ADCIRCWiki - User contributions [en]

Fort.19 file

2022-06-30T13:01:39Z

Cfulcher:

The fort.19 file contains non-periodic, time varying elevation boundary condition file for “elevation specified” boundary nodes. This file is only read when an “elevation specified” boundary condition has been specified in the [[fort.14 file]] ([[NOPE]]>0) and [[NBFR]]=0 in the [[fort.15 file]].

== File Format ==
The basic file structure is shown below. Each line of input data is represented by a line containing the input variable name(s). Blank lines are only to enhance readability. Loops indicate multiple lines of input.

[[ETIMINC]]

for k=1,[[NETA]]

: [[ESBIN(k)]]

end k loop

===Notes===

The first set of elevation values are provided at [[TIME]]=[[STATIM]]. Additional sets of elevation values are provided every [[ETIMINC]].

Enough sets of elevation values must be provided to extend for the entire model run, otherwise the run will crash!

[[Category:input files]]

Fort.19 file format

2022-06-30T13:01:05Z

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Fort.10 file format

2022-06-30T13:00:18Z

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Fort.11 file format

2022-06-30T12:59:51Z

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Fort.11 file

2022-06-30T12:58:12Z

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The fort.11 file is only used for a baroclinic run. Baroclinic 2DDI runs are not yet supported. Baroclinic 3D runs occur if [[IDEN]] is not equal to 0.

== File Format ==
The basic file structure is shown below. Each line of input data is represented by a line containing the input variable name(s). Blank lines are only to enhance readability. Loops indicate multiple lines of input.

===File structure for a baroclinic 2DDI run===

====IDEN = 1 or -1====
:Header Line 1
:Header Line 2
:[[NVP]]
:for k=1 to NVP
::[[jki]],[[DASIGT(jki)]]
:end k loop

====IDEN = 2 or -2====
:Header Line 1
:Header Line 2
:NVP
:for k=1 to NVP
::'jki,[[DASALT(jki)]]
:end k loop

====IDEN = 3 or -3====
:Header Line 1
:Header Line 2
:NVP
:for k=1 to NVP
::jki,[[DATEMP(jki)]]
:end k loop

====IDEN = 4 or -4====
:Header Line 1
:Header Line 2
:NVP
:for k=1 to NVP
::jki, DATEMP(jki), DASALT(jki)
:end k loop

===File structure for a baroclinic 3D run===

====IDEN = 1 or -1====
:Header Line 1
:Header Line 2
:[[NVN]], NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, [[SIGT(NHNN,NVNN)]]
::end j loop
:end k loop

====IDEN = 2 or -2====
:Header Line 1
:Header Line 2
:NVN, NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, [[SAL(k,j)]]
::end j loop
:end k loop

====IDEN = 3 or -3====
:Header Line 1
:Header Line 2
:NVN, NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, [[TEMP(k,j)]]
::end j loop
:end k loop

====IDEN = 4 or -4====
:Header Line 1
:Header Line 2
:NVN, NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, TEMP(k,j),SAL(k,j)
::end j loop
:end k loop

'''Note:''' j=1 at bottom, j=NVN at surface

[[Category:input files]]

Fort.20 file format

2022-06-28T19:27:41Z

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Fort.20 file

2022-06-28T19:27:03Z

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Non-periodic, normal flow boundary condition file for “specified non-zero normal flow” boundary nodes. This file is only read when a “specified non-zero normal flow” boundary condition has been specified in the Grid and Boundary Information File ([[IBTYPE]] =2, 12 or 22) and [[NFFR]] =0 in the [[fort.15 file]].

= File Format =
The basic file structure is shown below. Each line of input data is represented by a line containing the input variable name(s). Blank lines are only to enhance readability. Loops indicate multiple lines of input. Definitions of each variable are provided via hot links.

FTIMINC

for k=1,NFLBN

: QNIN(k)

end k loop

=Notes:=

The first set of normal flow values is provided at TIME=STATIM. Additional sets of normal flow values are provided every FTIMINC

Enough sets of normal flow values must be provided to extend for the entire model run, otherwise the run will crash!

Fort.19 file format

2022-06-28T19:26:06Z

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Fort.19 file

2022-06-28T19:25:29Z

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The fort.19 file contains non-periodic, time varying elevation boundary condition file for “elevation specified” boundary nodes. This file is only read when an “elevation specified” boundary condition has been specified in the [[fort.14 file]] ([[NOPE]]>0) and [[NBFR]]=0 in the [[fort.15 file]].

