Surface Roller

Table 1. CMS-Flow cards related to the surface roller

Card	Arguments	Range	Default	Description
CALC_ROLLER	CHARACTER	ON \| OFF	OFF	Turns on or off the surface roller model in CMS.
ROLLER_DISSIPATION_COEFFICIENT	REA	0.1	0.05-0.15	Roller dissipation coefficient.
ROLLER_EFFICIENCY_COEFFICIENT	REAL	1.0	0.5-1.0	Roller efficiency coefficient.
ROLLER_SCHEME	CHARACTER	UPWIND1 \| UPWIND2 \| LAX	UPWIND1	Determines the numerical scheme used for the surface roller calculation. UPWIND1 is a first order upwind scheme, UPWIND2 is a second order upwind scheme, and LAX is the second order Lax scheme.

Hot Start

The term Hot start refers to starting a simulation with an initial condition other zero (cold start). Hot starts are used for specifying initial conditions or restarting simulations at intermediate times. The hot start controls are set in the Flow tab of the CMS-Flow Model Control window.

Hot Start File

Figure 2. XMDFView showing the structure of the CMS Hot Start File.

The CMS hot start feature CMS lets the user restart simulations that have been stopped due to electric outages, hardware malfunctions, or model crashes. In the case of a model crash the user, may restart the model using larger solver iterations and/or time steps to stabilize the simulation. The user has the option to specify a hot start output time or an interval for outputting a recurring hot start file. Every time the hot start file is written, it overwrites the previous information. The CMS Hot Start file saves information on the water elevation (pressure), and current velocities. If the sediment transport is active, then the water depth, and sediment concentrations are also saved for each size class. The CMS hot start file is a binary XMDF file, has the name Hot_Start.h5 and is saved in the directory of the CMS-Flow files. Figure 1 shows the structure of the hot start file. After saving a CMS Hot Start file, it is a good idea to rename the file with a different name before using it as an initial conditions file. This way, the file will not be overwritten in future simulations.

Table 1. Hot Start CMS-Flow Cards

Card	Arguments	Default	Range	Description
HOT_START_OUTPUT_FILE	CHARACTER	none	none	Julian hour.
HOT_START_TIME	REAL	none	none	Sets the hot start output time.
AUTO_HOT_START_INTERVAL	REAL	none	none	Sets the recurring hot start output time.

Initial Conditions File

Figure 3. Dataset Toolbox showing a time step sample of the water elevation and current velocity datasets for use in a hot start (initial condition) file.

There are several situations where it is convenient to specify a user defined hot start file. For example, if the user forgets to setup the model output a hot start file or when running steady state conditions. A hot start file can easily be created and exported by the user from the SMS interface. The model requires at water levels, current velocities, concentrations, and water depths. Any datasets that are missing from the initial file. It is important to note that the names and paths of the initial condition datasets is important.

Table 2. Path and name for initial condition file variables.

Variable	Path and Name
Water surface elevation	Datasets\Water_Elevation
Current velocity	Datasets\Current_Velocity
Sediment concentrations	Datasets\Concentration
Salinity concentrations	Datasets\Salinity

The steps for creating a user defined hot start or initial condition file from a CMS-Flow solution file are outlined below.

Import CMS-Flow grid and solution file.
Sample a time step of the solution datasets for use in the initial condition
1. Click on Data | Data Calculator
  1. Under the Tools section, select Sample time steps.
  2. Under the Datasets section, click on the Water Elevation
Export the initial condition datasets to an XMDF file

Figure 3. Dataset Toolbox showing a time step sample of the water elevation and current velocity datasets for use in a hot start (initial condition) file.

Figure 4. Dataset Toolbox showing a time step sample of the water elevation and current velocity datasets for use in a hot start (initial condition) file.

Table 3. CMS-Flow card for specifying the initial condition file.

Card	Arguments	Default	Range	Description
INITIAL_STARTUP_FILE	CHARACTER	none	none	Julian data in YYDDD with YY being last two digits of the year, and DDD the Julian day of the year.

Output

In addition to the variables specified in the SMS interface, CMS has the option to output advanced mode output including the bed shear stress, bed composition, wind speed, etc. The following advanced cards have been added to CMS v4.0 and higher for outputting additional output information, ASCII file output, and more.

Table 2. Advanced output datasets.

