REMORA_ReadFromInitNetcdf.cpp File Reference

#include "REMORA_NCFile.H"
#include "AMReX_FArrayBox.H"
#include "REMORA_DataStruct.H"

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Functions
void	read_data_from_netcdf (int, const Box &domain, const std::string &fname, FArrayBox &NC_temp_fab, FArrayBox &NC_salt_fab, FArrayBox &NC_xvel_fab, FArrayBox &NC_yvel_fab)
	helper function for reading in initial state data from netcdf
void	read_data_full_domain_from_netcdf (int, const Box &domain, const std::string &fname, FArrayBox &NC_temp_fab, FArrayBox &NC_salt_fab, FArrayBox &NC_xvel_fab, FArrayBox &NC_yvel_fab, IntVect ngrow)
	helper function for reading in full domain high-resolution initial state data from netcdf
void	read_zeta_from_netcdf (int, const Box &domain, const std::string &fname, FArrayBox &NC_zeta_fab)
	helper function to read sea surface height from netcdf
void	read_zeta_full_domain_from_netcdf (int, const Box &domain, const std::string &fname, FArrayBox &NC_zeta_fab, IntVect ngrow)
	helper function to read high-resolution full-domain sea surface height from netcdf
void	read_bathymetry_from_netcdf (int, const Box &domain, const std::string &fname, FArrayBox &NC_h_fab)
	helper function to read bathymetry from netcdf
void	read_grid_vars_from_netcdf (int, const Box &domain, const std::string &fname, FArrayBox &NC_pm_fab, FArrayBox &NC_pn_fab, FArrayBox &NC_xr_fab, FArrayBox &NC_yr_fab, FArrayBox &NC_xu_fab, FArrayBox &NC_yu_fab, FArrayBox &NC_xv_fab, FArrayBox &NC_yv_fab, FArrayBox &NC_xp_fab, FArrayBox &NC_yp_fab)
	helper function to read grid variables from netcdf
bool	read_spherical_grid_vars_from_netcdf (int, const Box &domain, const std::string &fname, FArrayBox &NC_lonp_fab, FArrayBox &NC_latp_fab)
	helper function to read optional spherical psi coordinates from netcdf
void	read_bathymetry_full_domain_from_netcdf (const Box &domain, const std::string &fname, FArrayBox &NC_h_fab, IntVect ngrow)
	helper function to read full-domain high resolution bathymetry from netcdf
void	read_grid_vars_full_domain_from_netcdf (const Box &domain, const std::string &fname, FArrayBox &NC_pm_fab, FArrayBox &NC_pn_fab, IntVect ngrow)
	helper function to read full-domain high resolution grid variables from netcdf
void	read_coriolis_from_netcdf (int, const Box &domain, const std::string &fname, FArrayBox &NC_fcor_fab)
	helper function to read coriolis factor from netcdf
void	read_masks_from_netcdf (int, const Box &domain, const std::string &fname, FArrayBox &NC_mskr_fab, FArrayBox &NC_msku_fab, FArrayBox &NC_mskv_fab)
	helper function for reading in land-sea masks from netcdf
void	read_clim_nudg_coeff_from_netcdf (int, const Box &domain, const std::string &fname, bool do_m2_clim_nudg, bool do_m3_clim_nudg, bool do_temp_clim_nudg, bool do_salt_clim_nudg, FArrayBox &NC_M2NC_fab, FArrayBox &NC_M3NC_fab, FArrayBox &NC_TempNC_fab, FArrayBox &NC_SaltNC_fab)
	helper function to read climatology nudging from netcdf
void	read_vec_from_netcdf (int, const amrex::Vector< std::string > &fnames, const std::string &field_name, amrex::Vector< int > &vec_dat)
	helper function to read in vector of data from netcdf

Function Documentation

read_bathymetry_from_netcdf()

void read_bathymetry_from_netcdf	(	int	lev,
		const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_h_fab
	)

helper function to read bathymetry from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
NC_h_fab	container for bathymetry data

Definition at line 129 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_bathymetry_from_netcdf().

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read_bathymetry_full_domain_from_netcdf()

void read_bathymetry_full_domain_from_netcdf	(	const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_h_fab,
		IntVect	ngrow
	)

helper function to read full-domain high resolution bathymetry from netcdf

Parameters

domain	simulation domain at nc_hires_grid_level
fname	file name to read from
NC_h_fab	container for bathymetry data
ngrow	number of grow cells to read in, if not default

Definition at line 241 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_bathymetry_full_domain_from_netcdf().

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read_clim_nudg_coeff_from_netcdf()

void read_clim_nudg_coeff_from_netcdf	(	int	lev,
		const Box &	domain,
		const std::string &	fname,
		bool	do_m2_clim_nudg,
		bool	do_m3_clim_nudg,
		bool	do_temp_clim_nudg,
		bool	do_salt_clim_nudg,
		FArrayBox &	NC_M2NC_fab,
		FArrayBox &	NC_M3NC_fab,
		FArrayBox &	NC_TempNC_fab,
		FArrayBox &	NC_SaltNC_fab
	)

helper function to read climatology nudging from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
do_m2_clim_nudg	whether to do 2d momentum climatology nudging
do_m3_clim_nudg	whether to do 3d momentum climatology nudging
do_temp_clim_nudg	whether to do temperature climatology nudging
do_salt_clim_nudg	whether to do salinity climatology nudging
NC_M2NC_fab	container for 2d momentum climatology data
NC_M3NC_fab	container for 3d momentum climatology data
NC_TempNC_fab	container for temperature climatology data
NC_SaltNC_fab	container for salinity climatology data

Definition at line 351 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_clim_nudg_coeff_from_netcdf().