= File Format =
The basic file structure is shown below. Each line of input data is represented by a line containing the input variable name(s). Blank lines are only to enhance readability. Loops indicate multiple lines of input.

[[ETIMINC]]

for k=1,[[NETA]]

: [[ESBIN(k)]]

end k loop

=Notes=

The first set of elevation values are provided at [[TIME]]=[[STATIM]]. Additional sets of elevation values are provided every [[ETIMINC]].

Enough sets of elevation values must be provided to extend for the entire model run, otherwise the run will crash!

[[Category:input files]]

Fort.11 file format

2022-06-28T19:24:19Z

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#REDIRECT [[Fort.11_file]]

Fort.11 file

2022-06-28T17:55:07Z

Cfulcher: Move file format to this page, initial format edits to create page sections

The fort.11 file is only used for a baroclinic run. Baroclinic 2DDI runs are not yet supported. Baroclinic 3D runs occur if [[IDEN]] is not equal to 0.

= File Format =
The basic file structure is shown below. Each line of input data is represented by a line containing the input variable name(s). Blank lines are only to enhance readability. Loops indicate multiple lines of input.

=File structure for a baroclinic 2DDI run=

==IDEN = 1 or -1==
:Header Line 1
:Header Line 2
:[[NVP]]
:for k=1 to NVP
::[[jki]],[[DASIGT(jki)]]
:end k loop

==IDEN = 2 or -2==
:Header Line 1
:Header Line 2
:NVP
:for k=1 to NVP
::'jki,[[DASALT(jki)]]
:end k loop

==IDEN = 3 or -3==
:Header Line 1
:Header Line 2
:NVP
:for k=1 to NVP
::jki,[[DATEMP(jki)]]
:end k loop

==IDEN = 4 or -4==
:Header Line 1
:Header Line 2
:NVP
:for k=1 to NVP
::jki, DATEMP(jki), DASALT(jki)
:end k loop

=File structure for a baroclinic 3D run=

==IDEN = 1 or -1==
:Header Line 1
:Header Line 2
:[[NVN]], NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, [[SIGT(NHNN,NVNN)]]
::end j loop
:end k loop

==IDEN = 2 or -2==
:Header Line 1
:Header Line 2
:NVN, NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, [[SAL(k,j)]]
::end j loop
:end k loop

==IDEN = 3 or -3==
:Header Line 1
:Header Line 2
:NVN, NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, [[TEMP(k,j)]]
::end j loop
:end k loop

==IDEN = 4 or -4==
:Header Line 1
:Header Line 2
:NVN, NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, TEMP(k,j),SAL(k,j)
::end j loop
:end k loop

'''Note:''' j=1 at bottom, j=NVN at surface

[[Category:input files]]

Fort.11 file

2022-06-28T17:45:11Z

Cfulcher: Move file format to this page

The fort.11 file is only used for a baroclinic run. Baroclinic 2DDI runs are not yet supported. Baroclinic 3D runs occur if [[IDEN]] is not equal to 0.

== File Format ==
The basic file structure is shown below. Each line of input data is represented by a line containing the input variable name(s). Blank lines are only to enhance readability. Loops indicate multiple lines of input.

=File structure for a baroclinic 2DDI run=

If [[IDEN]] = 1 or -1
:Header Line 1
:Header Line 2
:[[NVP]]
:for k=1 to NVP
::[[jki]],[[DASIGT(jki)]]
:end k loop

If IDEN = 2 or -2
:Header Line 1
:Header Line 2
:NVP
:for k=1 to NVP
::'jki,[[DASALT(jki)]]
:end k loop

If IDEN = 3 or -3
:Header Line 1
:Header Line 2
:NVP
:for k=1 to NVP
::jki,[[DATEMP(jki)]]
:end k loop

If IDEN = 4 or -4
:Header Line 1
:Header Line 2
:NVP
:for k=1 to NVP
::jki, DATEMP(jki), DASALT(jki)
:end k loop

=File structure for a baroclinic 3D run=

If IDEN = 1 or -1
:Header Line 1
:Header Line 2
:[[NVN]], NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, [[SIGT(NHNN,NVNN)]]
::end j loop
:end k loop

