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='''Boundary Conditions'''=
= Hot Start =
CMS-Flow has multiple types of boundary conditions which are listed and discussed below.  All CMS-Flow boundary conditions are forced at the edges of the domain by use of cellstrings defined with the Surfacewater Modeling System.  
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.  


==Water Surface Elevation Forcing==
==Hot Start  File ==
Two types of Water Surface Elevation Forcing exist for CMS-FlowOnce a water surface elevation curve (or series of curves) is applied, the user is able to display the curve information graphically.
[[Image:Hot_Start_HDFView.png|thumb|right|500px| Figure 1. HDFView showing the structure of the CMS Hot Start File. ]]
# Single value for all cells on a cellstring
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. Only the very last record of information is preserved (no starting from earlier intervals).
# Multiple values on a cellstring (one for each cell)


=== Single Value ===
The CMS hot start files are written as binary XMDF files by default. Depending on the type of hot start (single file or recurring), the names are as follows are saved in the directory of the CMS-Flow files:
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.
* SingleHotStart.h5
* AutoHotStart.h5


=== Multiple Values ===
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.  
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.


==Water Surface Elevation and Velocity Forcing==
'''Table 1.  Hot Start CMS-Flow Cards'''
Users are able to extract both water surface elevations and velocity components from a larger domain solution (ie. Larger CMS-Flow or ADCIRC grid).
{| class=wikitable border="1"
! Card !!  Arguments !! Default !! Range !!  Description
|-
| HOT_START_TIME || REAL || none || none || Single time after start at which to output a single hot start file.
|-
| AUTO_HOT_START_INTERVAL || REAL || none || none || Sets the recurring hot start output interval .
|}


==River Flow Forcing==
<br style="clear:both" />
User creates a cellstring for the given boundary, chooses a River Flow type for the cellstring, then creates a time-series curve of flow rates. 
NOTES:
* Total flow rate specified is divided between the total number of cells in the cellstring with each carrying a portion of the total.
* 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


==Salinity Concentration Forcing==
==Initial Conditions File==
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.
[[Image:Hot_Start_XMDFView_Initial_Condition.png|thumb|right|300px|  Figure 2. Dataset  Toolbox showing a time step sample of the water  elevation and current velocity datasets for use in a hot start (initial condition) file.]]


=== Introduction ===
There are several situations where it is desired to specify a user-defined hot start file from which to start a simulation. If the user has previously specified a hot start file be written either at a specific time or at a recurring interval, they can simply indicate to start from that hot start as an initial condition from the SMS interface, or by adding a card to the parameter file. The card name and format are shown below.


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.
<br  style="clear:both" />
'''Table 2. CMS-Flow card for specifying the initial condition file.'''
{| class=wikitable border="1"
! Card !! Arguments !! Default !! Range !! Description
|-
| INITIAL_STARTUP_FILE <nowiki>|</nowiki> INITIAL_CONDITION_FILE || CHARACTER ||  none  || none || Hot start filename that contains the information for a Hot Start.
|}


=== Governing Equation ===
The depth-averaged 2-D salinity transport equation is given by


        <math> \frac{\partial ( h C_{sa} ) }{\partial t} + \frac{\partial (U_j h C_{sa})}{\partial x_j} = \frac{\partial }{\partial x_j} \biggl[ K_{sa}  h \frac{\partial C_{sa} }{\partial x_j} \biggr] </math>
Sometimes, the user may forget to set up the model output a hot start file or may have been running steady-state conditions. In these cases, a hot start file can easily be created and exported by the user from the SMS interface. The model requires records for water levels, current velocities, concentrations, and water depths and datasets that are missing from the initial file.
Note: It is important that the names and paths of the initial condition datasets are written correctly.


where <math> t </math> is time, <math> U_j </math> is the current velocity in the jth direction, <math> h </math> is the total water depth, <math> C_{sa} </math> is the salinity concentration, and <math> K_{sa} </math> is the salinity mixing coefficient.
'''Table 3. Path and name for initial condition file variables.'''
{| class=wikitable border="1"
! Variable !!  Path and Name
|-
| Water surface elevation ||  Datasets\Water_Elevation
|-
| Current velocity ||  Datasets\Current_Velocity
|-
| Sediment concentrations ||  Datasets\Concentration
|-
| Salinity concentrations || Datasets\Salinity
|}
<br  style="clear:both" />


=== Initial and Boundary Conditions ===
One example showing the steps for creating a user-defined hot start or initial condition file from a CMS-Flow solution file is outlined below.
The initial salinity is specified as a constant in the whole domain. The value of the constant is specified in the SMS 10.1 interface. Inflow salinity concentrations are applied at specified salinity boundary cell strings. Salinity cell strings are specified in the same manner as the hydrodynamic boundary cells strings.  
:1. Import CMS-Flow grid and solution file.
:2. Sample a time step of the solution datasets for use in the initial condition
::* Click on ''Data'' | ''Data Set Toolbox''
:::* Under the ''Tools'' section, select ''Sample time steps''.
:::* Under the ''Datasets'' section, click on the ''Water Elevation''
:3. Export the initial condition  datasets to an XMDF file


=== Numerical Methods ===
More to come about the process above.
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.