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read_coriolis_from_netcdf()

void read_coriolis_from_netcdf	(	int	lev,
		const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_fcor_fab
	)

helper function to read coriolis factor from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
NC_fcor_fab	container for Coriolis parameter data

Definition at line 290 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_coriolis_from_netcdf().

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read_data_from_netcdf()

void read_data_from_netcdf	(	int	,
		const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_temp_fab,
		FArrayBox &	NC_salt_fab,
		FArrayBox &	NC_xvel_fab,
		FArrayBox &	NC_yvel_fab
	)

helper function for reading in initial state data from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
NC_temp_fab	container for temperature data
NC_salt_fab	container for salinity data
NC_u_fab	container for u velocity data
NC_v_fab	container for v velocity data

Definition at line 18 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_data_from_netcdf().

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read_data_full_domain_from_netcdf()

void read_data_full_domain_from_netcdf	(	int	,
		const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_temp_fab,
		FArrayBox &	NC_salt_fab,
		FArrayBox &	NC_xvel_fab,
		FArrayBox &	NC_yvel_fab,
		IntVect	ngrow
	)

helper function for reading in full domain high-resolution initial state data from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
NC_temp_fab	container for temperature data
NC_salt_fab	container for salinity data
NC_u_fab	container for u velocity data
NC_v_fab	container for v velocity data
ngrow	number of grow cells to read

Definition at line 50 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_data_full_domain_from_netcdf().

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read_grid_vars_from_netcdf()

void read_grid_vars_from_netcdf	(	int	lev,
		const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_pm_fab,
		FArrayBox &	NC_pn_fab,
		FArrayBox &	NC_xr_fab,
		FArrayBox &	NC_yr_fab,
		FArrayBox &	NC_xu_fab,
		FArrayBox &	NC_yu_fab,
		FArrayBox &	NC_xv_fab,
		FArrayBox &	NC_yv_fab,
		FArrayBox &	NC_xp_fab,
		FArrayBox &	NC_yp_fab
	)

helper function to read grid variables from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
NC_pm_fab	container for pm data
NC_pn_fab	container for pn data
NC_xr_fab	container for x_rho data
NC_yr_fab	container for y_rho data
NC_xu_fab	container for x_u data
NC_yu_fab	container for y_u data
NC_xv_fab	container for x_v data
NC_yv_fab	container for y_v data
NC_xp_fab	container for x_p data
NC_yp_fab	container for y_p data

Definition at line 162 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_grid_vars_from_netcdf().

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read_grid_vars_full_domain_from_netcdf()

void read_grid_vars_full_domain_from_netcdf	(	const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_pm_fab,
		FArrayBox &	NC_pn_fab,
		IntVect	ngrow
	)

helper function to read full-domain high resolution grid variables from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
NC_pm_fab	container for pm data
NC_pn_fab	container for pn data
ngrow	number of grow cells to read in, if not default

Definition at line 266 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_grid_vars_full_domain_from_netcdf().

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read_masks_from_netcdf()

void read_masks_from_netcdf	(	int	,
		const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_mskr_fab,
		FArrayBox &	NC_msku_fab,
		FArrayBox &	NC_mskv_fab
	)

helper function for reading in land-sea masks from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
NC_mskr_fab	container for rho-point land/sea mask data
NC_msku_fab	container for u-point land/sea mask data
NC_mskv_fab	container for v-point land/sea mask data

Definition at line 316 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_masks_from_netcdf().

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read_spherical_grid_vars_from_netcdf()

bool read_spherical_grid_vars_from_netcdf	(	int	lev,
		const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_lonp_fab,
		FArrayBox &	NC_latp_fab
	)

helper function to read optional spherical psi coordinates from netcdf

Parameters

domain	simulation domain
fname	file name to read from
NC_lonp_fab	container for lon_psi data
NC_latp_fab	container for lat_psi data

Returns

whether the file carried spherical psi coordinates and they were read

ROMS grid files for spherical grids carry lon_psi/lat_psi alongside x_psi/y_psi, and those degree-valued corner arrays are what a coupled driver needs when the two components do not share a projected Cartesian frame (SCRIP/COAWST selects the same way; see Lib/SCRIP_COAWST/read_roms.f). Idealized grid files carry no spherical coordinates, so this read is optional and reports whether it happened rather than aborting.

Definition at line 207 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_grid_vars_from_netcdf().

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read_vec_from_netcdf()

void read_vec_from_netcdf	(	int	lev,
		const amrex::Vector< std::string > &	fnames,
		const std::string &	field_name,
		amrex::Vector< int > &	vec_dat
	)

helper function to read in vector of data from netcdf

Parameters

lev	level of data to read
fnames	file name(s) to read from
field_name	field name to read
vec_dat	vector to fill data

Definition at line 392 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_riv_pos_from_netcdf().

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read_zeta_from_netcdf()

void read_zeta_from_netcdf	(	int	lev,
		const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_zeta_fab
	)

helper function to read sea surface height from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
NC_zeta_fab	container for sea surface height data

Definition at line 79 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_zeta_from_netcdf().

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read_zeta_full_domain_from_netcdf()

void read_zeta_full_domain_from_netcdf	(	int	lev,
		const Box &	domain,
		const std::string &	fname,
		FArrayBox &	NC_zeta_fab,
		IntVect	ngrow
	)

helper function to read high-resolution full-domain sea surface height from netcdf

Parameters

lev	level of data to read
domain	simulation domain
fname	file name to read from
NC_zeta_fab	container for sea surface height data
ngrow	number of grow cells to read in, if not default

Definition at line 104 of file REMORA_ReadFromInitNetcdf.cpp.

Referenced by REMORA::init_zeta_full_domain_from_netcdf().

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