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4f2617d475 Jeff* .. _nonlinear-freesurface:
                 
                 Non-linear free-surface
                 -----------------------
                 
                 Options have been added to the model that concern the free surface formulation.
                 
                 Pressure/geo-potential and free surface
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 
0bad585a21 Navi* For the atmosphere, since :math:`\phi = \phi_{\rm topo} - \int^p_{p_s} \alpha dp`, subtracting the
4f2617d475 Jeff* reference state defined in section :numref:`hpe-p-geo-potential-split` :
                 
                 
                 .. math::
0bad585a21 Navi*      \phi_o = \phi_{\rm topo} - \int^p_{p_o} \alpha_o dp
                      \hspace{5mm}\mathrm{with}\hspace{3mm} \phi_o(p_o)=\phi_{\rm topo}
4f2617d475 Jeff* 
                 we get:
                 
                 .. math:: \phi' = \phi - \phi_o = \int^{p_s}_p \alpha dp - \int^{p_o}_p \alpha_o dp
                 
                 For the ocean, the reference state is simpler since :math:`\rho_c`
                 does not dependent on :math:`z` (:math:`b_o=g`) and the surface
                 reference position is uniformly :math:`z=0` (:math:`R_o=0`), and the
                 same subtraction leads to a similar relation. For both fluids, using
                 the isomorphic notations, we can write:
                 
0bad585a21 Navi* .. math:: \phi' = \int^{r_{\rm surf}}_r b~ dr - \int^{R_o}_r b_o dr
4f2617d475 Jeff* 
                 and re-write as:
                 
                 .. math::
0bad585a21 Navi*      \phi' = \int^{r_{\rm surf}}_{R_o} b~ dr + \int^{R_o}_r (b - b_o) dr
4f2617d475 Jeff*      :label: split-phi-Ro
                 
                 or:
                 
                 .. math::
0bad585a21 Navi*     \phi' = \int^{r_{surf}}_{R_o} b_o dr + \int^{r_{\rm surf}}_r (b - b_o) dr
4f2617d475 Jeff*     :label: split-phi-bo
                 
                 In section :numref:`finding_the_pressure_field`, following
                 eq. :eq:`split-phi-Ro`, the pressure/geo-potential :math:`\phi'` has been
                 separated into surface (:math:`\phi_s`), and hydrostatic anomaly
0bad585a21 Navi* (:math:`\phi'_{\rm hyd}`). In this section, the split between :math:`\phi_s`
                 and :math:`\phi'_{\rm hyd}` is made according to equation :eq:`split-phi-bo`.
4f2617d475 Jeff* This slightly different definition reflects the actual implementation in
                 the code and is valid for both linear and non-linear free-surface
                 formulation, in both r-coordinate and r\*-coordinate.
                 
                 Because the linear free-surface approximation ignores the tracer
                 content of the fluid parcel between :math:`R_o` and
0bad585a21 Navi* :math:`r_{\rm surf}=R_o+\eta`, for consistency reasons, this part is also
                 neglected in :math:`\phi'_{\rm hyd}` :
4f2617d475 Jeff* 
0bad585a21 Navi* .. math:: \phi'_{\rm hyd} = \int^{r_{\rm surf}}_r (b - b_o) dr \simeq \int^{R_o}_r (b - b_o) dr
4f2617d475 Jeff* 
                 Note that in this case, the two definitions of :math:`\phi_s` and
0bad585a21 Navi* :math:`\phi'_{\rm hyd}` from equations :eq:`split-phi-Ro` and
4f2617d475 Jeff* :eq:`split-phi-bo` converge toward the same (approximated) expressions:
0bad585a21 Navi* :math:`\phi_s = \int^{r_{\rm surf}}_{R_o} b_o dr` and
                 :math:`\phi'_{\rm hyd}=\int^{R_o}_r b' dr`.
dcaaa42497 Jeff* On the contrary, the unapproximated formulation
                 (see :numref:`free_surf_effect_col_thick`) retains the full expression:
0bad585a21 Navi* :math:`\phi'_{\rm hyd} = \int^{r_{\rm surf}}_r (b - b_o) dr` . This is
4f2617d475 Jeff* obtained by selecting :varlink:`nonlinFreeSurf` =4 in parameter file ``data``.
                 Regarding the surface potential:
                 