==Units for Boundary Conditions==
[[Image:Hot_Start_Sample.png|thumb|left|500px|  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.]]
* Water Surface Elevation - meters (<math>m</math>)
[[Image:Hot_Explorting_User_Defined_Arrows.png|thumb|right|500px| 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.]]
* Current Velocity - meters per second (<math>m/sec</math>)
* Flow Rate - cubic meters per second (<math> m^3/sec </math>)
* Salinity Concentration - parts per thousand (<math>PPT</math>)


='''Global Forcing'''=
<br style="clear:both" />
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==
= Global Output =
Temporally varying, spatially constant (ie. one value of wind applied for a given time to every computational cell in the domain.
[[image:Output_Tab.png|thumb|right|400px| Figure 1. ''Output'' tab in SMS 11.0 ]]
* In the near future a variable wind will be allowed and an interface within the SMS will be provided.
Global output refers to the variables that are output on every active cell on the grid. The global output options are specified in ''Output'' tab of the ''CMS-Flow Model Control'' window. More information on the global output variables, groups and CMS-Flow cards is provided in the sections below.


==Wave Forcing==
<br clear="all">
Temporally and spatially varying. 
== Output Datasets ==
* 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.
A description of the CMS-Flow cards used to specify the global output variable datasets is provided below.  
* 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
'''Table 4. Output datasets.'''
**Wave height
{| class=wikitable  style="text-align: center; border: 1px solid black;"
**Wave period
! Output Dataset !! Group  !!  Description !! <span style="color: red">Scalar</span>/<span style="color: darkblue">Vector</span> !! Units
**Wave direction
|- style="border-bottom: 1px solid red;"
**Wave dissipation
| Water_Elevation  || Water surface elevation|| Cell-centered water surface elevation || <span style="color: red">'''Scalar'''</span> || <math>m</math>
|-
| Current_Velocity  ||  Velocity || Depth-averaged and cell-centered current velocity '''Vector''' dataset and with respect to local grid coordinates || <span style="color: darkblue">'''Vector'''</span> || <math>m/s</math>
|-
| Current_Magnitude  || Velocity || Depth-averaged and cell-centered current velocity magnitude dataset || <span style="color: red">'''Scalar'''</span> || <math>m/s</math>
|-
| Eddy_Viscosity || Eddy viscosity || Cell-centered horizontal eddy viscosity || <span style="color: red">'''Scalar'''</span> || <math>m^2/s</math>
|-
| Concentration  ||  Sediment|| Depth-averaged and cell-centered sediment concentration  || <span style="color: red">'''Scalar'''</span> || <math>kg/m^3</math>
|-
| Capacity  ||  Sediment || Depth-averaged and cell-centered sediment concentration capacity || <span style="color: red">'''Scalar'''</span> || <math>kg/m^3</math>
|-
| Total_Sediment_Transport ||  Sediment || Depth-averaged and cell-centered total-load sediment transport || <span style="color: darkblue">'''Vector'''</span> || <math>kg/m/s</math>
|-
| Morphology_Change ||  Morphology ||  Cell-centered  morphology (bed) change. Positive is accretion and negative is erosion || <span style="color: red">'''Scalar'''</span> || <math>m</math>
|-
| Depth ||  Morphology ||  Cell-centered still water depth || <span style="color: red">'''Scalar'''</span> || <math>m</math>
|-
| Salinity  ||  Salinity Transport  || Depth-averaged and cell-centered sediment  concentration capacity || <span style="color: red">'''Scalar'''</span> || <math>ppt</math>
|-
| Wave_Height  ||  Waves ||  Cell-centered significant wave height || <span style="color: red">'''Scalar'''</span> || <math>m</math>
|-
| Wave_Height_Vec  ||  Waves ||  Cell-centered  significant wave height '''Vector''' || <span style="color: darkblue">'''Vector'''</span> || <math>m</math>
|-
| Wave_Period  ||  Waves ||  Cell-centered peak wave period || <span style="color: red">'''Scalar'''</span> || <math>s</math>
|-
| Wind_Magnitude  ||  Wind ||  Cell-centered wind speed || <span style="color: red">'''Scalar'''</span> || <math>m/s</math>
|-
| Wind_Velocity  ||  Wind ||  Cell-centered wind velocity '''Vector''' dataset with respect to local grid coordinates || <span style="color: darkblue">'''Vector'''</span> || <math>m/s</math>
|-
| Atm_Pressure  ||  Wind ||  Cell-centered atmospheric pressure || <span style="color: red">'''Scalar'''</span> || <math>Pa</math>
|-
| Atm_Pressure_GradX  ||  Wind ||  Cell-centered atmospheric pressure gradients in the X direction || <span style="color: red">'''Scalar'''</span> || <math>Pa/m</math>
|-
| Atm_Pressure_GradY  ||  Wind ||  Cell-centered atmospheric pressure gradients in the Y direction || <span style="color: red">'''Scalar'''</span> || <math>Pa/m</math>
|}


='''Transport Options'''=
== Output Time Series and Lists ==
==Sediment Transport==
The times at which each group is output is determined by the selecting one of four user defined output time series or lists. In SMS versions 10.1 and earlier, the output time series were used. However, because the output time series can become very large for long-term simulations, the time series have been replaced by lists in which the output times are specifying a list of starting, ending and increments. This option is more compact and also makes it easier to manually change the output options in the cmcards file.  
===Non-equilibrium Sediment Transport (NET)===
The 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.


