Combine SMS 8.1 and FVCOM for Modeling Estuary and Coastal

FVCOM User Manual (October 2011)

SMAST/UMASSD-11-1101 SMAST/UMASSD-11-1101

Chapter 20: Unstructured Triangular Mesh Generation FVCOM uses unstructured trianular rids and since no auto!atic !es" enerator is su##lied $it" t"e codin% users !ust use alternate so&t$are to build t"e !es"' T"ere are a !ult !ultit itude ude o& !es" !es" ener enerat ator orss aai aaila labl ble' e'

So!e So!e are are o#en o#en sour source ce and seera seerall are are

co!!ercial' An so&t$are $"ic" is ca#able o& eneratin t$o-di!ensional% t$o-di!ensional% unstructured trianular trianular rids rids $ould $or* &or FVCOM' +o$eer% +o$eer% "i" #o$ered #o$ered !es"in so&t$are so&t$are desined &or co!#le, -D rids% suc" as .riden% CM% or .AMT are e,#ensie% di&&icul di&&icultt to learn% learn% and are unnecessaril unnecessaril  #o$er&ul' e "ae listed listed so!e reco!!ended reco!!ended !es"es on t"e FVCOM users $ebsite' At MDM/SMAST% $e #ri!aril use t"e SMS (Sur&ace ater Model Sste!) to enerate unstructured rids in in FVCOM' SMS is !odule-based co!!ercial so&t$are t"at t"at can be #urc"ased in $"ole $"ole or b !odule' !odule' Onl t"ree t"ree !odules are necessar necessar &or !es" !es" eneration' eneration' T"e are t"e Mes" Module% Module% t"e Ma# Module% and t"e Scatter Scatter Module' Module' T"e beta ersion can be do$nloaded &ro! t"e SMS $ebsite3 "tt#3//$$$'e!s-i'co!/SMS/SMS4Oerie$/s!s4oerie$ "tt#3//$$$ 'e!s-i'co!/SMS/SMS4Oerie$/s!s4oerie$'"t!l/ '"t!l/ n t"is docu!ent% $e $ill uide ou t"rou" an e,a!#le !es" eneration usin SMS to teac" t"e basic #rocedure o& eneratin !es"es &or FVCOM' 20.1. Data Preparation

To enerate an unstructured rid% users need to "ae &irst ac5uired releant data includin3 1) coastlines and 2) bat"!etr'

a) Coastline preparation

FVCOM can be run in eit"er s#"erical or Cartesian Cartesian coordinates' For a##lications in t"e coastal ocean% $e reco!!end reco!!end t"at users use Cartesian Cartesian coordinates' coordinates' n eneral% t"e coastline data are in a eora#"ic &or!at o& lonitude and latitude' A #ro6ection #rora! is needed to conert t"e lonitude and latitude to t"e Cartesian coordinates relatie to a selected re&erence #oint' 7rocedures to #re#are t"e coastline coastline data are ien belo$' belo$'

Step 1: Download the coastline data

81


SMAST/UMASSD-11-1101 SMAST/UMASSD-11-1101

9eco!!ended $ebsite3 "tt#3//$$$'ndc'noaa'o/!/eodas/eodas'"t!l "tt#3//$$$'ndc'noaa'o/!/eodas/eodas'"t!l'' :OAA "as a .ODAS .ODAS CD aailable $it" .ODAS coastline e,tractor' e,tractor' T"e &or!at o& t"e do$nload coastline data is as &ollo$s3

1

41.5756

-70.5038

2

41.5756

-70.5041

2

41.5757

-70.5043

2

41.5760

-70.5043

2

41.5761

-70.5042

2

41.5761

-70.5039

2

41.5760

-70.5036

2

41.5757

-70.5036

3

41.5756

-70.5038

Colu!n 13 t"e data t#e3 1-start #oint; 2-#oints bet$een start and end #oints; -end #oint' Colu!n 23


Do$n Do$nlo load ad t"e t"e Cart Carto ora ra#" #"ic ic 7ro6 7ro6ect ectio ion n Tool ool call called ed =Pro#> &ro! &ro! $ebs $ebsit itee "tt#3//#ro6'!a#tools'or/ and install install it'



