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 Member Functions
	REMORA ()
virtual	~REMORA ()
void	Evolve ()
	Advance solution to final time.
virtual void	ErrorEst (int lev, amrex::TagBoxArray &tags, amrex::Real time, int ngrow) override
	Tag cells for refinement.
void	InitData ()
	Initialize multilevel data.
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	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 on level lev. Only works if using analytic initialization.
void	set_zeta_to_Ztavg (int lev)
	Set zeta components to be equal to time-averaged Zt_avg1.
void	update_mskp (int lev)
	Set psi-point mask to be consistent with rho-point mask.
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 ()
	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< std::string > &varnames, amrex::Real time, const amrex::Vector< int > &level_steps, const std::string &versionName="HyperCLaw-V1.1", const std::string &levelPrefix="Level_", const std::string &mfPrefix="Cell", const amrex::Vector< std::string > &extra_dirs=amrex::Vector< std::string >()) const
	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, amrex::Real time, const amrex::Vector< int > &level_steps, 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	bulk_fluxes (int lev, amrex::MultiFab *mf_cons, amrex::MultiFab *mf_uwind, amrex::MultiFab *mf_vwind, 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 (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 (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 (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 (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 > &DC, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &sstr, const amrex::Array4< amrex::Real const > &bstr, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const int iic, const int ntfirst, const int nnew, int nstp, int nrhs, int N, const amrex::Real lambda, const amrex::Real dt_lev)
	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 (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	t3dmix (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.
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	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=amrex::Real(0.0))
	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_bathymetry (int lev)
	Initialize bathymetry from file or analytic.
void	set_coriolis (int lev)
	Initialize Coriolis factor from file or analytic.
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_wind (int lev)
	Initialize or calculate wind speed from file or analytic.
void	set_hmixcoef (int lev)
	Initialize horizontal mixing coefficients.
void	init_flat_bathymetry (int lev)
	Initialize flat bathymetry to value from problo.
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=true, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=amrex::Real(0.0), 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=true)
	Fill a new MultiFab by copying in phi from valid region and filling ghost cells without applying boundary conditions.
void	fill_from_bdyfiles (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=amrex::Real(0.0))
	Fill boundary data from netcdf file.
void	init_beta_plane_coriolis (int lev)
	Calculate Coriolis parameters from beta plane parametrization.
void	init_data_from_netcdf (int lev)
	Problem initialization from NetCDF file.
void	init_bdry_from_netcdf ()
	Boundary data initialization from NetCDF file.
void	init_masks_from_netcdf (int lev)
	Mask data initialization from NetCDF file.
void	init_bathymetry_from_netcdf (int lev)
	Bathymetry data initialization from NetCDF file.
void	init_zeta_from_netcdf (int lev)
	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)
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	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.

Static Public Member Functions
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 scalar
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 scalar
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_hOfTheConfusingName
	Bathymetry data (2D, positive valued, h in ROMS)
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::Vector< std::unique_ptr< amrex::MultiFab > >	vec_s_r
	Scaled vertical coordinate (range [0,1]) that transforms to z, defined at rho points (cell centers)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_s_w
	Scaled vertical coordinate (range [0,1]) that transforms to z, defined at w-points (cell faces)
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_Cs_r
	Stretching coefficients at rho points.
amrex::Vector< std::unique_ptr< amrex::MultiFab > >	vec_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_lrflx
	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_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_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_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_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_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.

