::Real> REMORA::Cs_r

Stretching coefficients at rho points.

Definition at line 458 of file REMORA.H.

Referenced by calc_stretch_coeffs(), init_stretch_coeffs(), stretch_transform(), and WriteNCPlotFile_which().

Cs_w

amrex::Gpu::DeviceVector<amrex::Real> REMORA::Cs_w

Stretching coefficients at w points.

Definition at line 460 of file REMORA.H.

Referenced by calc_stretch_coeffs(), init_stretch_coeffs(), stretch_transform(), and WriteNCPlotFile_which().

cum_ref_ratios

amrex::Vector<amrex::IntVect> REMORA::cum_ref_ratios

private

Cumulative refinement ratio between level 0 and level i.

Definition at line 1853 of file REMORA.H.

Referenced by allocate_bathymetry_grid_vars_full_domain(), allocate_init_full_domain(), average_down_with_grow_cells(), coarsen_bathymetry_with_grow_cells(), coarsen_masks_with_grow_cells(), ensure_full_domain_masks(), init_bathymetry_full_domain_from_netcdf(), init_biology_full_domain_from_netcdf(), init_data_full_domain_from_netcdf(), init_grid_vars_full_domain_from_netcdf(), init_masks_full_domain_from_netcdf(), init_ref_ratios(), init_riv_pos_from_netcdf(), init_scalars_full_domain_from_netcdf(), init_zeta_full_domain_from_netcdf(), and refine_masks_with_grow_cells().

datalog

amrex::Vector<std::unique_ptr<std::fstream> > REMORA::datalog

private

Definition at line 1975 of file REMORA.H.

Referenced by DataLog(), NumDataLogs(), ReadParameters(), and setRecordDataInfo().

datalogname

amrex::Vector<std::string> REMORA::datalogname

private

Definition at line 1976 of file REMORA.H.

Referenced by DataLogName(), and ReadParameters().

derived_names_2d

const amrex::Vector<std::string> REMORA::derived_names_2d {}

private

Names of derived fields for 2d plotfile fields.

Definition at line 1773 of file REMORA.H.

Referenced by set2DPlotVariables().

derived_names_3d

const amrex::Vector<std::string> REMORA::derived_names_3d {"vorticity"}

private

Names of derived fields for 3d plotfile fields.

Definition at line 1771 of file REMORA.H.

Referenced by set3DPlotVariables().

dm_full_domain

amrex::DistributionMapping REMORA::dm_full_domain

the DistributionMapping every full-domain multifab is built on. Each of those covers the domain in a single box, so the map holds one entry, and which rank it names is whichever holds the least fab memory when it is built. Building one per allocator therefore put the mask and the data it weights on different ranks under MPI. Empty until full_domain_dmap first needs it.

Definition at line 1352 of file REMORA.H.

Referenced by full_domain_dmap().

do_substep

int REMORA::do_substep = 0

private

Whether to substep fine levels in time.

Definition at line 1737 of file REMORA.H.

Referenced by ReadParameters(), REMORA(), and REMORA().

domain_bc_type

amrex::Array<std::string,2*AMREX_SPACEDIM> REMORA::domain_bc_type

private

Array of strings describing domain boundary conditions.

Definition at line 1642 of file REMORA.H.

Referenced by init_bcs(), and writeJobInfo().

domain_bcs_type

amrex::Vector<amrex::BCRec> REMORA::domain_bcs_type

private

vector (over BCVars) of BCRecs

Definition at line 1637 of file REMORA.H.

Referenced by fill_from_bdyfiles(), FillCoarsePatchMap(), FillPatch(), FillPatchNoBC(), gls_corrector(), gls_prestep(), init_bcs(), init_stuff(), rhs_uv_2d(), update_massflux_3d(), and WritePlotFile().

domain_bcs_type_d

amrex::Gpu::DeviceVector<amrex::BCRec> REMORA::domain_bcs_type_d

private

GPU vector (over BCVars) of BCRecs.

Definition at line 1639 of file REMORA.H.

Referenced by init_bcs(), and init_stuff().

driver_atmos_forcing_mode

DriverAtmosForcingMode REMORA::driver_atmos_forcing_mode = DriverAtmosForcingMode::State

Active atmosphere-to-ocean forcing contract on the most recent driver apply.

Definition at line 520 of file REMORA.H.

Referenced by ApplyAtmosphericFluxes(), ApplyAtmosphericStates(), ConfigureDriverAtmosToOceanCoupling(), InitData(), SetDriverAtmosToOceanForcingMode(), and setup_step().

driver_atmos_state_from_driver

std::array<bool, AtmosState::NumTypes> REMORA::driver_atmos_state_from_driver {}

provenance flags for driver-supplied atmospheric forcing lanes

Definition at line 514 of file REMORA.H.

Referenced by ApplyAtmosphericFluxes(), ApplyAtmosphericStates(), and set_surface_state().

driver_uses_two_way_coupling

bool REMORA::driver_uses_two_way_coupling = false

Driver-level direction flag copied in before InitData.

Definition at line 518 of file REMORA.H.

Referenced by ConfigureDriverAtmosToOceanCoupling(), and InitData().

dt

amrex::Vector<amrex::Real> REMORA::dt

private

time step at each level

Definition at line 1619 of file REMORA.H.

Referenced by ComputeDt(), Evolve(), EvolveOneStep(), InitData(), ReadCheckpointFile(), REMORA(), REMORA(), set_zeta_to_Ztavg(), timeStep(), timeStepML(), and WriteCheckpointFile().

EminusP_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::EminusP_data_from_file

private

Data container for evaporation minus precipitation read from file.

Definition at line 1526 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

expand_plotvars_to_unif_rr

bool REMORA::expand_plotvars_to_unif_rr = false

private

whether plotfile variables should be expanded to a uniform refinement ratio

Definition at line 1779 of file REMORA.H.

Referenced by ReadParameters(), and WritePlotFile().

fennel_params

REMORABiology::FennelParameters REMORA::fennel_params

private

Runtime parameters for the Fennel biology package.

Definition at line 1707 of file REMORA.H.

Referenced by advance_biology(), init_biology_ic(), init_biology_ic_full_domain(), init_scalar_metadata(), and ReadParameters().

file_min_digits

int REMORA::file_min_digits = 5

staticprivate

Minimum number of digits in plotfile name or chunked history file.

Definition at line 1820 of file REMORA.H.

Referenced by ReadParameters(), WriteCheckpointFile(), WriteNCPlotFile(), and WritePlotFile().

fine_mask

amrex::MultiFab REMORA::fine_mask

private

Mask that zeroes out values on a coarse level underlying grids on the next finest level.

Definition at line 1896 of file REMORA.H.

Referenced by build_fine_mask().

fixed_dt

amrex::Real REMORA::fixed_dt = -one

staticprivate

User specified fixed baroclinic time step.

Definition at line 1730 of file REMORA.H.

Referenced by estTimeStep(), and ReadParameters().

FPr_c

amrex::Vector<REMORAFillPatcher> REMORA::FPr_c

private

Vector over levels of FillPatchers for scalars.

Definition at line 1568 of file REMORA.H.

Referenced by Construct_REMORAFillPatchers(), Define_REMORAFillPatchers(), FillPatch(), FillPatchNoBC(), and timeStepML().

FPr_u

amrex::Vector<REMORAFillPatcher> REMORA::FPr_u

private

Vector over levels of FillPatchers for u (3D)

Definition at line 1570 of file REMORA.H.

Referenced by Construct_REMORAFillPatchers(), Define_REMORAFillPatchers(), FillPatch(), FillPatchNoBC(), and timeStepML().

FPr_ubar

amrex::Vector<REMORAFillPatcher> REMORA::FPr_ubar

private

Vector over levels of FillPatchers for ubar (2D)

Definition at line 1578 of file REMORA.H.

Referenced by Construct_REMORAFillPatchers(), Define_REMORAFillPatchers(), FillPatch(), FillPatchNoBC(), and timeStepML().

FPr_v

amrex::Vector<REMORAFillPatcher> REMORA::FPr_v

private

Vector over levels of FillPatchers for v (3D)

Definition at line 1572 of file REMORA.H.

Referenced by Construct_REMORAFillPatchers(), Define_REMORAFillPatchers(), FillPatch(), FillPatchNoBC(), and timeStepML().

FPr_vbar

amrex::Vector<REMORAFillPatcher> REMORA::FPr_vbar

private

Vector over levels of FillPatchers for vbar (2D)

Definition at line 1580 of file REMORA.H.

Referenced by Construct_REMORAFillPatchers(), Define_REMORAFillPatchers(), FillPatch(), FillPatchNoBC(), and timeStepML().

FPr_w

amrex::Vector<REMORAFillPatcher> REMORA::FPr_w

private

Vector over levels of FillPatchers for w.

Definition at line 1574 of file REMORA.H.

