/[MITgcm]/manual/s_examples/text/model_examples.tex

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-revision 1.22 by jmc,
Fri Aug 27 18:21:43 2010 UTC
+revision 1.26 by jmc,
Fri Aug 29 17:08:21 2014 UTC
 Line 2
  % $Name$
  \section[MITgcm Example Experiments]{Example experiments}
- \label{sect:modelExamples}
+ \label{sec:modelExamples}
  \begin{rawhtml}
  <!-- CMIREDIR:modelExamples: -->
  \end{rawhtml}
 Line 13 
 The full MITgcm distribution comes with
  numerical experiments.  Some of these example experiments are tests of
  individual parts of the model code, but many are fully fledged
  numerical simulations. Full tutorials exist for a few of the examples,
- and are documented in sections \ref{sect:eg-baro} -
+ and are documented in sections \ref{sec:eg-baro} -
- \ref{sect:eg-tank}. The other examples follow the same general
+ \ref{sec:eg-tank}. The other examples follow the same general
  structure as the tutorial examples. However, they only include brief
  instructions in a text file called {\it README}.  The examples are
  located in subdirectories under the directory \texttt{verification}.
 Line 23 
 Each example is briefly described below.
  \subsection{Full list of model examples}
  \begin{enumerate}
  \item \texttt{tutorial\_advection\_in\_gyre} - Test of various
    advection schemes in a single-layer double-gyre experiment.
    This experiment is described in detail in section
-   \ref{sect:eg-adv-gyre}.
+   \ref{sec:eg-adv-gyre}.
  \item \texttt{tutorial\_baroclinic\_gyre} - Four layer, ocean double
    gyre. This experiment is described in detail in section
-   \ref{sect:eg-fourlayer}.
+   \ref{sec:eg-fourlayer}.
  \item \texttt{tutorial\_barotropic\_gyre} - Single layer, ocean double
    gyre (barotropic with free-surface).
-   This experiment is described in detail in section \ref{sect:eg-baro}.
+   This experiment is described in detail in section \ref{sec:eg-baro}.
  \item \texttt{tutorial\_cfc\_offline} - Offline form of the MITgcm to
    study advection of a passive tracer and CFCs.
-   This experiment is described in detail in section \ref{sect:eg-offline-cfc}.
+   This experiment is described in detail in section \ref{sec:eg-offline-cfc}.
- \item \texttt{tutorial\_deep\_convection} - Inhomogenously forced
+ \item \texttt{tutorial\_deep\_convection} - Non-uniformly forced
    ocean convection in a doubly periodic box. This experiment is
-   described in detail in section \ref{sect:eg-bconv}.
+   described in detail in section \ref{sec:eg-bconv}.
+ \item \texttt{tutorial\_dic\_adoffline} - Offline form of MITgcm
+   dynamics coupled to the dissolved inorganic carbon biogeochemistry model;
+   adjoint set-up.
  \item \texttt{tutorial\_global\_oce\_biogeo} - Ocean model coupled to
    the dissolved inorganic carbon biogeochemistry model. This
    experiment is described in detail in section
-   \ref{sect:eg-biogeochem_tutorial}.
+   \ref{sec:eg-biogeochem_tutorial}.
  \item \texttt{tutorial\_global\_oce\_in\_p} - Global ocean simulation in
    pressure coordinate (non-Boussinesq ocean model). Described in
-   detail in section \ref{sect:eg-globalpressure}.
+   detail in section \ref{sec:eg-globalpressure}.
  \item \texttt{tutorial\_global\_oce\_latlon} - 4x4 degree global ocean
    simulation with steady climatological forcing. This experiment is
-   described in detail in section \ref{sect:eg-global}.
+   described in detail in section \ref{sec:eg-global}.
  \item \texttt{tutorial\_global\_oce\_optim} - Global ocean state
    estimation at $4^\circ$ resolution.  This experiment is described in
-   detail in section \ref{sect:eg-global_state_estimate}.
+   detail in section \ref{sec:eg-global_state_estimate}.
  \item \texttt{tutorial\_held\_suarez\_cs} - 3D atmosphere dynamics
    using Held and Suarez (1994) forcing on cubed sphere grid.  This
-   experiment is described in detail in section \ref{sect:eg-hs}.
+   experiment is described in detail in section \ref{sec:eg-hs}.