Static Public Attributes
static int	total_nc_plot_file_step = 1

Private Member Functions
void	ReadParameters ()
	read in some parameters from inputs file
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_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.
void	FillCoarsePatch (int lev, amrex::Real time, amrex::MultiFab *mf_fine, amrex::MultiFab *mf_crse, const int icomp=0, const bool fill_all=true)
	fill an entire multifab by interpolating from the coarser level
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	setPlotVariables (const std::string &pp_plot_var_names)
void	appendPlotVariables (const std::string &pp_plot_var_names)
void	WriteNCPlotFile (int istep)
	Write plotfile using NetCDF (wrapper)
void	WriteNCPlotFile_which (int lev, int which_subdomain, 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.
AMREX_FORCE_INLINE int	ComputeGhostCells (const int &spatial_order)
	Helper function to determine number of ghost cells.
AMREX_FORCE_INLINE amrex::YAFluxRegister *	getAdvFluxReg (int lev)
	Get flux register.
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
amrex::Vector< amrex::Vector< amrex::FArrayBox > >	bdy_data_xlo
	Vectors (over time) of Vector (over variables) of FArrayBoxs for holding Western boundary data from file.
amrex::Vector< amrex::Vector< amrex::FArrayBox > >	bdy_data_xhi
	Vectors (over time) of Vector (over variables) of FArrayBoxs for holding Eastern boundary data from file.
amrex::Vector< amrex::Vector< amrex::FArrayBox > >	bdy_data_ylo
	Vectors (over time) of Vector (over variables) of FArrayBoxs for holding Southern boundary data from file.
amrex::Vector< amrex::Vector< amrex::FArrayBox > >	bdy_data_yhi
	Vectors (over time) of Vector (over variables) of FArrayBoxs for holding Northern boundary data from file.
amrex::Real	start_bdy_time
	Start time in the time series of boundary data.
amrex::Real	bdy_time_interval
	Interval between boundary data times.
NCTimeSeries *	sustr_data_from_file
	Data container for u-component surface momentum flux read from file.
NCTimeSeries *	svstr_data_from_file
	Data container for v-component surface momentum flux read from file.
NCTimeSeries *	Uwind_data_from_file
	Data container for u-direction wind read from file.
NCTimeSeries *	Vwind_data_from_file
	Data container for v-direction wind read from file.
NCTimeSeries *	ubar_clim_data_from_file
	Data container for ubar climatology data read from file.
NCTimeSeries *	vbar_clim_data_from_file
	Data container for vbar climatology data read from file.
NCTimeSeries *	u_clim_data_from_file
	Data container for u-velocity climatology data read from file.
NCTimeSeries *	v_clim_data_from_file
	Data container for v-velocity climatology data read from file.
NCTimeSeries *	temp_clim_data_from_file
	Data container for temperature climatology data read from file.
NCTimeSeries *	salt_clim_data_from_file
	Data container for salinity climatology data read from file.
amrex::Vector< NCTimeSeriesRiver * >	river_source_cons
	Vector of data containers for scalar data in rivers.
NCTimeSeriesRiver *	river_source_transport
	Data container for momentum transport in rivers.
NCTimeSeriesRiver *	river_source_transportbar
	Data container for vertically integrated momentum transport in rivers.
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< 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::Array< amrex::Array< amrex::Real, AMREX_SPACEDIM *2 >, AMREX_SPACEDIM+NCONS+8 >	m_bc_extdir_vals
	Array holding the Dirichlet values at walls which need them.
amrex::GpuArray< amrex::GpuArray< REMORA_BC, AMREX_SPACEDIM *2 >, BCVars::NumTypes >	phys_bc_type
	Array holding the "physical" boundary condition types (e.g. "inflow")
amrex::GpuArray< amrex::GpuArray< bool, AMREX_SPACEDIM *2 >, BdyVars::NumTypes+1 >	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()
	Time to stop.
amrex::Real	start_time = 0.0
	Time of the start of the simulation, in seconds.
std::string	restart_chkfile = ""
	If set, restart from this checkpoint file.
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(-1.0)
	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(-1.0)
	Checkpoint output interval in seconds.
bool	chunk_history_file = false
	Whether to chunk netcdf history file.
int	steps_per_history_file = -1
	Number of time steps per netcdf 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
	Names of variables to output to AMReX plotfile.
const amrex::Vector< std::string >	cons_names {"temp", "salt", "scalar"}
	Names of scalars for plotfile output.
const amrex::Vector< std::string >	derived_names {"vorticity"}
	Names of derived fields for plotfiles.
std::string	nc_frc_file
	NetCDF forcing file.
std::string	nc_riv_file
std::string	nc_clim_his_file
	NetCDF climatology history file.
std::string	nc_clim_coeff_file
	NetCDF climatology coefficient file.
std::string	bdry_time_varname = "ocean_time"
	Name of time field 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.
std::string	clim_salt_time_varname = "ocean_time"
	Name of time field for salinity climatology data.
std::string	clim_temp_time_varname = "ocean_time"
	Name of time field for temperature 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 = 0.8_rt
	CFL condition.
static amrex::Real	change_max = 1.1_rt
	Fraction maximum change in subsequent time steps.
static amrex::Real	fixed_dt = -1.0_rt
	User specified fixed baroclinic time step.
static amrex::Real	fixed_fast_dt = -1.0_rt
	User specified fixed barotropic time step.
static int	fixed_ndtfast_ratio = 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 = -1.0_rt
	Diagnostic sum output interval in time.
static int	file_min_digits = 5
	Minimum number of digits in plotfile name or chunked history file.
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 = 0.0_rt
	Variable for CPU timing.
static amrex::Real	previousCPUTimeUsed = 0.0_rt
	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 86 of file REMORA.H.

Constructor & Destructor Documentation

REMORA()

REMORA::REMORA

(

)

constructor:

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

Definition at line 61 of file REMORA.cpp.

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~REMORA()

REMORA::~REMORA ( )

virtual

Definition at line 135 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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appendPlotVariables()

void REMORA::appendPlotVariables ( const std::string &  pp_plot_var_names )

private

Parameters

pp_plot_var_names

variables to add to plot list

Definition at line 102 of file REMORA_Plotfile.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 = amrex::Real(0.0)
	)

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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AverageDown()

void REMORA::AverageDown ( )

private

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

Definition at line 1087 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 1099 of file REMORA.cpp.

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

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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 162 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_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,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 20 of file REMORA_bulk_flux.cpp.

Referenced by nonlin_eos(), and 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 1448 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 1416 of file REMORA.H.

Referenced by bulk_fluxes().

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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 657 of file REMORA_make_new_level.cpp.

ComputeDt()

void REMORA::ComputeDt ( )

private

a wrapper for estTimeStep()

Definition at line 6 of file REMORA_ComputeTimestep.cpp.

Referenced by Evolve(), 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 1312 of file REMORA.H.

Referenced by MakeNewLevelFromScratch(), and RemakeLevel().

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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 364 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 622 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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DataLog()

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

inlineprivate

Helper function for IO stream.

Definition at line 1347 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 1397 of file REMORA.H.

Define_REMORAFillPatchers()

void REMORA::Define_REMORAFillPatchers ( int  lev )

private

Define FillPatchers.

Parameters

[in]

lev

level to operate on

Definition at line 412 of file REMORA.cpp.

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

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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 15 of file REMORA_Tagging.cpp.

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estTimeStep()

Real REMORA::estTimeStep

(

int

level

)

const

compute dt from CFL considerations

Parameters

[in]

level

level of refinement

Definition at line 41 of file REMORA_ComputeTimestep.cpp.

Referenced by ComputeDt().

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Evolve()

void REMORA::Evolve

(

)

Advance solution to final time.

Definition at line 140 of file REMORA.cpp.

Referenced by main().

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fill_from_bdyfiles()

void REMORA::fill_from_bdyfiles	(	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	= amrex::Real(0.0)
	)

Fill boundary data from netcdf file.

Definition at line 19 of file REMORA_BoundaryConditions_netcdf.cpp.

Referenced by advance_3d(), 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)

Parameters

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

Definition at line 447 of file REMORA_FillPatch.cpp.