Referenced by Construct_REMORAFillPatchers(), Define_REMORAFillPatchers(), FillPatch(), FillPatchNoBC(), and timeStepML().

frc_time_varname

std::string REMORA::frc_time_varname = ""

private

Name of time field for forcing data.

Definition at line 1884 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

hires_grid_level

int REMORA::hires_grid_level = -1

private

Which level the high resolution bathymetry is at.

Definition at line 1839 of file REMORA.H.

Referenced by allocate_bathymetry_grid_vars_full_domain(), ensure_full_domain_masks(), init_bathymetry_full_domain_from_analytic(), init_bathymetry_full_domain_from_netcdf(), init_grid_vars_full_domain_from_netcdf(), init_masks_full_domain_from_analytic(), init_masks_full_domain_from_netcdf(), init_only(), MakeNewLevelFromCoarse(), ReadParameters(), RemakeLevel(), resize_stuff(), set_bathymetry(), set_grid_scale(), and set_masks().

hires_init_level

int REMORA::hires_init_level = -1

private

Which level the high resolution initialization data is at.

Definition at line 1846 of file REMORA.H.

Referenced by allocate_init_full_domain(), init_biology_full_domain_from_netcdf(), init_biology_ic_full_domain(), init_data_full_domain_from_netcdf(), init_full_domain_from_analytic(), init_full_domain_zeta_from_analytic(), init_only(), init_scalars_full_domain_from_netcdf(), init_zeta_full_domain_from_netcdf(), ReadParameters(), resize_stuff(), and set_zeta().

history_count

int REMORA::history_count = 0

private

Counter for which time index we are writing to in the netcdf history file.

Definition at line 1761 of file REMORA.H.

Referenced by InitData(), WriteAtFinalTime(), WriteAtIntermediateTime(), WriteNCPlotFile(), and WriteNCPlotFile_which().

istep

amrex::Vector<int> REMORA::istep

private

which step?

Definition at line 1611 of file REMORA.H.

Referenced by advance_2d(), advance_3d(), Evolve(), EvolveOneStep(), InitData(), ReadCheckpointFile(), REMORA(), REMORA(), restart(), setup_step(), timeStep(), timeStepML(), WriteAtFinalTime(), WriteCheckpointFile(), and WritePlotFile().

last_check_file_step

int REMORA::last_check_file_step

private

Step when we last output a checkpoint file.

Definition at line 1669 of file REMORA.H.

Referenced by InitData(), restart(), WriteAtFinalTime(), and WriteAtIntermediateTime().

last_check_file_time

amrex::Real REMORA::last_check_file_time

private

Simulation time when we last output a checkpoint file.

Definition at line 1671 of file REMORA.H.

Referenced by InitData(), restart(), and WriteAtIntermediateTime().

last_plot_file_step

int REMORA::last_plot_file_step

private

Step when we last output a plotfile.

Definition at line 1664 of file REMORA.H.

Referenced by InitData(), WriteAtFinalTime(), and WriteAtIntermediateTime().

last_plot_file_time

amrex::Real REMORA::last_plot_file_time

private

Simulation time when we last output a plotfile.

Definition at line 1666 of file REMORA.H.

Referenced by InitData(), restart(), and WriteAtIntermediateTime().

longwave_down_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::longwave_down_data_from_file

private

Data container for downward longwave radiation flux read from file.

Definition at line 1520 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

m_bc_extdir_vals

amrex::Vector<amrex::GpuArray<amrex::Real, AMREX_SPACEDIM*2> > REMORA::m_bc_extdir_vals

private

Array holding the Dirichlet values at walls which need them.

Definition at line 1645 of file REMORA.H.

Referenced by init_bcs(), and init_stuff().

max_step

int REMORA::max_step = std::numeric_limits<int>::max()

private

maximum number of steps

Definition at line 1679 of file REMORA.H.

Referenced by Evolve(), and ReadParameters().

nbio

int REMORA::nbio = 0

private

Number of biology tracers, set by the active biology model. Zero when no biology model is active.

Definition at line 1697 of file REMORA.H.

Referenced by init_biology_from_netcdf(), init_biology_full_domain_from_netcdf(), num_bio(), and ReadParameters().

nc_bdry_file

amrex::Vector< std::string > REMORA::nc_bdry_file = {""}

staticprivate

NetCDF boundary data.

Definition at line 58 of file REMORA.H.

Referenced by init_bdry_from_netcdf(), and ReadParameters().

nc_clim_coeff_file

std::string REMORA::nc_clim_coeff_file

private

NetCDF climatology coefficient file.

Definition at line 1863 of file REMORA.H.

Referenced by init_clim_nudg_coeff(), init_clim_nudg_coeff_from_netcdf(), and ReadParameters().

nc_clim_his_file

amrex::Vector<std::string> REMORA::nc_clim_his_file

private

NetCDF climatology history file(s)

Definition at line 1861 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

nc_frc_file

amrex::Vector<std::string> REMORA::nc_frc_file

private

NetCDF forcing file(s)

Definition at line 1856 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

nc_grid_file

amrex::Vector< amrex::Vector< std::string > > REMORA::nc_grid_file = {{""}}

staticprivate

NetCDF grid file.

Definition at line 60 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_coriolis_from_netcdf(), init_grid_vars_from_netcdf(), init_masks_from_netcdf(), and ReadParameters().

nc_grid_file_hires

std::string REMORA::nc_grid_file_hires

private

Grid file for high resolution bathymetry.

Definition at line 1841 of file REMORA.H.

Referenced by init_bathymetry_full_domain_from_netcdf(), init_grid_vars_full_domain_from_netcdf(), init_masks_full_domain_from_netcdf(), and ReadParameters().

nc_hires_grid_box

amrex::Box REMORA::nc_hires_grid_box

private

Box for the full domain at nc_hires_grid_level.

Definition at line 1843 of file REMORA.H.

Referenced by allocate_bathymetry_grid_vars_full_domain(), init_bathymetry_full_domain_from_netcdf(), init_grid_vars_full_domain_from_netcdf(), and init_masks_full_domain_from_netcdf().

nc_hires_init_box

amrex::Box REMORA::nc_hires_init_box

private

Box for the full domain at nc_hires_init_level.

Definition at line 1850 of file REMORA.H.

Referenced by allocate_init_full_domain(), init_biology_full_domain_from_netcdf(), init_data_full_domain_from_netcdf(), init_scalars_full_domain_from_netcdf(), and init_zeta_full_domain_from_netcdf().

nc_init_file

amrex::Vector< amrex::Vector< std::string > > REMORA::nc_init_file = {{""}}

staticprivate

NetCDF initialization file.

Definition at line 59 of file REMORA.H.

Referenced by init_biology_from_netcdf(), init_data_from_netcdf(), init_scalars_from_netcdf(), init_zeta_from_netcdf(), and ReadParameters().

nc_init_file_hires

std::string REMORA::nc_init_file_hires

private

Init file for high resolution.

Definition at line 1848 of file REMORA.H.

Referenced by init_biology_full_domain_from_netcdf(), init_data_full_domain_from_netcdf(), init_scalars_full_domain_from_netcdf(), init_zeta_full_domain_from_netcdf(), and ReadParameters().

nc_riv_file

amrex::Vector<std::string> REMORA::nc_riv_file

private

NetCDF river file(s)

Definition at line 1858 of file REMORA.H.

Referenced by init_only(), init_riv_pos_from_netcdf(), and ReadParameters().

ncons

int REMORA::ncons = Tracer_comp + 1

private

Number of conserved scalars in the state (temperature + salt + passive scalars + biology tracers)

Definition at line 1703 of file REMORA.H.

Referenced by advance_3d(), advance_3d_ml(), allocate_init_full_domain(), bdy_ubar(), bdy_vbar(), bdy_zeta(), ErrorEst(), fill_from_bdyfiles(), foextrap_bc(), foextrap_periodic_bc(), init_bcs(), init_bdry_from_netcdf(), init_biology_from_netcdf(), init_biology_full_domain_from_netcdf(), init_clim_nudg_coeff(), init_clim_nudg_coeff_from_netcdf(), init_data_from_netcdf(), init_data_full_domain_from_netcdf(), init_only(), init_scalar_metadata(), init_stuff(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), mask_arrays_for_write(), num_bc_vars(), num_bdy_vars(), prestep(), ReadCheckpointFile(), ReadParameters(), RemakeLevel(), resize_stuff(), set2DPlotVariables(), set3DPlotVariables(), set_hmixcoef(), set_init_data_averaged_down(), setup_step(), sum_integrated_quantities(), tke_bc(), u2d_simple_bc(), ubar_bc(), v2d_simple_bc(), vbar_bc(), WriteCheckpointFile(), WriteNCPlotFile_which(), WritePlotFile(), xvel_bc(), yvel_bc(), zeta_bc(), and zvel_bc().

ndtfast

int REMORA::ndtfast = 0

staticprivate

User specified, number of barotropic steps per baroclinic step.

Definition at line 1732 of file REMORA.H.

