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Next: 3.15 Surface Driven Convection Up: 3.14 Held-Suarez Atmosphere MITgcm Previous: 3.14.3 Set-up description   Contents

Subsections


3.14.4 Experiment Configuration

The model configuration for this experiment resides under the directory verification/tutorial_held_suarez_cs. The experiment files

  • input/data
  • input/data.pkg
  • input/eedata,
  • input/data.shap,
  • code/packages.conf,
  • code/CPP_OPTIONS.h,
  • code/SIZE.h,
  • code/DIAGNOSTICS_SIZE.h,
  • code/external_forcing.F,
contain the code customizations and parameter settings for these experiments. Below we describe the customizations to these files associated with this experiment.

3.14.4.1 File input/data

This file, reproduced completely below, specifies the main parameters for the experiment. The parameters that are significant for this configuration are:

  • Lines 7, 
     
 tRef=295.2, 295.5, 295.9, 296.3, 296.7, 297.1, 297.6, 298.1, 298.7, 299.3,
    $ \cdots$
    set reference values for potential temperature (in Kelvin units) at each model level. The entries are ordered like model level, from surface up to the top. Density is calculated from anomalies at each level evaluated with respect to the reference values set here.
    \fbox{ \begin{minipage}{5.0in} {\it S/R INI\_THETA}({\it ini\_theta.F}) \end{minipage}}

  • Line 10, 
     no_slip_sides=.FALSE.,
    this line selects a free-slip lateral boundary condition for the horizontal Laplacian friction operator e.g. $ \frac{\partial u}{\partial y}$ =0 along boundaries in $ y$ and $ \frac{\partial v}{\partial x}$ =0 along boundaries in $ x$ .

  • Lines 11, 
     no_slip_bottom=.FALSE.,
    this line selects a free-slip boundary condition at the top, in the vertical Laplacian friction operator e.g. $ \frac{\partial u}{\partial p}=\frac{\partial v}{\partial p}=0$

  • Line 12, 
     buoyancyRelation='ATMOSPHERIC',
    this line sets the type of fluid and the type of vertical coordinate to use, which, in this case, is air with a pressure like coordinate ($ p$ or $ p^*$ ).

  • Line 13, 
     eosType='IDEALGAS',
    Selects the Ideal gas equation of state.

  • Line 15, 
     implicitFreeSurface=.TRUE.,
    Selects the way the barotropic equation is solved, using here the implicit free-surface formulation.
    \fbox{ \begin{minipage}{5.0in} {\it S/R SOLVE\_FOR\_PRESSURE}~({\it solve\_for\_pressure.F}) \end{minipage}}

  • Line 16, 
     exactConserv=.TRUE.,
    Explicitly calculate again the surface pressure changes from the divergence of the vertically integrated horizontal flow, after the implicit free surface solver and filters are applied.
    \fbox{ \begin{minipage}{5.0in} {\it S/R INTEGR\_CONTINUITY}~({\it integr\_continuity.F}) \end{minipage}}

  • Line 17 and Line 18, 
     nonlinFreeSurf=4,
 select_rStar=2,
    Select the Non-Linear free surface formulation, using $ r^*$ vertical coordinate (here $ p^*$ ). Note that, except for the default ($ = 0$ ), other values of those 2 parameters are only permitted for testing/debuging purpose.
    \fbox{ \begin{minipage}{5.0in} {\it S/R CALC\_R\_STAR}~({\it calc\_r\_star.F})\\ {\it S/R UPDATE\_R\_STAR}~({\it update\_r\_star.F}) \end{minipage}}

  • Line 21 
     uniformLin_PhiSurf=.FALSE.,
    Select the linear relation between surface geopotential anomaly and surface pressure anomaly to be evaluated from $ \frac{\partial \Phi_s}{\partial p_s} = 1/\rho(\theta_{Ref})$ (see section 2.10.2.1). Note that using the default (=TRUE), the constant $ 1/\rho_0$ is used instead, and is not necessary consistent with other parts of the geopotential that relies on $ \theta_{Ref}$ .
    \fbox{ \begin{minipage}{5.0in} {\it S/R INI\_LINEAR\_PHISURF}~({\it ini\_linear\_phisurf.F}) \end{minipage}}

  • Line 23 and Line 24 
     saltStepping=.FALSE.,
 momViscosity=.FALSE.,
    Do not step forward Water vapour and do not compute viscous terms. This allow to save some computer time.