If IDEN = 2 or -2
:Header Line 1
:Header Line 2
:NVN, NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, [[SAL(k,j)]]
::end j loop
:end k loop

If IDEN = 3 or -3
:Header Line 1
:Header Line 2
:NVN, NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, [[TEMP(k,j)]]
::end j loop
:end k loop

If IDEN = 4 or -4
:Header Line 1
:Header Line 2
:NVN, NVP
:for k=1 to NVP
::for j=1 to NVN
:::k, j, TEMP(k,j),SAL(k,j)
::end j loop
:end k loop

'''Note:''' j=1 at bottom, j=NVN at surface

[[Category:input files]]

Fort.10 file format

2022-06-28T17:43:57Z

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Fort.38 file

2022-06-24T17:52:22Z

Cfulcher: Format edits

The surface temperature boundary condition input file (fort.38) is read in when the [[RES_BC_FLAG]] is set to -3, 3, -4, or 4 in the [[fort.15 file]] (i.e., when a lateral temperature boundary condition is being used) and its format depends on the [[BCFLAG_TEMP]] parameter in the [[fort.15 file]], which controls the surface heat flux parameterization in ADCIRC.

== File Format ==

The basic file structure is shown below. Each line of input is represented by a line containing the input variable name(s) in bold face type. Blank lines are to enhance readability. Loops indicate multiple lines of input.

==='''<code>BCFLAG_TEMP=1'''</code>===

''for i=1 to [[numberOfDataSets]]''

: ''for k=1 to [[NP]]''

:: '''<code>k'''</code>, '''<code>[[q_heat(k)]]'''</code>

:: ''end k loop''

: ''end i loop''

==='''<code>BCFLAG_TEMP=2'''</code>===

''for i=1 to [[numberOfDataSets]]''

:: ('''<code>K'''</code>, ('''<code>TMP(K,J)'''</code>, J=1,6),K=1,[[NP]])

''end i loop''

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

==='''<code>BCFLAG_TEMP=3'''</code>===

''for i=1 to [[numberOfDataSets]]''

:: ('''<code>K'''</code>, ('''<code>TMP(K,J)'''</code>, J=1,4),K=1,[[NP]])

''end i loop''

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

===Note===
In all the above cases, NP is the number of nodes in the horizontal mesh (i.e., the 2D fulldomain number of nodes). See the [[fort.15 file]] documentation on 3D baroclinic physics (particularly the explanation of various [[BCFLAG_TEMP]] values) for more details.

[[Category:input files]]

Fort.10 file

2022-06-24T15:34:36Z

Cfulcher: Format edits

The fort.10 file contains the concentration field needed for passive scalar transport.

== File Format ==
The basic file structure is shown below. Each line of input data is represented by a line containing the input variable name(s). Blank lines are only to enhance readability. Loops indicate multiple lines of input.

===File structure for a 2DDI run===

'''<code>Header Line 1'''</code>

'''<code>Header Line 2'''</code>

'''<code>[[NVP]]'''</code>

: for k=1 to [[NVP]]
:: [[jki]],'''<code>[[DACONC(jki)]]'''</code>
: end k loop

===File structure for a 3D run===

'''<code>Header Line 1'''</code>

'''<code>Header Line 2'''</code>

'''<code>[[NVN]]'''</code>, '''<code>[[NVP]]'''</code>

: for k=1 to [[NVP]]
:: for j=1 to [[NVN]]
::: '''<code>[[NHNN]]'''</code>,'''<code>[[NVNN]]'''</code>,'''<code>[[CONC(NHNN,NVNN)]]'''</code>
:: end j loop
: end k loop

[[Category:input files]]

Fort.10 file

2022-06-24T15:23:37Z

Cfulcher: Move file format to this page

The fort.10 file contains the concentration field needed for passive scalar transport.

== File Format ==
The basic file structure is shown below. Each line of input data is represented by a line containing the input variable name(s). Blank lines are only to enhance readability. Loops indicate multiple lines of input.