Card	Arguments	Description	Default value
WAVE_OUT_TIMES_LIST	integer	Output time series id	0
EDDY_OUT_TIMES_LIST	integer	Output time series id	0
VISC_OUT_TIMES_LIST	integer	Output time series id. Same as EDDY_OUT_TIMES_LIST	0
STRESS_OUT_TIMES_LIST	integer	Output time series id	0
BED_SHEAR_STRESS_OUT_TIMES_LIST	integer	Output time series id. Same as BED_SHEAR_STRESS_OUT_TIMES_LIST	0
GLOBAL_TECPLOT_FILES	ON \| OFF	Outputs Tecplot ASCII files	OFF
GLOBAL_SUPER_FILES	ON \| OFF	Outputs Tecplot ASCII files	OFF

XMDF File

The standard CMS-Flow output is written to an XMDF file with the name <Case Name>_sol.h5. The bindary file may be written in compressed format using the card described in the table below.

Table 3. CMS-Flow card for compressing the XMDF output file

Card	Arguments	Description	Default value
XMDF_COMPRESSION	ON \| OFF	Compresses the h5 file by a factor of about 7	OFF

Statistics

CMS V4.0 has the option to calculate statistics over the whole model domain for a user-specified time period. This option is accessed using the advanced cardss. The starting time, end time, and time interval should be specified in hours with respect to the model start time. The time interval should be larger or equal to the hydrodynamic time step. When activated the global statistics will be output in the same solution file within a subfolder named stats.

This option outputs the statistics for hydrodynamics, sediment and salinity transport. If only the statistics for one group

The hydrodynamic statistics output are:

Maximum current velocity
Maximum water level
Residual currents (vectors and magnitude)
Hydroperiod
Maximum spatial gradient for water levels
Maximum spatial gradient for current magnitude

Sediment Transport and Morphology Change

Maximum total load transport rate, m^2/hr
Net total load sediment transport rates, m^2/hr
Average total load sediment transport rates, m^2/hr
Gross total load sediment transport rates, m^2/hr
Positive and negative total load transport rates (in x and y directions), m^2/hr
Maximum spatial gradient of bathymetry

Salinity Statistics

Mean Salinity

Table 3. CMS-Flow cards related to output statistics

Card	Arguments	Description	Default value
GLOBAL_STATISTICS	[t0] [tn] [dt]	Calculates global statistics if specified	none
FLOW_STATISTICS	[t0] [tn] [dt]	Calculates flow statistics if specified	none
SEDIMENT_STATISTICS	[t0] [tn] [dt]	Calculates sediment statistics if specified	none
SALINITY_STATISTICS	[t0] [tn] [dt]	Calculates salinity statistics if specified	none

ASCII Output Files

In addition to the XMDF output file, CMS-Flow provides the output two types of ASCII output files:

Tecplot snap shot (*.dat), and history files (*.his)
SMS Super ASCII files (*.sup, *.xy, *.dat)

The CMS-Flow cards used for outputting these two types of files are described in the Table below.

Table 4. CMS-Flow cards used to output Tecplot and SMS Super ASCII files.

Card	Arguments	Description	Default value
GLOBAL_TECPLOT_FILES	ON \| OFF	Outputs Tecplot ASCII files	OFF
GLOBAL_SUPER_FILES	ON \| OFF	Outputs Tecplot ASCII files	OFF

Numerical Methods

Solution Scheme

This refers to the temporal discritization of the hydrodynamic, sediment and salinity transport equations. There are two options in CMS: 1. Implicit - First order backward Euler scheme. Uses a time step on the order of 5-15 minutes. Appropriate for cases which can be simulated with large computational time steps such as long term morphology change at inlets. 2. Explicit - First order forward Euler scheme. Uses a time step on the order of 0.5-1.0 second. Appropriate for cases that vary quickly in time such as flooding or barrier island breaching.

Matrix Solvers

The four different solvers implemented in the implicit solution scheme are the Gauss-Seidel, Gauss-Seidel with Successive-Over-Relaxation, BICGSTAB, and GMRES. The same solver is applied to flow, sediment and salinity. The default solver is the GMRES. The solver may be changed using the advanced card in the table below.

Advection scheme

As in the case of the implicit solution scheme, the same advection scheme is applied for the flow, sediment and salinity transport equations. There are three choices for advection schemes with upwinding in the implicit model: hybrid, exponential and HLPA. The hybrid scheme is fast but is the most diffusive. The exponential scheme is based on the 1D analytical solution to an advection-diffusion equation and produces very stable results. The HLPA is very stable and non-diffusive, but requires slightly more computational time. For most applications, the exponential scheme is recommended and is set as the default. The advection scheme may be change using the advanced card

Parallelization with OpenMP

Both Intel and AMD processors now are shipping chips with multiple cores/processors (henceforth referred to as "processors") available. CMS-Flow is now configured to make use of these extra processes that are available on newer machines.

