- Generated by
1.9.8
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REMORA
Regional Modeling of Oceans Refined Adaptively
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This is the complete list of members for REMORA, including all inherited members.
| Advance(int lev, amrex::Real time, amrex::Real dt_lev, int iteration, int ncycle) | 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) | REMORA | |
| advance_2d_onestep(int lev, amrex::Real dt_lev, amrex::Real dtfast_lev, int my_iif, int nfast_counter) | 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) | REMORA | |
| advance_3d_ml(int lev, amrex::Real dt_lev) | REMORA | |
| advflux_reg | REMORA | private |
| append2DPlotVariables(const std::string &pp_plot_var_names_2d) | REMORA | private |
| append3DPlotVariables(const std::string &pp_plot_var_names_3d) | REMORA | private |
| 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)) | REMORA | |
| AverageDown() | REMORA | private |
| AverageDownTo(int crse_lev) | REMORA | private |
| bdry_time_name_byvar | REMORA | private |
| bdry_time_varname | REMORA | private |
| bdy_index | REMORA | private |
| bdy_time_interval | REMORA | private |
| boundary_series | REMORA | private |
| boxes_at_level | REMORA | private |
| build_fine_mask(int lev) | 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) | REMORA | |
| bulk_psit(amrex::Real ZoL) | REMORA | inlinestatic |
| bulk_psiu(amrex::Real ZoL) | REMORA | inlinestatic |
| calc_stretch_coeffs() | REMORA | |
| calculate_nodal_masks(int lev) | REMORA | |
| cf_set_width | REMORA | private |
| cf_width | REMORA | private |
| cfl | REMORA | privatestatic |
| change_max | REMORA | privatestatic |
| check_file | REMORA | private |
| check_int | REMORA | private |
| check_int_time | REMORA | private |
| chunk_history_file | REMORA | private |
| ClearLevel(int lev) override | REMORA | virtual |
| clim_salt_time_varname | REMORA | private |
| clim_temp_time_varname | REMORA | private |
| clim_u_time_varname | REMORA | private |
| clim_ubar_time_varname | REMORA | private |
| clim_v_time_varname | REMORA | private |
| clim_vbar_time_varname | REMORA | private |
| ComputeDt() | REMORA | private |
| ComputeGhostCells(const int &spatial_order) | REMORA | inlineprivate |
| cons_names | REMORA | private |
| cons_new | REMORA | |
| cons_old | REMORA | |
| Construct_REMORAFillPatchers(int lev) | REMORA | private |
| convert_inv_days_to_inv_s(amrex::MultiFab *) | 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) | REMORA | |
| Cs_r | REMORA | |
| Cs_w | REMORA | |
| DataLog(int i) | REMORA | inlineprivate |
| datalog | REMORA | private |
| datalogname | REMORA | private |
| DataLogName(int i) const noexcept | REMORA | inlineprivate |
| Define_REMORAFillPatchers(int lev) | REMORA | private |
| derived_names | REMORA | private |
| do_substep | REMORA | private |
| domain_bc_type | REMORA | private |
| domain_bcs_type | REMORA | private |
| domain_bcs_type_d | REMORA | private |
| dt | REMORA | private |
| ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real time, int ngrow) override | REMORA | virtual |
| estTimeStep(int lev) const | REMORA | |
| Evolve() | REMORA | |
| expand_plotvars_to_unif_rr | REMORA | private |
| file_min_digits | REMORA | privatestatic |
| fill_3d_masks(int lev) | REMORA | |
