! 4DVar assimilation input parameters.
!
!git $Id$
!svn $Id: s4dvar.in 1202 2023-10-24 15:36:07Z arango $
!========================================================= Hernan G. Arango ===
! Copyright (c) 2002-2023 The ROMS/TOMS Group !
! Licensed under a MIT/X style license !
! See License_ROMS.md !
!==============================================================================
! !
! Input parameters can be entered in ANY order, provided that the parameter !
! KEYWORD (usually, upper case) is typed correctly followed by "=" or "==" !
! symbols. Any comment lines are allowed and must begin with an exclamation !
! mark (!) in column one. Comments may appear to the right of a parameter !
! specification to improve documentation. Comments will be ignored during !
! reading. Blank lines are also allowed and ignored. Continuation lines in !
! a parameter specification are allowed and must be preceded by a backslash !
! (\). In some instances, more than one value is required for a parameter. !
! If fewer values are provided, the last value is assigned for the entire !
! parameter array. The multiplication symbol (*), without blank spaces in !
! between, is allowed for a parameter specification. For example, in a two !
! grids nested application: !
! !
! AKT_BAK == 2*1.0d-6 2*5.0d-6 ! m2/s !
! !
! indicates that the first two entries of array AKT_BAK, in fortran column- !
! major order, will have the same value of "1.0d-6" for grid 1, whereas the !
! next two entries will have the same value of "5.0d-6" for grid 2. !
! !
! In multiple levels of nesting and/or multiple connected domains setups, !
! "Ngrids" entries are expected for some of these parameters. In such cases, !
! the order of the entries for a parameter is extremely important. It must !
! follow the same order (1:Ngrids) as in the state variable declaration. The !
! USER may follow the above guidelines for specifying his/her values. These !
! parameters are marked by "==" plural symbol after the KEYWORD. !
! !
!==============================================================================
!
! Number of iterations in the biconjugate gradient algorithm used to solve
! the elliptic equation for sea surface height in the error covariance
! balance operator, [1:Ngrids].
Nbico == 200
! Parameters used to compute balanced salinity in terms of temperature using
! empirical T-S relationships in the error covariance balance operator,
! [1:Ngrids].
dTdz_min == 0.001d0 ! minimum dT/dz (Celsius/m)
ml_depth == 100.0d0 ! mixed-layer depth (m; positive)
! Balance operator level of no motion depth (m) used when computing balanced
! free-surface contribution, [1:Ngrids].
LNM_depth == 1000.0d0 ! meters, positive
! Balance operator level of no motion flag used to compute balanced
! free-surface contribution:
!
! [0] Integrate from local bottom to the surface
! [1] Integrate from LNM_depth to surface or integrate from local bottom
! if shallower than LNM_depth
!
LNM_flag = 0
! Balance operator logical switches for state variables to consider in the
! error covariance multivariate constraints.
balance(isSalt) = T ! salinity
balance(isFsur) = T ! free-sruface
balance(isVbar) = F ! 2D momentum (ubar, vbar)
balance(isVvel) = T ! 3D momentum (u, v)
! Parameter to process the Nvct eigenvector of the stabilized representer
! matrix when computing array modes (here, Nvct=Ninner is the most important
! while Nvct=1 is the least important) OR cut-off parameter for the clipped
! analysis to disregard potentially unphysical array modes (that is, all
! the eigenvectors < Nctv are disgarded).
Nvct = 50
! Upper bound on the relative error of the gradient for the Lanczos
! conjugate gradient algorithm.
GradErr = 1.0d-4
! Maximum error bound on Hessian eigenvectors in the Lanczos conjugate
! gradient algorithm. Note that even quite inaccurate eigenvectors are
! useful for pre-conditioning purposes.
HevecErr = 1.0d-1
! Switch (T/F) to compute approximated Hessian eigenpairs in the Lanczos
! conjugate gradient algorithm.
LhessianEV = T
! Switch (T/F) to activate hot start in weak-constraint (R4DVAR and
! RBL4DVAR) algorithms of subsequent outer loops.
LhotStart = T
! Switch (T/F) to activate I4DVAR conjugate gradient preconditioning.
! Two types of Limited-Memory Preconditioner (LMP) are available
! (Tshimanga et al., 2008): spectral LMP and Ritz LMP.
Lprecond = F
! Switch to activate either Ritz Limited-Memory Preconditioner (T)
! or spectral Limited-Memory Preconditioner (F) to the I4DVAR algorithm.
Lritz = T
! If preconditioning, specify number of eigenpairs to use. If zero,
! use HevecErr parameter to determine the number of converged eigenpairs.
NritzEV = 0
! If weak constraint 4D-Var, set number of iterations in the Lanczos
! algorithm used to estimate the posterior analysis error covariance
! matrix.
NpostI = 50
! If observations impact or observations sensitivity, set the 4D-Var
! outer loop to process. It must be less or equal to Nouter.