Use =7ro6> to conert t"e lonitude and an d latitude &or!at data to t"e ,- coordinate' co ordinate'

T"e &or!at o& t"e out#ut data &ile loo*s li*e

?@1??'@ ?@1?8'1? ?@1?2'B?2B ?@1?2'?128 ?@1?1'188 ?@1?@B'21B ?@ ? @1801'18 ?@ ? @1801'0B ?@1??'@

Colu!n 13 x

-18BB'02@ -18B'828 -18B'@B -18B01'B1 -1880'B2 -1880'B0 -18B01'BB1 -18B'8?2B -18BB'02@

Colu!n 23 y

82


SMAST/UMASSD-11-1101

:ote3 $"en =7ro6> is used% be sure to *ee# t"e , and  locations o& t"e re&erence #oint used &or t"e #ro6ection' T"ese $ill be re5uired i& ou $is" to conert t"e , and  locations bac* to
=7ro6> can onl run $it" an in#ut &ile o& lonitude and latitude data% so a&ter t"e #ro6ection is co!#leted% $e need to add t"e 1st colu!n o& t"e oriinal data into t"e #ro6ected data to *ee# t"e identi&ication o& t"e data t#e' *. +un ,+eadCST.)- to create the coastline )ile )or&at co&patile with SMS.

e "ae a si!#le Fortran @@ #rora! called =readcst4ne$'&> on FVCOM user $ebsite' Users can use it or can $rite a er si!#le Matlab #rora! to do it' T"e &or!at o& t"e resultin out#ut &ile is3 COAST 11 0.0 9

11

0 871884.3125

-139646.0313

0.0

871859.3125

-139645.9219

0.0

871842.6875

-139634.7500

0.0

871842.8125

-139601.4375

0.0

871851.1875

-139590.3594

0.0

871876.1875

-139590.4531

0.0

871901.1875

-139601.6719

0.0

871901.0625

-139634.9844

0.0

871884.3125

-139646.0313

0.0

871775.5625

-139734.4531

0.0

871742.2500

-139723.2188

0.0

871720.3125

-139712.0000

0.0

871700.6875

-139689.7344

0.0

871700.7500

-139667.5156

0.0

871784.1875

-139667.8438

0.0

871825.8125

-139679.1094

0.0

871842.4375

-139701.3906

0.0

871834.0000

-139723.5781

0.0

871820.2500

-139734.6094

0.0

871775.5625

-139734.4531

0.0

0

b) Bathymetric data preparation

T"e bat"!etric data can be do$nloaded &ro! t"e US.S bat"!etric database or obtained &ro! ot"er data sources' n eneral% t"e data &or!at is3

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Colu!n 13 x (!eters) ; Colu!n 23 y (!eters); Colu!n 3 de#t" (!eters)' :ote3 FVCOM re5uires t"at t"e $ater de#t" is #ositie &or $et #oints' /ow "ou are read" to run ,SMS-.

20.2. Grid Generation

1' Clic* =SMS>% select =Start Usin SMS>

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2' .o to =File> at t"e u##er le&t corner' Select =O#en> and t"en &ind t"e 'cst> &ile in our co!#uter and o#en it' Select =ADC9C> and clic* on it' Eour coastline data s"ould a##ear on t"e screen' T"is is an e,a!#le o& a5uoit a on t"e sout"ern coast o& Ca#e Cod% Massac"usetts'

8



$. Create an initial open oundar"

S#eci& t"e o#en boundar line user =Create Feature Arc>'

Create Feature Arc

'

Start at a selected #oint at t"e coastline $it" one clic*% and t"en "old =s"i&t>% clic* #oints to build an o#en boundar' e sure to double clic* at t"e end #oint'

8B



T"e dots are t"e #oints ou clic*'

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*. S&ooth the open oundar" line

Select =Select Feature Verte,>% t"en use !ouse to !oe t"e line to et t"e s"a#e ou li*e' Eou can add additional #oints b selectin =Create Feature Verte,>

Select Feature Verte, Create Feature Verte,

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. Choose the horiontal resolution