Non-cohesive 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).  
'''Table 5. Time series and List Cards.'''
{| class=wikitable  border="1"
! Card !! Aguments/Format !! Default value !!  Description
|-
| TIME_SERIES_1 ||  [length of list 1] [output times for list 1] || 0 || Output time series  for list 1 in hours.
|-
| TIME_SERIES_2  || [length  of list 2] [output times for list 2] || 0 || Output time  series for list 2 in hours.
|-
|  TIME_SERIES_3 || [length  of list 3] [output times for list 3] || 0 ||  Output time series for list 3 in hours.
|-
| TIME_SERIES_4 || [length  of list 4] [output times for list  4] || 0 || Output time series for list 4 in hours.
|-
| TIME_LIST_1 || [number of sublists] [sublist 1: start, end,  increment] [sublist 2: start, end, increment]...|| 0 || Sublist(s) for  output time series 1. For each sublist, the arguments are starting time,  end time and increment in hours.
|-
|  TIME_LIST_2 || [number of sublist] [sublist 1: start, end, increment]  [sublist 2: start, end, increment]...|| 0 || Sublist(s) for output time  series 2. For each sublist, the arguments are starting time, end time  and increment in hours.
|-
| TIME_LIST_3  || [number of sublist] [sublist 1:  start, end, increment] [sublist 2:  start, end, increment]...|| 0 || Sublist(s) for output time series 3.  For each sublist, the arguments are starting time, end time and increment in hours.
|-
| TIME_LIST_4 ||  [number of sublist] [sublist 1:  start, end, increment] [sublist 2:  start, end, increment]...|| 0 || Sublist(s) for output time series 4.  For each sublist, the arguments are starting time, end time and  increment in hours..
|}


The governing equations are discretized using the Finite Volume Method on a staggered, non-uniform Cartesian grid. Time integration is calculated with a simple explicit forward Euler scheme. Diffusion terms are discretized with the standard central difference scheme. Advection terms are discretized with either the first order upwind scheme or the second order Hybrid Linear/Parabolic Approximation (HLPA) scheme of Zhu (1991).  
'''Table 6. Cards used to specify the output time series or list for each output group or dataset.'''
{| class=wikitable  border="1"
! Card !! Arguments !! Default  value !! Description
|-
| WSE_OUT_TIMES_LIST || INTEGER || 0 || Output time series  id for the water surface elevation in m.  
|-
| VEL_OUT_TIMES_LIST || INTEGER || 0 || Output time series  id for currentvelocity and magnitude in m/s.  
|-
| MORPH_OUT_TIMES_LIST || INTEGER || 0 || Output time series  id for the water depth and morphology (bed) change in m.
|-
| TRANS_OUT_TIMES_LIST || INTEGER || 0 || Output time series  id for sediment transport rates, concentations, and salinity.  
|-
| WAVES_OUT_TIMES_LIST || INTEGER || 0 || Output time series  id for the wave height in m, period in sec, and wave vectors.
|-
| EDDY_VISCOSITY_OUT_TIMES_LIST || INTEGER || 0 || Output time series  id for the eddy viscosity in m^2/s.
|-
| VISC_OUT_TIMES_LIST || INTEGER || 0 || Output time series  id for the eddy viscosity in m^2/s.
|-
| WIND_OUT_TIMES_LIST || INTEGER || 0 || Output time series  id for wind velocity and magnitude in m/s.
|-
| STRESS_OUT_TIMES_LIST || INTEGER || 0 || Output time series id for mean  bed shear stress in Pa.
|-
| WAVE_OUTPUT_DETAILS || ON  <nowiki>|</nowiki> OFF || OFF  || Outputs additional wave variables including wave direction, radiation stresses, breaking dissipation and roller energy.  
|}


Additional information on NET can be found [[CMS-Flow:Non-equilibrium_Sediment_Transport|here]].
== XMDF Output ==
The default option in CMS 4.2 and previous was to have all output information stored in one single XMDF file (*_sol.h5). That was fine, but this file could end up being really large and would take a long time to read into the SMS.  Starting in CMS version 5.0 and later is to output all output groups to the same individual XMDF files with according to information type (*_wse.h5, *_vel.h5, etc.).  


[[Media:Presentation.pdf | Powerpoint presentation on NET]]
=== Multiple Output Files ===
In the recent versions of CMS, all solution output is broken into multiple files.  If you want some of the output placed into the same file, you must specify cards in the CMCARDS file to change from the default. The following cards should be Advanced card section of the SMS interface or manually added to the parameter file.


==Salinity Transport==
Any of the following cards can be added to put only those datasets into one solution file.  Other datasets not specified will still go into separate files. The cards needed are as follows:
=== Introduction ===


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.
  WSE_OUT_FILE          project_sol.h5
  VEL_OUT_FILE          project_sol.h5
  VISC_OUT_FILE          project_sol.h5
  TRANS_OUT_FILE        project_sol.h5
  MORPH_OUT_FILE        project_sol.h5
  WAVES_OUT_FILE        project_sol.h5
  WIND_OUT_FILE          project_sol.h5


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.
To put all output into a single file, one simple card can be added (shown below). In SMS 12.3+ (CMS Version 5.1+), a simpler way has been created. There is an option in the interface named 'Use single XMDF solution file (_sol.h5)'.  