Nimpact = 1
! If multiple executables 4D-Var, set the current outer counter and
! its computation phase (string). The 4D-Var running script assigns
! their values.
OuterLoop = MyOuterLoop
Phase4DVAR = MyPhase4DVAR
! Number of extra-observation classes (NextraObs), observation type
! indices (ExtraIndex), and observation type names (ExtraName) to
! consider in addition to the 1-to-1 associated with the state
! variables. It is used in observation operators that require more than
! one state variable to evaluate a particular observation type like
! HF radials, travel time, pressure, etc.
!
! In any application, the number of observation types is computed as:
! NobsVar = NstateVar + NextraObs.
!
! NextraObs values are expected for keywords ExtraIndex and ExtraName.
! If NextraVar > 1, enter one observation type name per line and
! use a backslash as the continuation.
NextraObs = 0
ExtraIndex = 20
ExtraName = radial
! If weak constraint 4D-Var, set diffusive relaxation coefficients (m2/s)
! used to relax representer tangent linear solution to privious Picard
! iteration linearized trajectory.
tl_M2diff == 0.0d0 ! 2D momentum
tl_M3diff == 100.0d0 ! 3D momentum
tl_Tdiff == 50.0d0 50.0d0 ! NT tracers
! Switches (T/F) to create and write error covariance normalization
! factors for model, initial conditions, boundary conditions, and
! surface forcing. If TRUE, these factors are computed and written
! to NRMname(1:4) NetCDF files. If FALSE, they are read from NRMname(1:4)
! NetCDF file. The computation of these factors is very expensive and
! needs to be computed only once for a particular application provided
! that grid land/sea masking, and decorrelation scales remain
! the same. Notice that four values are needed (1=initial conditions,
! 2=model, 3=boundary conditions, 4=surface forcing) per each nested
! grid, [1:4,1:Ngrids].
LdefNRM == F F F F ! Create a new normalization files
LwrtNRM == F F F F ! Compute and write normalization
! Switches to compute the correlation normalization coefficients for
! model error covariance.
CnormM(isFsur) = T ! 2D variable at RHO-points
CnormM(isUbar) = T ! 2D variable at U-points
CnormM(isVbar) = T ! 2D variable at V-points
CnormM(isUvel) = T ! 3D variable at U-points
CnormM(isVvel) = T ! 3D variable at V-points
CnormM(isTvar) = T T ! NT tracers
! Switches to compute the correlation normalization coefficients for
! initial conditions error covariance.
CnormI(isFsur) = T ! 2D variable at RHO-points
CnormI(isUbar) = T ! 2D variable at U-points
CnormI(isVbar) = T ! 2D variable at V-points
CnormI(isUvel) = T ! 3D variable at U-points
CnormI(isVvel) = T ! 3D variable at V-points
CnormI(isTvar) = T T ! NT tracers
! Switches to compute the correlation normalization coefficients for
! boundary conditions error covariance.
CnormB(isFsur) = T ! 2D variable at RHO-points
CnormB(isUbar) = T ! 2D variable at U-points
CnormB(isVbar) = T ! 2D variable at V-points
CnormB(isUvel) = T ! 3D variable at U-points
CnormB(isVvel) = T ! 3D variable at V-points
CnormB(isTvar) = T T ! NT tracers
! Switches to compute the correlation normalization coefficients for
! surface forcing error covariance.
CnormF(isUstr) = T ! surface U-momentum stress
CnormF(isVstr) = T ! surface V-momentum stress
CnormF(isTsur) = T T ! NT surface tracers flux
! Correlation normalization method:
!
! [0] Exact, very expensive
! [1] Approximated, randomization
Nmethod == 0
! If randomization, select random number generation scheme:
!
! [1] Gaussian distributed deviates, numerical recipes
Rscheme == 1
! Number of iterations to compute correlation normalization coefficients
! via the randomization approach. A large number is required to be
! statistically meaningful and achieve zero expectation mean and unit
! variance. These factors insure that the error covariance diagonal
! elements are equal to unity.
Nrandom = 5000
! Horizontal and vertical stability and accuracy factors (< 1) used to
! time-step discretized convolution operators below its theoretical limit.
! Notice that four values [1:4] are needed for each factor to facilitate
! the error covariance modeling: 1=initial conditions, 2=model,
! 3=boundary conditions, and 4=surface forcing.
!
! IC Model OBC Sur For
Hgamma = 0.5 0.5 0.5 0.5 ! horizontal operator
Vgamma = 0.05 0.05 0.05 0.05 ! vertical operator
! Model error covariance: horizontal, isotropic decorrelation scales (m).
! This scales are only used in weak-constraint data assimilation.