  • Line 25 
     vectorInvariantMomentum=.TRUE.,
    Select the vector-invariant form to solve the momentum equation.
    \fbox{ \begin{minipage}{5.0in} {\it S/R MOM\_VECINV}~({\it mom\_vecinv.F}) \end{minipage}}

  • Line 26 
     staggerTimeStep=.TRUE.,
    Select the staggered time-stepping (rather than syncronous time stepping).

  • Line 27 and 28 
     readBinaryPrec=64,
 writeBinaryPrec=64,
    Sets format for reading binary input datasets and writing output fields to use 64-bit representation for floating-point numbers.
    \fbox{ \begin{minipage}{5.0in} {\it S/R READ\_WRITE\_FLD}~({\it read\_write\_fld.F})\\ {\it S/R READ\_WRITE\_REC}~({\it read\_write\_rec.F}) \end{minipage}}

  • Line 33, 
     cg2dMaxIters=200,
    Sets maximum number of iterations the two-dimensional, conjugate gradient solver will use, irrespective of convergence criteria being met.
    \fbox{ \begin{minipage}{5.0in} {\it S/R CG2D}~({\it cg2d.F}) \end{minipage}}

  • Line 35, 
     cg2dTargetResWunit=1.E-17,
    Sets the tolerance (in units of $ \omega$ ) which the two-dimensional, conjugate gradient solver will use to test for convergence in equation 2.20 to $ 1 \times 10^{-17} Pa/s$ . Solver will iterate until tolerance falls below this value or until the maximum number of solver iterations is reached.
    \fbox{ \begin{minipage}{5.0in} {\it S/R CG2D}~({\it cg2d.F}) \end{minipage}}

  • Line 40, 
     deltaT=450.,
    Sets the timestep $ \Delta t$ used in the model to $ 450~{\rm s}$ ( $ = 1/8 {\rm h}$ ).
    \fbox{ \begin{minipage}{5.0in} {\it S/R TIMESTEP}({\it timestep.F})\\ {\it S/R TIMESTEP\_TRACER}({\it timestep\_tracer.F}) \end{minipage}}

  • Line 42, 
     startTime=124416000.,
    Sets the starting time, in seconds, for the model time counter. A non-zero starting time requires to read the initial state from a pickup file. By default the pickup file is named according to the integer number (nIter0) of time steps in the startTime value ( $ nIter0 = startTime / deltaT $ ).

  • Line 44, 
    #nTimeSteps=69120,
    A commented out setting for the length of the simulation (in number of time-step) that corresponds to 1 year simulation.

  • Line 54 and 55, 
     nTimeSteps=16,
 monitorFreq=1.,
    Sets the length of the simulation (in number of time-step) and the frequency (in seconds) for "monitor" output. to 16 iterations and 1 seconds respectively. This choice corresponds to a short simulation test.

  • Line 48, 
     pChkptFreq=31104000.,
    Sets the time interval, in seconds, bewteen 2 consecutive "permanent" pickups ("permanent checkpoint frequency") that are used to restart the simuilation, to 1 year.

  • Line 49, 
     chkptFreq=2592000.,
    Sets the time interval, in seconds, bewteen 2 consecutive "temporary" pickups ("checkpoint frequency") to 1 month. The "temporary" pickup file name is alternatively "ckptA" and "ckptB" ; thoses pickup (as opposed to the permanent ones) are designed to be over-written by the model as the simulation progresses.

