General Parameters

The general parameters include solution scheme, time settings such as start time, duration and time step as well as wetting and drying depth. Most of the general parameters are set by going to "Model Parameters" tab within the "CMS-Flow Model Control" window. Below are some of the CMS cards related to the "Model Parameters" tab.

Card	Arguments	Default	Range	Description
HYDRO_TIME_STEP	REAL	Calculated based on solution scheme and courant number	none	Sets to the time step for hydrodynamics in seconds.
DURATION_RUN	REAL	48.0	>RAMP>0	Sets the duration of the model simulation in hours.
DURATION_RAMP	REAL	1.0	Sets the length of the ramp period in which the model forcing is slowly ramped from zero.

Boundary Conditions

CMS-Flow Boundary Conditions window

CMS-Flow has five types of boundary conditions which are listed and discussed below. The figure below shows the CMS-Flow Boundary Conditions window in SMS. All CMS-Flow boundary conditions are forced at the edges of the domain by use of cellstrings defined with the Surfacewater Modeling System (SMS). Cellstrings can either be created manually or using the SMS tool called Generate Along Boundary which is found under the Cellstring menu.

Land

The land boundary conditions is equivalent to a zero flux boundary condition. The land boundary condition is the default boundary condition when a cell string is created. It is not necessary to define land boundaries in the interior of the CMS-Flor domain, since land boundarys will automatically be detected by CMS-Flow based on the local water depths and the presence of inactive land cells.

Flow Rate-Forcing

The flow rate boundary condition specifies a time series of water fluxes in units of m^3/s per cell.

NOTES:

Total flow rate specified is divided between the total number of cells in the cellstring with each carrying a portion of the total.
This boundary type may only be specified along cell strings which are straight.
The sign of the flow rate curve is dependent on the direction of flow with respect to the origin (always lower-left hand corner of the grid).

This guide should assist in proper assignment:

- Flow rate from the East - Negative value
- Flow rate from the West - Positive value
- Flow rate from the North - Negative value
- Flow rate from the South - Positive value

Water Surface Elevation Forcing

Two types of Water Surface Elevation Forcing exist for CMS-Flow. Once a water surface elevation curve (or series of curves) is applied, the user is able to display the curve information graphically.

1. Define curve (single time series curve for each cell string)

User creates a cellstring for the given boundary and defines a time series curve. The value for each time on this curve is applied to all cells along the designated cellstring. The time series curve may be specified by either importing an SMS *.xys file, copying tabular data into SMS, or manually entered the time series information in SMS.

2. Extract from data set (time series curve for each cell on cell string)

User creates a cellstring for the given boundary and extracts multiple time series curves from a dataset or database. Each cell along the cellstring is given its own time-series curve information. Examples are:

Extraction of water surface elevation values from a larger domain solution (ie. Larger CMS-Flow or ADCIRC grid)
Extraction of tidal constituent information from a tidal database, from which a water surface elevation curve can be generated.

Tidal Constituent Forcing

Tidal Constituent Forcing window in SMS

CMS-Flow as the option of forcing with a harmonic tidal water surface elevation. To assign a boundary as a tidal boundary:

Select a cellstring
Click under CMS-Flow | Assign BC...
In the CMS-Flow Boundary Conditions window, click on Tidal constituent-forcing, and click OK.
Open the CMS-Flow Model Control window and click on the tab labeled Tidal.
Enter the amplitudes and phases of the tidal constituents. Note that the same amplitude and phase are applied to entire cellstring and click OK

Tidal constituents used in CMS

Constituent	Speed	Constituent	Speed	Constituent	Speed	Constituent	Speed
SA*	0.041067	SSA*	0.082137	MM*	0.54438	MSF*	1.0159
MF*	1.098	2Q1*	12.8543	Q1*	13.3987	RHO1*	13.4715
O1*	13.943	M1*	14.4967	P1*	14.9589	S1*	15.0
K1*	15.0411	J1*	15.5854	OO1*	16.1391	2N2*	27.8954
MU2*	27.9682	N2*	28.4397	NU2*	28.5126	M2	28.9841
LDA2*	29.4556	L2*	29.5285	T2*	29.9589	S2	30
R2*	30.0411	K2	30.0821	2SM2*	31.0159	2MK3*	42.9271
M3*	43.4762	MK3*	44.0252	MN4*	57.4238	M4	57.9682
MS4*	58.9841	S4*	60.0	M6	86.9523	S6*	90.0
M8*	115.9364

Only available through advanced cards for CMS >v4.0

Water Surface Elevation and Velocity Forcing

Users are able to extract both water surface elevations and velocity components from a larger domain solution (ie. Larger CMS-Flow or ADCIRC grid).