Referenced by Advance(), estTimeStep(), ReadParameters(), set_weights(), and timeStepML().

netcdf_fill_value

amrex::Real REMORA::netcdf_fill_value = amrex::Real(1.0e37)

private

fill value for masked arrays in netcdf output

Definition at line 1784 of file REMORA.H.

Referenced by ReadParameters(), WriteNCPlotFile_which(), and WritePlotFile().

nfast

int REMORA::nfast

private

Number of fast steps to take.

Definition at line 1734 of file REMORA.H.

Referenced by Advance(), advance_2d(), set_weights(), and timeStepML().

nscalar

int REMORA::nscalar = 0

private

Number of passive (dye) scalars carried in the state, beyond temperature and salinity. Does not count biology tracers. Dye is opt-in: a run carries one only when remora.nscalar asks for it.

Definition at line 1694 of file REMORA.H.

Referenced by init_scalar_metadata(), init_scalars_from_netcdf(), init_scalars_full_domain_from_netcdf(), num_passive_scalars(), num_scalar(), and ReadParameters().

nsubsteps

amrex::Vector<int> REMORA::nsubsteps

private

How many substeps on each level?

Definition at line 1613 of file REMORA.H.

Referenced by ComputeDt(), REMORA(), REMORA(), timeStep(), and timeStepML().

num_boxes_at_level

amrex::Vector<int> REMORA::num_boxes_at_level

private

how many boxes specified at each level by tagging criteria

Definition at line 1604 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_biology_from_netcdf(), init_clim_nudg_coeff_from_netcdf(), init_coriolis_from_netcdf(), init_data_from_netcdf(), init_grid_vars_from_netcdf(), init_masks_from_netcdf(), init_scalars_from_netcdf(), init_zeta_from_netcdf(), ReadParameters(), and refinement_criteria_setup().

num_files_at_level

amrex::Vector<int> REMORA::num_files_at_level

private

how many netcdf input files specified at each level

Definition at line 1606 of file REMORA.H.

Referenced by ReadParameters().

Pair_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::Pair_data_from_file

private

Data container for air pressure read from file.

Definition at line 1516 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

phys_bc_need_data

amrex::Vector<amrex::GpuArray<bool, AMREX_SPACEDIM*2> > REMORA::phys_bc_need_data

private

These are flags that indicate whether we need to read in boundary data from file.

Sized num_bdy_vars()+1; the extra trailing slot is a scratch entry that variables with no NetCDF boundary lane (see bdy_index) write into and nothing reads.

Definition at line 1655 of file REMORA.H.

Referenced by init_bcs(), and init_bdry_from_netcdf().

phys_bc_type

amrex::Vector<amrex::GpuArray<REMORA_BC, AMREX_SPACEDIM*2> > REMORA::phys_bc_type

private

Array holding the "physical" boundary condition types (e.g. "inflow")

Definition at line 1648 of file REMORA.H.

Referenced by FillBdyCCVels(), and init_bcs().

physbcs

amrex::Vector<std::unique_ptr<REMORAPhysBCFunct> > REMORA::physbcs

private

Vector (over level) of functors to apply physical boundary conditions.

Definition at line 1625 of file REMORA.H.

Referenced by advance_3d(), FillCoarsePatchMap(), FillPatch(), gls_corrector(), init_stuff(), init_zeta_from_netcdf(), REMORA(), REMORA(), and setup_step().

plot_file_name

std::string REMORA::plot_file_name {"plt_"}

private

Plotfile prefix.

Definition at line 1744 of file REMORA.H.

Referenced by ReadParameters(), WriteNCPlotFile(), and WritePlotFile().

plot_file_on_restart

int REMORA::plot_file_on_restart = 1

private

Whether to output a plotfile on restart from checkpoint.

Definition at line 1673 of file REMORA.H.

Referenced by InitData().

plot_int

int REMORA::plot_int = -1

private

Plotfile output interval in iterations.

Definition at line 1746 of file REMORA.H.

Referenced by InitData(), ReadParameters(), WriteAtFinalTime(), and WriteAtIntermediateTime().

plot_int_time

amrex::Real REMORA::plot_int_time = amrex::Real(-one)

private

Plotfile output interval in seconds.

Definition at line 1748 of file REMORA.H.

Referenced by InitData(), ReadParameters(), WriteAtFinalTime(), and WriteAtIntermediateTime().

plot_nodal_data

bool REMORA::plot_nodal_data = true

staticprivate

Whether to write nodal data (Nu_nd) to plotfiles.

Definition at line 1826 of file REMORA.H.

Referenced by ReadParameters(), WriteGenericPlotfileHeaderWithBathymetry(), WriteMultiLevelPlotfileWithBathymetry(), and WritePlotFile().

plot_staggered_vels

bool REMORA::plot_staggered_vels = false

staticprivate

Whether to write the staggered velocities (not averaged to cell centers)

Definition at line 1823 of file REMORA.H.

Referenced by ReadParameters(), WriteGenericPlotfileHeaderWithBathymetry(), WriteMultiLevelPlotfileWithBathymetry(), and WritePlotFile().

plot_var_names_2d

amrex::Vector<std::string> REMORA::plot_var_names_2d

private

Names of 2D variables to output to AMReX plotfile.

Definition at line 1766 of file REMORA.H.

Referenced by append2DPlotVariables(), set2DPlotVariables(), WriteNCPlotFile_which(), and WritePlotFile().

plot_var_names_3d

amrex::Vector<std::string> REMORA::plot_var_names_3d

private

Names of 3D variables to output to AMReX plotfile.

Definition at line 1764 of file REMORA.H.

Referenced by append3DPlotVariables(), set3DPlotVariables(), WriteNCPlotFile_which(), and WritePlotFile().

plotfile_fill_value

amrex::Real REMORA::plotfile_fill_value = zero

private

fill value for masked arrays in amrex plotfiles

Definition at line 1782 of file REMORA.H.

Referenced by ReadParameters(), and WritePlotFile().

plotfile_type

PlotfileType REMORA::plotfile_type = PlotfileType::amrex

staticprivate

Native or NetCDF plotfile output.

Definition at line 1829 of file REMORA.H.

Referenced by ReadParameters(), and WritePlotFile().

pp_prefix

std::string REMORA::pp_prefix {"remora"}

default prefix for input file parameters

Definition at line 371 of file REMORA.H.

Referenced by append2DPlotVariables(), append3DPlotVariables(), ReadParameters(), refinement_criteria_setup(), REMORA(), set2DPlotVariables(), and set3DPlotVariables().

previousCPUTimeUsed

amrex::Real REMORA::previousCPUTimeUsed = zero

staticprivate

Accumulator variable for CPU time used thusfar.

Definition at line 1944 of file REMORA.H.

Referenced by getCPUTime().

prob

std::unique_ptr<ProblemBase> REMORA::prob = nullptr

private

Pointer to container of analytical functions for problem definition.

Definition at line 1601 of file REMORA.H.

Referenced by init_analytic(), init_bathymetry_full_domain_from_analytic(), init_biology_ic(), init_biology_ic_full_domain(), init_full_domain_from_analytic(), init_full_domain_zeta_from_analytic(), init_masks_full_domain_from_analytic(), REMORA(), REMORA(), set_analytic_vmix(), set_bathymetry(), set_coriolis(), set_grid_scale(), set_hmixcoef(), set_masks(), set_smflux(), set_surface_state(), and set_zeta().

qair_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::qair_data_from_file

private

Data container for specific humidity read from file.

Definition at line 1514 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

rain_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::rain_data_from_file

private

Data container for precipitation rate read from file.

Definition at line 1522 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

ref_tags

Vector< AMRErrorTag > REMORA::ref_tags

staticprivate

Holds info for dynamically generated tagging criteria.

Definition at line 1893 of file REMORA.H.

Referenced by ErrorEst(), and refinement_criteria_setup().

regrid_int

int REMORA::regrid_int = 2

private

how often each level regrids the higher levels of refinement (after a level advances that many time steps)

Definition at line 1740 of file REMORA.H.

Referenced by ReadParameters(), timeStep(), and timeStepML().

restart_chkfile

std::string REMORA::restart_chkfile = ""

private

If set, restart from this checkpoint file.

Definition at line 1689 of file REMORA.H.

Referenced by InitData(), MakeNewLevelFromScratch(), ReadCheckpointFile(), and ReadParameters().

riv_time_varname

std::string REMORA::riv_time_varname = "river_time"

private

Name of time field for river time.

Definition at line 1882 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

river_direction

amrex::Gpu::DeviceVector<int> REMORA::river_direction

private

Vector over rivers of river direction: 0: u-face; 1: v-face; 2: w-face.

Definition at line 1555 of file REMORA.H.

Referenced by advance_2d(), advance_3d(), init_riv_pos_from_netcdf(), prestep_t_advection(), and rhs_t_3d().

river_source_cons

amrex::Vector<std::unique_ptr<NCTimeSeriesRiver> > REMORA::river_source_cons

private

Vector of data containers for scalar data in rivers.