Referenced by ErrorEst().

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FillCoarsePatch()

void REMORA::FillCoarsePatch ( int  lev, amrex::Real  time, amrex::MultiFab *  mf_fine, amrex::MultiFab *  mf_crse, const int  icomp = 0, const bool  fill_all = true  )

private

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]	icomp	component to fill
[in]	fill_all	whether to fill all components

Definition at line 364 of file REMORA_FillPatch.cpp.

Referenced by FillCoarsePatch(), init_only(), MakeNewLevelFromCoarse(), and set_bathymetry().

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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 = true,
		const int	n_not_fill = 0,
		const int	icomp_calc = 0,
		const amrex::Real	dt = amrex::Real(0.0),
		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(), gls_corrector(), gls_prestep(), init_bathymetry_from_netcdf(), InitData(), RemakeLevel(), set_2darrays(), set_analytic_vmix(), set_coriolis(), set_hmixcoef(), set_smflux(), set_wind(), 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 = true
	)

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 192 of file REMORA_FillPatch.cpp.

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

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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 1123 of file REMORA.cpp.

getAdvFluxReg()

AMREX_FORCE_INLINE amrex::YAFluxRegister * REMORA::getAdvFluxReg ( int  lev )

inlineprivate

Get flux register.

Definition at line 1339 of file REMORA.H.

getCPUTime()

amrex::Real REMORA::getCPUTime ( ) const

inlineprivate

Get CPU time used.

Definition at line 1366 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 293 of file REMORA_FillPatch.cpp.

Referenced by FillCoarsePatch(), and GetDataAtTime().

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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 246 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 183 of file REMORA_init_from_netcdf.cpp.

Referenced by set_bathymetry().

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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

(

)

Boundary data initialization from NetCDF file.

Parameters

lev	Integer specifying the current level

Definition at line 422 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 26 of file REMORA_init.cpp.

Referenced by set_coriolis().

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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 186 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 497 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 340 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 90 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only().

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init_flat_bathymetry()

void REMORA::init_flat_bathymetry

(

int

lev

)

Initialize flat bathymetry to value from problo.

Parameters

[in]

lev

level to operate on

Definition at line 658 of file REMORA.cpp.

Referenced by set_bathymetry().

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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 144 of file REMORA_init.cpp.

Referenced by init_set_vmix().

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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 427 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 375 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 704 of file REMORA.cpp.

Referenced by MakeNewLevelFromScratch().

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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 573 of file REMORA_init_from_netcdf.cpp.

Referenced by init_only().

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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 604 of file REMORA.cpp.

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

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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 451 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 141 of file REMORA_init_from_netcdf.cpp.

Referenced by set_zeta().

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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 258 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 197 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 254 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 662 of file REMORA_Plotfile.cpp.

Referenced by WriteNCPlotFile_which().

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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 157 of file REMORA_rho_eos.cpp.

Referenced by rho_eos().

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NumDataLogs()

AMREX_FORCE_INLINE int REMORA::NumDataLogs ( )

inlineprivatenoexcept

Definition at line 1354 of file REMORA.H.

Referenced by sum_integrated_quantities().

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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 226 of file REMORA.cpp.

Referenced by Evolve().

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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 > &	DC,
		const amrex::Array4< amrex::Real > &	FC,
		const amrex::Array4< amrex::Real const > &	sstr,
		const amrex::Array4< amrex::Real const > &	bstr,
		const amrex::Array4< amrex::Real const > &	z_r,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		const int	iic,
		const int	ntfirst,
		const int	nnew,
		int	nstp,
		int	nrhs,
		int	N,
		const amrex::Real	lambda,
		const amrex::Real	dt_lev
	)

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
	DC	temporary
	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 39 of file REMORA_prestep_diffusion.cpp.

Referenced by prestep().

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prestep_t_advection()

void REMORA::prestep_t_advection	(	const amrex::Box &	tbx,
		const amrex::Box &	gbx,
		const amrex::Array4< amrex::Real > &	tempold,
		const amrex::Array4< amrex::Real > &	tempcache,
		const amrex::Array4< amrex::Real > &	Hz,
		const amrex::Array4< amrex::Real > &	Huon,
		const amrex::Array4< amrex::Real > &	Hvom,
		const amrex::Array4< amrex::Real > &	W,
		const amrex::Array4< amrex::Real > &	DC,
		const amrex::Array4< amrex::Real > &	FC,
		const amrex::Array4< amrex::Real > &	sstore,
		const amrex::Array4< amrex::Real const > &	z_w,
		const amrex::Array4< amrex::Real const > &	h,
		const amrex::Array4< amrex::Real const > &	pm,
		const amrex::Array4< amrex::Real const > &	pn,
		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]	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 34 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 256 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 877 of file REMORA.cpp.

Referenced by REMORA().

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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 115 of file REMORA_Tagging.cpp.

Referenced by 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 116 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 323 of file REMORA_make_new_level.cpp.

Referenced by MakeNewLevelFromCoarse(), and MakeNewLevelFromScratch().

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restart()

void REMORA::restart

(

)

\briefRestart

Definition at line 458 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	(	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]	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 27 of file REMORA_rhs_t_3d.cpp.

Referenced by advance_3d().

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rhs_uv_2d()

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

RHS terms for 2D momentum.

Parameters

[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 17 of file REMORA_rhs_uv_2d.cpp.

Referenced by advance_2d().

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rhs_uv_3d()

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

RHS terms for 3D momentum.

Parameters

[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 28 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 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 50 of file REMORA_scale_rhs_vars.cpp.

Referenced by timeStepML().

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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 81 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 620 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 492 of file REMORA.cpp.

Referenced by init_only().

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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 581 of file REMORA.cpp.