  \item \texttt{tutorial\_offline} - Offline form of the MITgcm to study
    advection of a passive tracer.  This experiment is described in
-   detail in section \ref{sect:eg-offline}.
+   detail in section \ref{sec:eg-offline}.
  \item \texttt{tutorial\_plume\_on\_slope} - Gravity Plume on a
    continental slope.  This experiment is described in detail in
-   section \ref{sect:eg-gravityplume}.
+   section \ref{sec:eg-gravityplume}.
  \item \texttt{tutorial\_tracer\_adjsens} - Simple passive tracer
    experiment. Includes derivative calculation. This experiment is
-   described in detail in section \ref{sect:eg-simple-tracer-adjoint}.
+   described in detail in section \ref{sec:eg-simple-tracer-adjoint}.\\
+   Also contains an additional set-up using Secon Order Moment (SOM) advection
+   scheme ({\it input\_ad.som81/}).
+ \item \texttt{1D\_ocean\_ice\_column} - Oceanic column with seaice on top.
  \item \texttt{adjustment.128x64x1} - Barotropic adjustment problem on
    latitude longitude grid with 128x64 grid points ($2.8^\circ$ resolution).
  \item \texttt{adjustment.cs-32x32x1} - Barotropic adjustment problem on
    cube sphere grid with 32x32 points per face (roughly $2.8^\circ$
    resolution).\\
    Also contains a non-linear free-surface adjustment version ({\it input.nlfs/}).
- \item \texttt{advect\_cs} Two-dimensional passive advection test on
+ \item \texttt{advect\_cs} - Two-dimensional passive advection test on
-   cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$)
+   cube sphere grid (32x32 grid points per face, roughly $2.8^\circ$ resolution)
  \item \texttt{advect\_xy} - Two-dimensional (horizontal plane) passive
    advection test on Cartesian grid.\\
    Also contains an additional set-up using Adams-Bashforth 3 ({\it input.ab3\_c4/}).
  \item \texttt{advect\_xz} - Two-dimensional (vertical plane) passive
-   advection test on Cartesian grid.
+   advection test on Cartesian grid.\\
+   Also contains an additional set-up using non-linear free-surface
- \item \texttt{aim.5l\_Equatorial\_Channel}
+    with divergent barotropic flow and implicit vertical advection ({\it input.nlfs/}).
-   - 5-levels Intermediate Atmospheric physics,
+ \item \texttt{aim.5l\_Equatorial\_Channel} -
+-levels Intermediate Atmospheric physics,
 D Equatorial Channel configuration.
  \item \texttt{aim.5l\_LatLon} - 5-levels Intermediate Atmospheric physics,
    Global configuration, on latitude longitude grid with 128x64x5 grid
    points ($2.8^\circ$ resolution).
  \item \texttt{aim.5l\_cs} - 5-levels Intermediate Atmospheric physics,
    Global configuration on cube sphere grid
    (32x32 grid points per face, roughly $2.8^\circ$).\\
-   Also contains an additional set-up with an ocean mixed layer and thermodynamics
+   Also contains an additional set-up with a slab-ocean and thermodynamic
    sea-ice ({\it input.thSI/}).
  \item \texttt{bottom\_ctrl\_5x5} - Adjoint test using the bottom
-Line 116 
 Each example is briefly described below.
+Line 126 
 Each example is briefly described below.
  \item \texttt{cfc\_example} - Global ocean with online computation and
    advection of CFC11 and CFC12.
- \item \texttt{cpl\_aim+ocn} - Coupled Ocean - Atmosphere realistic
+ \item \texttt{cheapAML\_box} - Example using cheap atmospheric mixed layer
-   configuration on cubed-sphere cs32 horizontal grid,
+    (cheapAML) package.
+ \item \texttt{cpl\_aim+ocn} - Coupled Ocean - Atmosphere realistic
+   configuration on cubed-sphere cs32 horizontal grid,
    using Intermediate Atmospheric physics ({\it pkg/aim\_v23})
-   thermodynamics seaice ({\it pkg/thsice}) and land packages.
+   thermodynamic seaice ({\it pkg/thsice}) and land packages.
-   on cubed-sphere cs32 in a realistics configuration.
+   on cubed-sphere cs32 in a realistic configuration.