  • Line 50, 
     dumpFreq=2592000.,
    Set the frequencies (in seconds) for the snap-shot output to 1 month.

  • Line 51, 
    #monitorFreq=43200.,
    A commented out line setting the frequency (in seconds) for the "monitor" output to 12.h. This frequency fits better the longer simulation of 1 year.

  • Line 60, 
     usingCurvilinearGrid=.TRUE.,
    Set the horizontal type of grid to Curvilinear-Grid.

  • Line 61, 
     horizGridFile='grid_cs32',
    Set the root for the grid file name to "grid_cs32". The grid-file names are derived from the root, adding a suffix with the face number (e.g.: .face001.bin, .face002.bin $ \cdots$ )
    \fbox{ \begin{minipage}{5.0in} {\it S/R INI\_CURVILINEAR\_GRID}~({\it ini\_curvilinear\_grid.F}) \end{minipage}}

  • Lines 62 and 63, 
     delR=20*50.E2,
 Ro_SeaLevel=1.E5,
    Those 2 lines define the vertical discretization, in pressure units. The $ 1^{rst}$ one sets the increments in pressure units (Pa), to 20 equally thick levels of $ 50 \times 10^2 {\rm Pa}$ each. The $ 2^{nd}$ one sets the reference pressure at the sea-level, to $ 10^5 {\rm Pa}$ . This define the origin (interface $ k=1$ ) of the vertical pressure axis, with decreasing pressure as the level index $ k$ increases.
    \fbox{ \begin{minipage}{5.0in} {\it S/R INI\_VERTICAL\_GRID}~({\it ini\_vertical\_grid.F}) \end{minipage}}

  • Line 68, 
    #topoFile='topo.cs.bin'
    This commented out line would allow to set the file name of a 2-D orography file, in meters units, to 'topo.cs.bin'.
    \fbox{ \begin{minipage}{5.0in} {\it S/R INI\_DEPTH}~({\it ini\_depth.F}) \end{minipage}}

other lines in the file input/data are standard values that are described in the MITgcm Getting Started and MITgcm Parameters notes. 

     1	# ====================
     2	# | Model parameters |
     3	# ====================
     4	#
     5	# Continuous equation parameters
     6	 &PARM01
     7	 tRef=295.2, 295.5, 295.9, 296.3, 296.7, 297.1, 297.6, 298.1, 298.7, 299.3,
     8	      300.0, 300.7, 301.9, 304.1, 308.0, 315.1, 329.5, 362.3, 419.2, 573.8,
     9	 sRef=20*0.0,
    10	 no_slip_sides=.FALSE.,
    11	 no_slip_bottom=.FALSE.,
    12	 buoyancyRelation='ATMOSPHERIC',
    13	 eosType='IDEALGAS',
    14	 rotationPeriod=86400.,
    15	 implicitFreeSurface=.TRUE.,
    16	 exactConserv=.TRUE.,
    17	 nonlinFreeSurf=4,
    18	 select_rStar=2,
    19	 hFacInf=0.2,
    20	 hFacSup=2.0,
    21	 uniformLin_PhiSurf=.FALSE.,
    22	#hFacMin=0.2,
    23	 saltStepping=.FALSE.,
    24	 momViscosity=.FALSE.,
    25	 vectorInvariantMomentum=.TRUE.,
    26	 staggerTimeStep=.TRUE.,
    27	 readBinaryPrec=64,
    28	 writeBinaryPrec=64,
    29	 &
    30	
    31	# Elliptic solver parameters
    32	 &PARM02
    33	 cg2dMaxIters=200,
    34	#cg2dTargetResidual=1.E-12,
    35	 cg2dTargetResWunit=1.E-17,
    36	 &
    37	
    38	# Time stepping parameters
    39	 &PARM03
    40	 deltaT=450.,
    41	#nIter0=276480,
    42	 startTime=124416000.,
    43	#- run for 1 year (192.iterations x 450.s = 1.day, 360*192=69120):
    44	#nTimeSteps=69120,
    45	#forcing_In_AB=.FALSE.,
    46	 tracForcingOutAB=1,
    47	 abEps=0.1,
    48	 pChkptFreq=31104000.,
    49	 chkptFreq=2592000.,
    50	 dumpFreq=2592000.,
    51	#monitorFreq=43200.,
    52	 taveFreq=0.,
    53	#- to run a short test (2.h):
    54	 nTimeSteps=16,
    55	 monitorFreq=1.,
    56	 &
    57	
    58	# Gridding parameters
    59	 &PARM04
    60	 usingCurvilinearGrid=.TRUE.,
    61	 horizGridFile='grid_cs32',
    62	 delR=20*50.E2,
    63	 Ro_SeaLevel=1.E5,
    64	 &
    65	
    66	# Input datasets
    67	 &PARM05
    68	#topoFile='topo.cs.bin',
    69	 &