HdecayM(isFsur) == 50.0d+3 ! free-surface
HdecayM(isUbar) == 50.0d+3 ! 2D U-momentum
HdecayM(isVbar) == 50.0d+3 ! 2D V-momentum
HdecayM(isUvel) == 50.0d+3 ! 3D U-momentum
HdecayM(isVvel) == 50.0d+3 ! 3D V-momentum
HdecayM(isTvar) == 50.0d+3 50.0d+3 ! 1:NT tracers
! Model error covariance: vertical, isotropic decorrelation scales (m).
VdecayM(isUvel) == 100.0d0 ! 3D U-momentum
VdecayM(isVvel) == 100.0d0 ! 3D V-momentum
VdecayM(isTvar) == 100.0d0 100.0d0 ! 1:NT tracers
! Model error covariance: temporal decorrelation scales (days).
! This scales are only used in weak-constraint data assimilation.
TdecayM(isFsur) == 1.0d0 ! free-surface
TdecayM(isUbar) == 1.0d0 ! 2D U-momentum
TdecayM(isVbar) == 1.0d0 ! 2D V-momentum
TdecayM(isUvel) == 1.0d0 ! 3D U-momentum
TdecayM(isVvel) == 1.0d0 ! 3D V-momentum
TdecayM(isTvar) == 1.0d0 1.0d0 ! 1:NT tracers
! Initial conditions error covariance: horizontal, isotropic decorrelation
! scales (m).
HdecayI(isFsur) == 100.0d+3 ! free-surface
HdecayI(isUbar) == 100.0d+3 ! 2D U-momentum
HdecayI(isVbar) == 100.0d+3 ! 2D V-momentum
HdecayI(isUvel) == 100.0d+3 ! 3D U-momentum
HdecayI(isVvel) == 100.0d+3 ! 3D V-momentum
HdecayI(isTvar) == 100.0d+3 100.0d+3 ! 1:NT tracers
! Initial conditions error covariance: vertical, isotropic decorrelation
! scales (m).
VdecayI(isUvel) == 100.0d0 ! 3D U-momentum
VdecayI(isVvel) == 100.0d0 ! 3D V-momentum
VdecayI(isTvar) == 100.0d0 100.0d0 ! 1:NT tracers
! Boundary conditions error covariance: horizontal, isotropic decorrelation
! scales (m). A value is expected for each boundary edge in the following
! order:
! 1: west 2: south 3: east 4: north
HdecayB(isFsur) == 100.0d+3 100.0d+3 100.0d+3 100.0d+3 ! free-surface
HdecayB(isUbar) == 100.0d+3 100.0d+3 100.0d+3 100.0d+3 ! 2D U-momentum
HdecayB(isVbar) == 100.0d+3 100.0d+3 100.0d+3 100.0d+3 ! 2D V-momentum
HdecayB(isUvel) == 100.0d+3 100.0d+3 100.0d+3 100.0d+3 ! 3D U-momentum
HdecayB(isVvel) == 100.0d+3 100.0d+3 100.0d+3 100.0d+3 ! 3D V-momentum
HdecayB(isTvar) == 4*100.0d+3 4*100.0d+3 ! (4,1:NT) tracers
! Boundary conditions error covariance: vertical, isotropic decorrelation
! scales (m). A value is expected for each boundary edge in the following
! order:
! 1: west 2: south 3: east 4: north
VdecayB(isUvel) == 100.0d0 100.0d0 100.0d0 100.0d0 ! 3D U-momentum
VdecayB(isVvel) == 100.0d0 100.0d0 100.0d0 100.0d0 ! 3D V-momentum
VdecayB(isTvar) == 4*100.d0 4*100.d0 ! (4,1:NT) tracers
! Surface forcing error covariance: horizontal, isotropic decorrelation
! scales (m).
HdecayF(isUstr) == 100.0d+3 ! surface U-momentum stress
HdecayF(isVstr) == 100.0d+3 ! surface V-momentum stress
HdecayF(isTsur) == 100.0d+3 100.0d+3 ! 1:NT surface tracers flux
! Select flag for BackGround Quality Control (BGQC) of observations:
!
! [1] Quality control in terms of state variable indices
! [2] Quality control in terms of observation provenance
bgqc_type == 1
! If BGQC is in terms of state variables, set the threshold, squared number
! of standard deviations to use in the quality control rejection of
! observations.
!
! Use a large value (say, 1.0d+5) if you do not want to reject observations
! associated with a particular state variable.
!
! Use a small value (typically, 16 to rejecting based on on 4 standard
! deviations) to perform quality control of observations for a particular
! state variable.
S_bgqc(isFsur) == 1.0d+5 ! free-surface
S_bgqc(isUbar) == 1.0d+5 ! 2D U-momentum
S_bgqc(isVbar) == 1.0d+5 ! 2D V-momentum
S_bgqc(isUvel) == 1.0d+5 ! 3D U-momentum
S_bgqc(isVvel) == 1.0d+5 ! 3D V-momentum
S_bgqc(isTvar) == 16.0d0 16.0d0 ! 1:NT tracers
! If BGQC is in terms of observation provenance, set the threshold, squared
! number of standard deviations to use in the quality control rejection of
! observations.