===File structure for a 2DDI run===

Header Line 1

Header Line 2

[[NVP]]

: for k=1 to [[NVP]]
:: [[jki]],[[DACONC(jki)]]
: end k loop

===File structure for a 3D run===

Header Line 1

Header Line 2

[[NVN]], [[NVP]]

: for k=1 to [[NVP]]
:: for j=1 to [[NVN]]
::: [[NHNN]],[[NVNN]],[[CONC(NHNN,NVNN)]]
:: end j loop
: end k loop

[[Category:input files]]

Fort.38 file

2022-06-24T14:00:15Z

Cfulcher: /* File Format */

The surface temperature boundary condition input file (fort.38) is read in when the [[RES_BC_FLAG]] is set to -3, 3, -4, or 4 in the [[fort.15 file]] (i.e., when a lateral temperature boundary condition is being used) and its format depends on the [[BCFLAG_TEMP]] parameter in the [[fort.15 file]], which controls the surface heat flux parameterization in ADCIRC.

== File Format ==

The basic file structure is shown below. Each line of input is represented by a line containing the input variable name(s) in bold face type. Blank lines are to enhance readability. Loops indicate multiple lines of input.

===BCFLAG_TEMP=1===

for i=1 to [[numberOfDataSets]]

: for k=1 to [[NP]]

:: '''<code>k'''</code>, '''<code>[[q_heat(k)]]'''</code>

:: end k loop

: end i loop

===BCFLAG_TEMP=2===

for i=1 to [[numberOfDataSets]]

:: ('''<code>K'''</code>, ('''<code>TMP(K,J)'''</code>, J=1,6),K=1,[[NP]])

end i loop

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

===BCFLAG_TEMP=3===

for i=1 to [[numberOfDataSets]]

:: ('''<code>K'''</code>, ('''<code>TMP(K,J)'''</code>, J=1,4),K=1,[[NP]])

end i loop

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

===Note===
In all the above cases, NP is the number of nodes in the horizontal mesh (i.e., the 2D fulldomain number of nodes). See the [[fort.15 file]] documentation on 3D baroclinic physics (particularly the explanation of various [[BCFLAG_TEMP]] values) for more details.

[[Category:input files]]

Fort.38 file

2022-06-24T13:40:51Z

Cfulcher: Move file format to this page

The surface temperature boundary condition input file (fort.38) is read in when the [[RES_BC_FLAG]] is set to -3, 3, -4, or 4 in the [[fort.15 file]] (i.e., when a lateral temperature boundary condition is being used) and its format depends on the [[BCFLAG_TEMP]] parameter in the [[fort.15 file]], which controls the surface heat flux parameterization in ADCIRC.

== File Format ==

The basic file structure is shown below. Each line of input is represented by a line containing the input variable name(s) in bold face type. Blank lines are to enhance readability. Loops indicate multiple lines of input.

===BCFLAG_TEMP=1===

for i=1 to [[numberOfDataSets]]

: for k=1 to [[NP]]

:: k, [[q_heat(k)]]

:: end k loop

: end i loop

===BCFLAG_TEMP=2===

for i=1 to numberOfDataSets

:: (K, (TMP(K,J), J=1,6),K=1,NP)

end i loop

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

===BCFLAG_TEMP=3===

for i=1 to numberOfDataSets

:: (K, (TMP(K,J), J=1,4),K=1,NP)

end i loop

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

===Note===
In all the above cases, NP is the number of nodes in the horizontal mesh (i.e., the 2D fulldomain number of nodes). See the [[fort.15 file]] documentation on 3D baroclinic physics (particularly the explanation of various [[BCFLAG_TEMP]] values) for more details.

[[Category:input files]]

Fort.38 file

2022-06-24T13:04:28Z

Cfulcher: /* File Format */

The surface temperature boundary condition input file (fort.38) is read in when the [[RES_BC_FLAG]] is set to -3, 3, -4, or 4 in the [[fort.15 file]] (i.e., when a lateral temperature boundary condition is being used) and its format depends on the [[BCFLAG_TEMP]] parameter in the [[fort.15 file]], which controls the surface heat flux parameterization in ADCIRC.

The basic file structure is shown below. Each line of input is represented by a line containing the input variable name(s) in bold face type. Blank lines are to enhance readability. Loops indicate multiple lines of input.