                 .. math::
                     \phi_s = \int_{R_o}^{R_o+\eta} b_o dr = b_s \eta
                      \hspace{5mm}\mathrm{with}\hspace{5mm}
                      b_s = \frac{1}{\eta} \int_{R_o}^{R_o+\eta} b_o dr
                 
                 :math:`b_s \simeq b_o(R_o)` is an excellent approximation (better
                 than the usual numerical truncation, since generally :math:`|\eta|` is
                 smaller than the vertical grid increment).
                 
                 For the ocean, :math:`\phi_s = g \eta` and :math:`b_s = g` is uniform.
                 For the atmosphere, however, because of topographic effects, the
                 reference surface pressure :math:`R_o=p_o` has large spatial variations
                 that are responsible for significant :math:`b_s` variations (from 0.8 to
0bad585a21 Navi* 1.2 :math:`\rm [m^3/kg]`). For this reason, when :varlink:`uniformLin_PhiSurf`
4f2617d475 Jeff* =.FALSE. (parameter file ``data``, namelist ``PARAM01``) a non-uniform
                 linear coefficient :math:`b_s` is used and computed (:filelink:`INI_LINEAR_PHISURF <model/src/ini_linear_phisurf.F>`)
                 according to the reference surface pressure :math:`p_o`:
0bad585a21 Navi* :math:`b_s = b_o(R_o) = c_p \kappa (p_o / P^o_{\rm SLP})^{(\kappa - 1)} \theta_{ref}(p_o)`,
                 with :math:`P^o_{\rm SLP}` the mean sea-level pressure.
4f2617d475 Jeff* 
dcaaa42497 Jeff* .. _free_surf_effect_col_thick:
                 
4f2617d475 Jeff* Free surface effect on column total thickness (Non-linear free-surface)
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 
0bad585a21 Navi* The total thickness of the fluid column is :math:`r_{\rm surf} - R_{\rm fixed} =
                 \eta + R_o - R_{\rm fixed}`. In most applications, the free surface
4f2617d475 Jeff* displacements are small compared to the total thickness
0bad585a21 Navi* :math:`\eta \ll H_o = R_o - R_{\rm fixed}`. In the previous sections and in
4f2617d475 Jeff* older version of the model, the linearized free-surface approximation
0bad585a21 Navi* was made, assuming :math:`r_{\rm surf} - R_{\rm fixed} \simeq H_o` when
4f2617d475 Jeff* computing horizontal transports, either in the continuity equation or in
                 tracer and momentum advection terms. This approximation is dropped when
                 using the non-linear free-surface formulation and the total thickness,
                 including the time varying part :math:`\eta`, is considered when
                 computing horizontal transports. Implications for the barotropic part
                 are presented hereafter. In section :numref:`tracer-cons-nonlinear-freesurface`
                 consequences for tracer conservation is briefly discussed (more details
                 can be found in Campin et al. (2004) :cite:`cam:04`) ; the general
                 time-stepping is presented in section :numref:`nonlin-freesurf-timestepping`
                 with some limitations regarding the vertical resolution in section
                 :numref:`nonlin-freesurf-dzsurf`.
                 