| fill_from_bdyfiles(int lev, amrex::MultiFab &mf_to_fill, const amrex::MultiFab &mf_mask, const amrex::Real time, const int bccomp, const int bdy_var_type, const int icomp_to_fill, const int icomp_calc=0, const amrex::MultiFab &mf_calc=amrex::MultiFab(), const amrex::Real=amrex::Real(0.0)) | REMORA | |
| FillBdyCCVels(int lev, amrex::MultiFab &mf_cc_vel) | REMORA | |
| FillCoarsePatch(int lev, amrex::Real time, amrex::MultiFab *mf_fine, amrex::MultiFab *mf_crse, const int bccomp, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=amrex::Real(0.0), const amrex::MultiFab &mf_calc=amrex::MultiFab()) | REMORA | |
| FillCoarsePatchMap(int lev, amrex::Real time, amrex::MultiFab *mf_fine, amrex::MultiFab *mf_crse, const int bccomp, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=amrex::Real(0.0), const amrex::MultiFab &mf_calc=amrex::MultiFab(), amrex::Interpolater *mapper=nullptr) | REMORA | |
| FillCoarsePatchPC(int lev, amrex::Real time, amrex::MultiFab *mf_fine, amrex::MultiFab *mf_crse, const int bccomp, const int bdy_var_type=BdyVars::null, const int icomp=0, const bool fill_all=true, const int n_not_fill=0, const int icomp_calc=0, const amrex::Real dt=amrex::Real(0.0), const amrex::MultiFab &mf_calc=amrex::MultiFab()) | 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()) | 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) | REMORA | |
| fine_mask | REMORA | private |
| fixed_dt | REMORA | privatestatic |
| fixed_fast_dt | REMORA | privatestatic |
| fixed_ndtfast_ratio | REMORA | privatestatic |
| FPr_c | REMORA | private |
| FPr_u | REMORA | private |
| FPr_ubar | REMORA | private |
| FPr_v | REMORA | private |
| FPr_vbar | REMORA | private |
| FPr_w | REMORA | private |
| frc_time_varname | REMORA | private |
| get_t_old(int lev) const | REMORA | |
| getAdvFluxReg(int lev) | REMORA | inlineprivate |
| getCPUTime() const | REMORA | inlineprivate |
| GetDataAtTime(int lev, amrex::Real time) | REMORA | private |
| 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) | 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) | REMORA | |
| GotoNextLine(std::istream &is) | REMORA | privatestatic |
| history_count | REMORA | private |
| init_analytic(int lev) | REMORA | private |
| init_bathymetry_from_netcdf(int lev) | REMORA | |
| init_bcs() | REMORA | private |
| init_bdry_from_netcdf(int lev) | REMORA | |
| init_beta_plane_coriolis(int lev) | REMORA | |
| init_clim_nudg_coeff(int lev) | REMORA | |
| init_clim_nudg_coeff_from_netcdf(int lev) | REMORA | |
| init_coriolis_from_netcdf(int lev) | REMORA | |
| init_data_from_netcdf(int lev) | REMORA | |
| init_flat_bathymetry(int lev) | REMORA | |
| init_gls_vmix(int lev, SolverChoice solver_choice) | REMORA | |
| init_masks(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) | REMORA | private |
| init_masks_from_netcdf(int lev) | REMORA | |
| init_only(int lev, amrex::Real time) | REMORA | |
| init_riv_pos_from_netcdf(int lev) | REMORA | |
| init_set_vmix(int lev) | REMORA | |
| init_stretch_coeffs() | REMORA | |
| init_stuff(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) | REMORA | private |
| init_zeta_from_netcdf(int lev) | REMORA | |
| InitData() | REMORA | |
| InitializeFromFile() | REMORA | private |
| InitializeLevelFromData(int lev, const amrex::MultiFab &initial_data) | REMORA | private |
| is_it_time_for_action(int nstep, amrex::Real time, amrex::Real dt, int action_interval, amrex::Real action_per) | REMORA | |
| istep | REMORA | private |
