MS 698: 2014 Implementing a Hydrodynamic Model - Part 2 Julia Moriarty 14 February 2014
MS 698: 2014 Implementing a Hydrodynamic Model - Part 2 Julia Moriarty 14 February 2014.
Jan 03, 2016
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MS 698: 2014Implementing a Hydrodynamic Model
- Part 2
Julia Moriarty14 February 2014
Previously…• Governing Equations• Horizontal and Vertical Grid• Time-Stepping (Mode-splitting)• Compiling and Running 1D Test Case• Basic plots in MATLAB
This Week• Changing Inputs, Outputs • Practice Plotting
Types of Input
What types of input did we change last class?
Types of Input
1. Header file: sed_toy.h2. Analytical files: ana_smflux.h, etc. 3. NetCDF files: boundary_conditions.nc, etc.
Not in SED_TOY
4. ‘The’ input file: ocean_sed_toy.in
The Header File:ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…
Examples of header files for test cases
Header file for model run:sed_toy.h
The Header File:sed_toy.h
ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…
What does the header file do?• Defines or undefines options, usually related
to the model setup and parameterizations Model Code:e.g. *.h, *.F
What does the header file do?• Defines or undefines options, usually related
to the model setup and parameterizations Model Code:e.g. *.h, *.F
Model Code used for your model run:PROJECT/Build/*.f90
Compile
What does the header file do?• Defines or undefines options, usually related
to the model setup and parameterizations Model Code:e.g. *.h, *.F
Model Code used for your model run:PROJECT/Build/*.f90
Compile
What options are available for
header files?
ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…
cppdefs.h lists all options for header files
-also see ROMS wiki: https://www.myroms.org/wiki/index.php/Documentation
_Portal
Model Forcing:Analytical files vs. NetCDF files
• Both analytical and NetCDF files provide ways to force your model (e.g. winds, model bathymetry, boundary information)– Only use one at a time for a particular forcing
• NetCDF files provide timeseries of data, more complicated model grids
• Analytical files are useful for simple forcing functions, e.g. constant or sinusoidal wind forcing, constant water depth, etc.
Analytical Files:e.g. ana_smflux.h
ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…
Analytical Files:ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
… Original copies of analytical files:
ana_*.h
Edited copies of analytical files stored in one of these
directories
Analytical Files:ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…Original copies of
analytical files:ana_*.h
Edited copies of analytical files stored in one of these
directories
Steps:1. Specify directory for edited
analytical files in build.bash (In this class, we used Include, not Functionals)
2. Copy original ana_*.h file to your PROJECT/Functionals or Include directory
3. Edit ana_*.h file(s)4. (Re)compile code
NetCDF Files:ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…
NetCDF Files:ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
… Examples of NetCDF forcing files
(and *.in files)
NetCDF forcing files may be stored anywhere, but are
often stored here.
‘The’ Input Files
• Main input file: ocean.in
• Ocean.in calls other input files– sediment.in, floats.in,
stations.in, …
‘Input Files’: ocean.in,
sediment.in
ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
… Examples of input files (and NetCDF forcing
files)
Input files may be stored anywhere, but it are often
stored here.
What’s in ocean.in?• Timesteps• Open boundary conditions• Basic horizontal and vertical grid information• Directions for output files• Paths for other input and output files (e.g.
NetCDF files, sediment_sed_toy.in, ocean_his.nc)
• … and much more …The second half of the ocean.in file is a glossary explaining all of the different parameters in ocean.in
Editing Code and Input Files
Useful Linux Tools for Editing Code:
• Be creative: *, .., ., ‘|more’, ‘> outfile.txt’ work with most commands
Command Description
diff file1.txt file2.txt Prints out a line-by-line comparison of file1.txt and file2.txt to the command line.
diff file1.txt file2.txt > file1_vs_file2.txt Creates file1_vs_file2.txt, which is a line-by-line comparison of file1.txt and file2.txt
grep SED_TOY ana_smflux.h Prints out line numbers of all occurrences of “SED_TOY” in ana_smflux.h to the command line
grep SED_TOY ana_*.h Prints out line numbers of all occurrences of “SED_TOY” in all files starting with “ana_” and ending in (“.h”) to the command line
grep SED_TOY * |more Prints out line numbers of all occurrences of “SED_TOY” in all files in this directory in the command line. The “|more” makes Linux print out only one page’s worth of text at a time. Press the spacebar or Enter to scroll through results.
From within Emacs: Ctrl-sWhen prompted (at the bottom of the window) enter a string to search for, e.g. ‘SED_TOY’
Searches for “SED_TOY” within the file you have open in Emacs. This is case sensitive. Emacs begins searching from wherever your cursor is, moving downward in the document. To search upwards, use ‘Ctrl-r’ instead of ‘Ctrl-s’.
Other Useful Linux Tools:
• Be creative: ‘*’, ‘..’, ‘|more’, ‘> outfile.txt’ work with most commands• Be careful with case-sensitive commands
Command Description
more file.txt Scroll through file.txt in the command line
ls */*/*.in List any file ending in “.in” that is located two directories below the current working directory.
ls ../../ana_* List all files starting with “ana_” that are located two directories above the current working directory
ls ../../trunk/ROMS/Functionals/ana_* List all files starting with “ana_” that are located two directories up, and then within the trunk/ROMS/Functionals directory
tail ocean_sed_toy.log Print out the last few lines of the file ocean_sed_toy.log
tail –f ocean_sed_toy.log Print out the lines of the file ocean_sed_toy.log as the file is written
From within ROMS model code:write(6,*) ‘text’ variable
Prints out “ text value_of_variable” to the log file in ROMS.
Is ROMS doing what you think its
doing?
ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…
Check output files
*.f90 files are human-readable versions of the
compiled code
Is ROMS doing what you think its
doing?
ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…
Check, then check again
- Is the model code correct?- Does the model produce
reasonable output?- Trouble shoot:
- Look at *.f90’s, log file- Use write statements
Overview of Output Files• History Files: ocean_his.nc
– Stores time-series of instantaneous output.
• Time-Averaged Results: ocean_avg.nc– Stores time-series of time averaged values.
• Restart File: ocean_rst.nc– Used to restart a model run from exactly where it ended.
• Log File: ocean_sed_toy.log– Text file with information on model configuration, error messages, and
much more. – Only created if specified in the oceanS command:
• oceanS < External/ocean_sed_toy.in > Results/ocean_sed_toy.log &
ROMS OutputROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…
Output files may be stored anywhere, but are often
stored here.
ROMS Output:Location specified in
ocean.in
ROMS_OneD
trunk
PROJECT
Results
Build
External
ROMS
Include
Functionals
External
Include
Functionals
…
…
Manipulating Output Files• “Directions” for output
files in ocean_*.in:– NHIS – number of time-
steps between writing fields into history file
– NDEFHIS – number of time-steps between the creation of a new history file. NDEFHIS = 0 creates a single history file.
– HISNAME – name and path for history file
– Hout(*) – Tells model if it should prints out each variable to the history file
Questions?>> Start lab activity
Manipulating Time Steps
• DT – Time-step (baroclinic) in seconds• NDTFAST – number of barotropic time-steps
between each baroclinic time step• NTIMES – Total number of baroclinic
timesteps. • DSTART – First Timestamp of model
“Δt in history file” = DT * NHIS“Total Model Time” = DT*NTIMES
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