3.14.4.2 File input/data.pkg

This file, reproduced completely below, specifies the additional packages that the model uses for the experiment. Note that some packages are used by default (e.g.: pkg/generic_advdiff) and some others are selected according to parameter in input/data (e.g.: pkg/mom_vecinv). The additional packages that are used for this configuration are

  • Line 3, 
     
 useSHAP_FILT=.TRUE.,
    This line selects the Shapiro filter Shapiro [1970] (pkg/shap_filt) to be used in this experiment.

  • Line 4, 
     usediagnostics=.TRUE.,
    This line selects the pkg/diagnostics to be used in this experiment.

  • Line 5, 
    #useMNC=.TRUE.,
    This line that would selects the pkg/mnc for I/O is commented out.

The entire file input/data.pkg is reproduced here below: 

     1	# Packages
     2	 &PACKAGES
     3	 useSHAP_FILT=.TRUE.,
     4	 usediagnostics=.TRUE.,
     5	#useMNC=.TRUE.,
     6	 &

3.14.4.3 File input/eedata

This file uses standard default values except line 6: 

 useCubedSphereExchange=.TRUE.,
This line selects the cubed-sphere specific exchanges to to connect tiles and faces edges.

3.14.4.4 File input/data.shap

This file, reproduced completely below, specifies the parameters that the model uses for the Shapiro filter package (Shapiro [1970], section 2.20). The parameters that are significant for this configuration are:

  • Line 5, 
     
 Shap_funct=2,
    This line selects the shapiro filter function to use, here S2 in this experiment (see section 2.20).

  • Lines 6 and 7, 
     nShapT=0,
 nShapUV=4,
    Those lines select the order of the shapiro filter for active tracer ($ \theta $ and $ q$ ) and momentum ($ u,v$ ) respectively. In this case, no filter is applied to active tracers. Regarding the momentum, this sets the integer parameter $ n$ to 4, in the equations of section 2.20, which corresponds to a 8th order filter.

  • Line 9, 
     nShapUVPhys=4,
    This line selects the order of the physical space filter (filter function S2g, in section 2.20) that applies to $ u,v$ . The difference nShapUV - nShapUVPhys corresponds to the order of the computational filter (filter function S2c, in section 2.20).

  • Lines 12 and 13, 
    #Shap_Trtau=5400.,
#Shap_uvtau=1800.,
    Those commented lines would have set the time scale of the filter (in seconds), for $ \theta $ and $ q$ and for $ u$ and $ v$ respectively, to 5400 s (90 min) and 1800 s (30 min) respectively. Without explicitly setting those timescales, the default is used which corresponds to the model time-step.