| last_check_file_step | REMORA | private |
| last_check_file_time | REMORA | private |
| last_plot_file_step | REMORA | private |
| last_plot_file_time | REMORA | private |
| 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) | REMORA | |
| m_bc_extdir_vals | REMORA | private |
| MakeNewLevelFromCoarse(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override | REMORA | virtual |
| MakeNewLevelFromScratch(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override | REMORA | virtual |
| mask_arrays_for_write(int lev, amrex::Real fill_value, amrex::Real fill_where) | REMORA | |
| max_step | REMORA | private |
| nc_bdry_file | REMORA | privatestatic |
| nc_clim_coeff_file | REMORA | private |
| nc_clim_his_file | REMORA | private |
| nc_frc_file | REMORA | private |
| nc_grid_file | REMORA | privatestatic |
| nc_init_file | REMORA | privatestatic |
| nc_riv_file | REMORA | private |
| nfast | REMORA | private |
| 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) | REMORA | |
| nsubsteps | REMORA | private |
| num_boxes_at_level | REMORA | private |
| num_files_at_level | REMORA | private |
| NumDataLogs() noexcept | REMORA | inlineprivate |
| phys_bc_need_data | REMORA | private |
| phys_bc_type | REMORA | private |
| physbcs | REMORA | private |
| plot_file_name | REMORA | private |
| plot_file_on_restart | REMORA | private |
| plot_int | REMORA | private |
| plot_int_time | REMORA | private |
| plot_staggered_vels | REMORA | privatestatic |
| plot_var_names_2d | REMORA | private |
| plot_var_names_3d | REMORA | private |
| plotfile_type | REMORA | privatestatic |
| PlotFileName(int lev) const | REMORA | private |
| post_timestep(int nstep, amrex::Real time, amrex::Real dt_lev) | REMORA | |
| pp_prefix | 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) | REMORA | |
| prestep_diffusion(const amrex::Box &bx, const amrex::Box &gbx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &vel, const amrex::Array4< amrex::Real const > &vel_old, const amrex::Array4< amrex::Real > &rvel, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &Akv, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &sstr, const amrex::Array4< amrex::Real const > &bstr, const amrex::Array4< amrex::Real const > &z_r, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const int iic, const int ntfirst, const int nnew, int nstp, int nrhs, int N, const amrex::Real lambda, const amrex::Real dt_lev) | REMORA | |
| prestep_t_advection(int lev, const amrex::Box &tbx, const amrex::Box &gbx, const amrex::Array4< amrex::Real > &tempold, const amrex::Array4< amrex::Real > &tempcache, const amrex::Array4< amrex::Real > &Hz, const amrex::Array4< amrex::Real > &Huon, const amrex::Array4< amrex::Real > &Hvom, const amrex::Array4< amrex::Real > &W, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real > &sstore, const amrex::Array4< amrex::Real const > &z_w, const amrex::Array4< amrex::Real const > &h, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const amrex::Array4< int const > &river_pos, const amrex::Array4< amrex::Real const > &river_source, int iic, int ntfirst, int nrhs, int N, const amrex::Real dt_lev) | REMORA | |
| previousCPUTimeUsed | REMORA | privatestatic |
| print_banner(MPI_Comm, std::ostream &) | REMORA | static |
| print_error(MPI_Comm, const std::string &msg) | REMORA | static |
| print_summary(std::ostream &) | REMORA | static |
| print_tpls(std::ostream &) | REMORA | static |