Definition at line 1542 of file REMORA.H.

Referenced by advance_3d(), init_only(), and prestep().

river_source_transport

std::unique_ptr<NCTimeSeriesRiver> REMORA::river_source_transport

private

Data container for momentum transport in rivers.

Definition at line 1544 of file REMORA.H.

Referenced by advance_3d(), and init_only().

river_source_transportbar

std::unique_ptr<NCTimeSeriesRiver> REMORA::river_source_transportbar

private

Data container for vertically integrated momentum transport in rivers.

Definition at line 1546 of file REMORA.H.

Referenced by advance_2d(), and init_only().

running_with_coupling_driver

bool REMORA::running_with_coupling_driver = false

True once REMORA has received forcing through the coupling driver.

Definition at line 516 of file REMORA.H.

Referenced by ApplyAtmosphericFluxes(), ApplyAtmosphericStates(), ConfigureDriverAtmosToOceanCoupling(), InitData(), and setup_step().

s_r

amrex::Gpu::DeviceVector<amrex::Real> REMORA::s_r

Scaled vertical coordinate (range [0,1]) that transforms to z, defined at rho points (cell centers)

Definition at line 448 of file REMORA.H.

Referenced by calc_stretch_coeffs(), init_stretch_coeffs(), stretch_transform(), and WriteNCPlotFile_which().

s_w

amrex::Gpu::DeviceVector<amrex::Real> REMORA::s_w

Scaled vertical coordinate (range [0,1]) that transforms to z, defined at w-points (cell faces)

Definition at line 450 of file REMORA.H.

Referenced by calc_stretch_coeffs(), init_stretch_coeffs(), stretch_transform(), and WriteNCPlotFile_which().

set_bcs_by_var

bool REMORA::set_bcs_by_var

private

whether to set boundary conditions by variable rather than just by side

Definition at line 1622 of file REMORA.H.

Referenced by init_bcs().

solverChoice

SolverChoice REMORA::solverChoice

staticprivate

Container for algorithmic choices.

Definition at line 1776 of file REMORA.H.

Referenced by advance_2d(), advance_3d(), advance_biology(), ApplyAtmosphericFluxes(), average_down_with_grow_cells(), bulk_fluxes(), calc_stretch_coeffs(), check_mask_consistency(), ensure_full_domain_masks(), fill_from_bdyfiles(), FillCoarsePatchMap(), FillPatch(), GetDeckConfiguredAtmosStateLanes(), gls_corrector(), init_analytic(), init_bathymetry_full_domain_from_analytic(), init_bcs(), init_beta_plane_coriolis(), init_biology_ic(), init_biology_ic_full_domain(), init_clim_nudg_coeff(), init_clim_nudg_coeff_from_netcdf(), init_full_domain_from_analytic(), init_full_domain_zeta_from_analytic(), init_masks_full_domain_from_analytic(), init_only(), init_set_vmix(), init_stuff(), init_zeta_from_netcdf(), InitData(), lin_eos(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), nonlin_eos(), post_timestep(), prestep(), prestep_t_advection(), prsgrd(), ReadCheckpointFile(), ReadParameters(), RemakeLevel(), rho_eos(), rhs_t_3d(), rhs_uv_2d(), rhs_uv_3d(), set2DPlotVariables(), set_analytic_vmix(), set_bathymetry(), set_coriolis(), set_grid_scale(), set_hmixcoef(), set_masks(), set_smflux(), set_surface_state(), set_zeta(), set_zeta_to_Ztavg(), SetLongwaveFromDriver(), setup_step(), stretch_transform(), t3dmix2(), timeStep(), timeStepML(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

srflx_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::srflx_data_from_file

private

Data container for shortwave radiation flux read from file.

Definition at line 1518 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

start_time

amrex::Real REMORA::start_time = zero

private

Time of the start of the simulation, in seconds.

Definition at line 1686 of file REMORA.H.

Referenced by InitData(), ReadParameters(), SetStartTime(), and WriteNCPlotFile_which().

startCPUTime

amrex::Real REMORA::startCPUTime = zero

staticprivate

Variable for CPU timing.

Definition at line 1942 of file REMORA.H.

Referenced by getCPUTime(), and InitData().

steps_per_history_file

int REMORA::steps_per_history_file = -1

private

Time steps per netcdf history file. Must be > 0 if chunk_history_file.

Definition at line 1759 of file REMORA.H.

Referenced by ReadParameters(), WriteNCPlotFile(), and WriteNCPlotFile_which().

stop_time

amrex::Real REMORA::stop_time = std::numeric_limits<amrex::Real>::max()

private

Whether max_step was set in the inputs; the default above is not a distinguishable sentinel.

Time to stop

Definition at line 1683 of file REMORA.H.

Referenced by ComputeDt(), Evolve(), EvolveOneStep(), and ReadParameters().

sum_interval

int REMORA::sum_interval = -1

staticprivate

Diagnostic sum output interval in number of steps.

Definition at line 1815 of file REMORA.H.

Referenced by InitData(), post_timestep(), and ReadParameters().

sum_per

amrex::Real REMORA::sum_per = -one

staticprivate

Diagnostic sum output interval in time.

Definition at line 1817 of file REMORA.H.

Referenced by InitData(), post_timestep(), and ReadParameters().

sustr_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::sustr_data_from_file

private

Data container for u-component surface momentum flux read from file.

Definition at line 1504 of file REMORA.H.

Referenced by init_only(), and set_smflux().

svstr_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::svstr_data_from_file

private

Data container for v-component surface momentum flux read from file.

Definition at line 1506 of file REMORA.H.

Referenced by init_only(), and set_smflux().

t_new

amrex::Vector<amrex::Real> REMORA::t_new

private

new time at each level

Definition at line 1615 of file REMORA.H.

Referenced by advance_2d(), ComputeDt(), Evolve(), EvolveOneStep(), FillPatch(), FillPatchNoBC(), GetDataAtTime(), gls_corrector(), init_only(), init_zeta_from_netcdf(), InitData(), MakeNewLevelFromCoarse(), ReadCheckpointFile(), RemakeLevel(), REMORA(), REMORA(), restart(), set_2darrays(), set_init_data_averaged_down(), set_zeta_averaged_down(), setup_step(), timeStep(), timeStepML(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

t_old

amrex::Vector<amrex::Real> REMORA::t_old

private

old time at each level

Definition at line 1617 of file REMORA.H.

Referenced by advance_2d(), advance_3d(), advance_3d_ml(), advance_biology(), FillPatch(), FillPatchNoBC(), get_t_old(), GetDataAtTime(), gls_corrector(), gls_prestep(), init_only(), init_zeta_from_netcdf(), MakeNewLevelFromCoarse(), prestep(), RemakeLevel(), REMORA(), REMORA(), set_smflux(), set_surface_state(), timeStep(), and timeStepML().

Tair_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::Tair_data_from_file

private

Data container for air temperature read from file.

Definition at line 1512 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

total_nc_plot_file_step

int REMORA::total_nc_plot_file_step = 1

static

Definition at line 1409 of file REMORA.H.

Referenced by WriteNCPlotFile_which().

u_clim_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::u_clim_data_from_file

private

Data container for u-velocity climatology data read from file.

Definition at line 1533 of file REMORA.H.

Referenced by init_only(), and setup_step().

ubar_clim_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::ubar_clim_data_from_file

private

Data container for ubar climatology data read from file.

Definition at line 1529 of file REMORA.H.

Referenced by advance_2d(), and init_only().

use_biology_cpp_answer

int REMORA::use_biology_cpp_answer = 1

private

Select the native C++ biology kernel (1) or the ROMS Fortran bridge oracle (0). Only meaningful when built with USE_FENNEL_FORT=TRUE; ignored otherwise. Runtime-controlled so the two paths can be compared without a rebuild.

Definition at line 1715 of file REMORA.H.

Referenced by advance_biology(), and ReadParameters().

Uwind_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::Uwind_data_from_file

private

Data container for u-direction wind read from file.

Definition at line 1508 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

v_clim_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::v_clim_data_from_file

private

Data container for v-velocity climatology data read from file.

Definition at line 1535 of file REMORA.H.

Referenced by init_only(), and setup_step().

vbar_clim_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::vbar_clim_data_from_file

private

Data container for vbar climatology data read from file.

Definition at line 1531 of file REMORA.H.

Referenced by advance_2d(), and init_only().

vec_Akk

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Akk

Turbulent kinetic energy vertical diffusion coefficient.

Definition at line 648 of file REMORA.H.

Referenced by advance_3d(), gls_corrector(), init_gls_vmix(), init_stuff(), ReadCheckpointFile(), resize_stuff(), and WriteCheckpointFile().

vec_Akp

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Akp

Turbulent length scale vertical diffusion coefficient.

Definition at line 650 of file REMORA.H.