                 In the non-linear formulation, the continuous form of the model
                 equations remains unchanged, except for the 2D continuity equation
                 :eq:`discrete-time-backward-free-surface` which is now integrated from
0bad585a21 Navi* :math:`R_{\rm fixed}(x,y)` up to :math:`r_{\rm surf}=R_o+\eta` :
4f2617d475 Jeff* 
                 .. math::
0bad585a21 Navi*    \epsilon_{\rm fs} \partial_t \eta =
                    \left. \dot{r} \right|_{r=r_{\rm surf}} + \epsilon_{\rm fw} ({\mathcal{P-E}}) =
                    - {\bf \nabla}_h \cdot \int_{R_{\rm fixed}}^{R_o+\eta} \vec{\bf v} dr
94151a9b18 Jeff*    + \epsilon_{fw} ({\mathcal{P-E}})
4f2617d475 Jeff* 
                 Since :math:`\eta` has a direct effect on the horizontal velocity
0bad585a21 Navi* (through :math:`\nabla_h \Phi_{\rm surf}`), this adds a non-linear term to
4f2617d475 Jeff* the free surface equation. Several options for the time discretization
                 of this non-linear part can be considered, as detailed below.
                 
                 If the column thickness is evaluated at time step :math:`n`, and with
                 implicit treatment of the surface potential gradient, equations
                 :eq:`eq-solve2D` and :eq:`eq-solve2D_rhs` become:
                 
                 .. math::
                 
                    \begin{aligned}
0bad585a21 Navi*    \epsilon_{\rm fs} {\eta}^{n+1} -
                    {\bf \nabla}_h \cdot \Delta t^2 (\eta^{n}+R_o-R_{\rm fixed})
4f2617d475 Jeff*    {\bf \nabla}_h b_s {\eta}^{n+1}
                    = {\eta}^*\end{aligned}
                 
                 where
                 
                 .. math::
                 
                    \begin{aligned}
0bad585a21 Navi*    {\eta}^* = \epsilon_{\rm fs} \: {\eta}^{n} -
                    \Delta t {\bf \nabla}_h \cdot \int_{R_{\rm fixed}}^{R_o+\eta^n} \vec{\bf v}^* dr
                    \: + \: \epsilon_{\rm fw} \Delta_t ({\mathcal{P-E}})^{n}\end{aligned}
4f2617d475 Jeff* 
                 This method requires us to update the solver matrix at each time step.
                 
                 Alternatively, the non-linear contribution can be evaluated fully
                 explicitly:
                 
                 .. math::
                 
                    \begin{aligned}
0bad585a21 Navi*    \epsilon_{\rm fs} {\eta}^{n+1} -
                    {\bf \nabla}_h \cdot \Delta t^2 (R_o-R_{\rm fixed})
4f2617d475 Jeff*    {\bf \nabla}_h b_s {\eta}^{n+1}
                    = {\eta}^*
                    +{\bf \nabla}_h \cdot \Delta t^2 (\eta^{n})
                    {\bf \nabla}_h b_s {\eta}^{n}\end{aligned}
                 
                 This formulation allows one to keep the initial solver matrix unchanged
                 though throughout the integration, since the non-linear free surface
                 only affects the RHS.
                 
                
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 Finally, another option is a “linearized” formulation where the total
                 column thickness appears only in the integral term of the RHS
                 :eq:`eq-solve2D_rhs` but not directly in the equation :eq:`eq-solve2D`.
                 
                 Those different options (see :numref:`nonlinFreeSurf-flags`) have
                 been tested and show little differences. However, we recommend the use
                 of the most precise method (:varlink:`nonlinFreeSurf` =4) since the computation cost
                 involved in the solver matrix update is negligible.
                 
                 .. table:: Non-linear free-surface flags
                    :name: nonlinFreeSurf-flags
                 
