3.20.3 Code Configuration

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Next: 3.20.4 Running The Example Up: 3.20 Offline Example Previous: 3.20.2 Time-stepping of tracers Contents

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3.20.3 Code Configuration

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

input/data
input/data.off
input/data.pkg
input/data.ptracers
input/eedata
input/packages.conf
code/PTRACERS_SIZE.h
code/SIZE.h.

contain the code customisations and parameter settings required to run the example. In addition the following binary data files are required:

input/depth_g77.bin
input/tracer1_.bin
input/tracer2_.bin
input/input_off/uVeltave.0000000001-12.data
input/input_off/vVeltave.0000000001-12.data
input/input_off/wVeltave.0000000001-12.data
input/input_off/Convtave.0000000001-12.data

3.20.3.1 File input/data

This file, reproduced completely below, specifies the main parameters for the experiment.

Line 18, 19
```
 nIter0  = 0,
 nTimeSteps = 720,
```

nIter0 and nTimesteps control the start time and the length of the run (in timesteps). If nIter0 is non-zero the model will require appropriate pickup files to be present in the run directory. Where nIter0 is zero, as here, the model makes a fresh start. In this case the model has been prescribed to run for 720 timesteps or 1 year.

Line 20
```
 deltaTtracer= 43200.0,
```

deltaTtracer is the tracer timestep in seconds, in this case, 12 hours (43200s = 12 hours). Note that deltatTracer must be specified in input/data as well as specifying deltaToffline in input/data.off.

Line 21
```
 deltaTClock= 43200.0,
```

When using the MITgcm in offline mode deltaTClock (an internal model counter) should be made equal to the value assigned to deltatTtracer.

Line 27
```
 periodicExternalForcing=.TRUE.,
```

periodicExternalForcing is a flag telling the model whether to cyclically re-use forcing data where there is external forcing (see `A More Complcated Example', below). Where there is no external forcing, as here, but where there is to be cyclic re-use of the offline flow and mixing fields, periodicExternalForcing must be assigned the value .TRUE.

Line 28
```
 externForcingPeriod=2592000.,
```

externForcingPeriod specifies the period of the external forcing data in seconds. In the absence of external forcing, as in this example, it must be made equal to the value of externForcingPeriod in input/data.off, in this case, monthly (2592000s = 1 month).

Line 29
```
 externForcingCycle=31104000.,
```

externForcingCycle specifies the duration of the external forcing data cycle in seconds. In the absence of external forcing, as in this example, it must be made equal to the value of externForcingCycle in input/data.off, in this case, the cycle is one year(31104000s = 1 year).

Line 35
```
 usingSphericalPolarGrid=.TRUE.,
```

This line requests that the simulation be performed in a spherical polar coordinate system. It affects the interpretation of grid input parameters and causes the grid generation routines to initialize an internal grid based on spherical polar geometry.

Line 36

 delR=  50.,  70., 100., 140., 190., 
       240., 290., 340., 390., 440., 
       490., 540., 590., 640., 690.,

This line sets the vertical grid spacing between each z-coordinate line in the discrete grid. Here the total model depth is $5200\,{\rm m}$ .

Line 39
```
 ygOrigin=-90.,
```

This line sets the southern boundary of the modeled domain to $-90^{\circ}$ latitude N ( $90^{\circ }$ S). This value affects both the generation of the locally orthogonal grid that the model uses internally and affects the initialization of the coriolis force. Note - it is not required to set a longitude boundary, since the absolute longitude does not alter the kernel equation discretisation.

Line 40
```
 dxSpacing=2.8125,
```

This line sets the horizontal grid spacing between each y-coordinate line in the discrete grid to $2.8125^{\circ}$ in longitude.

Line 41
```
 dySpacing=2.8125,
```

This line sets the vertical grid spacing between each x-coordinate line in the discrete grid to $2.8125^{\circ}$ in latitude.

Line 46
```
bathyFile='depth_g77.bin',
```

This line specifies the name of the file, in this case depth_g77.bin, from which the domain bathymetry is read. This file contains a two-dimensional ( ) map of (assumed 64-bit) binary numbers giving the depth of the model at each grid cell, ordered with the x coordinate varying fastest. The points are ordered from low coordinate to high coordinate for both axes. The units and orientation of the depths in this file are the same as used in the MITgcm code. In this experiment, a depth of indicates land.

