REMORA
Regional Modeling of Oceans Refined Adaptively
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REMORA Member List

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_regREMORAprivate
appendPlotVariables(const std::string &pp_plot_var_names)REMORAprivate
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()REMORAprivate
AverageDownTo(int crse_lev)REMORAprivate
bdry_time_varnameREMORAprivate
bdy_data_xhiREMORAprivate
bdy_data_xloREMORAprivate
bdy_data_yhiREMORAprivate
bdy_data_yloREMORAprivate
bdy_indexREMORAprivate
bdy_time_intervalREMORAprivate
boxes_at_levelREMORAprivate
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)REMORAinlinestatic
bulk_psiu(amrex::Real ZoL)REMORAinlinestatic
cf_set_widthREMORAprivate
cf_widthREMORAprivate
cflREMORAprivatestatic
change_maxREMORAprivatestatic
check_fileREMORAprivate
check_intREMORAprivate
check_int_timeREMORAprivate
chunk_history_fileREMORAprivate
ClearLevel(int lev) overrideREMORAvirtual
clim_salt_time_varnameREMORAprivate
clim_temp_time_varnameREMORAprivate
clim_u_time_varnameREMORAprivate
clim_ubar_time_varnameREMORAprivate
clim_v_time_varnameREMORAprivate
clim_vbar_time_varnameREMORAprivate
ComputeDt()REMORAprivate
ComputeGhostCells(const int &spatial_order)REMORAinlineprivate
cons_namesREMORAprivate
cons_newREMORA
cons_oldREMORA
Construct_REMORAFillPatchers(int lev)REMORAprivate
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
datalogREMORAprivate
DataLog(int i)REMORAinlineprivate
datalognameREMORAprivate
DataLogName(int i) const noexceptREMORAinlineprivate
Define_REMORAFillPatchers(int lev)REMORAprivate
derived_namesREMORAprivate
do_substepREMORAprivate
domain_bc_typeREMORAprivate
domain_bcs_typeREMORAprivate
domain_bcs_type_dREMORAprivate
dtREMORAprivate
ErrorEst(int lev, amrex::TagBoxArray &tags, amrex::Real time, int ngrow) overrideREMORAvirtual
estTimeStep(int lev) constREMORA
Evolve()REMORA
file_min_digitsREMORAprivatestatic
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))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 icomp=0, const bool fill_all=true)REMORAprivate
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_maskREMORAprivate
fixed_dtREMORAprivatestatic
fixed_fast_dtREMORAprivatestatic
fixed_ndtfast_ratioREMORAprivatestatic
FPr_cREMORAprivate
FPr_uREMORAprivate
FPr_ubarREMORAprivate
FPr_vREMORAprivate
FPr_vbarREMORAprivate
FPr_wREMORAprivate
frc_time_varnameREMORAprivate
get_t_old(int lev) constREMORA
getAdvFluxReg(int lev)REMORAinlineprivate
getCPUTime() constREMORAinlineprivate
GetDataAtTime(int lev, amrex::Real time)REMORAprivate
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)REMORAprivatestatic
history_countREMORAprivate
init_analytic(int lev)REMORAprivate
init_bathymetry_from_netcdf(int lev)REMORA
init_bcs()REMORAprivate
init_bdry_from_netcdf()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_gls_vmix(int lev, SolverChoice solver_choice)REMORA
init_masks(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)REMORAprivate
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_stuff(int lev, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm)REMORAprivate
init_zeta_from_netcdf(int lev)REMORA
InitData()REMORA
InitializeFromFile()REMORAprivate
InitializeLevelFromData(int lev, const amrex::MultiFab &initial_data)REMORAprivate