Referenced by advance_3d(), gls_corrector(), init_gls_vmix(), init_stuff(), ReadCheckpointFile(), resize_stuff(), and WriteCheckpointFile().

vec_Akt

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Akt

Vertical diffusion coefficient (3D)

Definition at line 434 of file REMORA.H.

Referenced by advance_3d(), advance_3d_ml(), gls_corrector(), init_gls_vmix(), init_stuff(), prestep(), ReadCheckpointFile(), resize_stuff(), set_analytic_vmix(), and WriteCheckpointFile().

vec_Akv

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Akv

Vertical viscosity coefficient (3D)

Definition at line 432 of file REMORA.H.

Referenced by advance_3d(), advance_3d_ml(), gls_corrector(), init_gls_vmix(), init_stuff(), prestep(), ReadCheckpointFile(), resize_stuff(), set_analytic_vmix(), and WriteCheckpointFile().

vec_alpha

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_alpha

Thermal expansion coefficient (3D)

Definition at line 631 of file REMORA.H.

Referenced by init_stuff(), resize_stuff(), and setup_step().

vec_beta

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_beta

Saline contraction coefficient (3D)

Definition at line 633 of file REMORA.H.

Referenced by init_stuff(), resize_stuff(), and setup_step().

vec_btflux

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_btflux

Bottom tracer flux; input arrays.

Definition at line 502 of file REMORA.H.

Referenced by init_stuff(), resize_stuff(), and setup_step().

vec_btflx

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_btflx

Bottom tracer flux; working arrays.

Definition at line 500 of file REMORA.H.

Referenced by init_stuff(), prestep(), resize_stuff(), and setup_step().

vec_bustr

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_bustr

Bottom stress in the u direction.

Definition at line 530 of file REMORA.H.

Referenced by gls_corrector(), init_stuff(), resize_stuff(), setup_step(), and WritePlotFile().

vec_bvf

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_bvf

Brunt-Vaisala frequency (3D)

Definition at line 629 of file REMORA.H.

Referenced by gls_corrector(), init_stuff(), resize_stuff(), and setup_step().

vec_bvstr

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_bvstr

Bottom stress in the v direction.

Definition at line 532 of file REMORA.H.

Referenced by gls_corrector(), init_stuff(), resize_stuff(), setup_step(), and WritePlotFile().

vec_cloud

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_cloud

cloud cover fraction [0-1], defined at rho-points

Definition at line 509 of file REMORA.H.

Referenced by ApplyAtmosphericStates(), bulk_fluxes(), init_only(), init_stuff(), resize_stuff(), and set_surface_state().

vec_cons_full_domain

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_cons_full_domain

multilevel data container for high res initial data: temperature, salinity, passive tracer

Definition at line 392 of file REMORA.H.

Referenced by allocate_init_full_domain(), init_biology_full_domain_from_netcdf(), init_biology_ic_full_domain(), init_data_full_domain_from_netcdf(), init_full_domain_from_analytic(), init_scalars_full_domain_from_netcdf(), resize_stuff(), and set_init_data_averaged_down().

vec_diff2

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_diff2

Harmonic diffusivity for temperature / salinity.

Definition at line 440 of file REMORA.H.

Referenced by init_stuff(), mask_arrays_for_write(), resize_stuff(), set_hmixcoef(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_dmde

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_dmde

d(1/m)/d(eta)

Definition at line 619 of file REMORA.H.

Referenced by advance_2d(), init_stuff(), resize_stuff(), set_curvilinear_terms_from_grid_scale(), and setup_step().

vec_dndx

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_dndx

d(1/n)/d(xi)

Definition at line 617 of file REMORA.H.

Referenced by advance_2d(), init_stuff(), resize_stuff(), set_curvilinear_terms_from_grid_scale(), and setup_step().

vec_DU_avg1

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_DU_avg1

time average of barotropic x velocity flux (2D)

Definition at line 535 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d_ml(), init_stuff(), ReadCheckpointFile(), resize_stuff(), and WriteCheckpointFile().

vec_DU_avg2

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_DU_avg2

correct time average of barotropic x velocity flux for coupling (2D)

Definition at line 537 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d_ml(), init_stuff(), ReadCheckpointFile(), resize_stuff(), and WriteCheckpointFile().

vec_DV_avg1

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_DV_avg1

time average of barotropic y velocity flux

Definition at line 539 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d_ml(), init_stuff(), ReadCheckpointFile(), resize_stuff(), and WriteCheckpointFile().

vec_DV_avg2

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_DV_avg2

correct time average of barotropic y velocity flux for coupling (2D)

Definition at line 541 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d_ml(), init_stuff(), ReadCheckpointFile(), resize_stuff(), and WriteCheckpointFile().

vec_EminusP

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_EminusP

evaporation minus precipitation [kg/m^2/s], defined at rho-points

Definition at line 511 of file REMORA.H.

Referenced by bulk_fluxes(), init_only(), init_stuff(), resize_stuff(), set_surface_state(), and set_zeta_to_Ztavg().

vec_evap

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_evap

evaporation rate [kg/m^2/s]

Definition at line 507 of file REMORA.H.

Referenced by ApplyAtmosphericFluxes(), init_stuff(), resize_stuff(), set_zeta_to_Ztavg(), setup_step(), and WriteNCPlotFile_which().

vec_fcor

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_fcor

coriolis factor (2D)

Definition at line 587 of file REMORA.H.

Referenced by advance_2d_onestep(), init_beta_plane_coriolis(), init_coriolis_from_netcdf(), init_stuff(), resize_stuff(), set_coriolis(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_gls

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_gls

Turbulent generic length scale.

Definition at line 644 of file REMORA.H.

Referenced by advance_3d(), gls_corrector(), gls_prestep(), init_gls_vmix(), init_stuff(), ReadCheckpointFile(), resize_stuff(), setup_step(), and WriteCheckpointFile().

vec_h

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_h

multilevel data container for current step's z velocities (largely unused; W stored separately)

Bathymetry data (2D, positive valued, h in ROMS)

Definition at line 403 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d_ml(), allocate_bathymetry_grid_vars_full_domain(), check_mask_consistency(), estTimeStep(), fill_from_bdyfiles(), init_bathymetry_from_netcdf(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), resize_stuff(), set_bathymetry(), set_bathymetry_averaged_down(), setup_step(), stretch_transform(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

vec_h_full_domain

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_h_full_domain

Bathymetry data on the whole domain at each potential level.

Definition at line 406 of file REMORA.H.

Referenced by allocate_bathymetry_grid_vars_full_domain(), coarsen_bathymetry_with_grow_cells(), init_bathymetry_full_domain_from_analytic(), init_bathymetry_full_domain_from_netcdf(), init_grid_vars_full_domain_from_netcdf(), resize_stuff(), and set_bathymetry_averaged_down().

vec_Huon

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Huon

u-volume flux (3D)

Definition at line 416 of file REMORA.H.

Referenced by advance_3d_ml(), gls_corrector(), gls_prestep(), init_stuff(), prestep(), resize_stuff(), and setup_step().

vec_Hvom

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Hvom

v-volume flux (3D)

Definition at line 418 of file REMORA.H.

Referenced by advance_3d_ml(), gls_corrector(), gls_prestep(), init_stuff(), prestep(), resize_stuff(), and setup_step().

vec_Hz

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Hz

Width of cells in the vertical (z-) direction (3D, Hz in ROMS)

Definition at line 414 of file REMORA.H.

Referenced by advance_3d(), advance_3d_ml(), advance_biology(), estTimeStep(), gls_corrector(), gls_prestep(), init_stuff(), prestep(), resize_stuff(), set_2darrays(), setup_step(), stretch_transform(), and volWgtSumMF().

vec_latp

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_latp

latitude on psi-points (2D, degrees north); only filled when the grid NetCDF file carries lat_psi

Definition at line 614 of file REMORA.H.

Referenced by GetAtmosToOceanPsiLonLat(), init_grid_vars_from_netcdf(), and resize_stuff().

vec_lhflx

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_lhflx

latent heat flux

Definition at line 491 of file REMORA.H.

Referenced by ApplyAtmosphericFluxes(), init_stuff(), resize_stuff(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_longwave_down

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_longwave_down

Downward longwave radiation.

Definition at line 489 of file REMORA.H.

Referenced by ApplyAtmosphericStates(), init_only(), init_stuff(), resize_stuff(), set_surface_state(), and setup_step().

vec_lonp

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_lonp

longitude on psi-points (2D, degrees east); only filled when the grid NetCDF file carries lon_psi

Definition at line 611 of file REMORA.H.

Referenced by GetAtmosToOceanPsiLonLat(), init_grid_vars_from_netcdf(), and resize_stuff().

vec_lrflx

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_lrflx

longwave radiation

Definition at line 487 of file REMORA.H.

Referenced by ApplyAtmosphericFluxes(), init_stuff(), resize_stuff(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_Lscale

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Lscale

Vertical mixing turbulent length scale.

Definition at line 646 of file REMORA.H.