Additional information on using Multiple Processors with CMS-Flow can be found here.

Table 5. CMS-Flow cards related to numerical methods.

Card	Arguments	Default value	Description
SOLVER_TYPE	GAUSS-SEIDEL \| GAUSS-SEIDEL-SOR \| BICGSTAB \| GMRES	GMRES	Determines the numerical solver used
ADVECTION_SCHEME	HYBRID \| EXPONENTIAL \| HLPA	EXPONENTIAL	Determines the advection scheme
NUM_THREADS	INTEGER	1	Determines the number of threads used for parallel processing.
HYDRO_MAX_ITERATIONS	integer	20	Maximum number of iterations (outer loop) for the hydrodynamics
PRESSURE_ITERATIONS	integer	10	Number of solver iterations (inner loop) used to solver the pressure equation.
VELOCITY_ITERATIONS	integer	5	Number of solver iterations (inner loop) used to solver the momentum equations.
SEDIMENT_MAX_ITERATIONS	integer	20	Maximum number of iterations (outer loop) for the sediment transport
SALINITY_MAX_ITERATIONS	integer	20	Maximum number of iterations (outer loop) for the salinity transport
WATER_PONDING	CHARACTER	OFF	ON \| OFF	Turns On or Off water ponding. If water ponding is Off, isolated bodies of water will become dry.
ONE_CELL_WIDE_CHANNELS	CHARACTER	ON	ON \| OFF	Limits wetting and drying to areas with at least 3 cells wide. When turned off, the model stability is improved.

Card	Arguments	Default	Range	Description
SOLVER_TYPE	GAUSS-SEIDEL \| GAUSS-SEIDEL-SOR \| BICGSTAB \| GMRES	GMRES	Determines the numerical solver used
MATRIX_SOLVER	CHARACTER	GMRES	GAUSS-SEIDEL \| GAUSS-SEIDEL-SOR \| BICGSTAB \| GMRES	Selects the matrix solver for flow, sediment and salinity.
HYDRO_MAX_ITERATIONS	INTEGER	Function of grid size	>0	Sets the maximum number of iterations for the flow (hydro) solver (outer loop).
PRESSURE_ITERATIONS	INTEGER	Depends on Solver	>0	Sets the number of solver iterations for the pressure equation (inner loop).
VELOCITY_ITERATIONS	INTEGER	Depends on Solver	>0	Sets the number of solver iterations for the velocity or momentum equations (inner loop).
ADVECTION_SCHEME	CHARACTER	EXPONENTIAL	NONE \| HYBRID \| EXPONENTIAL \| HLPA	Sets the advection scheme for flow, sediment and salinity.

Scripting

Scipting refers to the automation of running multiple CMS runs with different parameters, without manually having to create and edit each alternative. The scripting process can include the following steps:

Setting up alternatives
Creating batch file
Plotting and analyzing results

Scripting can be done using a variety of software programs. The examples shown here were written in Matlab becase it is widely used, easy to read and convenient for plotting and analyzing results.

Setting Up Alternatives

‎

Figure 1. Example of scripting showing the files used.

In this example, 4 cases or alterantives are setup using the Matlab script below. The script copies the base setup files into subfolders and then modifies specific CMS-Flow cards in the *.cmcards file. The settings for each case are setup using a structure variable with field names corresponding to each CMS-Flow card (e.g. TIME_SERIES_INCREMENT). Separating each case into its own subfolder keeps the input and output separate and also allows for the different cases to be run at the same time.

 % Matlab Script: setup_cases.m
 flow = 'Flow_Shark';
 wave = 'Wave_Shark';
 ncases = 4; %Number of cases or alternatives  
 r(1).MANNINGS_N_DATASET = '"Manning_Alt1.h5" "Flow_Shark/Datasets/ManningsN"';
 r(1).WAVE_CURRENT_MEAN_STRESS = 'W09';
 r(1).TIME_SERIES_INCREMENT = 1800;
 r(2).MANNINGS_N_DATASET = '"Manning_Alt1.h5" "Flow_Shark/Datasets/ManningsN"';
 r(2).WAVE_CURRENT_MEAN_STRESS = 'DATA2';
 r(2).TIME_SERIES_INCREMENT = 900;
 r(3).MANNINGS_N_DATASET = '"Manning_Alt2.h5" "Flow_Shark/Datasets/ManningsN"';
 r(3).WAVE_CURRENT_MEAN_STRESS = 'W09';
 r(3).TIME_SERIES_INCREMENT = 900;
 r(4).MANNINGS_N_DATASET = '"Manning_Alt2.h5" "Flow_Shark/Datasets/ManningsN"';
 r(4).WAVE_CURRENT_MEAN_STRESS = 'DATA2';
 r(4).TIME_SERIES_INCREMENT = 600;
 for i=1:ncases
   d = ['Case',int2str(i)];
   if ~exist(d,'dir')
     mkdir(d)
   end
   copyfile([wave,'.*'],d)
   copyfile([flow,'.*'],d)
   copyfile([flow,'_mp.h5'],d);
   copyfile([flow,'_grid.h5'],d)
   cards = fieldnames(r(i));
   file = ['.\',d,'\Flow_Shark.cmcards'];
   fork=1:length(cards)
     setcard(file,cards{k},r(i).(cards{k})); 
   end
 end
 return