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

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set_drag()

void REMORA::set_drag

(

int

lev

)

Initialize or calculate bottom drag.

set_grid_scale()

void REMORA::set_grid_scale

(

int

lev

)

Set pm and pn arrays on level lev. Only works if using analytic initialization.

Parameters

[in]

lev

level to operate on

Definition at line 667 of file REMORA_make_new_level.cpp.

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

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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 633 of file REMORA.cpp.

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

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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 667 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_wind()

void REMORA::set_wind

(

int

lev

)

Initialize or calculate wind speed from file or analytic.

Parameters

[in]

lev

level to operate on

Definition at line 685 of file REMORA.cpp.

Referenced by setup_step().

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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 470 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 57 of file REMORA_init.cpp.

Referenced by set_zeta().

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set_zeta_to_Ztavg()

void REMORA::set_zeta_to_Ztavg

(

int

lev

)

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

Parameters

[in]

lev

level to operate on

Definition at line 724 of file REMORA_make_new_level.cpp.

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

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setPlotVariables()

void REMORA::setPlotVariables ( const std::string &  pp_plot_var_names )

private

Parameters

pp_plot_var_names

list of variable names to plot read in from parameter file

Definition at line 18 of file REMORA_Plotfile.cpp.

Referenced by REMORA().

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setRecordDataInfo()

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

inlineprivate

Definition at line 1380 of file REMORA.H.

Referenced by ReadParameters().

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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 15 of file REMORA_DepthStretchTransform.H.

Referenced by advance_3d(), 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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t3dmix()

void REMORA::t3dmix	(	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.

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 19 of file REMORA_t3dmix.cpp.

Referenced by setup_step().

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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(), 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().

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update_massflux_3d()

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

Correct mass flux.

Parameters

[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 22 of file REMORA_update_massflux_3d.cpp.

Referenced by advance_3d().

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update_mskp()

void REMORA::update_mskp

(

int

lev

)

Set psi-point mask to be consistent with rho-point mask.

Parameters

[in]

lev

level to operate on

Definition at line 766 of file REMORA_make_new_level.cpp.

Referenced by init_masks_from_netcdf().

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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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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 121 of file REMORA_SumIQ.cpp.

Referenced by sum_integrated_quantities().

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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 Evolve(), and InitData().

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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,
		amrex::Real	time,
		const amrex::Vector< int > &	level_steps,
		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	variable names to write out
time	time at which to output
level_steps	vector over level of iterations
versionName	version string for VisIt
levelPrefix	string to prepend to level number
mfPrefix	subdirectory for multifab data

Definition at line 570 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< std::string > &	varnames,
		amrex::Real	time,
		const amrex::Vector< int > &	level_steps,
		const std::string &	versionName = "HyperCLaw-V1.1",
		const std::string &	levelPrefix = "Level_",
		const std::string &	mfPrefix = "Cell",
		const amrex::Vector< std::string > &	extra_dirs = amrex::Vector<std::string>()
	)		const

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	variable names to write out
time	time at which to output
level_steps	vector over level of iterations
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 474 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  which_step )

private

Write plotfile using NetCDF (wrapper)

Parameters

which_step

current step for output

Definition at line 24 of file REMORA_NCPlotFile.cpp.

Referenced by Evolve(), and InitData().

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WriteNCPlotFile_which()

void REMORA::WriteNCPlotFile_which ( int  lev, int  which_subdomain, 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 109 of file REMORA_NCPlotFile.cpp.

Referenced by WriteNCPlotFile().

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WritePlotFile()

void REMORA::WritePlotFile

(

)

main driver for writing AMReX plotfiles

Definition at line 147 of file REMORA_Plotfile.cpp.

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

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Member Data Documentation

advflux_reg

amrex::Vector<amrex::YAFluxRegister*> REMORA::advflux_reg

private

array of flux registers for refluxing in multilevel

Definition at line 1114 of file REMORA.H.

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

bdry_time_varname

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

private

Name of time field for boundary data.

Definition at line 1281 of file REMORA.H.

Referenced by init_bdry_from_netcdf(), and ReadParameters().

bdy_data_xhi

amrex::Vector<amrex::Vector<amrex::FArrayBox> > REMORA::bdy_data_xhi

private

Vectors (over time) of Vector (over variables) of FArrayBoxs for holding Eastern boundary data from file.

Definition at line 995 of file REMORA.H.

Referenced by fill_from_bdyfiles(), FillCoarsePatch(), init_bdry_from_netcdf(), ReadCheckpointFile(), and WriteCheckpointFile().

bdy_data_xlo

amrex::Vector<amrex::Vector<amrex::FArrayBox> > REMORA::bdy_data_xlo

private

Vectors (over time) of Vector (over variables) of FArrayBoxs for holding Western boundary data from file.

Definition at line 993 of file REMORA.H.

Referenced by fill_from_bdyfiles(), FillCoarsePatch(), init_bdry_from_netcdf(), ReadCheckpointFile(), and WriteCheckpointFile().

bdy_data_yhi

amrex::Vector<amrex::Vector<amrex::FArrayBox> > REMORA::bdy_data_yhi

private

Vectors (over time) of Vector (over variables) of FArrayBoxs for holding Northern boundary data from file.

Definition at line 999 of file REMORA.H.

Referenced by fill_from_bdyfiles(), FillCoarsePatch(), init_bdry_from_netcdf(), ReadCheckpointFile(), and WriteCheckpointFile().

bdy_data_ylo

amrex::Vector<amrex::Vector<amrex::FArrayBox> > REMORA::bdy_data_ylo

private

Vectors (over time) of Vector (over variables) of FArrayBoxs for holding Southern boundary data from file.

Definition at line 997 of file REMORA.H.

Referenced by fill_from_bdyfiles(), FillCoarsePatch(), init_bdry_from_netcdf(), ReadCheckpointFile(), and WriteCheckpointFile().