is_it_time_for_action(int nstep, amrex::Real time, amrex::Real dt, int action_interval, amrex::Real action_per)REMORA
istepREMORAprivate
last_check_file_stepREMORAprivate
last_check_file_timeREMORAprivate
last_plot_file_stepREMORAprivate
last_plot_file_timeREMORAprivate
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_valsREMORAprivate
MakeNewLevelFromCoarse(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) overrideREMORAvirtual
MakeNewLevelFromScratch(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) overrideREMORAvirtual
mask_arrays_for_write(int lev, amrex::Real fill_value, amrex::Real fill_where)REMORA
max_stepREMORAprivate
nc_bdry_fileREMORAprivatestatic
nc_clim_coeff_fileREMORAprivate
nc_clim_his_fileREMORAprivate
nc_frc_fileREMORAprivate
nc_grid_fileREMORAprivatestatic
nc_init_fileREMORAprivatestatic
nc_riv_fileREMORAprivate
nfastREMORAprivate
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
nsubstepsREMORAprivate
num_boxes_at_levelREMORAprivate
num_files_at_levelREMORAprivate
NumDataLogs() noexceptREMORAinlineprivate
phys_bc_need_dataREMORAprivate
phys_bc_typeREMORAprivate
physbcsREMORAprivate
plot_file_nameREMORAprivate
plot_file_on_restartREMORAprivate
plot_intREMORAprivate
plot_int_timeREMORAprivate
plot_var_namesREMORAprivate
plotfile_typeREMORAprivatestatic
PlotFileName(int lev) constREMORAprivate
post_timestep(int nstep, amrex::Real time, amrex::Real dt_lev)REMORA
pp_prefixREMORA
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 > &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)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)REMORA
previousCPUTimeUsedREMORAprivatestatic
print_banner(MPI_Comm, std::ostream &)REMORAstatic
print_error(MPI_Comm, const std::string &msg)REMORAstatic
print_summary(std::ostream &)REMORAstatic
print_tpls(std::ostream &)REMORAstatic
print_usage(MPI_Comm, std::ostream &)REMORAstatic
probREMORAprivate
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()REMORAprivate
ReadNCMultiFab(amrex::FabArray< amrex::FArrayBox > &fab, const std::string &name, int coordinatorProc=amrex::ParallelDescriptor::IOProcessorNumber(), int allow_empty_mf=0)REMORAprivate
ReadParameters()REMORAprivate
ref_tagsREMORAprivatestatic
refinement_criteria_setup()REMORAprivate
regrid_intREMORAprivate
RemakeLevel(int lev, amrex::Real time, const amrex::BoxArray &ba, const amrex::DistributionMapping &dm) overrideREMORAvirtual
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)REMORAprivate
restart()REMORA
restart_chkfileREMORAprivate
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(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(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(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_varnameREMORAprivate
river_directionREMORAprivate
river_source_consREMORAprivate
river_source_transportREMORAprivate
river_source_transportbarREMORAprivate
salt_clim_data_from_fileREMORAprivate
scale_rhs_vars()REMORA
scale_rhs_vars_inv()REMORA
set_2darrays(int lev)REMORA
set_analytic_vmix(int lev)REMORA
set_bathymetry(int lev)REMORA
set_bcs_by_varREMORAprivate
set_coriolis(int lev)REMORA
set_drag(int lev)REMORA
set_grid_scale(int lev)REMORA
set_hmixcoef(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