| print_usage(MPI_Comm, std::ostream &) | REMORA | static |
| prob | REMORA | private |
| 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) | REMORA | |
| ReadCheckpointFile() | REMORA | private |
| ReadNCMultiFab(amrex::FabArray< amrex::FArrayBox > &fab, const std::string &name, int coordinatorProc=amrex::ParallelDescriptor::IOProcessorNumber(), int allow_empty_mf=0) | REMORA | private |
| ReadParameters() | REMORA | private |
| ref_tags | REMORA | privatestatic |
| refinement_criteria_setup() | REMORA | private |
| regrid_int | REMORA | private |
| RemakeLevel(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) override | REMORA | virtual |
| REMORA() | 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) | REMORA | |
| resize_stuff(int lev) | REMORA | private |
| restart() | REMORA | |
| restart_chkfile | REMORA | private |
| 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) | REMORA | |
| rhs_t_3d(int lev, const amrex::Box &bx, const amrex::Array4< amrex::Real > &t, const amrex::Array4< amrex::Real const > &tempstore, const amrex::Array4< amrex::Real const > &Huon, const amrex::Array4< amrex::Real const > &Hvom, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &W, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &mskr, const amrex::Array4< amrex::Real const > &msku, const amrex::Array4< amrex::Real const > &mskv, const amrex::Array4< int const > &river_pos, const amrex::Array4< amrex::Real const > &river_source, int nrhs, int nnew, int N, const amrex::Real dt_lev) | REMORA | |
| rhs_uv_2d(int lev, const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real const > &Duon, const amrex::Array4< amrex::Real const > &Dvom, const int nrhs) | REMORA | |
| rhs_uv_3d(int lev, const amrex::Box &xbx, const amrex::Box &ybx, const amrex::Array4< amrex::Real const > &uold, const amrex::Array4< amrex::Real const > &vold, const amrex::Array4< amrex::Real > &ru, const amrex::Array4< amrex::Real > &rv, const amrex::Array4< amrex::Real > &rufrc, const amrex::Array4< amrex::Real > &rvfrc, const amrex::Array4< amrex::Real const > &sustr, const amrex::Array4< amrex::Real const > &svstr, const amrex::Array4< amrex::Real const > &bustr, const amrex::Array4< amrex::Real const > &bvstr, const amrex::Array4< amrex::Real const > &Huon, const amrex::Array4< amrex::Real const > &Hvom, const amrex::Array4< amrex::Real const > &pm, const amrex::Array4< amrex::Real const > &pn, const amrex::Array4< amrex::Real const > &W, const amrex::Array4< amrex::Real > &FC, int nrhs, int N) | REMORA | |
| riv_time_varname | REMORA | private |
| river_direction | REMORA | private |
| river_source_cons | REMORA | private |
| river_source_transport | REMORA | private |
| river_source_transportbar | REMORA | private |
| s_r | REMORA | |
| s_w | REMORA | |
| salt_clim_data_from_file | REMORA | private |
| scale_rhs_vars() | REMORA | |
| scale_rhs_vars_inv() | REMORA | |
| set2DPlotVariables(const std::string &pp_plot_var_names_2d) | REMORA | private |
| set3DPlotVariables(const std::string &pp_plot_var_names_3d) | REMORA | private |
| set_2darrays(int lev) | REMORA | |
| set_analytic_vmix(int lev) | REMORA | |
| set_bathymetry(int lev) | REMORA | |
| set_bcs_by_var | REMORA | private |
| set_coriolis(int lev) | REMORA | |
| set_drag(int lev) | REMORA | |
| set_grid_scale(int lev) | REMORA | |
| set_hmixcoef(int lev) | REMORA | |
| set_masks(int lev) | REMORA | |