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 1143 of file REMORA.H.

Referenced by init_bcs().

bdy_time_interval

amrex::Real REMORA::bdy_time_interval

private

Interval between boundary data times.

Definition at line 1004 of file REMORA.H.

Referenced by fill_from_bdyfiles(), FillCoarsePatch(), init_bdry_from_netcdf(), ReadCheckpointFile(), and WriteCheckpointFile().

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 1094 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_clim_nudg_coeff_from_netcdf(), init_coriolis_from_netcdf(), init_data_from_netcdf(), init_masks_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 1051 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 1049 of file REMORA.H.

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

cfl

amrex::Real REMORA::cfl = 0.8_rt

staticprivate

CFL condition.

Definition at line 1173 of file REMORA.H.

Referenced by estTimeStep(), and ReadParameters().

change_max

amrex::Real REMORA::change_max = 1.1_rt

staticprivate

Fraction maximum change in subsequent time steps.

Definition at line 1175 of file REMORA.H.

Referenced by ComputeDt(), and ReadParameters().

check_file

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

private

Checkpoint file prefix.

Definition at line 1199 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 1201 of file REMORA.H.

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

check_int_time

amrex::Real REMORA::check_int_time = amrex::Real(-1.0)

private

Checkpoint output interval in seconds.

Definition at line 1203 of file REMORA.H.

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

chunk_history_file

bool REMORA::chunk_history_file = false

private

Whether to chunk netcdf history file.

Definition at line 1206 of file REMORA.H.

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

clim_salt_time_varname

std::string REMORA::clim_salt_time_varname = "ocean_time"

private

Name of time field for salinity climatology data.

Definition at line 1291 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

clim_temp_time_varname

std::string REMORA::clim_temp_time_varname = "ocean_time"

private

Name of time field for temperature climatology data.

Definition at line 1293 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 1287 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 1283 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 1289 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 1285 of file REMORA.H.

Referenced by ReadParameters().

cons_names

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

private

Names of scalars for plotfile output.

Definition at line 1218 of file REMORA.H.

Referenced by setPlotVariables(), and WritePlotFile().

cons_new

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

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

Definition at line 217 of file REMORA.H.

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

cons_old

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

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

Definition at line 208 of file REMORA.H.

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

datalog

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

private

Definition at line 1393 of file REMORA.H.

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

datalogname

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

private

Definition at line 1394 of file REMORA.H.

Referenced by DataLogName(), and ReadParameters().

derived_names

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

private

Names of derived fields for plotfiles.

Definition at line 1221 of file REMORA.H.

Referenced by setPlotVariables().

do_substep

int REMORA::do_substep = 0

private

Whether to substep fine levels in time.

Definition at line 1186 of file REMORA.H.

Referenced by ReadParameters(), 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 1128 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 1123 of file REMORA.H.

Referenced by fill_from_bdyfiles(), FillCoarsePatch(), 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 1125 of file REMORA.H.

Referenced by FillCoarsePatch(), init_bcs(), and init_stuff().

dt

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

private

time step at each level

Definition at line 1105 of file REMORA.H.

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

file_min_digits

int REMORA::file_min_digits = 5

staticprivate

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

Definition at line 1259 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 1307 of file REMORA.H.

Referenced by build_fine_mask().

fixed_dt

amrex::Real REMORA::fixed_dt = -1.0_rt

staticprivate

User specified fixed baroclinic time step.

Definition at line 1177 of file REMORA.H.

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

fixed_fast_dt

amrex::Real REMORA::fixed_fast_dt = -1.0_rt

staticprivate

User specified fixed barotropic time step.

Definition at line 1179 of file REMORA.H.

Referenced by ReadParameters(), and set_weights().

fixed_ndtfast_ratio

int REMORA::fixed_ndtfast_ratio = 0

staticprivate

User specified, number of barotropic steps per baroclinic step.

Definition at line 1181 of file REMORA.H.

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

FPr_c

amrex::Vector<REMORAFillPatcher> REMORA::FPr_c

private

Vector over levels of FillPatchers for scalars.

Definition at line 1054 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 1056 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 1064 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 1058 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 1066 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 1060 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 1297 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

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 1213 of file REMORA.H.

Referenced by Evolve(), InitData(), WriteNCPlotFile(), and WriteNCPlotFile_which().

istep

amrex::Vector<int> REMORA::istep

private

which step?

Definition at line 1097 of file REMORA.H.

Referenced by advance_2d(), advance_3d(), Evolve(), InitData(), ReadCheckpointFile(), REMORA(), restart(), setup_step(), timeStep(), timeStepML(), 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 1151 of file REMORA.H.

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

last_check_file_time

amrex::Real REMORA::last_check_file_time

private

Simulation time when we last output a checkpoint file.

Definition at line 1153 of file REMORA.H.

Referenced by Evolve(), and InitData().

last_plot_file_step

int REMORA::last_plot_file_step

private

Step when we last output a plotfile.

Definition at line 1146 of file REMORA.H.

Referenced by Evolve(), and InitData().

last_plot_file_time

amrex::Real REMORA::last_plot_file_time

private

Simulation time when we last output a plotfile.

Definition at line 1148 of file REMORA.H.

Referenced by Evolve(), and InitData().

m_bc_extdir_vals

amrex::Array<amrex::Array<amrex::Real, AMREX_SPACEDIM*2>,AMREX_SPACEDIM+NCONS+8> REMORA::m_bc_extdir_vals

private

Array holding the Dirichlet values at walls which need them.

Definition at line 1131 of file REMORA.H.

Referenced by FillCoarsePatch(), init_bcs(), and init_stuff().

max_step

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

private

maximum number of steps

Definition at line 1161 of file REMORA.H.

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

nc_bdry_file

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

staticprivate

NetCDF boundary data.