!
! Use a small value (say, 16 to rejecting based on on 4 standard deviations)
! to perform quality control for the desired observation provenance(s).
!
! Nprovenance: Number of observation provenances to quality control
! Iprovenance: Observation provenance indices to process [1:Nprovenance]
! P_bgqc: Standard deviation threshold [1:Nprovenance]
Nprovenance == 2
Iprovenance == 6 7 ! ARGO Temperature and Salinity
P_bgqc == 16.0d0 16.0d0
! If applicable, set switches (T/F) used to adjust surface tracer flux,
! [1:NT,1:Ngrids].
Lstflux == T T ! NT tracers
! If applicable, set switches to adjust state variables at the open
! boundaries. Notice that a value is expected for each boundary segment
! per nested grid, [1:4,1:Ngrids]. The boundary order is: 1=west,
! 2=south, 3=east, and 4=north. That is, anticlockwise starting at
! the western boundary.
!
! When processing momentum, you need to activate both components. If
! processing 2D momentum, you need to activate both free-surface and
! 3D-momentum at the processing boundary.
!
! W S E N _____N_____
! e o a o | 4 |
! s u s r | |
! t t t t 1 W E 3
! h h | |
! |_____S_____|
! 1 2 3 4 2
Lobc(isFsur) == F F F F ! free-surface
Lobc(isUbar) == F F F F ! 2D U-momentum
Lobc(isVbar) == F F F F ! 2D V-momentum
Lobc(isUvel) == F F F F ! 3D U-momentum
Lobc(isVvel) == F F F F ! 3D V-momentum
! If applicable, set switches to adjust state tracer variables at the
! open boundaries. Notice that a value is expected for each tracer at each
! boundary segment per nested grid, [1:4,1:NT,1:Ngrids]. The boundary order
! is the same as above. Notice that the first line has the values for
! temperature boundaries, the second is salinity, and so on.
Lobc(isTvar) == F F F F \
F F F F
! Input model, initial conditions, boundary conditions, and surface forcing
! standard deviation file names, [1:Ngrids].
STDnameM == roms_std_m.nc
STDnameI == roms_std_i.nc
STDnameB == roms_std_b.nc
STDnameF == roms_std_f.nc
! Input/output model, initial conditions, boundary conditions, and surface
! forcing error covariance normalization factors file name, [1:Ngrids].
NRMnameM == roms_nrm_m.nc
NRMnameI == roms_nrm_i.nc
NRMnameB == roms_nrm_b.nc
NRMnameF == roms_nrm_f.nc
! Input/output observation file name, [1:Ngrids].
OBSname == roms_obs.nc
! Input/output Hessian eigenvectors file name, [1:Ngrids].
HSSname == roms_hss.nc
! Input/output Lanczos vectors file name, [1:Ngrids].
LCZname == roms_lcz.nc
! Output time-evolved Lanczos vectors file name, [1:Ngrids].
LZEname == roms_lze.nc
! Output model data at observation locations file name, [1:Ngrids].
MODname == roms_mod.nc
! Output posterior error covariance matrix file name, [1:Ngrids].
ERRname == roms_err.nc
! Input forcing filenames at observation locations for computing observations
! impacts during the analysis-forecast cycle when the forecast is initialized
! with the 4D-Var analysis (OIFnameA) or the 4D-Var background (OIFnameB).
OIFnameA == roms_oif_a.nc
OIFnameB == roms_oif_b.nc
!
! GLOSSARY:
! =========
!
!------------------------------------------------------------------------------
! Error covariance matrix balance operator parameters. These parameters are
! only used when BALANCE_OPERATOR and ZETA_ELLIPTIC are activated.
!------------------------------------------------------------------------------
!
! Nbico Number of iterations in the biconjugate gradient algorithm
! used to solve the elliptic equation for sea surface height
! in the error covariance balance operator, [1:Ngrids]. We
! need as many iterations as required to decrease the error
! value of the reference free-surface to 1E-8 or smaller. In
! some applications Nbico=200 will do the job.
!
! Warning: be aware that there are 4 arrays that are
! ------- allocated with this parameter array and its
! value may be constrained by available memory:
!
! FOURDVAR(ng) % p_r2d (LBi:UBi,LBj:UBj,Nbico(ng))
! FOURDVAR(ng) % r_r2d (LBi:UBi,LBj:UBj,Nbico(ng))
! FOURDVAR(nd) % bp_r2d(LBi:UBi,LBj:UBj,Nbico(ng))
! FOURDVAR(ng) % br_r2d(LBi:UBi,LBj:UBj,Nbico(ng))
!
! All the iterations values are needed in the backward
! stepping of the adjoint.
!