==BCFLAG_TEMP=1==

for i=1 to [[numberOfDataSets]]

: for k=1 to [[NP]]

:: k, [[q_heat(k)]]

:: end k loop

: end i loop

==BCFLAG_TEMP=2==

for i=1 to numberOfDataSets

:: (K, (TMP(K,J), J=1,6),K=1,NP)

end i loop

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

==BCFLAG_TEMP=3==

for i=1 to numberOfDataSets

:: (K, (TMP(K,J), J=1,4),K=1,NP)

end i loop

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

==Note==
In all the above cases, NP is the number of nodes in the horizontal mesh (i.e., the 2D fulldomain number of nodes). See the [[fort.15 file]] documentation on 3D baroclinic physics (particularly the explanation of various [[BCFLAG_TEMP]] values) for more details.

[[Category:input files]]

Getting Started in Linux/Unix

2020-07-06T14:08:22Z

Cfulcher: /* Running the Serial Quarter Annular Harbor Test Case */

== Getting Started in Linux/Unix ==

This section of the wiki describes the most basic scenario of running ADCIRC on a Linux/Unix computer, using a simple test case as an example. If the user is running ADCIRC through the SMS application, please see the SMS documentation on running ADCIRC within SMS. This wiki does not cover that usage. And although the general process of running ADCIRC on a Windows computer or cluster is the same as for Linux/Unix, this section does not cover compiling ADCIRC on a Windows computer. See [[Getting Started in Windows]].

Initially, we will describe getting ADCIRC running on a simple test case in "serial" mode, meaning that only one cpu is used. Running ADCIRC in parallel mode is moderately more complex and will be described separately.

This section provides details on the following topics, with the serial, quarter annular harbor test case as a working example. Compiling the code for serial execution, the basic input/output files for ADCIRC, and what to do with the output. Overviews of the main input and output files are also described. This section assumes several things. The user ...
* knows ADCIRC is a finite element model, with linear triangular elements
* has access to a computer on which to run ADCIRC, and that the OS is Unix/Linux
* knows how to edit text files
* is familiar with working on computers via the "command line"
* has the source code
* has a compiler available (see notes below)

=== Compiling ADCIRC ===
The ADCIRC model is written in Fortran and needs to be compiled into executable code for the specific computer. Thus, the user needs a Fortran compiler available to translate the text source code into something the computer can execute. The mechanics of compiling ADCIRC are independent of the specific compiler. The [https://adcirc.org/files/2018/11/ADCIRCDevGuide.pdf ADCIRC Developers Guide] also has useful documentation on compiling, and readers may wish to look to it for further assistance.

==== Do you have a Fortran compiler? ====
If the answer to this question is "Huh?", then read this: [https://en.wikipedia.org/wiki/Fortran Fortran-Wikipedia] and this: [https://en.wikipedia.org/wiki/Compiler Compilers-Wikipedia].

==== Which compiler do I use? ====
If a compiler is not available and you have administrative access to the computer, install the GNU Fortran compiler. Otherwise, have an administrative user install it. The compiler is available [https://gcc.gnu.org/wiki/GFortranBinaries here]. If you are working on a High-Performance Computing (HPC) cluster maintained as a research and applications resource, then the chances are very high that a Fortran compiler exists on the cluster. In fact, there are probably several, typically including the GNU Fortran computer gfortran, and commercial compilers from Intel (ifort) and Portland Group (pgf). Which compiler you actually use depends on how your specific user environment is configured. Large clusters frequently use the "module" approach to add applications to the user's environment, or else just publish a list of compilers and how to add paths to them. Consult your system's documentation or an administrator if you cannot determine what compiler is available.

==== OK, actual compile time ====
The ADCIRC source code is packaged in directories ("folders"). The actual compiling is done in the "work" directory. In a terminal (i.e., on the command-line), go there. In this directory, there is a file called "makefile", which is a system for compiling software into executable code. There is also a file called cmplrflags.mk that contains sections for different compilers. You can either edit this file to specify the compiler or you can specify the compiler at the command line. For instance, assuming that you have the gfortran compiler available somewhere on your environment's PATH, do one of the following:
* Edit the cmplrflags.mk file by uncommenting the line that says <code>compiler=gnu</code>. This will tell the make process to use compiler information as defined in the "gnu" section for a Linux OS. At the command prompt, type <code>make adcirc</code>.
OR
* Skip editing the cmplrflags.mk file and just type <code>make adcirc compiler=gnu</code>.
This will compile the serial ADCIRC model. If compilation is successful, there should be an executable file named "adcirc" in the work directory. If you receive errors when compiling and are unsure how to deal with them, a quick search for the error on the internet may help you identify issues, such as compiler flag(s) or software libraries needed for your system. If you are not successful, you may need to reach out to an administrator for your system or to the ADCIRC listserv.