1    # ====================
2    # | Model parameters |
3    # ====================
4    #
5    # Continuous equation parameters
6    &PARM01
7    &
8    #
9    # Elliptic solver parameters
10   &PARM02
11   cg2dMaxIters=1000,
12   cg2dTargetResidual=1.E-13,
13   &
14   #
15
16   # Time stepping parameters
17   &PARM03
18   nIter0  = 0,
19   nTimeSteps = 720,
20   deltaTtracer= 43200.0,
21   deltaTClock = 43200.0,
22   pChkptFreq=31104000.,
23   chkptFreq= 31104000.,
24   dumpFreq=  2592000.,
25   taveFreq=  311040000.,
26   monitorFreq= 1.,
27   periodicExternalForcing=.TRUE.,
28   externForcingPeriod=2592000.,
29   externForcingCycle=31104000.,
30   &
31   #
32   # Gridding parameters
33   &PARM04
34   usingCartesianGrid=.FALSE.,
35   usingSphericalPolarGrid=.TRUE.,
36   delR=  50.,  70., 100., 140., 190., 
37         240., 290., 340., 390., 440., 
38         490., 540., 590., 640., 690.,
39   ygOrigin=-90.,
40   dxSpacing=2.8125,
41   dySpacing=2.8125,
42   &
43   #
44   # Input datasets
45   &PARM05
46   bathyFile=      'depth_g77.bin',
47   &

3.20.3.2 File input/data.off

input/data.off provides the MITgcm offline package with package specific parameters. input/data.off specifies the location (relative to the run directory) and prefix of files describing the flow field (UvelFile, VvelFile, WvelFile) and the corresponding convective mixing coefficients (ConvFile) which together prescribe the three dimensional, time varying dynamic system within which the offline model will advect the tracer.

Lines 2 to 5

  UvelFile= '../input/input_off/uVeltave',
  VvelFile= '../input/input_off/vVeltave',
  WvelFile= '../input/input_off/wVeltave',
  ConvFile= '../input/input_off/Convtave',

In the example the offline data is located in the sub-directory input/input_off. In this directory are fields describing the velocity and convective mixing histories of a prior forward integration of the MITgcm required for the offline package and identified in input/data_off. Based on the values of deltatToffline, offlineForcingPeriod and offlineForcingCycle specified in input/data.off, since offlineForcingCycle corresponds to 12 forcing periods offlineForcingPeriod and since offlineIter0 is zero, there needs to be 12 uVeltave, 12 vVeltave, 12 wVeltave and 12 Convtave files each having a 10 digit sequence identifier between 0000000001 to 0000000012, that is, a total of 48 files.

Line 9
```
  offlineIter0=0,
```

offlineIter0, here specified to be 0 timesteps, corresponds to the timestep at which the tracer model is initialised. Note that offlineIter0 and nIter0 (set in input/data) need not be the same.

Line 10
```
  deltaToffline=43200.,
```

deltatToffline sets the timestep associated with the offline model data in seconds, here 12 hours (43200s = 12 hours).

Line 11
```
  offlineForcingPeriod=43200.,
```

offlineForcingPeriod sets the forcing period associated with the offline model data in seconds.

Line 12
```
  offlineForcingCycle=518400.,
```

offlineForcingCycle sets the forcing cycle length associated with the offline model data in seconds. In this example the offline forcing cycle is 6 days, or 12 offline forcing periods. Together deltatToffline, offlineForcingPeriod and offlineForcingCycle determine the value of the 10 digit sequencing tag the model expects files in input/input_off to have.

1   &OFFLINE_PARM01
2    UvelFile= 'input_off/uVeltave',
3    VvelFile= 'input_off/vVeltave',
4    WvelFile= 'input_off/wVeltave',
5    ConvFile= 'input_off/Convtave',
6   &end

7   &OFFLINE_PARM02
8    offlineIter0=0,
9    deltaToffline=43200.,
10   offlineForcingPeriod=43200.,
11   offlineForcingCycle=518400.,
12  &end

3.20.3.3 File input/data.pkg

File input/data.pkg, reproduced completely below, specifies which MITgcm packages ( /MITgcm/pkg) are to be used.