0bad585a21 Navi*    +---------------------------+---------+-----------------------------------------------------------------------------------------+
                    | Parameter                 | Value   | Description                                                                             |
                    +===========================+=========+=========================================================================================+
                    | :varlink:`nonlinFreeSurf` | -1      | linear free-surface, restart from a pickup file                                         |
                    |                           |         | produced with #undef :varlink:`EXACT_CONSERV` code                                      |
                    +---------------------------+---------+-----------------------------------------------------------------------------------------+
                    |                           | 0       | linear free-surface (= default)                                                         |
                    +---------------------------+---------+-----------------------------------------------------------------------------------------+
                    |                           | 4       | full non-linear free-surface                                                            |
                    +---------------------------+---------+-----------------------------------------------------------------------------------------+
                    |                           | 3       | same as 4 but neglecting :math:`\int_{R_o}^{R_o+\eta} b' dr` in :math:`\Phi'_{\rm hyd}` |
                    +---------------------------+---------+-----------------------------------------------------------------------------------------+
                    |                           | 2       | same as 3 but do not update cg2d solver matrix                                          |
                    +---------------------------+---------+-----------------------------------------------------------------------------------------+
                    |                           | 1       | same as 2 but treat momentum as in linear free-surface                                  |
                    +---------------------------+---------+-----------------------------------------------------------------------------------------+
                    | :varlink:`select_rStar`   | 0       | do not use :math:`r^*` vertical coordinate (= default)                                  |
                    +---------------------------+---------+-----------------------------------------------------------------------------------------+
                    |                           | 2       | use :math:`r^*` vertical coordinate                                                     |
                    +---------------------------+---------+-----------------------------------------------------------------------------------------+
                    |                           | 1       | same as 2 but without the contribution of the                                           |
                    |                           |         | slope of the coordinate in :math:`\nabla \Phi`                                          |
                    +---------------------------+---------+-----------------------------------------------------------------------------------------+
4f2617d475 Jeff* 
                 
                 .. _tracer-cons-nonlinear-freesurface:
                 
                 Tracer conservation with non-linear free-surface
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 
                 To ensure global tracer conservation (i.e., the total amount) as well as
                 local conservation, the change in the surface level thickness must be
                 consistent with the way the continuity equation is integrated, both in
                 the barotropic part (to find :math:`\eta`) and baroclinic part (to find
                 :math:`w = \dot{r}`).
                 
                 To illustrate this, consider the shallow water model, with a source of
94151a9b18 Jeff* fresh water (:math:`\mathcal{P}`):
4f2617d475 Jeff* 
0bad585a21 Navi* .. math:: \partial_t h +  \nabla  \cdot h \vec{\bf v} = \mathcal{P}
4f2617d475 Jeff* 
                 where :math:`h` is the total thickness of the water column. To conserve
                 the tracer :math:`\theta` we have to discretize:
                 
                 .. math::
0bad585a21 Navi*    \partial_t (h \theta) +  \nabla  \cdot ( h \theta \vec{\bf v})
                      = \mathcal{P} \theta_{\rm rain}
4f2617d475 Jeff* 
                 Using the implicit (non-linear) free surface described above
                 (:numref:`press_meth_linear`) we have:
                 
                 .. math::
                    \begin{aligned}
0bad585a21 Navi*    h^{n+1} = h^{n} - \Delta t  \nabla  \cdot (h^n \, \vec{\bf v}^{n+1} ) + \Delta t \mathcal{P} \\\end{aligned}
4f2617d475 Jeff* 
                
** Warning **
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 The discretized form of the tracer equation must adopt the same “form”
                 in the computation of tracer fluxes, that is, the same value of
                 :math:`h`, as used in the continuity equation:
                 
                 .. math::
                    \begin{aligned}
                    h^{n+1} \, \theta^{n+1} = h^n \, \theta^n
0bad585a21 Navi*            - \Delta t  \nabla  \cdot (h^n \, \theta^n \, \vec{\bf v}^{n+1})
                            + \Delta t \mathcal{P} \theta_{\rm rain}\end{aligned}
4f2617d475 Jeff* 
                 The use of a 3 time-levels time-stepping scheme such as the
                 Adams-Bashforth make the conservation sightly tricky. The current
                 implementation with the Adams-Bashforth time-stepping provides an exact
                 local conservation and prevents any drift in the global tracer content
                 (Campin et al. (2004) :cite:`cam:04`). Compared to the linear free-surface
                 method, an additional step is required: the variation of the water
                 column thickness (from :math:`h^n` to :math:`h^{n+1}`) is not
                 incorporated directly into the tracer equation. Instead, the model uses
                 the :math:`G_\theta` terms (first step) as in the linear free surface
                