  \item \texttt{cpl\_atm2d+ocn} - Coupled Ocean - Atmosphere realistic
    configuration using 2-D Atmospheric Model ({\it pkg/atm2d}).
  \item \texttt{deep\_anelastic} - Convection simulation on a giant planet:
-Line 131 
 Each example is briefly described below.
+Line 144 
 Each example is briefly described below.
  \item \texttt{dome} - Idealized 3D test of a density-driven bottom current.
  \item \texttt{exp2} - Old version of the global ocean experiment (no GM,
        no partial-cells).\\
-   Also contains an additional set-up with ridid-lid ({\it input.rigidLid/}).
+   Also contains an additional set-up with rigid-lid ({\it input.rigidLid/}).
  \item \texttt{exp4} - Flow over a Gaussian bump in open-water or
-   channel with open boundaries.
+   channel with open boundaries.\\
+   Also contains an additional set-up using non-linear free-surface ({\it input.nlfs/}).
- \item \texttt{exp5} - Deep convection.
  \item \texttt{fizhi-cs-32x32x40} - Global atmospheric simulation with
    realistic topography, 40 vertical levels, a cubed sphere grid and
-Line 154 
 Each example is briefly described below.
+Line 166 
 Each example is briefly described below.
    dynamical forcing running on different vertical grids.
  \item \texttt{flt\_example} - Example of using float package.
  \item \texttt{front\_relax} - Relaxation of an ocean thermal front
-   (test for Gent/McWilliams scheme). 2D (Y-Z).\\
+   (test for Gent/McWilliams scheme). 2D (y-z).\\
-   Also contains an additional set-up with Mixed-Layer Eddy parameterization
+   Also contains additional set-ups:
-   (Ferrari \& McWilliams, 2007) ({\it input.mxl/}).
+   \begin{enumerate}
+    \item using the Boundary-Value Problem method
- \item \texttt{global1x1\_tot} - ECCO-GODAE production configuration
+           (Ferrari et al., 2010) ({\it input.bvp/}).
-  version 1, 2 \& 3
+    \item with Mixed-Layer Eddy parameterization
+           (Ferrari \& McWilliams, 2007) ({\it input.mxl/}).
- \item \texttt{global2x2\_tot} - ECCO production configuration version 0
+   \end{enumerate}
- \item \texttt{global\_ocean.90x40x15} Global ocean simulation at 4x4
-   degree resolution. Similar to tutorial\_global\_oce\_latlon, with
-   quasi-non-hydrostatics and non-hydrostatic metric terms.\\
-   Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
- \item \texttt{global\_ocean.cs32x15} - Global ocean experiment on the
+ \item \texttt{global\_ocean.90x40x15} - Global ocean simulation at 4x4
-   cubed sphere grid.\\
+   degree resolution. Similar to tutorial\_global\_oce\_latlon, but using
+   $z^*$ coordinates with quasi-non-hydrostatic and non-hydrostatic metric terms.
+   This experiment also illustrate the use of SBO package.
    Also contains additional set-ups:
    \begin{enumerate}
-    \item non-hydrostratic with biharmonic viscosity ({\it input.viscA4/})
+    \item using down-slope package ({\it pkg/down\_slope}) ({\it input.dwnslp/})
+    \item an Open-AD adjoint set-up ({\it code\_oad/, input\_oad/}).
+    \item four TAF adjoint set-ups ({\it code\_ad/}):
+    \begin{enumerate}
+      \item standard experiment ({\it input\_ad/}).
+      \item with bottom drag as a control ({\it input\_ad.bottomdrag/}).
+      \item with kappa GM as a control ({\it input\_ad.kapgm/}).
+      \item with kappa Redi as a control ({\it input\_ad.kapredi/}).
+    \end{enumerate}
+   \end{enumerate}
+ \item \texttt{global\_ocean.cs32x15} - Global ocean experiment on the
+   cubed sphere grid.\\
+   Also contains additional forward set-ups:
+   \begin{enumerate}
+    \item non-hydrostatic with biharmonic viscosity ({\it input.viscA4/})
     \item using thermodynamic sea ice and bulk force ({\it input.thsice/})
-    \item using thermodynamic ({\it pkg/thsice}) dynamics ({\it pkg/seaice}) sea-ice
+    \item using thermodynamic ({\it pkg/thsice}) dynamic ({\it pkg/seaice}) sea-ice
-          and EXF package ({\it input.icedyn/})
+          and {\it exf} package ({\it input.icedyn/})
+    \item using thermodynamic - dynamic ({\it pkg/seaice}) sea-ice
+          with {\it exf} package ({\it input.seaice/})
+   \end{enumerate}
+   and few additional adjoint set-ups ({\it code\_ad/}):
+   \begin{enumerate}
+    \item standard experiment without sea-ice ({\it input\_ad/}).