Referenced by gls_corrector(), init_gls_vmix(), init_stuff(), ReadCheckpointFile(), resize_stuff(), and WriteCheckpointFile().

vec_mskp

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_mskp

land/sea mask at cell corners (2D)

Definition at line 565 of file REMORA.H.

Referenced by advance_2d_onestep(), calculate_nodal_masks(), check_mask_consistency(), init_masks(), resize_stuff(), setup_step(), and update_nodal_masks().

vec_mskr

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_mskr

land/sea mask at cell centers (2D)

Definition at line 559 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), advance_biology(), allocate_bathymetry_grid_vars_full_domain(), ApplyAtmosphericFluxes(), AverageDownTo(), bulk_fluxes(), calculate_nodal_masks(), check_mask_consistency(), ensure_full_domain_masks(), ErrorEst(), estTimeStep(), fill_3d_masks(), FillCoarsePatchMap(), FillPatch(), GetLandSeaMasks(), init_masks(), init_masks_from_netcdf(), init_zeta_from_netcdf(), mask_arrays_for_write(), ReadCheckpointFile(), resize_stuff(), set_hmixcoef(), set_masks(), set_masks_averaged_down(), setup_step(), update_avgdown_masks(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

vec_mskr3d

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_mskr3d

land/sea mask at cell centers, copied to all z levels (3D)

Definition at line 567 of file REMORA.H.

Referenced by ErrorEst(), fill_3d_masks(), init_masks(), and resize_stuff().

vec_mskr_crse_on_fine

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_mskr_crse_on_fine

the level's rho-, u- and v-masks copied onto the layout of the level above it coarsened, which is the layout the two-way average-down computes on. Indexed by the coarse level of the pair. Built on demand and reused until a regrid, since the masks are a function of position alone and so do not change between them.

Definition at line 573 of file REMORA.H.

Referenced by AverageDownTo(), clear_avgdown_masks(), resize_stuff(), and update_avgdown_masks().

vec_mskr_full_domain

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_mskr_full_domain

Land/sea mask at cell centers on the whole domain at each potential level. Specified at hires_grid_level and coarsened down from there, so that a refined coastline and the bathymetry it goes with come from the same grid.

Definition at line 411 of file REMORA.H.

Referenced by allocate_bathymetry_grid_vars_full_domain(), average_down_with_grow_cells(), coarsen_bathymetry_with_grow_cells(), coarsen_masks_with_grow_cells(), ensure_full_domain_masks(), init_masks_full_domain_from_analytic(), init_masks_full_domain_from_netcdf(), refine_masks_with_grow_cells(), resize_stuff(), and set_masks_averaged_down().

vec_msku

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_msku

land/sea mask at x-faces (2D)

Definition at line 561 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), ApplyAtmosphericFluxes(), AverageDownTo(), bulk_fluxes(), calculate_nodal_masks(), check_mask_consistency(), fill_from_bdyfiles(), FillCoarsePatchMap(), FillPatch(), GetLandSeaMasks(), init_masks(), init_zeta_from_netcdf(), mask_arrays_for_write(), ReadCheckpointFile(), resize_stuff(), setup_step(), update_avgdown_masks(), update_nodal_masks(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

vec_msku_crse_on_fine

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_msku_crse_on_fine

Definition at line 574 of file REMORA.H.

Referenced by AverageDownTo(), clear_avgdown_masks(), resize_stuff(), and update_avgdown_masks().

vec_mskv

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_mskv

land/sea mask at y-faces (2D)

Definition at line 563 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), ApplyAtmosphericFluxes(), AverageDownTo(), bulk_fluxes(), calculate_nodal_masks(), check_mask_consistency(), fill_from_bdyfiles(), FillCoarsePatchMap(), FillPatch(), GetLandSeaMasks(), init_masks(), init_zeta_from_netcdf(), mask_arrays_for_write(), ReadCheckpointFile(), resize_stuff(), setup_step(), update_avgdown_masks(), update_nodal_masks(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

vec_mskv_crse_on_fine

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_mskv_crse_on_fine

Definition at line 575 of file REMORA.H.

Referenced by AverageDownTo(), clear_avgdown_masks(), resize_stuff(), and update_avgdown_masks().

vec_nudg_coeff

amrex::Vector<amrex::Vector<std::unique_ptr<amrex::MultiFab> > > REMORA::vec_nudg_coeff

Climatology nudging coefficients.

Definition at line 653 of file REMORA.H.

Referenced by advance_2d(), advance_3d(), fill_from_bdyfiles(), init_clim_nudg_coeff(), init_clim_nudg_coeff_from_netcdf(), init_stuff(), resize_stuff(), and setup_step().

vec_Pair

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Pair

Air pressure [mb], defined at rho-points.

Definition at line 482 of file REMORA.H.

Referenced by ApplyAtmosphericStates(), init_only(), init_stuff(), resize_stuff(), set_surface_state(), setup_step(), and WriteNCPlotFile_which().

vec_pm

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_pm

horizontal scaling factor: 1 / dx (2D)

Definition at line 578 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), allocate_bathymetry_grid_vars_full_domain(), ErrorEst(), estTimeStep(), fill_from_bdyfiles(), gls_corrector(), gls_prestep(), init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), scale_rhs_vars(), scale_rhs_vars_inv(), set_curvilinear_terms_from_grid_scale(), set_grid_coords_from_grid_scale(), set_grid_scale(), set_grid_vars_averaged_down(), set_hmixcoef(), setup_step(), volWgtSumMF(), WriteNCPlotFile_which(), and WritePlotFile().

vec_pm_full_domain

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_pm_full_domain

horizontal scaling factor: 1 / dx (2D) on whole domain

Definition at line 582 of file REMORA.H.

Referenced by allocate_bathymetry_grid_vars_full_domain(), init_grid_vars_full_domain_from_netcdf(), resize_stuff(), and set_grid_vars_averaged_down().

vec_pn

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_pn

horizontal scaling factor: 1 / dy (2D)

Definition at line 580 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), allocate_bathymetry_grid_vars_full_domain(), ErrorEst(), estTimeStep(), fill_from_bdyfiles(), gls_corrector(), gls_prestep(), init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), scale_rhs_vars(), scale_rhs_vars_inv(), set_curvilinear_terms_from_grid_scale(), set_grid_coords_from_grid_scale(), set_grid_scale(), set_grid_vars_averaged_down(), set_hmixcoef(), setup_step(), volWgtSumMF(), WriteNCPlotFile_which(), and WritePlotFile().

vec_pn_full_domain

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_pn_full_domain

horizontal scaling factor: 1 / dy (2D) on whole domain

Definition at line 584 of file REMORA.H.

Referenced by allocate_bathymetry_grid_vars_full_domain(), init_grid_vars_full_domain_from_netcdf(), resize_stuff(), and set_grid_vars_averaged_down().

vec_qair

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_qair

Specific humidity [kg/kg], defined at rho-points.

Definition at line 480 of file REMORA.H.

Referenced by ApplyAtmosphericStates(), init_only(), init_stuff(), resize_stuff(), set_surface_state(), and setup_step().

vec_rain

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rain

precipitation rate [kg/m^2/s]

Definition at line 505 of file REMORA.H.

Referenced by ApplyAtmosphericFluxes(), ApplyAtmosphericStates(), bulk_fluxes(), init_only(), init_stuff(), resize_stuff(), set_surface_state(), set_zeta_to_Ztavg(), and WriteNCPlotFile_which().

vec_rdrag

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rdrag

Linear drag coefficient [m/s], defined at rho points.

Definition at line 523 of file REMORA.H.

Referenced by init_stuff(), ReadCheckpointFile(), resize_stuff(), setup_step(), and WriteCheckpointFile().

vec_rdrag2

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rdrag2

Quadratic drag coefficient [unitless], defined at rho points.

Definition at line 525 of file REMORA.H.

Referenced by init_stuff(), ReadCheckpointFile(), resize_stuff(), setup_step(), and WriteCheckpointFile().

vec_rhoA

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rhoA

vertically-averaged density

Definition at line 627 of file REMORA.H.

Referenced by advance_2d_onestep(), init_stuff(), resize_stuff(), and setup_step().

vec_rhoS

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rhoS

density perturbation

Definition at line 625 of file REMORA.H.

Referenced by Advance(), advance_2d_onestep(), init_stuff(), resize_stuff(), and setup_step().

vec_river_position

amrex::Vector<std::unique_ptr<amrex::iMultiFab> > REMORA::vec_river_position

private

iMultiFab for river positions; contents are indices of rivers

Definition at line 1553 of file REMORA.H.

Referenced by advance_2d(), advance_3d(), init_riv_pos_from_netcdf(), init_stuff(), prestep(), and resize_stuff().

vec_ru

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_ru

u velocity RHS (3D, includes horizontal and vertical advection)

Definition at line 420 of file REMORA.H.

Referenced by advance_3d_ml(), init_only(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), resize_stuff(), scale_rhs_vars(), scale_rhs_vars_inv(), setup_step(), and WriteCheckpointFile().

vec_ru2d

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_ru2d

u velocity RHS (2D, includes horizontal and vertical advection)

Definition at line 424 of file REMORA.H.