Clic* =Select Feature Arc>% t"en !oe t"e !ouse to t"e #art o& t"e coastline (t"e line $it" ra color is t"e #art o& t"e coastline ou select); o to t"e u##er !anual line to select =Feature Ob6ects> to select =9edistribute Vertices>

Feature Ob6ects 9edistribute Vertices

Select Feature Arc

88



Clic* =9edistribute Vertices>' n t"e sub-$indo$ o& =distribute ertices>% ou can select t"e s#acin interal' T"e unit o& t"e lent" is t"e sa!e as our in#ut data' For e,a!#le% $e t#e =0> in =s#acin>% it !eans $e $ant to "ae a "oriontal resolution o& about 0 ! in t"e se!ents $e c"oose'

C"oose t"e s#acin

9e#eat t"is e,ercise until ou select all se!ents o& t"e coastline and o#en boundar line' e sure to sae our !a# &ile' SMS does not sae as our #roceed and ou cannot o bac*$ards' A&ter all t"ese are co!#leted% t"e screen s"ould loo* li*e3

100



/et step is to uild &esh3

101



4. 5uild the &esh

Clic* =Select Feature Arc>' Use our !ouse to select all lines in t"e screen ou $ant to include in buildin !es"es' T"en o to GFeature Ob6ectsG !enu and select Huild #olonsG'

Select Feature Arc

102



Clic* =Select Feature 7olons> on t"e le&t !enu bar% t"en !oe t"e !ouse bac* to t"e !es" do!ain% "old t"e s"i&t *e% and clic* it% t"e entire do!ain s"ould beco!e blac*' & ou &ind so!e reions are not colored blac*% it !eans t"at our #reious ste#s are not done correctl% eit"er t"e line is not closed or #er"a#s anot"er issue' e sure to o bac* to &i, it' "en correct% our screen s"ould loo* li*e t"is3

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.o to t"e u##er !enu bar to and select =Ma#2D Mes"> &ro! t"e =Feature Ob6ects>G #ull-do$n !enu' Clic* on it to start buildin o ur !es"'

Ma#I2D Mes"

10



:o$% t"e !es" is built' See belo$ &or t"e result'

10



e sure to sae t"is !es" First% clic* >Mes" Module> on t"e le&t side !anual bar% t"en o to t"e u##er !enu =File> to select =Sae Mes">' Clic* on it% our !es" is saed'

Mes" Module

10B



6. Mesh 7ualit" Control Step 1: unloc* t"e !es"' 9e!ain in =Mes" Module>% o to t"e u##er !enu to select

=:odes>' n t"e sub-$indo$ o& =:odes>% ou $ill &ind =loc*ed> bo, $"ic" $ill be c"ec*ed' T"at !eans t"at t"e !es" is loc*ed' Clic* =loc*ed> to unloc* t"e !es"' Step 2: o to t"e le&t !enu bar to select =Dis#la O#tions>' Clic* on it% ou s"ould

see a screen li*e t"is3

Dis#la O#tions

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Step $: c"ec* t"e bo, =Mes" 5ualit>% clic* =o#tions> ne,t to =Mes" 5ualit>% an

ele!ent 5ualit c"ec*s screen a##ears' Users need to in#ut t"eir 5ualit re5uire!ent #ara!eters into eac" ro$' elo$ are our reco!!endations3 Mini!u! interior anle3 0'0 Ma,i!u! interior anle3 10'0 Ma,i!u! slo#e3 0'1 le!ent area c"ane3 0' Connectin ele!ents3 ? or less (? is t"e !a,i!u! ele!ents allo$ed &or FVCOM)' A&ter all selections% clic* =o*>'

10?



elo$ is t"e result o& t"e 5ualit selection' 9ed colors s"o$ t"at t"e anle o& an ele!ent is out o& t"e rane $e s#eci&ied% and blue colors s"o$ t"at t"e ele!ent area c"ane o& t"ose trianles are out o& t"e rane $e e,#ected'

108



Step *3 start ad6ustin t"e !es" anles and area' T"e si!#lest $a is to ad6ust usin

t"e !ouse' .o to t"e le&t !anual bar to clic* on =Select Mes" :ode>' Use t"e !ouse to o to t"e colored area% and !oe t"e nodes until t"e color disa##ears' 9e#eat &or all colored reions'