setPlotVariables(const std::string &pp_plot_var_names)REMORAprivate
setRecordDataInfo(int i, const std::string &filename)REMORAinlineprivate
setup_step(int lev, amrex::Real time, amrex::Real dt_lev)REMORA
solverChoiceREMORAprivatestatic
start_bdy_timeREMORAprivate
start_timeREMORAprivate
startCPUTimeREMORAprivatestatic
steps_per_history_fileREMORAprivate
stop_timeREMORAprivate
stretch_transform(int lev)REMORA
sum_integrated_quantities(amrex::Real time)REMORA
sum_intervalREMORAprivatestatic
sum_perREMORAprivatestatic
sustr_data_from_fileREMORAprivate
svstr_data_from_fileREMORAprivate
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_newREMORAprivate
t_oldREMORAprivate
temp_clim_data_from_fileREMORAprivate
timeStep(int lev, amrex::Real time, int iteration)REMORAprivate
timeStepML(amrex::Real time, int iteration)REMORAprivate
total_nc_plot_file_stepREMORAstatic
u_clim_data_from_fileREMORAprivate
ubar_clim_data_from_fileREMORAprivate
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)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_fileREMORAprivate
v_clim_data_from_fileREMORAprivate
vbar_clim_data_from_fileREMORAprivate
vec_AkkREMORA
vec_AkpREMORA
vec_AktREMORA
vec_AkvREMORA
vec_alphaREMORA
vec_betaREMORA
vec_btfluxREMORA
vec_btflxREMORA
vec_bustrREMORA
vec_bvfREMORA
vec_bvstrREMORA
vec_Cs_rREMORA
vec_Cs_wREMORA
vec_diff2REMORA
vec_DU_avg1REMORA
vec_DU_avg2REMORA
vec_DV_avg1REMORA
vec_DV_avg2REMORA
vec_evapREMORA
vec_fcorREMORA
vec_glsREMORA
vec_hOfTheConfusingNameREMORA
vec_HuonREMORA
vec_HvomREMORA
vec_HzREMORA
vec_lhflxREMORA
vec_lrflxREMORA
vec_LscaleREMORA
vec_mskpREMORA
vec_mskrREMORA
vec_mskuREMORA
vec_mskvREMORA
vec_nudg_coeffREMORA
vec_pmREMORA
vec_pnREMORA
vec_rainREMORA
vec_rdragREMORA
vec_rdrag2REMORA
vec_rhoAREMORA
vec_rhoSREMORA
vec_river_positionREMORAprivate
vec_ruREMORA
vec_ru2dREMORA
vec_rubarREMORA
vec_rufrcREMORA
vec_rvREMORA
vec_rv2dREMORA
vec_rvbarREMORA
vec_rvfrcREMORA
vec_rzetaREMORA
vec_s_rREMORA
vec_s_wREMORA
vec_shflxREMORA
vec_sstoreREMORA
vec_stfluxREMORA
vec_stflxREMORA
vec_sustrREMORA
vec_svstrREMORA
vec_tkeREMORA
vec_ubarREMORA
vec_uwindREMORA
vec_vbarREMORA
vec_visc2_pREMORA
vec_visc2_rREMORA
vec_vwindREMORA
vec_weight1REMORA
vec_weight2REMORA
vec_xpREMORA
vec_xrREMORA
vec_xuREMORA
vec_xvREMORA
vec_ypREMORA
vec_yrREMORA
vec_yuREMORA
vec_yvREMORA
vec_z_phys_ndREMORA
vec_z_rREMORA
vec_z_wREMORA
vec_zetaREMORA
vec_ZoBotREMORA
vec_Zt_avg1REMORA
verboseREMORAprivatestatic
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_fileREMORAprivate
write_history_fileREMORAprivatestatic
writeBuildInfo(std::ostream &os)REMORAstatic
WriteCheckpointFile()REMORAprivate
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) constREMORA
writeJobInfo(const std::string &dir) constREMORA
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 >()) constREMORA
WriteNCMultiFab(const amrex::FabArray< amrex::FArrayBox > &fab, const std::string &name, bool set_ghost=false) constREMORAprivate
WriteNCPlotFile(int istep)REMORAprivate
WriteNCPlotFile_which(int lev, int which_subdomain, bool write_header, ncutils::NCFile &ncf, bool is_history)REMORAprivate
WritePlotFile()REMORA
xvel_newREMORA
xvel_oldREMORA
yvel_newREMORA
yvel_oldREMORA
zvel_newREMORA
zvel_oldREMORA
~REMORA()REMORAvirtual