Additional information on Salinity Transport in CMS-Flow can be found [[CMS-Flow:Salinity_Calculation|here]].
  USE_COMMON_SOLUTION_FILE            ON


='''Other Processes'''=
=== File Compression ===
==Bottom Friction==
The standard CMS-Flow output is written to an XMDF file with the name <Case Name>_sol.h5. The binary file may be written in compressed format using the card described in the table below. An option exists in the SMS named 'XMDF file compression' that enables this from the interface.
==Hard Bottom==
==Variable D50==


='''Other Features'''=
'''Table 7. CMS-Flow card for compressing the XMDF output file'''
==Parallelization with OpenMP==
{| class=wikitable border="1"
Both Intel and AMD processors now are shipping chips with multiple cores/processors (henceforth referred to as "processors") available.
! Card !! Arguments !!  Default  value !! Description
|-
| XMDF_COMPRESSION || ON  <nowiki>|</nowiki> OFF  || OFF || Compresses the h5 file by a factor of about 7
|}


Presently (08/4/2009) - To enable use of more than one processor (or more than one thread) in CMS-Flow, the user must specify the corresponding "Card" in the "Advanced" tab in the CMS-Flow model control in SMS 10.1 (unavailable in version SMS 10.0 and earlier):
== ASCII Output ==
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)


OPENMP_THREADS  <# of threads>
The CMS-Flow cards used for outputting these two types of files are described in the Table below.
This card takes as an argument the number of threads to use for a given application with the following rules:


# If more threads are requested than are available, only the maximum on the machine are used.
'''Table 8. CMS-Flow cards used to output Tecplot and SMS Super ASCII files.'''
# If hyperthreading is allowed on that chip's architecture, all threads are used, up to the number requested.
{| class=wikitable border="1"
! Card !! Arguments !!  Description !! Default value
|-
|  GLOBAL_TECPLOT_FILES || ON  <nowiki>|</nowiki> OFF ||  Outputs Tecplot ASCII files || OFF
|-
|  GLOBAL_SUPER_FILES || ON  <nowiki>|</nowiki> OFF || Outputs general ASCII solution files || OFF
|}


  EXAMPLE 1
= Statistics =
    Your machine has 8 cores, and you want to start a CMS-Flow run that 5 threads.
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''.  
    "OPENMP_THREADS <white space> 5" is specified in the Advanced Card section.


===Hyperthreading===
This option outputs the statistics for hydrodynamics, sediment and salinity transport. If only the statistics for one group
*'''''Some''''' of the higher-end chips have a feature called "Hyperthreading" which allows each processor to split further into two "threads" which could further increase throughput of the work that processor performs.  For example, on an Intel Extreme Quad-core processor there are 4 cores, but with hyperthreading, there is a possibility of using '''8''' separate threads.
*If you know that your computer has hyperthreading, you can actually specify "OPENMP_THREADS  2" and get better performance while still only using one '''physical''' processor.


  EXAMPLE 2
* '''Hydrodynamics:'''
    Your machine has 4 Hyperthreading cores, and you want to start a CMS-Flow run that
:# Maximum  current velocity
    uses 5 threads (leaving 3 threads for other system and user processes).  
:# Maximum water level
    You would enter the card "OPENMP_THREADS <white space> 5" and CMS-Flow would use 5
:# Residual currents  (vectors and magnitude)
    threads.
:# Hydroperiod
:# Maximum spatial gradient for water levels
:# Maximum spatial gradient for current  magnitude


===Requesting too many threads===
* '''Sediment Transport and Morphology Change''':
*If you specify a number that is too large for your particular machine to use, CMS-Flow will use the maximum number of threads available.
:# Maximum total load transport rate, m^2/s
:# Net total load sediment transport rates, m^2/s
:# Average  total  load sediment transport rates, m^2/s
:# Gross  total load sediment  transport rates, m^2/s
:# Positive  and negative total load  transport rates (in x and y directions), m^2/s
:# Maximum spatial  gradient of bathymetry


  EXAMPLE 3
* '''Salinity Statistics''':
    Your machine has 2 cores, and you start a CMS-Flow run with the card: 
:# Mean Salinity
      "OPENMP_THREADS  3".
    CMS-Flow will realize that your machine has only 2 cores and is not capable of
    hyperthreading.  The number of processors that will be used is '''2'''.