Select Mes" :ode

:ote3 To !a*e t"e radiation o#en boundar condition $or* #ro#erl% $e suest t"at users !a*e one o& t"e interior edes o& an o#en boundar trianle nor!al to t"e o#en boundar' FVCOM $ill run $it"out t"is restriction% but $it" increased nu!erical noise due to t"e "i" &re5uenc $ae re&lection &ro! t"e o#en boundar'

110



8. Select the open oundar" nodes to uild an input )ile )or the open oundar" condition treat&ent. Step 1: .o to t"e le&t !anual bar to clic* =Create :odestrin>' Moe our !ouse to t"e

&irst node o& t"e o#en boundar line connected to t"e coastline' +old =s"i&t> and t"en continue to clic* t"e o#en boundar nodes' "en ou et to t"e last end node #oint connected to t"e ot"er side o& t"e coastline% double clic* it' C"ec* t"e screen to !a*e sure all boundar nodes are selected'

Create :odestrin

111



Step 2: 9e-nu!ber t"e o#en boundar nodes' .o to t"e le&t !anual bar to clic* on

=Select :odestrin>' A s!all bo, $ill a##ear on t"e o#en boundar line' Clic* t"is bo,% all t"e o#en boundar nodes $ill be colored' .o to t"e u##er !anual bar to select =:odestrin>' On t"at sub-$indo$% clic* on =renu!ber>' All nodes on t"e o#en boundar $ill be renu!bered'

9enu!ber

Select :odestrin

A&ter ou "ae &inis"ed t"is ste#% be sure to o to =File> to clic* =Save Mesh>% so t"at t"e !es" &ile $ill be u#dated $it" t"e ne$ nu!berin o& t"e o#en boundar nodes' T"is nu!berin $ill &acilitate s#eci&in t"e o#en boundar &orcin in later !odel setu# staes'

112



9. %nterpolation o) ath"&etric data into the &esh

Step 1: .o to t"e u##er !anual to =File> and select =O#en>' Find t"e bat"!etric &ile in

our co!#uter% t"en clic* it' Jee# clic*in =ne,t> in t"e .U selection' All t"e data $ill a##ear on t"e screen% oerla##in oer t"e !es"' An e,a!#le is ien belo$' :ote3 t"is is 6ust used to de!onstrate "o$ $e can inter#olate t"e bat"!etric data into t"e !es"% so $e did not use t"e co!#lete bat"!etric data set "ere'

11



Step 2: .o to t"e u##er !anual bar% select =Scatter>' n t"e sub-$indo$ !anual% select

=nter#olate to Mes">' See t"e screen belo$ &or e,a!#le'

11



Step $3 Clic* =nter#olate to Mes"> Eou can select di&&erent inter#olation !et"ods in t"e

bo, o& =inter#olation>' A&ter our !a*e our selection% clic* =o*>' T"e bat"!etric data $ill be inter#olated to nodes o& t"e !es"'

11



Step *: Select =sae as> &ro! t"e &ile !enu and create an out#ut &ile na!e $it" t"e

e,tension >#ts> (e,a!#le3 !&ile'#ts)' Clic* =Sae>% a sub-$indo$ titled =,#ort S"oal File> screen $ill a##ear' Fro! "ere% ou !ust do t$o t"ins3 1) in =,#ort O#tion> c"ec* =Sae Mes">; and 2) o to =Colu!n +eader>% select =K> ro$ and t"en c"oose t"e last o#tion =eleation (K) inter(Scalar)>' A&ter ou co!#lete t"ese t$o ste#s% clic* =o*> and our bat"!etric data &ile is saed'

11B



10. Displa"ing the Mesh and %nterpolated 5ath"&etr"

Users can o to =Dis#la O#tions> on t"e le&t !anual bar to see di&&erent !et"ods o& dis#lain t"e !es" and inter#olated bat"!etr' S"o$n belo$ is an e,a!#le o& t"e bat"!etr i!ae and !es" #roduced b selectin =2D Mes"> and =Contour O#tions>'

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Combine SMS 8.1 and FVCOM for Modeling Estuary and Coastal

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