Salinity Concentration Forcing

If salinity transport is active for the simulation, the user has the ability to use existing hydrodynamic cellstrings in the interface in order to provide a time-series curve of salinity concentrations. The salinity concentrations must be provided in units of ppt.

Global Forcing

There are two main types of global forcing available in CMS-Flow, wind and wave. Global forcing means that the forcing is applied on a cell-by-cell nature, rather than forcing along a boundary.

Wind Forcing

Wind Curve

SMS 10.1

Temporally varying, spatially constant winds are input in CMS in the Wind Section of the CMS-Flow Model Control Window. To add wind forcing to a current CMS-Flow project click on CMS-Flow | Model Control and then on the Wind/Wave tab. Activate wind forcing by clicking on the Include Wind check box. Winds may be imported using an *.m2w file or by specifying a curve for wind speed and direction. To specify a curve for each click on the respective box which says Curve undefined which will open the XY Series Editor. The time series may be manually entered, copied or imported from an *.xys file in the XY Series Editor.

Spatially Variable Wind and Atmospheric Pressure CMS-Flow V4.0 and higher have the option to use spatially variable wind and atmospheric pressure forcing. Currently, this feature is specified in the advanced card section using the cards listed in the table below.

CMS-Flow cards related to wind

Card	Arguments	Type
WIND_OUT_TIMES_LIST	Id number of output times list	integer
WIND_DRAG_COEFFICIENT	kappa in Hsu (1988) (default 0.4)	real
WIND_INPUT_CURVE	Name of model parameter file followed wind curve path	character
ANEMOMETER_HEIGHT	Height of wind speeds	meter
OCEANWEATHER_WIND_FILE	Name of Oceanweather, Inc. wind file (*.win)	character
OCEANWEATHER_PRES_FILE	Name of Oceanweather, Inc. pressure file (*.pre)	character
OCEANWEATHER_XY_FILE	Name of Oceanweather, Inc. coordinate file (*.xy)	character
WIND_PRESSURE_FLEET_FILE	Name of fleet wind and pressure file	character
WIND_PRESSURE_GRID_PARAM	Nwlat,Nwlon,wLatMax,wLonMin,wLatInc,wLonInc	integer and real
WIND_PRESSURE_TIME_INCREMENT	wTimeInc	real

Wave Forcing

Temporally and spatially varying.

Wave forcing is generally provided by the user selecting to use the Steering Module within SMS. The mapping of wave data from wave grid to flow grid is automated during the course of the steering process.
If a choice is made not to use the steering process, the user must provide several datasets of information which has been mapped to the flow grid geometery.
- Radiation stress gradient
- Wave height
- Wave period
- Wave direction
- Wave dissipation

CMS-Flow cards related to wave forcing (one-way coupling)

Card	Arguments	Type
WAVE_RSTRESS_DATASET	"File name" "Dataset path"	character
WAVE_HEIGHT_DATASET	"File name" "Dataset path"	character
WAVE_PERIOD_DATASET	"File name" "Dataset path"	character
WAVE_DIRECTION_DATASET	"File name" "Dataset path"	character
WAVE_DISSIPATION_DATASET	"File name" "Dataset path"	character

Transport Options

Sediment Transport

SMS 10.1

The sediment transport controls are located in the Transport section of the CMS-Flow Model Control window as shown in the figure below. The sediment transport is activated by going to the Transport section of the CMS-Flow Model Control and checking the box labeles Calculate sediment transport. The CMS card used to turn on or off the sediment transport is described in the table below.