Referenced by advance_2d_onestep(), init_only(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), resize_stuff(), scale_rhs_vars(), scale_rhs_vars_inv(), and WriteCheckpointFile().

vec_rubar

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rubar

barotropic x velocity for the RHS (2D)

Definition at line 543 of file REMORA.H.

Referenced by advance_2d_onestep(), init_stuff(), and resize_stuff().

vec_rufrc

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rufrc

u velocity RHS, integrated, including advection and bottom/surface stresses (2D)

Definition at line 428 of file REMORA.H.

Referenced by advance_2d_onestep(), init_stuff(), resize_stuff(), and setup_step().

vec_rv

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rv

v velocity RHS (3D, includes horizontal and vertical advection)

Definition at line 422 of file REMORA.H.

Referenced by advance_3d_ml(), init_only(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), resize_stuff(), scale_rhs_vars(), scale_rhs_vars_inv(), setup_step(), and WriteCheckpointFile().

vec_rv2d

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rv2d

v velocity RHS (2D, includes horizontal and vertical advection)

Definition at line 426 of file REMORA.H.

Referenced by advance_2d_onestep(), init_only(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), resize_stuff(), scale_rhs_vars(), scale_rhs_vars_inv(), and WriteCheckpointFile().

vec_rvbar

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rvbar

barotropic y velocity for the RHS (2D)

Definition at line 545 of file REMORA.H.

Referenced by advance_2d_onestep(), init_stuff(), and resize_stuff().

vec_rvfrc

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rvfrc

v velocity RHS, integrated, including advection and bottom/surface stresses (2D)

Definition at line 430 of file REMORA.H.

Referenced by advance_2d_onestep(), init_stuff(), resize_stuff(), and setup_step().

vec_rzeta

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_rzeta

free surface height for the RHS (2D)

Definition at line 547 of file REMORA.H.

Referenced by advance_2d_onestep(), init_stuff(), and resize_stuff().

vec_shflx

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_shflx

sensible heat flux

Definition at line 493 of file REMORA.H.

Referenced by ApplyAtmosphericFluxes(), init_stuff(), resize_stuff(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_srflx

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_srflx

Shortwave radiation flux [W/m²], defined at rho-points.

Definition at line 485 of file REMORA.H.

Referenced by advance_biology(), ApplyAtmosphericFluxes(), ApplyAtmosphericStates(), GetAtmosToOceanRhoLayout(), init_only(), init_stuff(), resize_stuff(), set_surface_state(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_sstore

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_sstore

additional scratch space for calculations on temp, salt, etc

Definition at line 622 of file REMORA.H.

Referenced by advance_3d_ml(), init_stuff(), prestep(), resize_stuff(), and setup_step().

vec_stflux

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_stflux

Surface tracer flux; input arrays.

Definition at line 498 of file REMORA.H.

Referenced by ApplyAtmosphericFluxes(), init_stuff(), resize_stuff(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_stflx

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_stflx

Surface tracer flux; working arrays.

Definition at line 496 of file REMORA.H.

Referenced by init_stuff(), prestep(), resize_stuff(), and setup_step().

vec_sustr

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_sustr

Surface stress in the u direction.

Definition at line 469 of file REMORA.H.

Referenced by advance_biology(), ApplyAtmosphericFluxes(), GetAtmosToOceanUFaceLayout(), gls_corrector(), init_only(), init_stuff(), resize_stuff(), set_smflux(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_svstr

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_svstr

Surface stress in the v direction.

Definition at line 471 of file REMORA.H.

Referenced by advance_biology(), ApplyAtmosphericFluxes(), GetAtmosToOceanVFaceLayout(), gls_corrector(), init_only(), init_stuff(), resize_stuff(), set_smflux(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_Tair

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Tair

Air temperature [°C], defined at rho-points.

Definition at line 478 of file REMORA.H.

Referenced by ApplyAtmosphericStates(), init_only(), init_stuff(), resize_stuff(), set_surface_state(), setup_step(), and WriteNCPlotFile_which().

vec_tke

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_tke

Turbulent kinetic energy.

Definition at line 642 of file REMORA.H.

Referenced by advance_3d(), gls_corrector(), gls_prestep(), init_gls_vmix(), init_stuff(), ReadCheckpointFile(), resize_stuff(), setup_step(), and WriteCheckpointFile().

vec_ubar

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_ubar

barotropic x velocity (2D)

Definition at line 549 of file REMORA.H.

Referenced by advance_2d(), advance_2d_onestep(), advance_3d_ml(), init_only(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), mask_arrays_for_write(), ReadCheckpointFile(), RemakeLevel(), resize_stuff(), set_2darrays(), timeStepML(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

vec_uwind

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_uwind

Wind in the u direction, defined at rho-points.

Definition at line 474 of file REMORA.H.

Referenced by advance_biology(), ApplyAtmosphericStates(), init_only(), init_stuff(), resize_stuff(), set_surface_state(), and setup_step().

vec_vbar

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_vbar

barotropic y velocity (2D)

Definition at line 551 of file REMORA.H.

Referenced by advance_2d(), advance_2d_onestep(), advance_3d_ml(), init_only(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), mask_arrays_for_write(), ReadCheckpointFile(), RemakeLevel(), resize_stuff(), set_2darrays(), timeStepML(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

vec_visc2_p

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_visc2_p

Harmonic viscosity defined on the psi points (corners of horizontal grid cells)

Definition at line 436 of file REMORA.H.

Referenced by advance_2d_onestep(), init_stuff(), resize_stuff(), set_hmixcoef(), and setup_step().

vec_visc2_r

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_visc2_r

Harmonic viscosity defined on the rho points (centers)

Definition at line 438 of file REMORA.H.

Referenced by advance_2d_onestep(), init_stuff(), mask_arrays_for_write(), resize_stuff(), set_hmixcoef(), setup_step(), WriteNCPlotFile_which(), and WritePlotFile().

vec_vwind

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_vwind

Wind in the v direction, defined at rho-points.

Definition at line 476 of file REMORA.H.

Referenced by advance_biology(), ApplyAtmosphericStates(), init_only(), init_stuff(), resize_stuff(), set_surface_state(), and setup_step().

vec_weight1

amrex::Vector<amrex::Real> REMORA::vec_weight1

Weights for calculating avg1 in 2D advance.

Definition at line 636 of file REMORA.H.

Referenced by advance_2d(), and set_weights().

vec_weight2

amrex::Vector<amrex::Real> REMORA::vec_weight2

Weights for calculating avg2 in 2D advance.

Definition at line 638 of file REMORA.H.

Referenced by advance_2d(), and set_weights().

vec_xp

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_xp

x_grid on psi-points (2D)

Definition at line 605 of file REMORA.H.

Referenced by GetAtmosToOceanPsiCoordinates(), init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), set_grid_coords_from_grid_scale(), and WriteNCPlotFile_which().

vec_xr

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_xr

x_grid on rho points (2D)

Definition at line 590 of file REMORA.H.

Referenced by init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), set_grid_coords_from_grid_scale(), and WriteNCPlotFile_which().

vec_xu

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_xu

x_grid on u-points (2D)

Definition at line 595 of file REMORA.H.

Referenced by init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), set_grid_coords_from_grid_scale(), and WriteNCPlotFile_which().

vec_xv

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_xv

x_grid on v-points (2D)

Definition at line 600 of file REMORA.H.

Referenced by init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), set_grid_coords_from_grid_scale(), and WriteNCPlotFile_which().

vec_xvel_full_domain

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_xvel_full_domain

multilevel data container for high res initial x velocities (u in ROMS)

Definition at line 394 of file REMORA.H.

Referenced by allocate_init_full_domain(), init_data_full_domain_from_netcdf(), init_full_domain_from_analytic(), resize_stuff(), and set_init_data_averaged_down().

vec_yp

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_yp

y_grid on psi-points (2D)

Definition at line 607 of file REMORA.H.

Referenced by GetAtmosToOceanPsiCoordinates(), init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), set_grid_coords_from_grid_scale(), and WriteNCPlotFile_which().

vec_yr

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_yr

y_grid on rho points (2D)

Definition at line 592 of file REMORA.H.

Referenced by init_beta_plane_coriolis(), init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), set_grid_coords_from_grid_scale(), and WriteNCPlotFile_which().

vec_yu

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_yu

y_grid on u-points (2D)

Definition at line 597 of file REMORA.H.

Referenced by init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), set_grid_coords_from_grid_scale(), and WriteNCPlotFile_which().

vec_yv

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_yv

y_grid on v-points (2D)

Definition at line 602 of file REMORA.H.

Referenced by init_grid_vars_from_netcdf(), init_stuff(), resize_stuff(), set_grid_coords_from_grid_scale(), and WriteNCPlotFile_which().

vec_yvel_full_domain

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_yvel_full_domain

multilevel data container for high res initial y velocities (v in ROMS)

Definition at line 396 of file REMORA.H.