| set_smflux(int lev) | REMORA | |
| set_weights(int lev) | REMORA | |
| set_wind(int lev) | REMORA | |
| set_zeta(int lev) | REMORA | |
| set_zeta_average(int lev) | REMORA | |
| set_zeta_to_Ztavg(int lev) | REMORA | |
| setRecordDataInfo(int i, const std::string &filename) | REMORA | inlineprivate |
| setup_step(int lev, amrex::Real time, amrex::Real dt_lev) | REMORA | |
| solverChoice | REMORA | privatestatic |
| start_bdy_time | REMORA | private |
| start_time | REMORA | private |
| startCPUTime | REMORA | privatestatic |
| steps_per_history_file | REMORA | private |
| stop_time | REMORA | private |
| stretch_transform(int lev) | REMORA | |
| sum_integrated_quantities(amrex::Real time) | REMORA | |
| sum_interval | REMORA | privatestatic |
| sum_per | REMORA | privatestatic |
| sustr_data_from_file | REMORA | private |
| svstr_data_from_file | REMORA | private |
| 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) | REMORA | |
| t_new | REMORA | private |
| t_old | REMORA | private |
| temp_clim_data_from_file | REMORA | private |
| timeStep(int lev, amrex::Real time, int iteration) | REMORA | private |
| timeStepML(amrex::Real time, int iteration) | REMORA | private |
| total_nc_plot_file_step | REMORA | static |
| u_clim_data_from_file | REMORA | private |
| ubar_clim_data_from_file | REMORA | private |
| update_massflux_3d(int lev, const amrex::Box &bx, const int ioff, const int joff, const amrex::Array4< amrex::Real > &phi, const amrex::Array4< amrex::Real > &phibar, const amrex::Array4< amrex::Real > &Hphi, const amrex::Array4< amrex::Real const > &Hz, const amrex::Array4< amrex::Real const > &pm_or_pn, const amrex::Array4< amrex::Real const > &Dphi1, const amrex::Array4< amrex::Real const > &Dphi2, const amrex::Array4< amrex::Real > &DC, const amrex::Array4< amrex::Real > &FC, const amrex::Array4< amrex::Real const > &msk, const int nnew) | REMORA | |
| update_mskp(int lev) | 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) | REMORA | |
| Uwind_data_from_file | REMORA | private |
| v_clim_data_from_file | REMORA | private |
| vbar_clim_data_from_file | REMORA | private |
| vec_Akk | REMORA | |
| vec_Akp | REMORA | |
| vec_Akt | REMORA | |
| vec_Akv | REMORA | |
| vec_alpha | REMORA | |
| vec_beta | REMORA | |
| vec_btflux | REMORA | |
| vec_btflx | REMORA | |
| vec_bustr | REMORA | |
| vec_bvf | REMORA | |
| vec_bvstr | REMORA | |
| vec_diff2 | REMORA | |
| vec_DU_avg1 | REMORA | |
| vec_DU_avg2 | REMORA | |
| vec_DV_avg1 | REMORA | |
| vec_DV_avg2 | REMORA | |
| vec_evap | REMORA | |
| vec_fcor | REMORA | |
| vec_gls | REMORA | |
| vec_h | REMORA | |
| vec_Huon | REMORA | |
| vec_Hvom | REMORA | |
| vec_Hz | REMORA | |
| vec_lhflx | REMORA | |
| vec_lrflx | REMORA | |
| vec_Lscale | REMORA | |
| vec_mskp | REMORA | |
| vec_mskr | REMORA | |
| vec_mskr3d | REMORA | |
| vec_msku | REMORA | |
| vec_mskv | REMORA | |
| vec_nudg_coeff | REMORA | |
| vec_pm | REMORA | |
| vec_pn | REMORA | |
| vec_rain | REMORA | |
| vec_rdrag | REMORA | |
| vec_rdrag2 | REMORA | |
| vec_rhoA | REMORA | |
| vec_rhoS | REMORA | |
| vec_river_position | REMORA | private |
| vec_ru | REMORA | |
| vec_ru2d | REMORA | |
| vec_rubar | REMORA | |
| vec_rufrc | REMORA | |
| vec_rv | REMORA | |
| vec_rv2d | REMORA | |
| vec_rvbar | REMORA | |
| vec_rvfrc | REMORA | |
| vec_rzeta | REMORA | |
| vec_shflx | REMORA | |
| vec_sstore | REMORA | |