** Warning **
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 formulation (with the “*surface correction*” turned “on”, see tracer
                 section):
                 
                 .. math::
0bad585a21 Navi*    G_\theta^n = \left(-  \nabla  \cdot (h^n \, \theta^n \, \vec{\bf v}^{n+1})
                             - \dot{r}_{\rm surf}^{n+1} \theta^n \right) / h^n
4f2617d475 Jeff* 
                 Then, in a second step, the thickness variation (expansion/reduction)
                 is taken into account:
                 
                 .. math::
                    \theta^{n+1} = \theta^n + \Delta t \frac{h^n}{h^{n+1}}
94151a9b18 Jeff*       \left( G_\theta^{(n+1/2)} + \mathcal{P} (\theta_{\mathrm{rain}} - \theta^n )/h^n \right)
4f2617d475 Jeff* 
                 Note that with a simple forward time step (no Adams-Bashforth), these
                 two formulations are equivalent, since
0bad585a21 Navi* :math:`(h^{n+1} - h^{n})/ \Delta t = \mathcal{P} -  \nabla  \cdot (h^n \, \vec{\bf v}^{n+1} ) = P + \dot{r}_{\rm surf}^{n+1}`
4f2617d475 Jeff* 
                 .. _nonlin-freesurf-timestepping:
                 
                 Time stepping implementation of the non-linear free-surface
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 
                 The grid cell thickness was hold constant with the linear free-surface;
                 with the non-linear free-surface, it is now varying in time, at least at
                 the surface level. This implies some modifications of the general
                 algorithm described earlier in sections :numref:`adams-bashforth-sync` and
                 :numref:`adams-bashforth-staggered`.
                 
                 A simplified version of the staggered in time, non-linear free-surface
                 algorithm is detailed hereafter, and can be compared to the equivalent
                 linear free-surface case (eq. :eq:`Gv-n-staggered` to
                 :eq:`t-n+1-staggered`) and can also be easily transposed to the
                 synchronous time-stepping case. Among the simplifications, salinity
                 equation, implicit operator and detailed elliptic equation are
                 omitted. Surface forcing is explicitly written as fluxes of
                 temperature, fresh water and momentum,
94151a9b18 Jeff* :math:`\mathcal{Q}^{n+1/2}, \mathcal{P}^{n+1/2}, \mathcal{F}_{\bf v}^n` respectively. :math:`h^n`
4f2617d475 Jeff* and :math:`dh^n` are the column and grid box thickness in
                 r-coordinate.
                 
                   .. math::
0bad585a21 Navi*      \phi^{n}_{\rm hyd} = \int b(\theta^{n},S^{n},r) dr
4f2617d475 Jeff*      :label: phi-hyd-nlfs
                 
                   .. math::
                      \vec{\bf G}_{\vec{\bf v}}^{n-1/2}\hspace{-2mm} =
                      \vec{\bf G}_{\vec{\bf v}} (dh^{n-1},\vec{\bf v}^{n-1/2})
                      \hspace{+2mm};\hspace{+2mm}
                      \vec{\bf G}_{\vec{\bf v}}^{(n)} =
                         \frac{3}{2} \vec{\bf G}_{\vec{\bf v}}^{n-1/2}
                      -  \frac{1}{2} \vec{\bf G}_{\vec{\bf v}}^{n-3/2}
                      :label: Gv-n-nlfs
                 
                   .. math::
                      \vec{\bf v}^{*} = \vec{\bf v}^{n-1/2} + \Delta t \frac{dh^{n-1}}{dh^{n}} \left(
                      \vec{\bf G}_{\vec{\bf v}}^{(n)} + F_{\vec{\bf v}}^{n}/dh^{n-1} \right)
0bad585a21 Navi*      - \Delta t \nabla \phi_{\rm hyd}^{n}
4f2617d475 Jeff*      :label: vstar-nlfs
                 