===SMS 10.1+ How-to===
'''Table 9. CMS-Flow cards related to output statistics'''
The following animation quickly goes through the steps needed to add this capability to a CMS-Flow simulation.
{| class=wikitable border="1"
[http://cirp.usace.army.mil/products/tutorials/MultiProcesses.html Animation]
! Card !! Arguments !! Description !! Default value !! Notes
|-
| GLOBAL_STATISTICS ||  [t0] [tn] [dt]  || Calculates  global statistics if specified || none || [start] [end] [increment]
|-
| FLOW_STATISTICS || [t0] [tn] [dt] || Calculates  flow statistics if specified || none || [start] [end] [increment]
|-
| SEDIMENT_STATISTICS || [t0] [tn] [dt] || Calculates sediment statistics if specified || none || [start] [end] [increment]
|-
| SALINITY_STATISTICS || [t0] [tn]  [dt] ||  Calculates salinity  statistics if specified || none || [start] [end] [increment]
|}


=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.
{| class=wikitable border="1"
!  Card !! Arguments !! Default !! Range !!  Description
|-
| SOLUTION_SCHEME || CHARACTER || EXPLICIT || EXPLICIT <nowiki>|</nowiki> 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.
{| class=wikitable border="1"
!  Card !! Arguments !! Default  !! Range !!  Description
|-
| MATRIX_SOLVER  ||  CHARACTER || GMRES ||  GAUSS-SEIDEL <nowiki>|</nowiki>  GAUSS-SEIDEL-SOR  <nowiki>|</nowiki> BICGSTAB  <nowiki>|</nowiki>  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). Typical range: 30-50 for GAUSS-SEIDEL and GAUSS-SEIDEL-SOR, and 20-30 for BICGSTAB and GMRES.
|-
|  PRESSURE_ITERATIONS ||  INTEGER || Depends on Solver || >0 ||  Sets  the number of solver  iterations for the pressure equation (inner loop). Typical range: 80-100 for GAUSS-SEIDEL and GAUSS-SEIDEL-SOR, and 15-25 for BICGSTAB and GMRES.
|-
| VELOCITY_ITERATIONS || INTEGER || Depends  on Solver || >0  ||  Sets the number of solver iterations for the  velocity or momentum  equations (inner loop). Typical range: 20-30 for GAUSS-SEIDEL and GAUSS-SEIDEL-SOR, and 5-10 for BICGSTAB and GMRES.
|-
| SEDIMENT_MAX_ITERATIONS || integer  ||  20 ||  >0 || Maximum number  of iterations (outer loop) for the sediment  transport
|-
| SALINITY_MAX_ITERATIONS ||  integer  || 20 || >0|| 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 10. CMS-Flow cards  related to numerical methods.'''
{| class=wikitable border="1"
!  Card !! Arguments !! Default !! Range !!  Description
|-
| ADVECTION_SCHEME  || CHARACTER ||  EXPONENTIAL || NONE  <nowiki>|</nowiki> HYBRID  <nowiki>|</nowiki>  EXPONENTIAL  <nowiki>|</nowiki> HLPA || Sets the advection  scheme for  flow, sediment and salinity.
|}
== Wetting and Drying ==
'''Table 11. CMS-Flow cards  related to numerical methods.'''
{| class=wikitable border="1"
|-
| 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      <nowiki>|</nowiki> 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  <nowiki>|</nowiki> 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  [[CMS-Flow:Multiple_Processor_Capability|'''here''']].
'''Table 12. CMS-Flow cards related to numerical methods.'''
{| class=wikitable border="1" style="text-align:center"
! Card !! Arguments !! Default !! Solver Range !! Description
|-
| NUM_THREADS
|| INTEGER || 1
|width="230px"| '''Explicit''' - 1 to number of threads<br>'''Implicit''' -  1 to 4
|| 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:
# 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 ==
‎[[Image:Scripting_Explorer.png|thumb|right|700px|Figure  1. Example of scripting showing the files used.]]
<br clear="all">
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.
<br style="clear:both" />
<font size=2>
<font color=green>% Matlab Script: setup_cases.m</font>
clear <font color=magenta>all</font>
flow = <font color=magenta>'Flow_Shark'</font>;
wave = <font color=magenta>'Wave_Shark'</font>;
ncases = 4; <font color=green>%Number of cases or alternatives</font> 
r(1).MANNINGS_N_DATASET = <font color=magenta>'"Manning_Alt1.h5" "Flow_Shark/Datasets/ManningsN"'</font>;
r(1).WAVE_CURRENT_MEAN_STRESS = <font color=magenta>'W09'</font>;
r(1).TIME_SERIES_INCREMENT = 1800;
r(2).MANNINGS_N_DATASET = <font color=magenta>'"Manning_Alt1.h5" "Flow_Shark/Datasets/ManningsN"'</font>;
r(2).WAVE_CURRENT_MEAN_STRESS = <font color=magenta>'DATA2'</font>;
r(2).TIME_SERIES_INCREMENT = 900;
r(3).MANNINGS_N_DATASET = <font color=magenta>'"Manning_Alt2.h5" "Flow_Shark/Datasets/ManningsN"'</font>;
r(3).WAVE_CURRENT_MEAN_STRESS = <font color=magenta>'W09'</font>;
r(3).TIME_SERIES_INCREMENT = 900;
r(4).MANNINGS_N_DATASET = <font color=magenta>'"Manning_Alt2.h5" "Flow_Shark/Datasets/ManningsN"'</font>;
r(4).WAVE_CURRENT_MEAN_STRESS = <font color=magenta>'DATA2'</font>;
r(4).TIME_SERIES_INCREMENT = 600;
<font color=blue>for</font> i=1:ncases
  d = [<font color=magenta>'Case'</font>,int2str(i)];
  <font color=blue>if</font> ~exist(d,<font color=magenta>'dir'</font>)