Card	Arguments	Default	Range	Description
CALC_SEDIMENT_TRANSPORT	CHARACTER	OFF	ON \| OFF	Turns on or off the sediment transport calculation.

Transport model

There are currently three sediment transport models available in CMS: (1) Equilibrium total load, (2) Equilibrium bed load plus advection-diffusion for suspended load, and (3) Non-equilibrium total load. The first two models are selected by unchecking the checkbox which says "Use non-equilibrium transport" and selecting either "Total load" for the first model, or "Advection-diffusion" for the second next to input item named "Formulation". The third model is selected by checking the box "Use non-equilibrium transport".

Card	Arguments	Default	Range	Description	Versions
SED_TRAN_FORMULATION	CHARACTER	NET	WATANABE \| LUND_CIRP \| A-D \| NET	Selects the sediment transport model.	>1.0
SED_TRAN_CALC_INTERVAL	REAL		greater or equal to hydro time step for explicit scheme, or equal hydro time step for implicit scheme	Time step used for transport equation
MORPH_UPDATE_INTERVAL	REAL		greater or equal to hydro time step for explicit scheme, or equal hydro time step for implicit scheme	Time step used for updating bed elevation

Note that the when selecting the equilibrium total load model, the SED_TRAN_FORMULATION card is set to either WATANABE or LUND_CIRP depending on the transport formula chosen. When selecting the equilibrium A-D model, the transport formula is specified through the concentration profile formula (described below).

1. Equilibrium Total load

In this model, both the bed load and suspended load are assumed to be in equilibrium. The bed change is solved using a simple mass balance equation known as the Exner equation. More information on the this model can be found here.

2. Equilibrium Bed load plus Advection-Diffusion Suspended Load

Calculations of suspended load and bed load are conducted separately. The bed load is assumed to be in equilibrium and is included in the bed change equation while the suspended load is solved through the solution of an advection-diffusion equation. Actually the advection diffusion equation is a non-equilibrium formulation, but because the bed load is assumed to be in equilibrium, this model is referred to the "Equilibrium A-D" model.

More information on the this model can be found here.

3. Non-equilibrium Total Load

The non-equilibrium sediment transport algorithm (NET) simulates non-cohesive, single size sediment transport and bed change using a Finite Volume method and includes advection, diffusion, hiding and exposure, and avalanching. NET sediment transport is calculated with a non-equilibrium bed-material (total load) formulation. In this approach, the suspended- and bed-load transport equations are combined into a single equation and thus there is one less empirical parameter to estimate (adaptation length).

Additional information on NET can be found here.

All of the previously mentioned models account for hard bottom and effect of the bed slope on bed load.

Transport Formula

The nearbed sediment concentation or concentration capacity are calculated with one of the following transport formula:

Lund-CIRP (2006)
Van Rijn (1998)
Watanabe (1987)
Soulsby-van Rijn (1997) (>=V4.0)

Card	Arguments	Default	Range	Description
NET_TRANSPORT_CAPACITY	CHARACTER	LUND-CIRP	LUND-CIRP \| VAN_RIJN \| WATANABE \| SOULSBY	Selects the transport formula. Note that SOULSBY is only available in v>=4.0
TRANSPORT_FORMULA	CHARACTER	LUND-CIRP	LUND-CIRP \| VAN_RIJN \| WATANABE \| SOULSBY	Selects the transport formula. Note that SOULSBY is only available in v>=4.0.
SED_TRANS_FORMULATION	CHARACTER	LUND-CIRP	LUND-CIRP \| A-D \| WATANABE \| NET	Selects the transport formula for the equilibrium total load model. Does not specify the transport formula for the equilibrium A-D and non-equilibrium total load models.
CONCENTRATION_PROFILE	CHARACTER	LUND-CIRP	LUND-CIRP\|EXPONENTIAL\| ROUSE\| VAN_RIJN	Selects the concentration profile to be used either in the equilibrium A-D or total load nonequilibrium models.
A_COEFFICIENT_WATANABE	REAL	0.1	0.05-0.5	Empirical coefficient which goes into the Watanabe transport formula.