=== Running the Serial Quarter Annular Harbor Test Case ===
The test case is the so-called serial quarter annular problem. It is described in some detail [https://adcirc.org/home/documentation/example-problems/quarter-annular-harbor-with-tidal-forcing-example/ here]. The ADCIRC grid is only 63 nodes (triangle vertices) and 96 elements. A plot of the grid is shown to the right. The red arc indicates open boundary nodes, and the green lines represent land (i.e., no flow) boundaries. The forcing for this test is a 0.3048 meter M2 tide on the open boundary, run for 5 days with a 180 sec timestep and a 2 day ramp up of the boundary forcing.

[[File:Screenshot 2018-08-13 15.02.38.png|200px|thumb|Quarter Annular Harbor Test Case Grid]]

# Get the test case [https://cdr.lib.unc.edu/downloads/dj52wb456?locale=en here].
# Extract the downloaded file. It will expand into a directory called "serial_quarter_annular_v51_52_20/". Go there and extract the contents.
# There are several files in this directory. The fort.14 and fort.15 files are input files. The rest are output by ADCIRC and contain various parts of the solution.
# Run the previously compiled ADCIRC serial executable by either copying it to this test case directory and executing it by typing <code>./adcirc</code>, or by using the relative or absolute path to the executable (e.g., <code>/home/MyUserName/ADCIRC/work/adcirc</code>).
This serial case is very fast. It will produce these '''output''' files:
*adcirc.log - runtime diagnostic log file
*fort.16 - another runtime diagnostic log file
*fort.33 - iterative solver diagnostic file
*fort.61 - station output file
*fort.67 - alternating hotstart file
*fort.68 - alternating hotstart file
*maxele.63 - maximum water level over duration of simulation
*maxvel.63 - maximum depth-averaged water speed over duration of simulation

If you get this far, then the case ran. Now it's time to [[visualization|visualize]] the results.

Getting Started in Linux/Unix

2020-07-06T14:07:44Z

Cfulcher: /* Running the Serial Quarter Annular Harbor Test Case */

== Getting Started in Linux/Unix ==

This section of the wiki describes the most basic scenario of running ADCIRC on a Linux/Unix computer, using a simple test case as an example. If the user is running ADCIRC through the SMS application, please see the SMS documentation on running ADCIRC within SMS. This wiki does not cover that usage. And although the general process of running ADCIRC on a Windows computer or cluster is the same as for Linux/Unix, this section does not cover compiling ADCIRC on a Windows computer. See [[Getting Started in Windows]].

Initially, we will describe getting ADCIRC running on a simple test case in "serial" mode, meaning that only one cpu is used. Running ADCIRC in parallel mode is moderately more complex and will be described separately.

This section provides details on the following topics, with the serial, quarter annular harbor test case as a working example. Compiling the code for serial execution, the basic input/output files for ADCIRC, and what to do with the output. Overviews of the main input and output files are also described. This section assumes several things. The user ...
* knows ADCIRC is a finite element model, with linear triangular elements
* has access to a computer on which to run ADCIRC, and that the OS is Unix/Linux
* knows how to edit text files
* is familiar with working on computers via the "command line"
* has the source code
* has a compiler available (see notes below)

=== Compiling ADCIRC ===
The ADCIRC model is written in Fortran and needs to be compiled into executable code for the specific computer. Thus, the user needs a Fortran compiler available to translate the text source code into something the computer can execute. The mechanics of compiling ADCIRC are independent of the specific compiler. The [https://adcirc.org/files/2018/11/ADCIRCDevGuide.pdf ADCIRC Developers Guide] also has useful documentation on compiling, and readers may wish to look to it for further assistance.

==== Do you have a Fortran compiler? ====
If the answer to this question is "Huh?", then read this: [https://en.wikipedia.org/wiki/Fortran Fortran-Wikipedia] and this: [https://en.wikipedia.org/wiki/Compiler Compilers-Wikipedia].