| vec_stflux | REMORA | |
| vec_stflx | REMORA | |
| vec_sustr | REMORA | |
| vec_svstr | REMORA | |
| vec_tke | REMORA | |
| vec_ubar | REMORA | |
| vec_uwind | REMORA | |
| vec_vbar | REMORA | |
| vec_visc2_p | REMORA | |
| vec_visc2_r | REMORA | |
| vec_vwind | REMORA | |
| vec_weight1 | REMORA | |
| vec_weight2 | REMORA | |
| vec_xp | REMORA | |
| vec_xr | REMORA | |
| vec_xu | REMORA | |
| vec_xv | REMORA | |
| vec_yp | REMORA | |
| vec_yr | REMORA | |
| vec_yu | REMORA | |
| vec_yv | REMORA | |
| vec_z_phys_nd | REMORA | |
| vec_z_r | REMORA | |
| vec_z_w | REMORA | |
| vec_zeta | REMORA | |
| vec_ZoBot | REMORA | |
| vec_Zt_avg1 | REMORA | |
| verbose | REMORA | privatestatic |
| 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) | 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) | REMORA | |
| volWgtSumMF(int lev, const amrex::MultiFab &mf, int comp, bool local, bool finemask) | REMORA | |
| Vwind_data_from_file | REMORA | private |
| write_history_file | REMORA | privatestatic |
| writeBuildInfo(std::ostream &os) | REMORA | static |
| WriteCheckpointFile() | REMORA | private |
| WriteGenericPlotfileHeaderWithBathymetry(std::ostream &HeaderFile, int nlevels, const amrex::Vector< amrex::BoxArray > &bArray, const amrex::Vector< std::string > &varnames_3d, const amrex::Vector< std::string > &varnames_2d_rho, const amrex::Vector< std::string > &varnames_2d_u, const amrex::Vector< std::string > &varnames_2d_v, const amrex::Vector< amrex::Geometry > &my_geom, amrex::Real time, const amrex::Vector< int > &level_steps, const amrex::Vector< amrex::IntVect > &rr, const std::string &versionName, const std::string &levelPrefix, const std::string &mfPrefix) const | REMORA | |
| writeJobInfo(const std::string &dir) const | REMORA | |
| WriteMultiLevelPlotfileWithBathymetry(const std::string &plotfilename, int nlevels, const amrex::Vector< const amrex::MultiFab * > &mf, const amrex::Vector< const amrex::MultiFab * > &mf_nd, const amrex::Vector< const amrex::MultiFab * > &mf_u, const amrex::Vector< const amrex::MultiFab * > &mf_v, const amrex::Vector< const amrex::MultiFab * > &mf_w, const amrex::Vector< const amrex::MultiFab * > &mf_2d_rho, const amrex::Vector< const amrex::MultiFab * > &mf_2d_u, const amrex::Vector< const amrex::MultiFab * > &mf_2d_v, const amrex::Vector< std::string > &varnames_3d, const amrex::Vector< std::string > &varnames_2d_rho, const amrex::Vector< std::string > &varnames_2d_u, const amrex::Vector< std::string > &varnames_2d_v, const amrex::Vector< amrex::Geometry > &my_geom, amrex::Real time, const amrex::Vector< int > &level_steps, const amrex::Vector< amrex::IntVect > &rr, const std::string &versionName="HyperCLaw-V1.1", const std::string &levelPrefix="Level_", const std::string &mfPrefix="Cell", const amrex::Vector< std::string > &extra_dirs=amrex::Vector< std::string >()) const | REMORA | |
| WriteNCMultiFab(const amrex::FabArray< amrex::FArrayBox > &fab, const std::string &name, bool set_ghost=false) const | REMORA | private |
| WriteNCPlotFile(int istep) | REMORA | private |
| WriteNCPlotFile_which(int lev, int which_subdomain, bool write_header, ncutils::NCFile &ncf, bool is_history) | REMORA | private |
| WritePlotFile() | REMORA | |
| xvel_new | REMORA | |
| xvel_old | REMORA | |
| yvel_new | REMORA | |
| yvel_old | REMORA | |
| zvel_new | REMORA | |
| zvel_old | REMORA | |
| ~REMORA() | REMORA | virtual |
1.9.8