Definition at line 48 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 1278 of file REMORA.H.

Referenced by init_clim_nudg_coeff_from_netcdf(), and ReadParameters().

nc_clim_his_file

std::string REMORA::nc_clim_his_file

private

NetCDF climatology history file.

Definition at line 1276 of file REMORA.H.

Referenced by init_only(), and ReadParameters().

nc_frc_file

std::string REMORA::nc_frc_file

private

NetCDF forcing file.

Definition at line 1272 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 50 of file REMORA.H.

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

nc_init_file

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

staticprivate

NetCDF initialization file.

Definition at line 49 of file REMORA.H.

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

nc_riv_file

std::string REMORA::nc_riv_file

private

Definition at line 1273 of file REMORA.H.

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

nfast

int REMORA::nfast

private

Number of fast steps to take.

Definition at line 1183 of file REMORA.H.

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

nsubsteps

amrex::Vector<int> REMORA::nsubsteps

private

How many substeps on each level?

Definition at line 1099 of file REMORA.H.

Referenced by ComputeDt(), 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 1090 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_clim_nudg_coeff_from_netcdf(), init_coriolis_from_netcdf(), init_data_from_netcdf(), init_masks_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 1092 of file REMORA.H.

Referenced by ReadParameters().

phys_bc_need_data

amrex::GpuArray<amrex::GpuArray<bool, AMREX_SPACEDIM*2>,BdyVars::NumTypes+1> REMORA::phys_bc_need_data

private

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

Definition at line 1137 of file REMORA.H.

Referenced by init_bcs(), and init_bdry_from_netcdf().

phys_bc_type

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

private

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

Definition at line 1134 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 1111 of file REMORA.H.

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

plot_file_name

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

private

Plotfile prefix.

Definition at line 1193 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 1155 of file REMORA.H.

Referenced by InitData().

plot_int

int REMORA::plot_int = -1

private

Plotfile output interval in iterations.

Definition at line 1195 of file REMORA.H.

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

plot_int_time

amrex::Real REMORA::plot_int_time = amrex::Real(-1.0)

private

Plotfile output interval in seconds.

Definition at line 1197 of file REMORA.H.

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

plot_var_names

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

private

Names of variables to output to AMReX plotfile.

Definition at line 1216 of file REMORA.H.

Referenced by appendPlotVariables(), setPlotVariables(), and WritePlotFile().

plotfile_type

PlotfileType REMORA::plotfile_type = PlotfileType::amrex

staticprivate

Native or NetCDF plotfile output.

Definition at line 1262 of file REMORA.H.

Referenced by Evolve(), InitData(), ReadParameters(), and WritePlotFile().

pp_prefix

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

default prefix for input file parameters

Definition at line 205 of file REMORA.H.

Referenced by appendPlotVariables(), ReadParameters(), refinement_criteria_setup(), and setPlotVariables().

previousCPUTimeUsed

amrex::Real REMORA::previousCPUTimeUsed = 0.0_rt

staticprivate

Accumulator variable for CPU time used thusfar.

Definition at line 1362 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 1087 of file REMORA.H.

Referenced by init_analytic(), REMORA(), set_analytic_vmix(), set_bathymetry(), set_coriolis(), set_grid_scale(), set_hmixcoef(), set_smflux(), set_wind(), and set_zeta().

ref_tags

Vector< AMRErrorTag > REMORA::ref_tags

staticprivate

Holds info for dynamically generated tagging criteria.

Definition at line 1304 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 1189 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 1169 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 1295 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 1041 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<NCTimeSeriesRiver*> REMORA::river_source_cons

private

Vector of data containers for scalar data in rivers.

Definition at line 1032 of file REMORA.H.

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

river_source_transport

NCTimeSeriesRiver* REMORA::river_source_transport

private

Data container for momentum transport in rivers.

Definition at line 1034 of file REMORA.H.

Referenced by advance_3d(), and init_only().

river_source_transportbar

NCTimeSeriesRiver* REMORA::river_source_transportbar

private

Data container for vertically integrated momentum transport in rivers.

Definition at line 1036 of file REMORA.H.

Referenced by advance_2d(), and init_only().

salt_clim_data_from_file

NCTimeSeries* REMORA::salt_clim_data_from_file

private

Data container for salinity climatology data read from file.

Definition at line 1029 of file REMORA.H.

Referenced by advance_3d(), and init_only().

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 1108 of file REMORA.H.

Referenced by init_bcs().

solverChoice

SolverChoice REMORA::solverChoice

staticprivate

Container for algorithmic choices.

Definition at line 1224 of file REMORA.H.

Referenced by Advance(), advance_2d(), advance_3d(), bulk_fluxes(), fill_from_bdyfiles(), FillPatch(), gls_corrector(), init_analytic(), init_beta_plane_coriolis(), init_clim_nudg_coeff(), init_clim_nudg_coeff_from_netcdf(), init_only(), init_set_vmix(), init_stuff(), InitData(), lin_eos(), MakeNewLevelFromScratch(), nonlin_eos(), post_timestep(), prestep(), prestep_t_advection(), prsgrd(), ReadCheckpointFile(), ReadParameters(), RemakeLevel(), rho_eos(), rhs_t_3d(), rhs_uv_2d(), rhs_uv_3d(), set_analytic_vmix(), set_bathymetry(), set_coriolis(), set_grid_scale(), set_hmixcoef(), set_smflux(), set_wind(), set_zeta(), set_zeta_to_Ztavg(), setup_step(), stretch_transform(), timeStep(), timeStepML(), WriteCheckpointFile(), and WriteNCPlotFile_which().

start_bdy_time

amrex::Real REMORA::start_bdy_time

private

Start time in the time series of boundary data.

Definition at line 1002 of file REMORA.H.