! dTdz_min Minimum d(T)/d(z) above which the balanced salinity
! (deltaS_b) is computed, [1:Ngrids]:
!
! deltaS_b = cff * dSdT * deltaT; dSdT = dSdz / dTdz
!
! where cff is a coefficient that depends on the mixed-layer
! depth (ml_depth):
!
! cff = 1.0 - EXP (z_r / ml_depth)
!
! ml_depth Mixed-layer depth (m; positive) used above in smoothing
! coefficient (cff), [1:Ngrids].
!
! LNM_depth Level of no motion depth (m; positive) used to compute the
! balanced free-surface contribution in the error covariance
! balance operator. It is only relevant when LNM_flag=1,
! balance(isFsur)=T, and ZETA_ELLIPTIC is NOT activated. It
! is used to integrate the non-hydrostatic equation.
!
! LNM_flag Level of no motion integration flag used to used to compute
! the balanced free-surface contribution:
!
! LNM_flag = 0, integrate from local bottom to the surface
!
! LNM_flag = 1, integrate from LNM_depth to surface or
! integrate from local bottom if shallower
! than LNM_depth
!
! balance Balance operator logical switches for state variables to
! consider in the error covariance off-diagonal multivariate
! constraints:
!
! balance(isSalt) = T, salinity
! balance(isFsur) = T, free-sruface
! balance(isVbar) = F, 2D momentum (ubar, vbar)
! balance(isVvel) = T, 3D momentum (u, v)
!
! Guidelines:
!
! 1) The salinity contribution, balance(isSalt), depends
! only on temperature. Notice that temperature is used
! to establish the balanced part of the other state
! variables.
!
! 2) The free-surface contribution, balance(isFsur), depends
! on salinity since we need to compute balanced density
! and integrate properly using LNM_flag and LNM_depth.
! This implies that balance(isSalt) needs to be TRUE too.
! It is independent of the 2D or 3D balance velocity terms.
!
! 3) The 3D momentum, balance(isVvel), depends on salinity
! since we need to compute balanced density. This
! implies that balance(isSalt) needs to be TRUE too.
!
!------------------------------------------------------------------------------
! Array modes parameter.
!------------------------------------------------------------------------------
!
! Nvct Which eigenvector of the stabilized representer matrix to
! process to computing array modes when option ARRAY_MODES is
! activated. In this case, Nvct =< Ninner,
!
! Nvct=1 least important eigenvector
! Nvct=Ninner most important eigenvector
!
! or cut-off eigenvector for the clipped analysis when
! the option CLIPPING is activated to remove potentially
! unphysical array modes. In this case, Nvct =< Ninner. All
! the eigenvectors are ordered according to their significance,
! Nvct=Ninner is the most important.
!
! Nvct:Ninner eigenvectors will be processed
! 1:Nvct-1 eigenvectors will be disgarded
!
!------------------------------------------------------------------------------
! Lanczos conjugate gradient algorithm parameters.
!------------------------------------------------------------------------------
!
! GradErr Upper bound on the relative error of the gradient.
!
! HevecErr Maximum error bound on Hessian eigenvectors. Note that
! even quite inaccurate eigenvectors are useful
! for pre-conditioning purposes.
!
! LhessianEV Switch (T/F) to compute approximated Hessian eigenvalues
! and eigenvectors.
!
!
! LhotStart Switch (T/F) to activate hot start in weak-constraint
! (R4DVAR and RBL4DVAR) algorithms.
!
! Lprecond Switch (T/F) to activate preconditioning in the I4DVAR
! algorithm. Two types of Limited-Memory preconditioner (LMP)
! are available Tshimanga et al., 2008): Spectral and Ritz.
!
! If Lprecond=T and Lritz=F, Spectral LMP
! If Lprecond=T and Lritz=T, Ritz LMP
!
! Lritz Switch to activate either Ritz Limited-Memory Preconditioner
! (T) or spectral Limited-Memory Preconditioner (F) to the
! I4DVAR algorithm using eigenpairs approximation for the
! Hessian matrix. The accuracy of the Hessian eigenvectors
! (HevecErr) can be used to fine tune the minimization. That
! is, HevecErr can be used to control number of eigenvalues
! of the preconditioning Hessian matrix. See Tshimanga et al.
! (2008) Q. J. R. Met. Soc. paper for details.
!
! NritzEV If preconditioning, specify number of eigenpairs to use.
! If zero, use HevecErr parameter to determine the number
! of converged eigenpairs.
!
! NpostI If weak constraint 4D-Var (RBL4DVAR or R4DVAR), set number
! of iterations in the Lanczos algorithm used to estimate the
! posterior analysis error covariance matrix.
!
!------------------------------------------------------------------------------
! Observations impact or observations sensitivity.
!------------------------------------------------------------------------------
!