    mkdir(d)
  <font color=blue>end</font>
  copyfile([wave,<font color=magenta>'.*'</font>],d)
  copyfile([flow,<font color=magenta>'.*'</font>],d)
  copyfile([flow,<font color=magenta>'_mp.h5'</font>],d);
  copyfile([flow,<font color=magenta>'_grid.h5'</font>],d)
  cards = fieldnames(r(i));
  file = [<font color=magenta>'.\'</font>,d,<font color=magenta>'\'</font>,flow,<font color=magenta>'.cmcards'</font>];
  <font color=blue>for</font>k=1:length(cards)
    setcard(file,cards{k},r(i).(cards{k}));
  <font color=blue>end</font>
<font color=blue>end</font>
<font color=blue>return</font>
</font>
The script above requires the subroutine below.
<font size=2>
<font color=blue>function</font> setcard(cmcardsfile,card,value)
<font color=green>% setcard(file,card,value)</font>
<font color=green>% Overwrites or appends a CMS-Flow card</font>
<font color=green>% in the *.cmcards file</font>
copyfile(cmcardsfile,<font color=magenta>'temp'</font>)
fid=fopen(<font color=magenta>'temp'</font>,<font color=magenta>'r'</font>);
fid2=fopen(cmcardsfile,<font color=magenta>'w'</font>);
nc=length(card);
ok = false(1);
<font color=blue>if </font>~ischar(value)   
  value = num2str(value);
<font color=blue>end</font>
<font color=blue>while</font> 1   
  tline = fgets(fid);       
  <font color=blue>if</font> ~ischar(tline), <font color=blue>break</font>, <font color=blue>end</font>   
  <font color=blue>if</font> strncmp(card,tline,nc)       
    fprintf(fid2,<font color=magenta>'%s      %s %s'</font> ,card,value,tline(end));               
    ok = true(1);       
    <font color=blue>continue </font> 
  <font color=blue>end</font>   
  nline = length(tline);   
  <font color=blue>if</font> (~ok && strcmp(tline(1:min(nline,14)),<font color=magenta>'END_PARAMETERS'</font>))       
    fprintf(fid2,<font color=magenta>'%s      %s %s'</font>,card,value,tline(end));       
    fprintf(fid2,<font color=magenta>'%s'</font> ,tline);       
    <font color=blue>break</font>
  <font color=blue>end</font>   
  fprintf(fid2,<font color=magenta>'%s'</font> ,tline);
<font color=blue>end</font>
fclose(fid);
fclose(fid2);
delete(<font color=magenta>'temp'</font>)
<font color=blue>return</font>
</font>
== 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.
<font size=2>
<font color=green>% Matlab Script: create_bat.m</font>
cmsexe = <font color=magenta>'cms2d_v4b42_x64p.exe'</font>; <font color=green>%CMS-Flow executable</font>
batfile = <font color=magenta>'run_cases.bat'</font>; <font color=green>%Output batch file</font>
fid = fopen(batfile,<font color=magenta>'w'</font>);
<font color=blue>for</font> i=1:ncases
  cmcards = [<font color=magenta>'.\Case'</font>,int2str(i),<font color=magenta>'\'</font>,flow,<font color=magenta>'.cmcards'</font>]; <font color=green>%CMS-Flow cmcards file</font>
  fprintf(fid,<font color=magenta>'START %s %s %s'</font>,cmsexe,cmcards,char(10));
<font color=blue>end</font>
fclose(fid);
<font color=blue>return</font>
</font>
The following text shows what the resulting batch file (*.bat) looks like
<font size=2>
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
</font>
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
----
<font size=2>
<font color=green>% Matlab Script: plot_cases.m</font>
close <font color=magenta>all</font>
eta = cell(ncases,1);
<font color=blue>for</font>  i=1:ncases   
  etafile = [<font color=magenta>'.\Case'</font> ,int2str(i),<font color=magenta>'\'</font>,flow,<font color=magenta>'_eta.txt'</font> ]; <font color=green>%Water elevation</font>
  eta{i} = load(etafile);   
<font color=blue>end</font>
figure
hold on
<font color=blue>for</font> i=1:ncases   
  h = plot(eta{i}(:,1),eta{i}(:,3),'-');  <font color=green>%3 is the index is the observation point index</font>
<font color=blue>end</font>
ylabel(<font color=magenta>'Water elevation, m'</font>)
xlabel(<font color=magenta>'Elapsed Time, hr'</font>)
<font color=blue>return</font>
</font>
----
=Units of Measurement=
{| class=wikitable border="1"
! Variable !! Units !! Symbol
|-
| Water Surface Elevation || meters || <math>m</math>
|-
| Current Velocity || meters per second  || <math>m/sec</math>
|-
| Flow Rate || cubic meters per second || <math> m^3/sec </math>
|-
| Salinity Concentration || parts per thousand || <math>ppt</math>
|-
| Sediment Concentration || kilogram per meter cubed || <math>kg/m^3</math>
|-
| Sediment Transport || kilogram per meter per second || <math>kg/m/sec</math>
|-
| Bed Shear Stress || kilogram per meter per second squared (Pascals) || <math>Pa</math>
|}
---------------------------------
[[CMS-Flow]]
[[CMS-Flow]]

Latest revision as of 14:55, 7 April 2022

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 1. HDFView 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. Only the very last record of information is preserved (no starting from earlier intervals).