The script above requires the subroutine below.

 function setcard(cmcardsfile,card,value)
 % setcard(file,card,value)
 % Overwrites or appends a CMS-Flow card
 % in the *.cmcards file
 copyfile(cmcardsfile,'temp')
 fid=fopen('temp','r');
 fid2=fopen(cmcardsfile,'w');
 nc=length(card);
 ok = false(1);
 if ~ischar(value)    
   value = num2str(value);
 end
 while 1    
   tline = fgets(fid);        
   if ~ischar(tline), break, end    
   if strncmp(card,tline,nc)        
     fprintf(fid2,'%s       %s %s' ,card,value,tline(end));                
     ok = true(1);        
     continue    
   end    
   nline = length(tline);    
   if (~ok && strcmp(tline(1:min(nline,14)),'END_PARAMETERS'))        
     fprintf(fid2,'%s       %s %s',card,value,tline(end));        
     fprintf(fid2,'%s' ,tline);        
     break 
   end    
   fprintf(fid2,'%s' ,tline);
 end
 fclose(fid);
 fclose(fid2);
 delete('temp')
 return

Batch File

Although it is possible to launch CMS from Matlab a batch file is preferable to use a batch file because it allows running all of the cases without opening Matlab.

 % Matlab Script: create_bat.m
 cmsexe = 'cms2d_v4b42_x64p.exe'; %CMS-Flow executable
 batfile = 'run_cases.bat'; %Output batch file
 fid = fopen(batfile,'w');
 for i=1:ncases 
   cmcards = ['.\Case',int2str(i),'\',flow,'.cmcards']; %CMS-Flow cmcards file
   fprintf(fid,'START %s %s %s',cmsexe,cmcards,char(10)); 
 end
 fclose(fid);
 return

The following text shows what the resulting batch file (*.bat) looks like

    START cms2d_v4b42_x64p.exe .\Case1\Flow_Shark.cmcards
    START cms2d_v4b42_x64p.exe .\Case2\Flow_Shark.cmcards

To run the batch file, simply double click on the file and each case will launch separately in its own MS-DOS window.

Plotting

The following example reads the Observation Point time series output file (*_eta.txt) and plots the 3rd

 % Matlab Script: plot_cases.m
 close all 
 eta = cell(ncases,1); 
 for  i=1:ncases    
   etafile = ['.\Case' ,int2str(i),'\',flow,'_eta.txt' ]; %Water elevation
   eta{i} = load(etafile);    
 end
 figure
 hold on
 for i=1:ncases    
   h = plot(eta{i}(:,1),eta{i}(:,3),'-');  %3 is the index is the observation point index
 end
 ylabel('Water elevation, m')
 xlabel('Elapsed Time, hr')
 return

Units of Measurement

Variable	Units	Symbol
Water Surface Elevation	meters	$m$
Current Velocity	meters per second	$m/sec$
Flow Rate	cubic meters per second	$m^{3}/sec$
Salinity Concentration	parts per thousand	$ppt$
Sediment Concentration	kilogram per meter cubed	$kg/m^{3}$
Sediment Transport	meter squared per second	$m^{2}/sec$
Bed Shear Stress	kilogram per meter per second squared	$Pa$

CMS-Flow

CMS-Flow:Features

Contents

Surface Roller

Hot Start

Hot Start File

Initial Conditions File

Output

XMDF File

Statistics

ASCII Output Files

Numerical Methods

Solution Scheme

Matrix Solvers

Advection scheme

Parallelization with OpenMP

Scripting

Setting Up Alternatives

Batch File

Plotting

Units of Measurement

Navigation menu

CMS-Flow:Features

Surface Roller

Hot Start

Hot Start File

Initial Conditions File

Output

XMDF File

Statistics

ASCII Output Files

Numerical Methods

Solution Scheme

Matrix Solvers

Advection scheme

Parallelization with OpenMP

Scripting

Setting Up Alternatives

Batch File

Plotting

Units of Measurement

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