Referenced by allocate_init_full_domain(), init_data_full_domain_from_netcdf(), init_full_domain_from_analytic(), resize_stuff(), and set_init_data_averaged_down().

vec_z_phys_nd

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_z_phys_nd

z coordinates at psi points (cell nodes)

Definition at line 463 of file REMORA.H.

Referenced by advance_3d_ml(), init_stuff(), MakeNewLevelFromScratch(), resize_stuff(), stretch_transform(), and WritePlotFile().

vec_z_r

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_z_r

z coordinates at rho points (cell centers)

Definition at line 443 of file REMORA.H.

Referenced by init_stuff(), resize_stuff(), setup_step(), and stretch_transform().

vec_z_w

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_z_w

z coordinates at w points (faces between z-cells)

Definition at line 446 of file REMORA.H.

Referenced by advance_3d_ml(), advance_biology(), gls_corrector(), init_stuff(), resize_stuff(), setup_step(), and stretch_transform().

vec_zeta

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_zeta

free surface height (2D)

Definition at line 553 of file REMORA.H.

Referenced by advance_2d(), advance_2d_onestep(), allocate_init_full_domain(), fill_from_bdyfiles(), init_stuff(), init_zeta_from_netcdf(), ReadCheckpointFile(), resize_stuff(), set_zeta(), set_zeta_average(), set_zeta_averaged_down(), set_zeta_to_Ztavg(), and WriteCheckpointFile().

vec_zeta_full_domain

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_zeta_full_domain

high resolution initial free surface height (2D)

Definition at line 556 of file REMORA.H.

Referenced by allocate_init_full_domain(), init_full_domain_zeta_from_analytic(), init_zeta_full_domain_from_netcdf(), resize_stuff(), and set_zeta_averaged_down().

vec_ZoBot

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_ZoBot

Bottom roughness length [m], defined at rho points.

Definition at line 527 of file REMORA.H.

Referenced by gls_corrector(), init_stuff(), ReadCheckpointFile(), resize_stuff(), setup_step(), and WriteCheckpointFile().

vec_Zt_avg1

amrex::Vector<std::unique_ptr<amrex::MultiFab> > REMORA::vec_Zt_avg1

Average of the free surface, zeta (2D)

Definition at line 466 of file REMORA.H.

Referenced by advance_2d_onestep(), AverageDownTo(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), mask_arrays_for_write(), ReadCheckpointFile(), RemakeLevel(), resize_stuff(), set_zeta_average(), set_zeta_to_Ztavg(), stretch_transform(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

verbose

int REMORA::verbose = 0

staticprivate

Verbosity level of output.

Definition at line 1812 of file REMORA.H.

Referenced by check_mask_consistency(), estTimeStep(), Evolve(), init_riv_pos_from_netcdf(), prestep_diffusion(), ReadParameters(), sum_integrated_quantities(), and vert_visc_3d().

Vwind_data_from_file

std::unique_ptr<NCTimeSeries> REMORA::Vwind_data_from_file

private

Data container for v-direction wind read from file.

Definition at line 1510 of file REMORA.H.

Referenced by init_only(), and set_surface_state().

write_history_file

bool REMORA::write_history_file = true

staticprivate

Whether to output NetCDF files as a single history file with several time steps.

Definition at line 1501 of file REMORA.H.

Referenced by ReadParameters(), and WriteNCPlotFile().

xvel_new

amrex::Vector<amrex::MultiFab*> REMORA::xvel_new

multilevel data container for current step's x velocities (u in ROMS)

Definition at line 385 of file REMORA.H.

Referenced by advance_3d_ml(), allocate_init_full_domain(), AverageDownTo(), ClearLevel(), ErrorEst(), estTimeStep(), init_analytic(), init_data_from_netcdf(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), mask_arrays_for_write(), ReadCheckpointFile(), RemakeLevel(), REMORA(), REMORA(), set_2darrays(), set_init_data_averaged_down(), setup_step(), sum_integrated_quantities(), timeStep(), timeStepML(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

xvel_old

amrex::Vector<amrex::MultiFab*> REMORA::xvel_old

multilevel data container for last step's x velocities (u in ROMS)

Definition at line 376 of file REMORA.H.

Referenced by advance_3d(), ClearLevel(), gls_corrector(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), REMORA(), REMORA(), setup_step(), timeStep(), timeStepML(), and WriteCheckpointFile().

yvel_new

amrex::Vector<amrex::MultiFab*> REMORA::yvel_new

multilevel data container for current step's y velocities (v in ROMS)

Definition at line 387 of file REMORA.H.

Referenced by advance_3d_ml(), allocate_init_full_domain(), AverageDownTo(), ClearLevel(), ErrorEst(), estTimeStep(), init_analytic(), init_data_from_netcdf(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), mask_arrays_for_write(), ReadCheckpointFile(), RemakeLevel(), REMORA(), REMORA(), set_2darrays(), set_init_data_averaged_down(), setup_step(), sum_integrated_quantities(), timeStep(), timeStepML(), WriteCheckpointFile(), WriteNCPlotFile_which(), and WritePlotFile().

yvel_old

amrex::Vector<amrex::MultiFab*> REMORA::yvel_old

multilevel data container for last step's y velocities (v in ROMS)

Definition at line 378 of file REMORA.H.

Referenced by advance_3d(), ClearLevel(), gls_corrector(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), REMORA(), REMORA(), setup_step(), timeStep(), timeStepML(), and WriteCheckpointFile().

zvel_new

amrex::Vector<amrex::MultiFab*> REMORA::zvel_new

multilevel data container for current step's z velocities (largely unused; W stored separately)

Definition at line 389 of file REMORA.H.

Referenced by advance_3d_ml(), AverageDownTo(), ClearLevel(), ErrorEst(), estTimeStep(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), REMORA(), REMORA(), setup_step(), timeStep(), timeStepML(), WriteCheckpointFile(), and WritePlotFile().

zvel_old

amrex::Vector<amrex::MultiFab*> REMORA::zvel_old

multilevel data container for last step's z velocities (largely unused; W stored separately)

Definition at line 380 of file REMORA.H.

Referenced by ClearLevel(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), REMORA(), REMORA(), setup_step(), timeStep(), timeStepML(), and WriteCheckpointFile().

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The documentation for this class was generated from the following files:

• /home/runner/work/REMORA/REMORA/Source/REMORA.H
• /home/runner/work/REMORA/REMORA/Source/Biology/REMORA_Biology.cpp
• /home/runner/work/REMORA/REMORA/Source/BoundaryConditions/REMORA_BoundaryConditions_netcdf.cpp
• /home/runner/work/REMORA/REMORA/Source/BoundaryConditions/REMORA_FillPatch.cpp
• /home/runner/work/REMORA/REMORA/Source/Initialization/REMORA_init.cpp
• /home/runner/work/REMORA/REMORA/Source/Initialization/REMORA_init_bcs.cpp
• /home/runner/work/REMORA/REMORA/Source/Initialization/REMORA_init_from_netcdf.cpp
• /home/runner/work/REMORA/REMORA/Source/Initialization/REMORA_make_new_level.cpp
• /home/runner/work/REMORA/REMORA/Source/IO/REMORA_Checkpoint.cpp
• /home/runner/work/REMORA/REMORA/Source/IO/REMORA_console_io.cpp
• /home/runner/work/REMORA/REMORA/Source/IO/REMORA_NCPlotFile.cpp
• /home/runner/work/REMORA/REMORA/Source/IO/REMORA_Plotfile.cpp
• /home/runner/work/REMORA/REMORA/Source/IO/REMORA_SetPlotVars.cpp
• /home/runner/work/REMORA/REMORA/Source/IO/REMORA_writeJobInfo.cpp
• /home/runner/work/REMORA/REMORA/Source/REMORA.cpp
• /home/runner/work/REMORA/REMORA/Source/REMORA_Coupling.cpp
• /home/runner/work/REMORA/REMORA/Source/REMORA_SumIQ.cpp
• /home/runner/work/REMORA/REMORA/Source/REMORA_Tagging.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_Advance.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_advance_2d.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_advance_2d_onestep.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_advance_3d.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_advance_3d_ml.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_apply_clim_nudg.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_bulk_flux.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_bulk_flux_test.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_ComputeTimestep.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_coriolis.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_curvilinear.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_gls.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_prestep.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_prestep_diffusion.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_prestep_t_advection.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_prsgrd.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_rho_eos.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_rhs_t_3d.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_rhs_uv_2d.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_rhs_uv_3d.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_scale_rhs_vars.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_set_weights.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_setup_step.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_t3dmix.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_TimeStep.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_TimeStepML.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_update_massflux_3d.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_uv3dmix.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_vert_mean_3d.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_vert_visc_3d.cpp
• /home/runner/work/REMORA/REMORA/Source/Utils/REMORA_DepthStretchTransform.H