Draft
Basic Description of the Directory Structure and Associated Files used by
The Comprehensive Aquatic Systems Model (CASM)
Developed for the UACSE Sacramento District
CASM SAC Version 1.0
Steven M. Bartell
Cardno ENTRIX
Maryville, TN 37801
Prepared for
Dynamic Solutions, LLC
Knoxville, TN
August 2011
CASM SAC Version 1.0 July 2011
DRAFT – Do not cite or quote S.M. Bartell
The following CASM_SAC directory and identified subdirectories need to be created on
your c:\ drive.
(Note: the Ammonia subdirectory is not needed at this time, but create it if you desire.)
The Debug directory contains the executable file: casm_sac100.exe
The SAC_Advect subdirectory includes the following files:
advect_St01.out
advect_St02.out
advect_St03.out
advect_St04.out
SAC_geo.dat
The SAC_geo file is an input file. The *.out files are created by the CASM_SAC if the
avection option is selected in the model control file (to be described later).
2
CASM SAC Version 1.0 July 2011
DRAFT – Do not cite or quote S.M. Bartell
The SAC_Bio_Data contains the following files:
casmSAC_bio_bioinit_100.dat initial biomass values per population and segment
casmSCA_bio_parms_100.dat bioenergetics and habitat preference/tolerance
values (apply across all segments)
SAC_CASM_Out contains:
casmSAC-jnk.out echoes selected input information for QA/QC
light_St01.out summary of light extinction calculations for
location 1
light_St02.out location 2
light_St03.out location 3
light_St04.out location 4
The above 4 files are generated by the model given filenames defined in the control file.
The first filename (i.e., casmSAC_jnk.out) is coded in the program.
SAC_CASM_Test
Casm_ended.txt signals Visual Basic shell that model has concluded
(Note: not relevant to the SAC application, but inherited from a previous CASM
application.)
SAC_Env_DataCV contains the input files:
SAC_Stn01_UD_NDL_50y.dat 50 y of daily environmental inputs used for
location 1 (Northern Delta)
SAC_Stn02_UD_SDL_50y.dat 50 y of daily environmental inputs used for
location 2 (Southern Delta)
SAC_Stn02_UD_ESB_50y.dat 50 y of daily environmental inputs used for
location 3 (Eastern Suisin Bay)
SAC_Stn02_UD_WSB_50y.dat 50 y of daily environmental inputs used for
location 4 (Western Suisin Bay)
These are critical files to be developed by DSL for the Sacramento application. Perhaps
we don’t need 50 y of data for 50-y simulations. But the model can run at a daily time
step for 50 y (longer with some programming changes). The number of simulated years is
defined in the control file, which is listed later in this document.
SAC_Env_Mod normally contains files used to systematically alter some of the
environmental input values for “scenario” development. Only one file is needed:
3
CASM SAC Version 1.0 July 2011
DRAFT – Do not cite or quote S.M. Bartell
Morph_mod_base.dat retains baseline bathymetry conditions across multiple
years of simulation.
SAC_SimPlot contains subdirectories as described in the above figure. Each
subdirectory contains separate output files for each of the modeled populations and
selected water quality parameters, as well as some aggregated population values (e.g.,
total zooplankton). The filenames are defined in the casm_sac100 control file and the
model generates these files during the course of a simulation.
SAC_SimResult contains additional output files generated by the model.
casmSAC_BLN.out total annual production for the entire system for each
model population
casmSAC_gas.out ecosystem goods and services (gas) calculated by the model
casmSAC_sys.out summary of annual production for each population,
segment, and year
SAC_Stn01_UD_NDL.dat daily values for selected water quality parameters and
population biomass for station 1 (Northern Delta)
SAC_Stn02_UD_NDL.dat daily values for selected water quality parameters and
population biomass for station 2 (Southern Delta)
SAC_Stn03_UD_NDL.dat daily values for selected water quality parameters and
population biomass for station 3 (East Suisin Bay)
SAC_Stn04_UD_NDL.dat daily values for selected water quality parameters and
population biomass for station 4 (West Suisin Bay)
SAC_Web_Data contains a file that specifies the grazing and predator-prey interactions
among the modeled populations:
web_casmSAC.dat
4
CASM SAC Version 1.0 July 2011
DRAFT – Do not cite or quote S.M. Bartell
Control file for setting up simulations using the CASM_SAC Version 1.0
The following file controls simulation of the CASM_SAC Version 1.0. The file is located
in the main c:\CASM_SAC directory and should not be relocated.
Filename: c:\CASM_SAC\casm_SAC_cntrl_100.dat for use with CASM_SAC version 1.00
CASM_SAC Program Version 1.00 control file
Enter the number of stations used to describe the system: (i3 format)
004 Number of stations
Select option for advective transport (000=no transport, 111=include transport)
000
Enter the number of simulated years (format i3)
001
Specify the output interval in days (format i3)
010
Provide a message that describes the particular simulation (a80)
Message: baseline model testing...
