Variables

H

Hz

Vertical level thicknesses, $\,H_{z}\,(\xi ,\eta ,s)$.

dimension = Hz(LBi:UBi,LBj:UBj,N(ng))

pointer = GRID(ng)%Hz

tangent = tl_Hz

adjoint = ad_Hz

units = meter

grid = ρ-points

option = SOLVE3D

routine = set_depths.F

I

Iend

Non-overlaping upper bound tile index in the i-direction. Its value depends on the tile rank (sub-domain patition).

routine = tile.h, get_tile.F

Istr

Non-overlaping lower bound tile index in the i-direction. Its value depends on the tile rank (sub-domain patition).

routine = tile.h, get_tile.F

idbio

Identification indeces for biological tracer variables, t(:,:,:,:,idbio(:)).

dimension = idbio(NBT)

option = BIOLOGY

routine = mod_scalars.F

idsed

Identification indeces for biological tracer variables, t(:,:,:,:,idsed(:)).

dimension = idsed(NST)

option = SEDIMENT

routine = mod_scalars.F

inert

Identification indeces for inert tracer variables, t(:,:,:,:,inert(:)).

dimension = inert(NPT)

option = T_PASSIVE

routine = mod_scalars.F

isalt

Tracer identification index for salinity, t(:,:,:,:,isalt).

routine = mod_scalars.F

itemp

Tracer identification index for potential temperature, t(:,:,:,:,itemp).

routine = mod_scalars.F

J

Jend

Non-overlaping upper bound tile index in the j-direction. Its value depends on the tile rank (sub-domain patition).

routine = tile.h, get_tile.F

Jstr

Non-overlaping lower bound tile index in the j-direction. Its value depends on the tile rank (sub-domain patition).

routine = tile.h, get_tile.F

L

LBi

Array lower bound dimension in the i-direction. In serial and shared-memory applications its value is LBi=-2 for East-West periodic grids or LBi=0 for non-periodic grids . In distributed-memory its value is a function of the tile partition, LBi=Istr-NghostPoints.

option = LOWER_BOUND_I

routine = get_bounds.F, get_tile.F

LBj

Array lower bound dimension in the j-direction. In serial and shared-memory applications its value is LBj=-2 for North-South periodic grids or LBj=0 for non-periodic grids . In distributed-memory its value is a function of the tile partition, LBj=Jstr-NghostPoints.

option = LOWER_BOUND_J

routine = get_bounds.F, get_tile.F

N

N

Number of vertical levels for each nested grid.

dimension = N(Ngrids)

routine = mod_param.F

NAT

Number of active tracer-type variables. Usually, it has a value of two for potential temperature and salinty.

option = SOLVE3D

routine = mod_param.F

NBT

Number of biological tracer-type variables.

option = BIOLOGY

routine = mod_param.F

NCS

Number of cohesive (mud) sediment tracer-type variables.

option = SEDIMENT

routine = mod_param.F

NghostPoints

Number of ghost points in the halo region used in distributed-memory configurations.

option = GHOST_POINTS

routine = mod_param.F

Ngrids

Number of nested and/or multiple connected grids to solve.

routine = mod_param.F

NNS

Number of non-cohesive (sand) sediment tracer-type variables.

option = SEDIMENT

routine = mod_param.F

NPT

Number of inert tracer-type variables. Currently, an inert passive tracer is one that it is only advected and diffused. Other processes are ignored. These tracers include, for example, dyes, pollutants, oil spills, etc.

option = T_PASSIVE

routine = mod_param.F

NST

Number of sediment tracer-type variables, NST=NCS+NNS.

option = SEDIMENT

routine = mod_param.F

NT

Total number of tracer-type variables for each nested grid. Currently, NT=NAT+NPT+NST+NBT.

dimension = NT(Ngrids)

option = SOLVE3D

routine = mod_param.F

R

rho

In situ density anomaly computed as a function of potential temperature, salinity, and depth.

$\,\sigma (\xi ,\eta ,s)=\rho (\xi ,\eta ,s)-1000$.

dimension = rho(LBi:UBi,LBj:UBj,N(ng))

pointer = OCEAN(ng)%rho

tangent = tl_rho

adjoint = ad_rho

units = kilogram meter^-3

grid = ρ-points

option = SOLVE3D, NONLIN_EOS

routine = rho_eos.F

It can computed using a linear or nonlinear equation of state. The nonlinear equation of state is based on Jackett and McDougall (1992) polynomial expressions.

T

t

Tracer-type variables, $\,T(\xi ,\eta ,s,t,itrc)$.

dimension = t(LBi:UBi,LBj:UBj,N(ng),3,NT(ng))

pointer = OCEAN(ng)%t

tangent = tl_t

adjoint = ad_t

grid = ρ-points

option = SOLVE3D

routine = step3d_t.F

This array contains all the tracer fields. They are classified as active (potential temperature, salinity), inert (dyes, pollutants, oil spills, etc), passive (sediment, biology). There is a index identifier for each tracer field (see table below). Notice that salinity does not have physical units. Usually PSU is used to indicate that the practical salinity scale was used to determine conductivity.