                   .. math::
0bad585a21 Navi*      \longrightarrow \rm update \phantom{x} \rm model \phantom{x} \rm geometry : {\bf hFac}(dh^n)
4f2617d475 Jeff* 
                   .. math::
                      \begin{aligned}
                      \eta^{n+1/2} \hspace{-1mm} & =
                      \eta^{n-1/2} + \Delta t P^{n+1/2} - \Delta t
0bad585a21 Navi*       \nabla  \cdot \int \vec{\bf v}^{n+1/2} dh^{n} \\
4f2617d475 Jeff*      & = \eta^{n-1/2} + \Delta t P^{n+1/2} - \Delta t
0bad585a21 Navi*       \nabla  \cdot \int \!\!\! \left( \vec{\bf v}^* - g \Delta t \nabla \eta^{n+1/2} \right) dh^{n}\end{aligned}
4f2617d475 Jeff*      :label: nstar-nlfs
                 
                   .. math::
                      \vec{\bf v}^{n+1/2}\hspace{-2mm} =
                      \vec{\bf v}^{*} - g \Delta t \nabla \eta^{n+1/2}
                      :label: v-n+1-nlfs
                 
                   .. math::
                      h^{n+1} = h^{n} + \Delta t P^{n+1/2} - \Delta t
0bad585a21 Navi*         \nabla  \cdot \int \vec{\bf v}^{n+1/2} dh^{n}
4f2617d475 Jeff*      :label: h-n+1-nlfs
                 
                   .. math::
                      G_{\theta}^{n} = G_{\theta} ( dh^{n}, u^{n+1/2}, \theta^{n} )
                      \hspace{+2mm};\hspace{+2mm}
                      G_{\theta}^{(n+1/2)} = \frac{3}{2} G_{\theta}^{n} - \frac{1}{2} G_{\theta}^{n-1}
                      :label: Gt-n-nlfs
                 
                   .. math::
                      \theta^{n+1} =\theta^{n} + \Delta t \frac{dh^n}{dh^{n+1}} \left(
                      G_{\theta}^{(n+1/2)}
94151a9b18 Jeff*      +( P^{n+1/2} (\theta_{\mathrm{rain}}-\theta^n) + \mathcal{Q}^{n+1/2})/dh^n \right)
4f2617d475 Jeff*      :label: t-n+1-nlfs
                 
                 Two steps have been added to linear free-surface algorithm (eq.
                 :eq:`Gv-n-staggered` to :eq:`t-n+1-staggered`): Firstly, the model
                
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 “geometry” (here the **hFacC,W,S**) is updated just before entering
                 :filelink:`SOLVE_FOR_PRESSURE <model/src/solve_for_pressure.F>`,
                 using the current :math:`dh^{n}` field.
                 Secondly, the vertically integrated continuity equation
                 :eq:`h-n+1-nlfs` has been added (:varlink:`exactConserv` =.TRUE., in
                 parameter file ``data``, namelist ``PARM01``) just before computing the
                 vertical velocity, in subroutine :filelink:`INTEGR_CONTINUITY <model/src/integr_continuity.F>`. Although this
                 equation might appear redundant with :eq:`nstar-nlfs`, the
                 integrated column thickness :math:`h^{n+1}` will be different from
                 :math:`\eta^{n+1/2} + H`  in the following cases:
                 
                 -  when Crank-Nicolson time-stepping is used (see :numref:`crank-nicolson_baro`).
                 
                 -  when filters are applied to the flow field, after :eq:`v-n+1-nlfs`,
                    and alter the divergence of the flow.
                 
                 -  when the solver does not iterate until convergence; for example,
                    because a too large residual target was set (:varlink:`cg2dTargetResidual`,
                    parameter file ``data``, namelist ``PARM02``).
                 