+    \item using thermodynamic - dynamic sea-ice ({\it input\_ad.seaice/})
+    \item same as above without adjoint sea-ice dynamics ({\it input\_ad.seaice\_dynmix/})
+    \item using thermodynamic sea-ice from {\it thsice} package ({\it input\_ad.thsice/})
    \end{enumerate}
  \item \texttt{global\_ocean\_ebm} - Global ocean experiment on a lat-lon
-Line 186 
 Each example is briefly described below.
+Line 219 
 Each example is briefly described below.
    Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
  \item \texttt{global\_with\_exf} - Global ocean experiment on a lat-lon
-   grid using the exf package. Similar to global\_ocean.90x40x15
+   grid using the {\it exf} package. Similar to tutorial\_global\_oce\_latlon
-   experiment.
+   experiment.\\
+   Also contains a secondary set-up with yearly {\it exf} fields ({\it input\_ad.yearly/}).
+ \item \texttt{halfpipe\_streamice} - Example using package "streamice".\\
+   Also contains adjoint set-ups using TAF ({\it code\_ad/, input\_ad/})
+    and using Open-AD ({\it code\_oad/, input\_oad/}).
  \item \texttt{hs94.128x64x5} - 3D atmosphere dynamics on lat-lon grid,
    using Held and Suarez '94 forcing.
  \item \texttt{hs94.1x64x5} - Zonal averaged atmosphere dynamics
    using Held and Suarez '94 forcing.\\
-   Also contains an adjoint set-up ({\it code\_ad/, input\_ad/}).
+   Also contains adjoint set-ups using TAF ({\it code\_ad/, input\_ad/})
+    and using Open-AD ({\it code\_oad/, input\_oad/}).
  \item \texttt{hs94.cs-32x32x5} - 3D atmosphere dynamics using Held and
-   Suarez (1994) forcing on the cubed sphere. 5 vertical levels.\\
+   Suarez (1994) forcing on the cubed sphere, similar to tutorial\_held\_suarez\_cs
+   experiment but using linear free-surface and only 5 levels.\\
    Also contains an additional set-up with Implicit Internal gravity waves
-   treatment ({\it input.impIGW/}).
+   treatment and Adams-Bashforth 3 ({\it input.impIGW/}).
  \item \texttt{ideal\_2D\_oce} - Idealized 2D global ocean simulation on
    an aqua planet.
  \item \texttt{internal\_wave} - Ocean internal wave forced by open
-   boundary conditions.
+   boundary conditions.\\
+   Also contains an additional set-up using {\it pkg/kl10} (see section
+    \ref{sec:pkg:kl10}, Klymak and Legg, 2010) ({\it input.kl10/}).
  \item \texttt{inverted\_barometer} - Simple test of ocean response to
    atmospheric pressure loading.
  \item \texttt{isomip} - ISOMIP like set-up including ice-shelf cavities
    ({\it pkg/shelfice}).\\
-   Also contains an additional set-up with ({\it input.htd/})
+   Also contains additional set-ups:
-   but only Martin knows what "htd" stands for.
+   \begin{enumerate}
+    \item with "htd" ({\it input.htd/})
+           but only Martin knows what "htd" stands for.
+    \item using package {\it icefront} ({\it input.icefront})
+   \end{enumerate}
+   and also adjoint set-ups using TAF ({\it code\_ad/, input\_ad/, input\_ad.htd/})
+   or using Open-AD ({\it code\_oad/, input\_oad/}).