Index	Field	Units	CPP
itemp	Potential temperature	Celsius	SOLVE3D
isalt	Salinity	None	SALINITY
inert(1:NPT)	NPT inert tracers	kilogram meter-3	T_PASSIVE
idsed(1:NST)	NST sediment tracers	kilogram meter-3	SEDIMENT
idbio(1:NBT)	NBT biology tracers	millimole meter-3	BIOLOGY

U

UBi

Array upper bound dimension in the i-direction. In serial and shared-memory applications its value is govern by the value of UPPER_BOUND_I. In distributed-memory its value is a function of the tile partition, UBi=Iend+NghostPoints.

option = UPPER_BOUND_I

routine = get_bounds.F, get_tile.F

UBj

Array upper bound dimension in the j-direction. In serial and shared-memory applications its value is govern by the value of UPPER_BOUND_J. In distributed-memory its value is a function of the tile partition, UBj=Jend+NghostPoints.

option = UPPER_BOUND_J

routine = get_bounds.F, get_tile.F

u

Total momentum component in the ξ-direction, $\,u(\xi ,\eta ,s,t)$.

dimension = u(LBi:UBi,LBj:UBj,N(ng),2)

pointer = OCEAN(ng)%u

tangent = tl_u

adjoint = ad_u

units = meter second^-1

grid = u-points

option = SOLVE3D

routine = step3d_uv.F

ubar

Vertically-integrated momentum component in the ξ-direction, ${\bar {u}}(\xi ,\eta ,t)$.

${\bar {u}}={\frac {1}{D}}\int _{-h}^{\zeta }u\,H_{z}\,dz$

dimension = ubar(LBi:UBi,LBj:UBj,3)

pointer = OCEAN(ng)%ubar

tangent = tl_ubar

adjoint = ad_ubar

units = meter second^-1

grid = u-points

routine = step2d.F

V

v

3D momentum component in the η-direction, $\,v(\xi ,\eta ,s,t)$.

dimension = v(LBi:UBi,LBj:UBj,N(ng),2)

pointer = OCEAN(ng)%v

tangent = tl_u

adjoint = ad_u

units = meter second^-1

grid = v-points

option = SOLVE3D

routine = step3d_uv.F

vbar

Vertically-integrated momentum component in the η-direction, ${\bar {v}}(\xi ,\eta ,t)$.

${\bar {v}}={\frac {1}{D}}\int _{-h}^{\zeta }v\,H_{z}\,dz$

dimension = vbar(LBi:UBi,LBj:UBj,3)

pointer = OCEAN(ng)%vbar

tangent = tl_vbar

adjoint = ad_vbar

units = meter second^-1

grid = v-points

routine = step2d.F

W

W

Terrain-following, vertical velocity component, $\,\Omega (\xi ,\eta ,s)\,Hz/mn$.

dimension = W(LBi:UBi,LBj:UBj,0:N(ng))

pointer = OCEAN(ng)%W

tangent = tl_W

adjoint = ad_W

units = meter³ second^-1

sign = positive downwards (downwelling), negative upwards (upwelling)

grid = w-points

option = SOLVE3D

routine = omega.F

wvel

True vertical velocity component, $\,w(\xi ,\eta ,s)$. It is computed only for output purposes.

dimension = wvel(LBi:UBi,LBj:UBj,0:N(ng))

pointer = OCEAN(ng)%wvel

units = meter second^-1

sign = positive downwards (downwelling), negative upwards (upwelling

grid = w-points

option = SOLVE3D

routine = wvelocity.F

Z

zeta

Free-surface, $\,\zeta (\xi ,\eta ,t)$.

dimension = zeta(LBi:UBi,LBj:UBj,3)

pointer = OCEAN(ng)%zeta

tangent = tl_zeta

adjoint = ad_zeta

units = meter

grid = ρ-points

routine = step2d.F

z_r

Actual depths of variables at ρ-points, $\,Z_{r}(\xi ,\eta ,s)$.

dimension = z_r(LBi:UBi,LBj:UBj,N(ng))

pointer = GRID(ng)%z_r

units = meter

sign = negative downwards

grid = ρ-points

option = SOLVE3D

routine = set_depths.F

z_w

Actual depths of variables at w-points, $\,Z_{w}(\xi ,\eta ,s)$.

dimension = z_w(LBi:UBi,LBj:UBj,0:N(ng))

pointer = GRID(ng)%z_w

units = meter

sign = negative downwards

grid = w-points

option = SOLVE3D

routine = set_depths.F