! Nimpact Outer loop to consider in the computation of the observations
! impact or observation sensitivity, Nimpact =< Nouter. This
! facilitates the computations with multiple outer loop 4D-Var
! applications. The observation analysis needs to be computed
! separately for each outer loop. The full analysis for all
! outer loops is combined offline.
!
!------------------------------------------------------------------------------
! Outer loop counter and phase for split 4D-Var in multiple executables.
!------------------------------------------------------------------------------
!
! OuterLoop Current outer loop counter. It is set by the running shell
! script.
!
! Phase4DVAR Current split 4D-Var algorithm elementary phases to compute:
!
! Phase4DVAR = 'background' Xb
! Phase4DVAR = 'increment' dXa
! Phase4DVAR = 'analysis' Xa = Xb + dXa
! Phase4DVAR = 'post_analysis' (posterior analysis)
! Phase4DVAR = 'post_error' (posterior error)
!
! There is a 'prior_error' phase that it is always done in
! 'ROMS_initialize'.
!
!------------------------------------------------------------------------------
! Additional observation operators.
!------------------------------------------------------------------------------
!
! Currently, only one extra-observation operator has been implemented to
! process radial velocities from HF radars instruments.
!
! NextraObs Number of extra-observation classes to consider in addition
! to those associated with the state variables (one-to-one
! correspondence. They are used in observation operators that
! require more than one state variable to evaluate a particular
! extra-observation type like HF radials, travel time,
! pressure, etc.
!
! In any application, the number of observation types is
! computed as:
!
! NobsVar(ng) = NstateVar(ng) + NextraObs
!
! If not processing extra-observation classes, set NextraObs
! to zero.
!
! ExtraIndex Extra-observation class identification indices, as specified
! in input observation NetCDF file variable "obs_type". The
! index has to be a number greater than 7+2*NT, where NT is
! the total of active plus passive tracers. NextraObs values
! are expected for this Keyword. This parameter is only
! processed when NextraObs > 0.
!
! ExtraName Extra-observation class names. NextraObs values are expected.
! This parameter is only processed when NextraObs > 0. Enter
! one class type name per line and use a backslash for
! continuation. For example:
!
! ExtraName = radials \
! pressure
!
! Currently, however, only the radials operator is coded.
!
!------------------------------------------------------------------------------
! Diffusive relaxation coefficients.
!------------------------------------------------------------------------------
!
! If weak constraint 4D-Var and RPM_RELAXATION flag is activated, these
! coefficients are used to relax the representer tangent linear solution
! to the previous outer loop linearized trajectory during the Picard
! iterations. The user may turn off relaxation on a particular variable
! by setting the coefficient to zero.
!
! tl_M2diff 2D momentum diffusion relaxation coefficient (m2/s).
!
! tl_M3diff 3D momentum diffusion relaxation coefficient (m2/s).
!
! tl_Tdiff Tracers type variables diffusion relaxation coefficients
! (m2/s). NT values are expected.
!
!------------------------------------------------------------------------------
! Background/model correlation parameters.
!------------------------------------------------------------------------------
!
! LdefNRM Switch (T/F) to create a new normalization NetCDF file
! for, [4,1:Ngrids]:
!
! LdefNRM(1,:) initial conditions error covariance
! LdefNRM(2,:) model error covariance
! LdefNRM(3,:) boundary conditions error covariance
! LdefNRM(4,:) surface forcing error covariance
!
! The computation of the correlation normalization
! coefficients is very expensive and needs to be computed
! only once for a particular application provided that grid,
! land/sea masking (if any), and decorrelation scales (see
! below) remain the same. The user can use this switch
! in conjunction with the CnormM, CnormI, CnormB, CnormF
! (see below) switches to compute each coefficient separately.
! The normalization NetCDF only needs to be created once
! and simultaneous runs can write to the same NetCDF. If
! using this approach, compute the normalization factors
! with the CORRELATION CPP-option and not I4DVAR, RBL4DVAR
! or R4DVAR.
!
! LwrtNRM Switch (T/F) to write out correlation normalization factors
! for, [4,1:Ngrids]:
!
! LwrtNRM(1,:) initial conditions error covariance
! LwrtNRM(2,:) model error covariance
! LwrtNRM(3,:) boundary conditions error covariance
! LwrtNRM(4,:) surface forcing error covariance
!
! If TRUE, these factors are computed and written to NRMnameI,
! NRMnameM, NRMnameB, and NRMnameF NetCDF files, respectively.
! If FALSE, they are read from NRMname NetCDF file.
!
! CnormM Compute (T/F) model error covariance
! normalization factors:
!
! CnormM(isFsur) free-surface
! CnormM(isUbar) 2D U-momentum
! CnormM(isVbar) 2D V-momentum
! CnormM(isUvel) 3D U-momentum
! CnormM(isVvel) 3D V-momentum
! CnormM(isTvar) tracers (1:NT)
!