                 In this staggered time-stepping algorithm, the momentum tendencies are
                 computed using :math:`dh^{n-1}` geometry factors :eq:`Gv-n-nlfs`
                 and then rescaled in subroutine :filelink:`TIMESTEP <model/src/timestep.F>`, :eq:`vstar-nlfs`,
                 similarly to tracer tendencies (see :numref:`tracer-cons-nonlinear-freesurface`).
                 The tracers are stepped forward later,
                 using the recently updated flow field :math:`{\bf v}^{n+1/2}` and the
                 corresponding model geometry :math:`dh^{n}` to compute the tendencies
                 :eq:`Gt-n-nlfs`; then the tendencies are rescaled by
                 :math:`dh^n/dh^{n+1}` to derive the new tracers values
                 :math:`(\theta,S)^{n+1}` (:eq:`t-n+1-nlfs`, in subroutines :filelink:`CALC_GT <model/src/calc_gt.F>`,
                 :filelink:`CALC_GS <model/src/calc_gs.F>`).
                 
                 Note that the fresh-water input is added in a consistent way in the
                 continuity equation and in the tracer equation, taking into account the
                 fresh-water temperature :math:`\theta_{\mathrm{rain}}`.
                 
                 Regarding the restart procedure, two 2D fields :math:`h^{n-1}` and
                 :math:`(h^n-h^{n-1})/\Delta t` in addition to the standard state
                 variables and tendencies (:math:`\eta^{n-1/2}`,
                 :math:`{\bf v}^{n-1/2}`, :math:`\theta^n`, :math:`S^n`,
                 :math:`{\bf G}_{\bf v}^{n-3/2}`, :math:`G_{\theta,S}^{n-1}`) are
                
** Warning **
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 stored in a “*pickup*” file. The model restarts reading this
                 pickup file, then updates the model geometry according to
                 :math:`h^{n-1}`, and compute :math:`h^n` and the vertical velocity
                 before starting the main calling sequence (eq. :eq:`phi-hyd-nlfs` to
                 :eq:`t-n+1-nlfs`, :filelink:`FORWARD_STEP <model/src/forward_step.F>`).
                 
                 .. admonition:: S/R  :filelink:`INTEGR_CONTINUITY <model/src/integr_continuity.F>`
                   :class: note
                 
                     | :math:`h^{n+1} - H_o` : :varlink:`etaH` ( :filelink:`DYNVARS.h <model/inc/DYNVARS.h>` )
                     | :math:`h^n - H_o` : :varlink:`etaHnm1` ( :filelink:`SURFACE.h <model/inc/SURFACE.h>` )
                     | :math:`(h^{n+1} - h^n ) / \Delta t` : :varlink:`dEtaHdt` ( :filelink:`SURFACE.h <model/inc/SURFACE.h>` )
                 
                 
                 .. _nonlin-freesurf-dzsurf:
                 
                 Non-linear free-surface and vertical resolution
                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                 
                 When the amplitude of the free-surface variations becomes as large as
                 the vertical resolution near the surface, the surface layer thickness
                 can decrease to nearly zero or can even vanish completely. This later
                 possibility has not been implemented, and a minimum relative thickness
                 is imposed (:varlink:`hFacInf`, parameter file ``data``, namelist ``PARM01``) to
                 prevent numerical instabilities caused by very thin surface level.
                 
                 A better alternative to the vanishing level problem relies on a different vertical coordinate
                 :math:`r^*` : The time variation of the total column thickness becomes
                 part of the :math:`r^*` coordinate motion, as in a :math:`\sigma_{z},\sigma_{p}`
                 model, but the fixed part related to topography is treated as in a
                 height or pressure coordinate model. A complete description is given in
                 Adcroft and Campin (2004) :cite:`adcroft:04a`.
                 
                 The time-stepping implementation of the :math:`r^*` coordinate is
                 identical to the non-linear free-surface in :math:`r` coordinate, and
                 differences appear only in the spacial discretization.
                 

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