Referenced by fill_from_bdyfiles(), init_bdry_from_netcdf(), ReadCheckpointFile(), WriteCheckpointFile(), and WriteNCPlotFile_which().

start_time

amrex::Real REMORA::start_time = 0.0

private

Time of the start of the simulation, in seconds.

Definition at line 1166 of file REMORA.H.

Referenced by InitData(), and ReadParameters().

startCPUTime

amrex::Real REMORA::startCPUTime = 0.0_rt

staticprivate

Variable for CPU timing.

Definition at line 1360 of file REMORA.H.

Referenced by getCPUTime(), and InitData().

steps_per_history_file

int REMORA::steps_per_history_file = -1

private

Number of time steps per netcdf history file.

-1 is the default and means code will automatically compute number of steps per file based on grid size to keep files < 2 GB

Definition at line 1211 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

Time to stop.

Definition at line 1163 of file REMORA.H.

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

sum_interval

int REMORA::sum_interval = -1

staticprivate

Diagnostic sum output interval in number of steps.

Definition at line 1254 of file REMORA.H.

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

sum_per

amrex::Real REMORA::sum_per = -1.0_rt

staticprivate

Diagnostic sum output interval in time.

Definition at line 1256 of file REMORA.H.

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

sustr_data_from_file

NCTimeSeries* REMORA::sustr_data_from_file

private

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

Definition at line 1010 of file REMORA.H.

Referenced by init_only(), and set_smflux().

svstr_data_from_file

NCTimeSeries* REMORA::svstr_data_from_file

private

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

Definition at line 1012 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 1101 of file REMORA.H.

Referenced by advance_2d(), ComputeDt(), Evolve(), FillPatch(), FillPatchNoBC(), GetDataAtTime(), gls_corrector(), init_only(), init_zeta_from_netcdf(), InitData(), MakeNewLevelFromCoarse(), ReadCheckpointFile(), RemakeLevel(), REMORA(), set_2darrays(), 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 1103 of file REMORA.H.

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

temp_clim_data_from_file

NCTimeSeries* REMORA::temp_clim_data_from_file

private

Data container for temperature climatology data read from file.

Definition at line 1027 of file REMORA.H.

Referenced by advance_3d(), and init_only().

total_nc_plot_file_step

int REMORA::total_nc_plot_file_step = 1

static

Definition at line 908 of file REMORA.H.

Referenced by WriteNCPlotFile_which().

u_clim_data_from_file

NCTimeSeries* REMORA::u_clim_data_from_file

private

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

Definition at line 1023 of file REMORA.H.

Referenced by init_only(), and setup_step().

ubar_clim_data_from_file

NCTimeSeries* REMORA::ubar_clim_data_from_file

private

Data container for ubar climatology data read from file.

Definition at line 1019 of file REMORA.H.

Referenced by advance_2d(), and init_only().

Uwind_data_from_file

NCTimeSeries* REMORA::Uwind_data_from_file

private

Data container for u-direction wind read from file.

Definition at line 1014 of file REMORA.H.

Referenced by init_only(), and set_wind().

v_clim_data_from_file

NCTimeSeries* REMORA::v_clim_data_from_file

private

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

Definition at line 1025 of file REMORA.H.

Referenced by init_only(), and setup_step().

vbar_clim_data_from_file

NCTimeSeries* REMORA::vbar_clim_data_from_file

private

Data container for vbar climatology data read from file.

Definition at line 1021 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 409 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 411 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 252 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 250 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 392 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 394 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 305 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 303 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 320 of file REMORA.H.

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

vec_bvf

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

Brunt-Vaisala frequency (3D)

Definition at line 390 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 322 of file REMORA.H.

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

vec_Cs_r

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

Stretching coefficients at rho points.

Definition at line 271 of file REMORA.H.

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

vec_Cs_w

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

Stretching coefficients at w points.

Definition at line 273 of file REMORA.H.

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

vec_diff2

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

Harmonic diffusivity for temperature / salinity.

Definition at line 258 of file REMORA.H.

Referenced by init_stuff(), resize_stuff(), set_hmixcoef(), 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 325 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 327 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 329 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 331 of file REMORA.H.

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

vec_evap

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

evaporation rate [kg/m^2/s]

Definition at line 310 of file REMORA.H.

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

vec_fcor

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

coriolis factor (2D)

Definition at line 360 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(), and WriteNCPlotFile_which().

vec_gls

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

Turbulent generic length scale.

Definition at line 405 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_hOfTheConfusingName

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

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

Definition at line 229 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d_ml(), fill_from_bdyfiles(), init_bathymetry_from_netcdf(), init_flat_bathymetry(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), resize_stuff(), set_bathymetry(), setup_step(), stretch_transform(), WriteCheckpointFile(), and WriteNCPlotFile_which().

vec_Huon

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

u-volume flux (3D)

Definition at line 234 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 236 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 232 of file REMORA.H.

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

vec_lhflx

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

latent heat flux

Definition at line 294 of file REMORA.H.

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

vec_lrflx

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

longwave radiation

Definition at line 292 of file REMORA.H.

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

vec_Lscale

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

Vertical mixing turbulent length scale.

Definition at line 407 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 352 of file REMORA.H.

Referenced by advance_2d_onestep(), init_masks(), init_masks_from_netcdf(), resize_stuff(), setup_step(), and update_mskp().

vec_mskr

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

land/sea mask at cell centers (2D)

Definition at line 346 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), bulk_fluxes(), FillPatch(), init_masks(), init_masks_from_netcdf(), init_zeta_from_netcdf(), mask_arrays_for_write(), ReadCheckpointFile(), resize_stuff(), setup_step(), update_mskp(), and WriteCheckpointFile().

vec_msku

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

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

Definition at line 348 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), bulk_fluxes(), fill_from_bdyfiles(), FillPatch(), init_masks(), init_masks_from_netcdf(), mask_arrays_for_write(), ReadCheckpointFile(), resize_stuff(), setup_step(), and WriteCheckpointFile().

vec_mskv

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

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

Definition at line 350 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), bulk_fluxes(), fill_from_bdyfiles(), FillPatch(), init_masks(), init_masks_from_netcdf(), mask_arrays_for_write(), ReadCheckpointFile(), resize_stuff(), setup_step(), and WriteCheckpointFile().

vec_nudg_coeff

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

Climatology nudging coefficients.