! CnormI Compute (T/F) initial conditions error covariance
! normalization factors:
!
! CnormI(isFsur) free-surface
! CnormI(isUbar) 2D U-momentum
! CnormI(isVbar) 2D V-momentum
! CnormI(isUvel) 3D U-momentum
! CnormI(isVvel) 3D V-momentum
! CnormI(isTvar) tracers (1:NT)
!
! CnormB Compute (T/F) open boundary conditions error covariance
! normalization factors:
!
! CnormB(isFsur) free-surface
! CnormB(isUbar) 2D U-momentum
! CnormB(isVbar) 2D V-momentum
! CnormB(isUvel) 3D U-momentum
! CnormB(isVvel) 3D V-momentum
! CnormB(isTvar) tracers (1:NT)
!
! CnormF Compute (T/F) surface forcing error covariance
! normalization factors:
!
! CnormF(isTsur) tracer flux (1:NT)
! CnormF(isUstr) wind U-stress
! CnormF(isVstr) wind V-stress
!
! Nmethod Correlation normalization method:
!
! [0] Exact, very expensive
! [1] Approximated, randomization
!
! Rscheme Random number generation scheme if randomization:
!
! [1] Gaussian distributed deviates, numerical recipes
!
! Nrandom Number of iterations to compute correlation normalization
! factors using the randomization approach of Fisher and
! Courtier (1995). A large number is required to be
! statistically meaningful and achieve zero expectation
! mean and unit variance, approximately. These factors ensure
! that the error covariance diagonal elements are equal to
! unity.
!
! Hgamma Horizontal stability and accuracy factor (< 1) used to
! scale the time-step of the convolution operator below its
! theoretical limit, [1:4]. Notice that four values are
! needed for Hgamma to facilitate the error covariance
! modeling for initial conditions (1), model (2), boundary
! conditions (3), and surface forcing (4).
!
! Vgamma Vertical stability and accuracy factor (< 1) used to
! scale the time-step of the convolution operator below its
! theoretical limit, [1:4]. Notice that four values are
! needed for Vgamma to facilitate the error covariance
! modeling for initial conditions (1), model (2), boundary
! conditions (3), and surface forcing (4).
!
! HdecayM Model error covariance, [1:Ngrids],
! horizontal, isotropic decorrelation scales (m):
!
! HdecayM(isFsur) free-surface
! HdecayM(isUbar) 2D U-momentum
! HdecayM(isVbar) 2D V-momentum
! HdecayM(isUvel) 3D U-momentum
! HdecayM(isVvel) 3D V-momentum
! HdecayM(isTvar) tracers (1:NT,1:Ngrids)
!
! VdecayM Model error covariance, [1:Ngrids],
! vertical, isotropic decorrelation scale (m):
!
! VdecayM(isUvel) 3D U-momentum
! VdecayM(isVvel) 3D V-momentum
! VdecayM(isTvar) tracers (1:NT,1:Ngrids)
!
! HdecayI Initial conditions error covariance, [1:Ngrids],
! horizontal, isotropic decorrelation scales (m):
!
! HdecayI(isFsur) free-surface
! HdecayI(isUbar) 2D U-momentum
! HdecayI(isVbar) 2D V-momentum
! HdecayI(isUvel) 3D U-momentum
! HdecayI(isVvel) 3D V-momentum
! HdecayI(isTvar) tracers (1:NT,1:Ngrids)
!
! VdecayI Model error covariance, [1:Ngrids],
! vertical, isotropic decorrelation scale (m):
!
! VdecayI(isUvel) 3D U-momentum
! VdecayI(isVvel) 3D V-momentum
! VdecayI(isTvar) tracers (1:NT)
!
! HdecayB Open boundary conditions error covariance, [4,1:Ngrids],
! horizontal, isotropic decorrelation scales (m):
!
! HdecayB(:,isFsur) free-surface
! HdecayB(:,isUbar) 2D U-momentum
! HdecayB(:,isVbar) 2D V-momentum
! HdecayB(:,isUvel) 3D U-momentum
! HdecayB(:,isVvel) 3D V-momentum
! HdecayB(:,isTvar) tracers (4,1:NT,1:Ngrids)
!
! boundary index 1: west 2: south 3: east 4: north
!
! VdecayB Model error covariance, [4,1:Ngrids],
! vertical, isotropic decorrelation scale (m):
!
! VdecayB(isUvel) 3D U-momentum
! VdecayB(isVvel) 3D V-momentum
! VdecayB(isTvar) tracers (4,1:NT,1:Ngrids)
!
! boundary index 1: west 2: south 3: east 4: north
!
! HdecayF Surface forcing error covariance, [1:Ngrids],
! horizontal, isotropic decorrelation scales (m):
!
! HdecayF(isTsur) tracers flux (1:NT,1:Ngrids)
! HdecayF(isUstr) wind U-stress
! HdecayF(isVstr) wind V-stress
!