  \item \texttt{lab\_sea} - Regional Labrador Sea simulation on a lat-lon
    grid using the sea ice package.\\
    Also contains additional set-ups:
    \begin{enumerate}
-    \item using the LSR solver (instead of EVP dynamics) ({\it input.lsr/})
+    \item using the simple "free-drift" assumption for seaice ({\it input.fd/})
-    \item using Hibler and Bryan (1987) sea-ice ocean stress ({\it input.hb87/})
+    \item using EVP dynamics (instead of LSR solver) and Hibler \& Bryan (1987)
+          sea-ice ocean stress ({\it input.hb87/})
     \item using package {\it salt\_plume} ({\it input.salt\_plume/})
    \end{enumerate}
    and also 3 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.noseaicedyn/,
-   input\_ad.noseaice/}).
+    input\_ad.noseaice/}).
  \item \texttt{matrix\_example} - Test of experimental method to
-   accelerated convergence towards equillibrium.
+   accelerated convergence towards equilibrium.
  \item \texttt{MLAdjust} - Simple tests for different viscosity formulations.\\
-   Also contains additional set-ups:
+   Also contains additional set-ups (see: {\it verification/MLAdjust/README}):
    \begin{enumerate}
-    \item ({\it input.0.leith/})
+    \item ({\it input.A4FlxF/})
-    \item ({\it input.0.leithD/})
+    \item ({\it input.AhFlxF/})
-    \item ({\it input.0.smag/})
+    \item ({\it input.AhVrDv/})
-    \item ({\it input.1.leith/})
+    \item ({\it input.AhStTn/})
    \end{enumerate}
  \item \texttt{natl\_box} - Eastern subtropical North Atlantic with KPP
    scheme; 1 month integration
- \item \texttt{natl\_box\_adjoint} - Eastern subtropical North Atlantic with KPP
+ \item \texttt{obcs\_ctrl} - Adjoint test using Open-Boundary conditions
-   scheme; adjoint set-up.
+   as control parameters.
- \item \texttt{offline\_exf\_seaice} - oceanic surface forcing computed
+ \item \texttt{offline\_exf\_seaice} - Seaice on top of oceanic surface layer
-   by bulk-formulae ({\it pkg/exf}) and inposed SST (offline ocean).\\
+   in an idealized channel. Forcing is computed by bulk-formulae ({\it pkg/exf})
+   with temperature relaxation to prescribed SST (offline ocean).\\
    Also contains additional set-ups:
    \begin{enumerate}
-    \item with sea-ice ({\it pkg/seaice}) thermodynamics ({\it input.seaicetd/})
+    \item sea-ice dynamics-only using JFNK solver
-    \item an adjoint test ({\it code\_ad/, input\_ad/}).
+          and {\it pkg/thsice} advection ({\it input.dyn\_jfnk/})
+    \item sea-ice dynamics-only using LSR solver
+          and {\it pkg/seaice} advection ({\it input.dyn\_lsr/})
+    \item sea-ice thermodynamics-only using {\it pkg/seaice} ({\it input.thermo/})
+    \item sea-ice thermodynamics-only using {\it pkg/thsice} ({\it input.thsice/})
    \end{enumerate}
+   and also 2 adjoint set-ups ({\it code\_ad/, input\_ad/, input\_ad.thsice/}).
- \item \texttt{OpenAD} simple Adjoint experiement (used also to test
-   open-AD compiler)
- \item \texttt{rotating\_tank} Rotating tank simulation in cylindrical
+ \item \texttt{OpenAD} - Simple Adjoint experiment (used also to test
+   Open-AD compiler)
+ \item \texttt{rotating\_tank} - Rotating tank simulation in cylindrical
    coordinates.  This experiment is described in detail in section
-   \ref{sect:eg-tank}.
+   \ref{sec:eg-tank}.
+ \item \texttt{seaice\_itd} - Seaice example using Ice Thickness Distribution (ITD).\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item ({\it input.thermo/})
+    \item ({\it input.lipscomb07/})
+   \end{enumerate}
- \item \texttt{seaice\_obcs} similar to "lab\_sea" ({\it input.salt\_plume/})
+ \item \texttt{seaice\_obcs} - Similar to "lab\_sea" ({\it input.salt\_plume/})
    experiment with only a fraction of the domain and open-boundary conditions
-   derived from "lab\_sea" experiment.
+   derived from "lab\_sea" experiment.\\
+   Also contains additional set-ups:
+   \begin{enumerate}
+    \item ({\it input.seaiceSponge/})
+    \item ({\it input.tides/})
+   \end{enumerate}
+ \item \texttt{short\_surf\_wave} - Short surface wave adjusment
+    (non-hydrostatic) in homogeneous 2-D vertical section (x-z).