Scaling Factors

Transport Scaling Factors

The bed and suspended transport scaling factors multiply directly by the transport capacity or near-bed sediment concentration calculated from the transport formula. These factors should be used to calibrate sediment transport rates and due to the large uncertainty in the transport formula, it is generally acceptable to use scaling factors in the range of 0.5-2.0.

Card	Arguments	Default	Range	Description
BED_LOAD_SCALE_FACTOR	REAL	1.0	0.5-2.0	Calibration factor for bed load transport capacity formula
SUSP_LOAD_SCALE_FACTOR	REAL	1.0	0.5-2.0	Calibration factor for suspended load transport capacity formula

Morphologic Scaling Factor

The morphologic scaling factor is directly multiplied by the calculated bed change at every time step and is intended as a means of speeding up the computational time. It is only recommended for periodic boundary conditions or conditions that do not change rapidly over time.

Card	Arguments	Default	Range	Description
MORPH_ACCEL_FACTOR	REAL	1.0	1-100	Morphologic acceleracion factor. Directly multiplies by calculated bed change.

Sediment Characteristics

Card	Arguments	Default	Range	Description	Versions
SEDIMENT_POROSITY	REAL	0.4	0-1	Sets the sediment porosity
SEDIMENT_DENSITY	REAL	2650	none	Sets the sediment density in kg/m^3
SEDIMENT_FALL_VELOCITY	REAL	none	4.0e-4 - 0.4	Sets the sediment fall velocity to a constant in m/s	v>=3.5

Bedslope term

Card	Arguments	Default	Range	Description	Versions
SLOPE_COEFFICIENT	REAL	1.0	0-5	Bed slope coefficient which controls enters a diffusion term which moves sediment down slope

Advanced

Card	Arguments	Default	Range	Description	Versions
HIDING_EXPOSURE_COEFFICIENT	REAL	0.7	0.6-1.0	Hiding and exposure coefficient.	v>=3.5
SCHMIDT_NUMBER	REAL	1.0	none	Controls the sediment mixing strength	v>=4.0

Boundary and Initial Conditions

Card	Arguments	Default	Range	Description	Versions
NET_LOADING_FACTOR	REAL	1.0	0.5-2.0	Used to specify under- or overloading at sediment inflow boundaries. Only for NET.	3.5=>v<=4.0
SEDIMENT_INFLOW_LOADING_FACTOR	REAL	1.0	0.5-2.0	Used to specify under- or overloading at sediment inflow boundaries.	>=4.0
CALC_MORPH_DURING_RAMP	CHARACTER	ON	ON \| OFF	Determines whether to calculate the morphology change during the ramp period	v>=3.5

Salinity Transport

In many estuaries, the density gradients caused by spatial variations in salinity can be an important driving force in the circulation. Salinity is also a key water quality variable in estuaries, since it affects the chemical and biological processes. Salinity is simulated in the Coastal Modeling System (CMS) in a depth-averaged sense. This means that the estuary or body of water is assumed to be well mixed vertically and the salinity is constant over the water column.

The salinity transport equation is solved with an explicit, finite volume method. The advection term is discretized with upwind scheme, and the diffusion term is discretized with the standard central difference scheme.

The CMS-Flow salinity cards are listed in the table below.

Card	Arguments	Description	Versions
CALC_SALINITY	ON \| OFF	Turns salinity on or off	>=v3.75
SALT_OUT_TIMES_LIST	integer	Index of times list of output times	>=v3.75
SALINITY_IC	real	Specifies the initial salinity value in ppt for the whole computational domain	>=v3.75
SALINITY_IC_ASCII	character	Specifies the file name of a scatter set file (*.pts) containing the coordiantes and initial salinity values to be interpolated using the Laplacian interpolation	>=4.0

Additional information on Salinity Transport in CMS-Flow can be found here.

Other Processes

Bottom Friction

SMS Project Explorer showing CMS-Flow project.

The bottom friction parameter (related to Manning $n$ ) is spatially varying (cell-specific) over the grid domain. The default value upon grid creation is 0.025. At times a user may desire to represent locations where added friction is needed due to structures or increased turbulence due to sharp changes in current speed. More information on using this feature of CMS-Flow can be found here.