Specify information on derivatives (i3:000=no info,111=give info); specify debug station (1-4)
000 1
Specify initial biomass input file:
c:\CASM_SAC\SAC_Bio_Data\casmSAC_bio_binit_100.dat
Specify bioenergetics parameter input file:
c:\CASM_SAC\SAC_Bio_Data\casmSAC_bio_parms_100.dat
Specify food web input file:
c:\CASM_SAC\SAC_Web_Data\web_casmSAC.dat
Specify environment input files for each station:
c:\CASM_SAC\SAC_Env_DataCV\SAC_Stn01_UD_NDL_50y.dat
c:\CASM_SAC\SAC_Env_DataCV\SAC_Stn02_UD_SDL_50y.dat
c:\CASM_SAC\SAC_Env_DataCV\SAC_Stn03_UD_ESB_50y.dat
c:\CASM_SAC\SAC_Env_DataCV\SAC_Stn04_UD_WSB_50y.dat
Specify geomorphology input file:
c:\CASM_SAC\SAC_Advect\SAC_geo.dat
Specify geomorphology modification input file:
c:\CASM_SAC\SAC_Env_Mod\Morph_mod.dat
Specify goods and services output file
c:\CASM_SAC\SAC_SimResult\casmSAC_gas.out
Specify system summary output file
c:\CASM_SAC\SAC_SimResult\casmSAC_sys.out
Specify system bottom-line result file
c:\CASM_SAC\SAC_SimResult\casmSAC_BLN.out
Specify simulation output files for each station:
c:\CASM_SAC\SAC_SimResult\SAC_Stn01_UD_NDL.dat
c:\CASM_SAC\SAC_SimResult\SAC_Stn02_UD_SDL.dat
c:\CASM_SAC\SAC_SimResult\SAC_Stn03_UD_ESB.dat
c:\CASM_SAC\SAC_SimResult\SAC_Stn04_UD_WSB.dat
Specify plot files for individual populations for all stations
c:\CASM_SAC\SAC_SimPlot\Phyto\phyto_diat.dat
c:\CASM_SAC\SAC_SimPlot\Phyto\phyto_othr.dat
c:\CASM_SAC\SAC_SimPlot\Perip\perip_peri.dat
c:\CASM_SAC\SAC_SimPlot\Macro\macro_macr.dat
c:\CASM_SAC\SAC_SimPlot\Emerg\emerg_emrg.dat
c:\CASM_SAC\SAC_SimPlot\Zoopl\zoopl_mcro.dat
c:\CASM_SAC\SAC_SimPlot\Zoopl\zoopl_limn.dat
c:\CASM_SAC\SAC_SimPlot\Zoopl\zoopl_eury.dat
5
CASM SAC Version 1.0 July 2011
DRAFT – Do not cite or quote S.M. Bartell
c:\CASM_SAC\SAC_SimPlot\Zoopl\zoopl_psdp.dat
c:\CASM_SAC\SAC_SimPlot\Zoopl\zoopl_acar.dat
c:\CASM_SAC\SAC_SimPlot\PFish\pfish_mysd.dat
c:\CASM_SAC\SAC_SimPlot\PFish\pfish_ofsh.dat
c:\CASM_SAC\SAC_SimPlot\PFish\pfish_pfsh.dat
c:\CASM_SAC\SAC_SimPlot\Decom\decom_bctp.dat
c:\CASM_SAC\SAC_SimPlot\BInvt\binvt_clam.dat
c:\CASM_SAC\SAC_SimPlot\BFish\pfish_ofsh.dat
c:\CASM_SAC\SAC_SimPlot\BFish\pfish_pfsh.dat
c:\CASM_SAC\SAC_SimPlot\Decom\decom_bcts.dat
Specify plot files for aggregated populations for all stations
c:\CASM_SAC\SAC_SimPlot\PopAg\popag_phyt.dat
c:\CASM_SAC\SAC_SimPlot\PopAg\popag_peri.dat
c:\CASM_SAC\SAC_SimPlot\PopAg\popag_macr.dat
c:\CASM_SAC\SAC_SimPlot\PopAg\popag_emrg.dat
c:\CASM_SAC\SAC_SimPlot\PopAg\popag_zoop.dat
c:\CASM_SAC\SAC_SimPlot\PopAg\popag_binv.dat
c:\CASM_SAC\SAC_SimPlot\PopAg\popag_pfsh.dat
c:\CASM_SAC\SAC_SimPlot\PopAg\popag_bfsh.dat
Specify plot files for environmental parameters for all stations
c:\CASM_SAC\SAC_SimPlot\Envir\envir_DINe.dat
c:\CASM_SAC\SAC_SimPlot\Envir\envir_DIPe.dat
c:\CASM_SAC\SAC_SimPlot\Envir\envir_DisO.dat
c:\CASM_SAC\SAC_SimPlot\Envir\envir_DOCe.dat
c:\CASM_SAC\SAC_SimPlot\Envir\envir_POCe.dat
c:\CASM_SAC\SAC_SimPlot\Envir\envir_Cvel.dat
c:\CASM_SAC\SAC_SimPlot\Envir\envir_Dpth.dat
c:\CASM_SAC\SAC_SimPlot\Envir\envir_PChl.dat
Note: filenames may be changed to define specific scenarios or simulations.
Many of the key input and output files listed above have been described previously. Also,
several of the output files will contain biomass values of zero (e.g., macrophytes,
emergent aquatic plants) because specific populations within these guilds have not been
defined. However, the current model requires at least one population (even a generic one)
to be defined for each producer and consumer guild.
As long as the format of the file is maintained, changes can be made with any text editor.
Any saved changes will be enforced during future simulations.
6
CASM SAC Version 1.0 July 2011
DRAFT – Do not cite or quote S.M. Bartell
Performing a Simulation using the CASM-SAC Version 1.0
(To be added.)
7