Definition at line 414 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_pm

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

horizontal scaling factor: 1 / dx (2D)

Definition at line 355 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), ErrorEst(), fill_from_bdyfiles(), gls_corrector(), gls_prestep(), init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), scale_rhs_vars(), scale_rhs_vars_inv(), set_grid_scale(), setup_step(), volWgtSumMF(), WriteNCPlotFile_which(), and WritePlotFile().

vec_pn

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

horizontal scaling factor: 1 / dy (2D)

Definition at line 357 of file REMORA.H.

Referenced by advance_2d_onestep(), advance_3d(), advance_3d_ml(), ErrorEst(), fill_from_bdyfiles(), gls_corrector(), gls_prestep(), init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), scale_rhs_vars(), scale_rhs_vars_inv(), set_grid_scale(), setup_step(), volWgtSumMF(), WriteNCPlotFile_which(), and WritePlotFile().

vec_rain

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

precipitation rate [kg/m^2/s]

Definition at line 308 of file REMORA.H.

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

vec_rdrag

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

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

Definition at line 313 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 315 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 388 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 386 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 1039 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 238 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 242 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 333 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 246 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 240 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 244 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 335 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 248 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 337 of file REMORA.H.

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

vec_s_r

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

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

Definition at line 266 of file REMORA.H.

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

vec_s_w

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

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

Definition at line 268 of file REMORA.H.

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

vec_shflx

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

sensible heat flux

Definition at line 296 of file REMORA.H.

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

vec_sstore

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

additional scratch space for calculations on temp, salt, etc

Definition at line 383 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 301 of file REMORA.H.

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

vec_stflx

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

Surface tracer flux; working arrays.

Definition at line 299 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 282 of file REMORA.H.

Referenced by gls_corrector(), init_only(), init_stuff(), resize_stuff(), set_smflux(), setup_step(), and WriteNCPlotFile_which().

vec_svstr

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

Surface stress in the v direction.

Definition at line 284 of file REMORA.H.

Referenced by gls_corrector(), init_only(), init_stuff(), resize_stuff(), set_smflux(), setup_step(), and WriteNCPlotFile_which().

vec_tke

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

Turbulent kinetic energy.

Definition at line 403 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 339 of file REMORA.H.

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

vec_uwind

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

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

Definition at line 287 of file REMORA.H.

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

vec_vbar

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

barotropic y velocity (2D)

Definition at line 341 of file REMORA.H.

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

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 254 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 256 of file REMORA.H.

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

vec_vwind

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

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

Definition at line 289 of file REMORA.H.

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

vec_weight1

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

Weights for calculating avg1 in 2D advance.

Definition at line 397 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 399 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 378 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), set_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 363 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), set_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 368 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), set_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 373 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), set_grid_scale(), and WriteNCPlotFile_which().

vec_yp

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

y_grid on psi-points (2D)

Definition at line 380 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), set_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 365 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), set_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 370 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), set_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 375 of file REMORA.H.

Referenced by init_bathymetry_from_netcdf(), init_stuff(), resize_stuff(), set_grid_scale(), and WriteNCPlotFile_which().

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 276 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 261 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 264 of file REMORA.H.

Referenced by advance_3d_ml(), 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 343 of file REMORA.H.

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

vec_ZoBot

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

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

Definition at line 317 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 279 of file REMORA.H.

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

verbose

int REMORA::verbose = 0

staticprivate

Verbosity level of output.

Definition at line 1251 of file REMORA.H.

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

Vwind_data_from_file

NCTimeSeries* REMORA::Vwind_data_from_file

private

Data container for v-direction wind read from file.

Definition at line 1016 of file REMORA.H.

Referenced by init_only(), and set_wind().

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 1007 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 219 of file REMORA.H.

Referenced by advance_3d_ml(), AverageDownTo(), ClearLevel(), ErrorEst(), estTimeStep(), init_analytic(), init_data_from_netcdf(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), mask_arrays_for_write(), ReadCheckpointFile(), RemakeLevel(), REMORA(), set_2darrays(), 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 210 of file REMORA.H.

Referenced by advance_3d(), ClearLevel(), gls_corrector(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), 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 221 of file REMORA.H.

Referenced by advance_3d_ml(), AverageDownTo(), ClearLevel(), ErrorEst(), estTimeStep(), init_analytic(), init_data_from_netcdf(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), mask_arrays_for_write(), ReadCheckpointFile(), RemakeLevel(), REMORA(), set_2darrays(), 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 212 of file REMORA.H.

Referenced by advance_3d(), ClearLevel(), gls_corrector(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), 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 223 of file REMORA.H.

Referenced by advance_3d_ml(), AverageDownTo(), ClearLevel(), ErrorEst(), estTimeStep(), init_analytic(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), 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 214 of file REMORA.H.

Referenced by ClearLevel(), init_only(), InitData(), MakeNewLevelFromCoarse(), MakeNewLevelFromScratch(), ReadCheckpointFile(), RemakeLevel(), 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/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_writeJobInfo.cpp
• /home/runner/work/REMORA/REMORA/Source/REMORA.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_ComputeTimestep.cpp
• /home/runner/work/REMORA/REMORA/Source/TimeIntegration/REMORA_coriolis.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