The CMS hot start files are written as binary XMDF files by default. Depending on the type of hot start (single file or recurring), the names are as follows are saved in the directory of the CMS-Flow files:

  • SingleHotStart.h5
  • AutoHotStart.h5

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_TIME REAL none none Single time after start at which to output a single hot start file.
AUTO_HOT_START_INTERVAL REAL none none Sets the recurring hot start output interval .


Initial Conditions File

Figure 2. 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 desired to specify a user-defined hot start file from which to start a simulation. If the user has previously specified a hot start file be written either at a specific time or at a recurring interval, they can simply indicate to start from that hot start as an initial condition from the SMS interface, or by adding a card to the parameter file. The card name and format are shown below.


Table 2. CMS-Flow card for specifying the initial condition file.

Card Arguments Default Range Description
INITIAL_STARTUP_FILE | INITIAL_CONDITION_FILE CHARACTER none none Hot start filename that contains the information for a Hot Start.


Sometimes, the user may forget to set up the model output a hot start file or may have been running steady-state conditions. In these cases, a hot start file can easily be created and exported by the user from the SMS interface. The model requires records for water levels, current velocities, concentrations, and water depths and datasets that are missing from the initial file. Note: It is important that the names and paths of the initial condition datasets are written correctly.

Table 3. 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


One example showing the steps for creating a user-defined hot start or initial condition file from a CMS-Flow solution file is 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
  • Click on Data | Data Set Toolbox
  • Under the Tools section, select Sample time steps.
  • Under the Datasets section, click on the Water Elevation
3. Export the initial condition datasets to an XMDF file

More to come about the process above.

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.


Global Output

Figure 1. Output tab in SMS 11.0

Global output refers to the variables that are output on every active cell on the grid. The global output options are specified in Output tab of the CMS-Flow Model Control window. More information on the global output variables, groups and CMS-Flow cards is provided in the sections below.


Output Datasets

A description of the CMS-Flow cards used to specify the global output variable datasets is provided below.

Table 4. Output datasets.

Output Dataset Group Description Scalar/Vector Units
Water_Elevation Water surface elevation Cell-centered water surface elevation Scalar
Current_Velocity Velocity Depth-averaged and cell-centered current velocity Vector dataset and with respect to local grid coordinates Vector
Current_Magnitude Velocity Depth-averaged and cell-centered current velocity magnitude dataset Scalar
Eddy_Viscosity Eddy viscosity Cell-centered horizontal eddy viscosity Scalar
Concentration Sediment Depth-averaged and cell-centered sediment concentration Scalar
Capacity Sediment Depth-averaged and cell-centered sediment concentration capacity Scalar
Total_Sediment_Transport Sediment Depth-averaged and cell-centered total-load sediment transport Vector
Morphology_Change Morphology Cell-centered morphology (bed) change. Positive is accretion and negative is erosion Scalar
Depth Morphology Cell-centered still water depth Scalar
Salinity Salinity Transport Depth-averaged and cell-centered sediment concentration capacity Scalar
Wave_Height Waves Cell-centered significant wave height Scalar
Wave_Height_Vec Waves Cell-centered significant wave height Vector Vector
Wave_Period Waves Cell-centered peak wave period Scalar
Wind_Magnitude Wind Cell-centered wind speed Scalar
Wind_Velocity Wind Cell-centered wind velocity Vector dataset with respect to local grid coordinates Vector
Atm_Pressure Wind Cell-centered atmospheric pressure Scalar
Atm_Pressure_GradX Wind Cell-centered atmospheric pressure gradients in the X direction Scalar
Atm_Pressure_GradY Wind Cell-centered atmospheric pressure gradients in the Y direction Scalar

Output Time Series and Lists

The times at which each group is output is determined by the selecting one of four user defined output time series or lists. In SMS versions 10.1 and earlier, the output time series were used. However, because the output time series can become very large for long-term simulations, the time series have been replaced by lists in which the output times are specifying a list of starting, ending and increments. This option is more compact and also makes it easier to manually change the output options in the cmcards file.

Table 5. Time series and List Cards.

Card Aguments/Format Default value Description
TIME_SERIES_1 [length of list 1] [output times for list 1] 0 Output time series for list 1 in hours.
TIME_SERIES_2 [length of list 2] [output times for list 2] 0 Output time series for list 2 in hours.
TIME_SERIES_3 [length of list 3] [output times for list 3] 0 Output time series for list 3 in hours.
TIME_SERIES_4 [length of list 4] [output times for list 4] 0 Output time series for list 4 in hours.
TIME_LIST_1 [number of sublists] [sublist 1: start, end, increment] [sublist 2: start, end, increment]... 0 Sublist(s) for output time series 1. For each sublist, the arguments are starting time, end time and increment in hours.
TIME_LIST_2 [number of sublist] [sublist 1: start, end, increment] [sublist 2: start, end, increment]... 0 Sublist(s) for output time series 2. For each sublist, the arguments are starting time, end time and increment in hours.
TIME_LIST_3 [number of sublist] [sublist 1: start, end, increment] [sublist 2: start, end, increment]... 0 Sublist(s) for output time series 3. For each sublist, the arguments are starting time, end time and increment in hours.
TIME_LIST_4 [number of sublist] [sublist 1: start, end, increment] [sublist 2: start, end, increment]... 0 Sublist(s) for output time series 4. For each sublist, the arguments are starting time, end time and increment in hours..