Card	Arguments	Default	Range	Description	Versions
USE_WALL_FRICTION	CHARACTER	ON	ON \| OFF	Turns on or off wall friction	>=3.5
MANNING_N_DATASET	CHARACTER CHARACTER	[<grid file>] [<grid name>//"Datasets/ManningsN"]	none	Grid file name and dataset path for the input Manning's n dataset	>=v3.5
MANNING_N_CONSTANT	real number	none	0.001-0.5	Specifies input Manning n dataset	>=v3.5
WAVE-CURRENT_MEAN_STRESS	character	W09	W09 \| DATA2 \| DATA13 \| F85 \| HT95	Defines the model used for calculating the mean bottom shear stress used in hydro	>=4.0

Hard Bottom

SMS Project Explorer showing Hard bottom dataset

Hard Bottom is a morphologic constraint that provides the capability to simulate mixed bottom types within a single simulation. This cell-specific feature limits the erodibility of the constrained cells down to a specified depth below the water surface. More information on the use of hard bottom within the SMS can be found here.

CMS-Flow Model Control window showing the location where the hard bottom dataset is specified.

Variable D50

When sediment transport and morphology change are activated, sometimes it may be desired to designate areas of the grid to have a certain grain size. This cell-specific parameter allows each cell to take on the characteristics of a certain sediment grain size. More information on the use of variable grain size (D50) can be found here.

Eddy Viscosity

Eddy Viscosity in CMS-Flow is not a user definable parameter. A description of the advanced cards related to eddy viscosity is shown in the table below.

Card	Arguments	Default	Range	Description	Versions
TURBULENCE_MODEL	CHARACTER	SUBGRID	SUBGRID \|FALCONER\| PARABOLIC \| MIXING-LENGTH	Specifies the turbulence model used	>=3.5
EDDY_VISCOSITY_CONSTANT	REAL	1.0E-6	>=1.0E-6	Constant contribution or base value of eddy viscosity	>=3.5
EDDY_VISCOSITY_BOTTOM	REAL	0.0667	0.01-0.2	Coefficient related to the contribution to eddy viscosity from the bottom shear	>=3.5
EDDY_VISCOSITY_HORIZONTAL	REAL	0.4	0.2-0.6	Coefficient related to the contribution to eddy viscosity from horizontal velocity gradients	>=3.5
EDDY_VISCOSITY_WAVE	REAL	0.5	0.2-1.0	Coefficient related to the wave bottom friction contribution to eddy viscosity	>=4.0
EDDY_VISCOSITY_BREAKING	REAL	0.05	0.04-0.08	Coefficient related to the wave breaking contribution to eddy viscosity	>=4.0

More information can be found here.

Other Features

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.

Advanced Output

The following advanced cards have been added to CMS v4.0 and higher for outputting additional output information, ASCII file output, and more.

Card	Arguments	Description	Default value
XMDF_COMPRESSION	ON \| OFF	Compresses the h5 file by a factor of about 7	OFF
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	0
STRESS_OUT_TIMES_LIST	integer	Output time series id	0
BED_SHEAR_STRESS_OUT_TIMES_LIST	integer	Output time series id	0
GLOBAL_TECPLOT_FILES	ON \| OFF	Outputs Tecplot ASCII files	OFF
GLOBAL_SUPER_FILES	ON \| OFF	Outputs Tecplot ASCII files	OFF
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

Matrix solver

The four different solvers implemented in the implicit model 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	Description	Default value
SOLVER_TYPE	GAUSS-SEIDEL \| GAUSS-SEIDEL-SOR \| BICGSTAB \| GMRES	Determines the numerical solver used	GMRES
HYDRO_MAX_ITER	integer	Maximum number of iterations (outer loop) for the hydrodynamics	20
SEDIMENT_MAX_ITER	integer	Maximum number of iterations (outer loop) for the sediment transport	20
SALINITY_MAX_ITER	integer	Maximum number of iterations (outer loop) for the salinity transport	20

Advection scheme

As in the case of the solver, 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

Card	Arguments	Description	Default value
ADVECTION_SCHEME	HYBRID \| EXPONENTIAL \| HLPA	Determines the advection scheme	EXPONENTIAL

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