The entire file input/data.shap is reproduced here below: 

     1	# Shapiro Filter parameters
     2	 &SHAP_PARM01
     3	 shap_filt_uvStar=.FALSE.,
     4	 shap_filt_TrStagg=.TRUE.,
     5	 Shap_funct=2,
     6	 nShapT=0,
     7	 nShapUV=4,
     8	#nShapTrPhys=0,
     9	 nShapUVPhys=4,
    10	#Shap_TrLength=140000.,
    11	#Shap_uvLength=110000.,
    12	#Shap_Trtau=5400.,
    13	#Shap_uvtau=1800.,
    14	#Shap_diagFreq=2592000.,
    15	 &

3.14.4.5 File code/SIZE.h

Four lines are customized in this file for the current experiment

  • Line 39, 
     sNx=32,
    sets the lateral domain extent in grid points along the x-direction, for 1 face.

  • Line 40, 
     sNy=32,
    sets the lateral domain extent in grid points along the y-direction, for 1 face.

  • Line 43, 
     nSx=6,
    sets the number of tiles in the x-direction, for the model domain decomposition. In this simple case (one processor and 1 tile per face), this number corresponds to the total number of faces.

  • Line 49, 
     Nr=20,
    sets the vertical domain extent in grid points.

3.14.4.6 File code/packages.conf

This file, reproduced completely below, specifies the packages that are compiled and made available for this experiment. The additional packages that are used for this configuration are

  • Line 4, 
     
 gfd
    This line selects the standard set of packages that are used by default.

  • Line 5, 
     
 shap_filt
    This line makes the Shapiro filter package available for this experiment.

  • Line 6, 
     
 exch2
    This line selects the exch2 pacakge to be compiled and used in this experiment. Note that, with the present structure of the model, the parameter useEXCH2 does not exists and therefore, this package is always used when it is compiled.

  • Line 8, 
     diagnostics
    This line selects the pkg/diagnostics to be compiled, and makes it available for this experiment.

  • Line 9, 
     mnc
    This line selects the pkg/mnc to be compiled, and makes it available for this experiment.

The entire file code/packages.conf is reproduced here below: 

     1	# $Header: /u/gcmpack/MITgcm/verification/tutorial_held_suarez_cs/code/packages.conf,v 1.1 2005/07/15 21:25:20 jmc Exp $
     2	# $Name:  $
     3	
     4	gfd
     5	shap_filt
     6	exch2
     7	timeave
     8	diagnostics
     9	mnc

3.14.4.7 File code/CPP_OPTIONS.h

This file uses standard default except for Line 40
(diff CPP_OPTIONS.h ../../../model/inc): 

#define NONLIN_FRSURF
This line allow to use the non-linear free-surface part of the code, which is required for the $ p^*$ coordinate formulation.

3.14.4.8 Other Files

Other files relevant to this experiment are

  • code/external_forcing.F
  • input/grid_cs32.face00[n].bin, with $ n=1,2,3,4,5,6$
contain the code customisations and binary input files for this experiments. Below we describe the customisations to these files associated with this experiment.

The file code/external_forcing.F contains 4 subroutines that calculate the forcing terms (Right-Hand side term) in the momentum equation (3.63, S/R EXTERNAL_FORCING_U and EXTERNAL_FORCING_V) and in the potential temperature equation (3.64, S/R EXTERNAL_FORCING_T). The water-vapour forcing subroutine (S/R EXTERNAL_FORCING_S) is left empty for this experiment.

The grid-files input/grid_cs32.face00[n].bin, with $ n=1,2,3,4,5,6$ , are binary files (direct-access, big-endian 64.bits real) that contains all the cubed-sphere grid lengths, areas and grid-point positions, with one file per face. Each file contains 18 2-D arrays (dimension $ 33 \times 33$ ) that correspond to the model variables: XC YC DXF DYF RA XG YG DXV DYU RAZ DXC DYC RAW RAS DXG DYG AngleCS AngleSN (see GRID.h file)

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Next: 3.15 Surface Driven Convection Up: 3.14 Held-Suarez Atmosphere MITgcm Previous: 3.14.3 Set-up description   Contents
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