Table 6. Cards used to specify the output time series or list for each output group or dataset.

Card Arguments Default value Description
WSE_OUT_TIMES_LIST INTEGER 0 Output time series id for the water surface elevation in m.
VEL_OUT_TIMES_LIST INTEGER 0 Output time series id for currentvelocity and magnitude in m/s.
MORPH_OUT_TIMES_LIST INTEGER 0 Output time series id for the water depth and morphology (bed) change in m.
TRANS_OUT_TIMES_LIST INTEGER 0 Output time series id for sediment transport rates, concentations, and salinity.
WAVES_OUT_TIMES_LIST INTEGER 0 Output time series id for the wave height in m, period in sec, and wave vectors.
EDDY_VISCOSITY_OUT_TIMES_LIST INTEGER 0 Output time series id for the eddy viscosity in m^2/s.
VISC_OUT_TIMES_LIST INTEGER 0 Output time series id for the eddy viscosity in m^2/s.
WIND_OUT_TIMES_LIST INTEGER 0 Output time series id for wind velocity and magnitude in m/s.
STRESS_OUT_TIMES_LIST INTEGER 0 Output time series id for mean bed shear stress in Pa.
WAVE_OUTPUT_DETAILS ON | OFF OFF Outputs additional wave variables including wave direction, radiation stresses, breaking dissipation and roller energy.

XMDF Output

The default option in CMS 4.2 and previous was to have all output information stored in one single XMDF file (*_sol.h5). That was fine, but this file could end up being really large and would take a long time to read into the SMS. Starting in CMS version 5.0 and later is to output all output groups to the same individual XMDF files with according to information type (*_wse.h5, *_vel.h5, etc.).

Multiple Output Files

In the recent versions of CMS, all solution output is broken into multiple files. If you want some of the output placed into the same file, you must specify cards in the CMCARDS file to change from the default. The following cards should be Advanced card section of the SMS interface or manually added to the parameter file.

Any of the following cards can be added to put only those datasets into one solution file. Other datasets not specified will still go into separate files. The cards needed are as follows:

 WSE_OUT_FILE           project_sol.h5
 VEL_OUT_FILE           project_sol.h5
 VISC_OUT_FILE          project_sol.h5
 TRANS_OUT_FILE         project_sol.h5
 MORPH_OUT_FILE         project_sol.h5
 WAVES_OUT_FILE         project_sol.h5
 WIND_OUT_FILE          project_sol.h5

To put all output into a single file, one simple card can be added (shown below). In SMS 12.3+ (CMS Version 5.1+), a simpler way has been created. There is an option in the interface named 'Use single XMDF solution file (_sol.h5)'.

 USE_COMMON_SOLUTION_FILE            ON

File Compression

The standard CMS-Flow output is written to an XMDF file with the name <Case Name>_sol.h5. The binary file may be written in compressed format using the card described in the table below. An option exists in the SMS named 'XMDF file compression' that enables this from the interface.

Table 7. CMS-Flow card for compressing the XMDF output file

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

ASCII Output

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 8. 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 general ASCII solution files 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

  • Hydrodynamics:
  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/s
  2. Net total load sediment transport rates, m^2/s
  3. Average total load sediment transport rates, m^2/s
  4. Gross total load sediment transport rates, m^2/s
  5. Positive and negative total load transport rates (in x and y directions), m^2/s
  6. Maximum spatial gradient of bathymetry
  • Salinity Statistics:
  1. Mean Salinity

Table 9. CMS-Flow cards related to output statistics

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

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). Typical range: 30-50 for GAUSS-SEIDEL and GAUSS-SEIDEL-SOR, and 20-30 for BICGSTAB and GMRES.
PRESSURE_ITERATIONS INTEGER Depends on Solver >0 Sets the number of solver iterations for the pressure equation (inner loop). Typical range: 80-100 for GAUSS-SEIDEL and GAUSS-SEIDEL-SOR, and 15-25 for BICGSTAB and GMRES.
VELOCITY_ITERATIONS INTEGER Depends on Solver >0 Sets the number of solver iterations for the velocity or momentum equations (inner loop). Typical range: 20-30 for GAUSS-SEIDEL and GAUSS-SEIDEL-SOR, and 5-10 for BICGSTAB and GMRES.
SEDIMENT_MAX_ITERATIONS integer 20 >0 Maximum number of iterations (outer loop) for the sediment transport
SALINITY_MAX_ITERATIONS integer 20 >0 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 10. 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 11. 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 12. CMS-Flow cards related to numerical methods.

Card Arguments Default Solver Range Description
NUM_THREADS INTEGER 1 Explicit - 1 to number of threads
Implicit - 1 to 4
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,'.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


Units of Measurement

Variable Units Symbol
Water Surface Elevation meters
Current Velocity meters per second
Flow Rate cubic meters per second
Salinity Concentration parts per thousand
Sediment Concentration kilogram per meter cubed
Sediment Transport kilogram per meter per second
Bed Shear Stress kilogram per meter per second squared (Pascals)

CMS-Flow