CMS-Flow:Features

Steering

Steering refers to the coupling process between CMS-Flow and CMS-Wave. In CMS versions < 4.0, the steering process is handled by the SMS interface while in newer versions >= 4.0, the steering process is done internally. The steering process in either is similar. First the wave model is run twice at time zero to the first steering interval. The wave information is then interpolated on to the flow grid and the flow model is run from time zero to the first steering interval. The flow information is then interpolated on the wave grid and the wave model is run for the second steering interval and the process is repeated until the simulation is complete.

Inline Steering (CMS Versions>=4.0)

The significant wave height, peak wave period, wave unit vectors, and wave dissipation were linearly interpolated to the flow grid every steering interval and then linearly interpolated in time at every hydrodynamic time step. Wave variables such as wave length and bottom orbital velocities were updated every time step for wave-current interaction.

When using such a large steering interval, it is important to consider how the water levels, current velocities and bed elevations, which are passed from the flow to the wave model, are estimated.

For this application, and for most open coast applications, the nearshore waves are most sensitive to variations in water levels and not currents. Therefore, improved results can be obtained by predicting the water levels at the wave model time step based on a decomposition of the water levels into spatially constant and variable components. The spatially constant component is assumed to be equal to the tidal water surface elevation and the spatially variable component which includes wind and wave setup is estimated based on the last flow time step. The currents and bed elevations which are passed from the wave to flow grid are simply set to the last time step value. Other types of prediction methods could be used; however, the approach described above has been found to be sufficient for most applications and is simple to calculate. After each wave run, a surface roller model is also calculated on the wave grid and the roller stresses are added to the wave stresses before interpolating on to the flow grid. Even though CMS-Flow and CMS-Wave use different grids, the two models are in a single code which facilitates the model coupling and speeds up the computation by avoiding communication files, variable allocation and model initialization at every steering interval.

Table 1. CMS-Flow cards related to steering

Card	Arguments	Default	Range	Description
CMS-WAVE_SIM_FILE	CHARACTER	none	none	File name including path for the CMS-Wave sim file.
WAVE_SIM_FILE	CHARACTER	none	none	Same as CMS-WAVE_SIM_FILE.
STEERING_INTERVAL	REAL	none	none	Sets the recurring hot start output time.
WAVE_WATER_LEVEL	CHARACTER	TIDAL_PLUS_VARIATION	LAST | TIDAL | TIDAL_PLUS_VARIATION	Determines the method used to calculate the water levels passed to the wave model.
FLOW_EXTRAPOLATION_DISTANCE	REAL	Calculated based on grid geometry	none	Determines the extrapolation distance used for flow variables on the wave grid.
WAVE_EXTRAPOLATION_DISTANCE	REAL	Calculated based on grid geometry	none	Determines the extrapolation distance used for wave variables on the flow grid.

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.

1. Import CMS-Flow grid and solution file.
2. 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
3. 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:

1. Maximum current velocity
2. Maximum water level
3. Residual currents (vectors and magnitude)
4. Hydroperiod
5. Maximum spatial gradient for water levels
6. Maximum spatial gradient for current magnitude

• Sediment Transport and Morphology Change

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

• Salinity Statistics

1. 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:

1. Tecplot snap shot (*.dat), and history files (*.his)
2. 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.

Card	Arguments	Default	Range	Description
SOLUTION_SCHEME	CHARACTER	EXPLICIT	EXPLICIT | IMPLICIT	Determines the solution scheme used in CMS-Flow.

Solver Options

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.

Card	Arguments	Default	Range	Description
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).
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

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

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

Card	Arguments	Default	Range	Description
ADVECTION_SCHEME	CHARACTER	EXPONENTIAL	NONE | HYBRID | EXPONENTIAL | HLPA	Sets the advection scheme for flow, sediment and salinity.

Wetting and Drying

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

DRYING_DEPTH	REAL	Calculated based on solution scheme and courant number	none	Sets to the time step for hydrodynamics in seconds.
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.

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	Range	Description
NUM_THREADS	INTEGER	1	Determines the number of threads used for parallel processing.
OPENMP_THREADS	INTEGER	1	Determines the number of threads used for parallel processing.

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:

1. Setting up alternatives
2. Creating batch file
3. 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
clear all
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
START cms2d_v4b42_x64p.exe .\Case3\Flow_Shark.cmcards
START cms2d_v4b42_x64p.exe .\Case4\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

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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	$Pa$

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CMS-Flow