!------------------------------------------------------------------------------
! Background Quality Control (BCQC) of observations parameters.
!------------------------------------------------------------------------------
!
! bgqc_type Flag to determine the type of background quality control:
!
! bgqc_type = 1 Background quality control in terms of
! the state variable index (1 - MstateVar)
! read from the input observation NetCDF,
! variable "obs_type".
!
! It is general because it includes all the
! observation provenances for a particular
! state variable. For example, all the
! temperature observations.
!
! bgqc_type = 2 Background quality control in terms of
! the observation provenance index read
! from the input observation NetCDF,
! variable "obs_provenance".
!
! It is specific because it only includes
! the observations for a particular
! provenance or instrument. For example,
! temperature observation from ARGO buoys.
!
! S_bgqc Threshold, squared number of standard deviations to use in
! the quality control rejection of observations in terms of
! the state variable index.
!
! S_bgqc(isFsur) free-surface
! S_bgqc(isUbar) 2D U-momentum
! S_bgqc(isVbar) 2D V-momentum
! S_bgqc(isUvel) 3D U-momentum
! S_bgqc(isVvel) 3D V-momentum
! S_bgqc(isTvar) NT tracers (4,NT,Ngrids)
!
! It used when bgqc_type = 1. Use a large value (say 1.0d+5)
! to indicate that the observations are spread out over a wider
! range of background values. Otherwise, you use values like
! 16 for rejecting observations based on 2 standard deviations.
!
! Nprovenance Number of observation provenances to consider for background
! quality control. Used when bgqc_type = 2.
!
! Iprovenance Observation provenance index to consider for background
! quality control. Use the same index value as specified
! in input observations NetCDF, variable "obs_provenance".
! 1:Nprovenance values are expected for each nested grid.
! Used when bgqc_type = 2.
!
! P_bgqc Threshold, squared number of standard deviations to use in
! the quality control rejection of observations in terms of
! the provenance index, 1:Nprovenance values are expected for
! each nested grid. Used when bgqc_type = 2.
!
!------------------------------------------------------------------------------
! 4D-Var adjustment switches.
!------------------------------------------------------------------------------
!
! Lstflux Logical switches (T/F) used to adjust surface tracer flux,
! including active and passive tracers, [1:NT, 1:Ngrids].
! These switches are used when ADJUST_STFLUX is activated.
!
! Lobc Logical switches (T/F) used to adjust state variables at
! the open boundaries. A value is expected for each boundary
! segment per nested grid, [1:4, 1:Ngrids].
!
! The boundary order is anticlockwise starting at the western
! edge as follows:
!
! 1 = western edge
! 2 = southern edge
! 3 = eastern edge
! 4 = northern edge
!
! Lobc(isFsur) free-surface
! Lobc(isUbar) 2D U-momentum
! Lobc(isVbar) 2D V-momentum
! Lobc(isUvel) 3D U-momentum
! Lobc(isVvel) 3D V-momentum
! Lobc(isTvar) NT tracers (4,NT,Ngrids)
!
! WARNING: When processing momentum, you need to activate both
! ======= components. If processing 2D momentum, you need to
! activate both free-surface and 3D-momentum at the processing
! boundary. The 2D momentum adjustment is computed by vertically
! integretating the 3D momentum increments.
!
!------------------------------------------------------------------------------
! Input/Output NetCDF files (a string with a maximum of 256 characters).
!------------------------------------------------------------------------------
!
! STDnameM Input model error covariance
! standard deviation file name.
!
! STDnameI Input initial conditions error covariance
! standard deviation file name.
!
! STDnameB Input open boundary conditions error covariance
! standard deviation file name.
!
! STDnameF Input surface forcing error covariance
! standard deviation file name.
!
! NRMnameM Input/output model error covariance
! normalization factors file name.
!
! NRMnameI Input/output initial conditions error covariance
! normalization factors file name.
!
! NRMnameB Input/output open boundary conditions error covariance
! normalization factors file name.
!
! NRMnameF Input/output surface forcing error covariance
! normalization factors file name.
!
! OBSname Input/Output observations data file name.
!
! HSSname Input/Output Hessian eigenvectors file name.
!
! LCZname Input/output Lanczos vectors file name.
!
! LZEname Output time-evolved Lanczos vectors file name.
!
! MODname Output model data at observations locations file name.
!
! ERRname Output posterior error covariance matrix file name.
!
! Input forcing filenames at observation locations for computing observations
! impacts during the analysis-forecast cycle when RBL4DVAR_FCT_SENSITIVITY and
! OBS_SPACE are activated:
!
! (See www.myroms.org/wiki/Analysis-Forecast_Cycle_Observation_Impacts)
!
! OIFnameA Forecast initialized with 4D-Var analysis (red curve)
!
! OIFnameB Forecast initialized with 4D_Var background (blue curve)
!