- \item \texttt{solid-body.cs-32x32x1} Solid body rotation test for cube
+ \item \texttt{so\_box\_biogeo} - Open-boundary Southern ocean box around
+  Drake passage, using same model parameters and forcing as experiment
+   "tutorial\_global\_oce\_biogeo" from which initial conditions
+  and OB conditions have been extracted.
+ \item \texttt{solid-body.cs-32x32x1} - Solid body rotation test for cube
    sphere grid.
- \item \texttt{tidal\_basin\_2d} 2-D vertical section (X-Z) with tidal forcing
+ \item \texttt{tidal\_basin\_2d} - 2-D vertical section (x-z) with tidal forcing
+  (untested)
- \item \texttt{vermix} Simple test in a small domain (3 columns) for
+ \item \texttt{vermix} - Simple test in a small domain (3 columns) for
    ocean vertical mixing schemes. The standard set-up ({\it input/}) uses
-   KPP scheme.\\
+   KPP scheme \cite[]{lar-eta:94}.\\
    Also contains additional set-ups:
    \begin{enumerate}
-    \item with Gaspar et al. (1990) ({\it pkg/ggl90}) scheme ({\it input.ggl90/})
+    \item with Double Diffusion scheme from KPP ({\it input.dd/})
-    \item with Mellor \& Yamada (1982) level 2. ({\it pkg/my82}) scheme ({\it input.my82/})
+    \item with \cite{gas-eta:90} ({\it pkg/ggl90}) scheme ({\it input.ggl90/})
-    \item with Paluszkiewicz \& Romea (1997) ({\it pkg/opps}) scheme ({\it input.opps/})
+    \item with \cite{Mellor:Yamada1982} level 2. ({\it pkg/my82}) scheme ({\it input.my82/})
-    \item with Pacanowski \& Philander (1981) ({\it pkg/pp81}) scheme ({\it input.pp81/})
+    \item with \cite{pal-rom:97} ({\it pkg/opps}) scheme ({\it input.opps/})
+    \item with \cite{Pacanowski:Philander1981} ({\it pkg/pp81}) scheme ({\it input.pp81/})
    \end{enumerate}
  \end{enumerate}
-Line 302 
 Each example directory has the following
+Line 379 
 Each example directory has the following
    \item \texttt{code/CPP\_EEOPTIONS.h}: declares CPP keys relative to
      the ``execution environment'' part of the code. The default
      version is located in \texttt{eesupp/inc}.
    \item \texttt{code/CPP\_OPTIONS.h}: declares CPP keys relative to
      the ``numerical model'' part of the code. The default version is
      located in \texttt{model/inc}.
    \item \texttt{code/SIZE.h}: declares size of underlying
      computational grid.  The default version is located in
      \texttt{model/inc}.
    \end{itemize}
    In addition, other include files and subroutines might be present in
    \texttt{code} depending on the particular experiment. See Section 2
    for more details.
  \item \texttt{input}: contains the input data files required to run
    the example. At a minimum, the \texttt{input} directory contains the
    following files:
-Line 323 
 Each example directory has the following
+Line 400 
 Each example directory has the following
    \begin{itemize}
    \item \texttt{input/data}: this file, written as a namelist,
      specifies the main parameters for the experiment.
    \item \texttt{input/data.pkg}: contains parameters relative to the
      packages used in the experiment.
    \item \texttt{input/eedata}: this file contains ``execution
      environment'' data. At present, this consists of a specification
-     of the number of threads to use in $X$ and $Y$ under multithreaded
+     of the number of threads to use in $X$ and $Y$ under multi-threaded
      execution.
    \end{itemize}
    In addition, you will also find in this directory the forcing and
    topography files as well as the files describing the initial state
    of the experiment.  This varies from experiment to experiment. See
-Line 343 
 Each example directory has the following
+Line 420 
 Each example directory has the following
    useful for comparison with your own output when you run the
    experiment.
- \item \texttt{build}: this directory is where the model is compiled
+ \item \texttt{build}: this directory is initially empty and is used
-   and loaded, and where the executable resides.
+   to compile and load the model, and to generate the executable.
+ \item \texttt{run}: this directory is initially empty and is used
+   to run the executable.
  \end{itemize}

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+Added in v.1.26

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