Line 3
```
 usePTRACERS=.TRUE.,
```

usePTRACERS is a flag invoking the ptracers package which is responsible for the advection of the tracer within the model.

1  # Packages
2   &PACKAGES
3   usePTRACERS=.TRUE.,
4   &

3.20.3.4 File input/data.ptracers

File input/data.ptracers, reproduced completely below, provides the MITgcm ptracers package with package specific parameters, prescribing the nature of the the tracer/tracers as well as the variables associated with their advection.

Line 2
```
 PTRACERS_numInUse=2,
```

PTRACERS_numInUse tells the model how many separate tracers are to be advected, in this case 2. Note: The value of PTRACERS_numInUse must agree with the value specified in code/PTRACERS_SIZE.h - see code/PTRACERS_SIZE.h below.

Line 3
```
 PTRACERS_Iter0= 0,
```

PTRACERS_Iter0 specifies the iteration at which the tracer is to be introduced. In this case the tracer is initialised at the start of the simulation. i.e. PTRACERS_Iter0 = PTRACERS_nIter0.

Lines 5 and 10
```
 PTRACERS_advScheme(1)=77,
```

PTRACERS_advScheme(n) identifies which advection scheme will be used for tracer n, where n is the number of the tracer up to PTRACERS_numInUse. See section 2.18, 'Comparison of advection schemes', to identify the numerical codes used to specify different advection schemes (e.g. centered 2nd order, 3rd order upwind) as well as details of each.

Lines 6 and 11
```
 PTRACERS_diffKh(1)=1.E3,
```

PTRACERS_diffKh(n) is the horizontal diffusion coefficient for tracer n, where n is the number of the tracer up to PTRACERS_numInUse.

Lines 7 and 12
```
 PTRACERS_diffKr(1)=5.E-5,
```

PTRACERS_diffKr(n) is the vertical diffusion coefficient for tracer n, where n is the number of the tracer up to PTRACERS_numInUse.

Lines 8 and 13

 PTRACERS_initialFile(1)='tracer1.bin',

PTRACERS_initialFile(n) identifies the initial tracer field to be associated with tracer n, where n is the number of the tracer up to PTRACERS_numInUse. In this example file input/tracer1.bin contains localised tracer, input/tracer2.bin contains an arbitrary global distribution. Included Matlab script input/makeinitialtracer.m provides a template for generating or manipulating initial tracer fields.

1   &PTRACERS_PARM01
2   PTRACERS_numInUse=2,
3   PTRACERS_Iter0= 0,
4  # tracer 1 
5   PTRACERS_advScheme(1)=77,
6   PTRACERS_diffKh(1)=1.E3,
7   PTRACERS_diffKr(1)=5.E-5,
8   PTRACERS_initialFile(1)='tracer1.bin',
9  # tracer 2 
10  PTRACERS_advScheme(2)=77,
11  PTRACERS_diffKh(2)=1.E3,
12  PTRACERS_diffKr(2)=5.E-5,
13  PTRACERS_initialFile(2)='tracer2.bin',
14  &

Note input/data.ptracers requires a set of entries for each tracer.

3.20.3.5 File input/eedata

This file uses standard default values and does not contain customisations for this experiment.

The following code changes are required to run this exaperiment.

3.20.3.6 File code/packages.conf

This file is used to invoke the model components required for a particuylar implementation of the MITgcm. In this case the code/packages.conf contains the component names:

ptracers
generic_advdiff
mdsio
mom_fluxform
mom_vecinv
timeave
rw
monitor
offline

3.20.3.7 File code/PTRACERS_SIZE.h

Line
```
     PARAMETER(PTRACERS_num = 2 )
```

This line sets the parameters PTRACERS_num (the number of tracers to be integrated) to 2 (in agreement with input/data.ptracers).

3.20.3.8 File code/SIZE.h

Two lines are customized in this file for the current experiment

Line 39,
```
 sNx=128,
```
this line sets the lateral domain extent in grid points for the axis aligned with the x-coordinate.
Line 40,
```
 sNy=64,
```
this line sets the lateral domain extent in grid points for the axis aligned with the y-coordinate.
Line 49,
```
 Nr=15,
```
this line sets the vertical domain extent in grid points.

Next: 3.20.4 Running The Example Up: 3.20 Offline Example Previous: 3.20.2 Time-stepping of tracers Contents

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Last update 2018-01-23