==== Which compiler do I use? ====
If a compiler is not available and you have administrative access to the computer, install the GNU Fortran compiler. Otherwise, have an administrative user install it. The compiler is available [https://gcc.gnu.org/wiki/GFortranBinaries here]. If you are working on a High-Performance Computing (HPC) cluster maintained as a research and applications resource, then the chances are very high that a Fortran compiler exists on the cluster. In fact, there are probably several, typically including the GNU Fortran computer gfortran, and commercial compilers from Intel (ifort) and Portland Group (pgf). Which compiler you actually use depends on how your specific user environment is configured. Large clusters frequently use the "module" approach to add applications to the user's environment, or else just publish a list of compilers and how to add paths to them. Consult your system's documentation or an administrator if you cannot determine what compiler is available.

==== OK, actual compile time ====
The ADCIRC source code is packaged in directories ("folders"). The actual compiling is done in the "work" directory. In a terminal (i.e., on the command-line), go there. In this directory, there is a file called "makefile", which is a system for compiling software into executable code. There is also a file called cmplrflags.mk that contains sections for different compilers. You can either edit this file to specify the compiler or you can specify the compiler at the command line. For instance, assuming that you have the gfortran compiler available somewhere on your environment's PATH, do one of the following:
* Edit the cmplrflags.mk file by uncommenting the line that says <code>compiler=gnu</code>. This will tell the make process to use compiler information as defined in the "gnu" section for a Linux OS. At the command prompt, type <code>make adcirc</code>.
OR
* Skip editing the cmplrflags.mk file and just type <code>make adcirc compiler=gnu</code>.
This will compile the serial ADCIRC model. If compilation is successful, there should be an executable file named "adcirc" in the work directory. If you receive errors when compiling and are unsure how to deal with them, a quick search for the error on the internet may help you identify issues, such as compiler flag(s) or software libraries needed for your system. If you are not successful, you may need to reach out to an administrator for your system or to the ADCIRC listserv.

=== Running the Serial Quarter Annular Harbor Test Case ===
The test case is the so-called serial quarter annular problem. It is described in some detail [https://adcirc.org/home/documentation/example-problems/quarter-annular-harbor-with-tidal-forcing-example/ here]. The ADCIRC grid is only 63 nodes (triangle vertices) and 96 elements. A plot of the grid is shown to the right. The red arc indicates open boundary nodes, and the green lines represent land (i.e., no flow) boundaries. The forcing for this test is a 0.3048 meter M2 tide on the open boundary, run for 5 days with a 180 sec timestep and a 2 day ramp up of the boundary forcing.

[[File:Screenshot 2018-08-13 15.02.38.png|200px|thumb|Quarter Annular Harbor Test Case Grid]]

# Get the test case [https://cdr.lib.unc.edu/concern/data_sets/12579z98c?locale=en here].
# Extract the downloaded file. It will expand into a directory called "serial_quarter_annular_v51_52_20/". Go there and extract the contents.
# There are several files in this directory. The fort.14 and fort.15 files are input files. The rest are output by ADCIRC and contain various parts of the solution.
# Run the previously compiled ADCIRC serial executable by either copying it to this test case directory and executing it by typing <code>./adcirc</code>, or by using the relative or absolute path to the executable (e.g., <code>/home/MyUserName/ADCIRC/work/adcirc</code>).
This serial case is very fast. It will produce these '''output''' files:
*adcirc.log - runtime diagnostic log file
*fort.16 - another runtime diagnostic log file
*fort.33 - iterative solver diagnostic file
*fort.61 - station output file
*fort.67 - alternating hotstart file
*fort.68 - alternating hotstart file
*maxele.63 - maximum water level over duration of simulation
*maxvel.63 - maximum depth-averaged water speed over duration of simulation

If you get this far, then the case ran. Now it's time to [[visualization|visualize]] the results.

Getting Started in Linux/Unix

2020-07-06T13:54:51Z

Cfulcher: /* Running the Serial Quarter Annular Harbor Test Case */

== Getting Started in Linux/Unix ==

This section of the wiki describes the most basic scenario of running ADCIRC on a Linux/Unix computer, using a simple test case as an example. If the user is running ADCIRC through the SMS application, please see the SMS documentation on running ADCIRC within SMS. This wiki does not cover that usage. And although the general process of running ADCIRC on a Windows computer or cluster is the same as for Linux/Unix, this section does not cover compiling ADCIRC on a Windows computer. See [[Getting Started in Windows]].

Initially, we will describe getting ADCIRC running on a simple test case in "serial" mode, meaning that only one cpu is used. Running ADCIRC in parallel mode is moderately more complex and will be described separately.

This section provides details on the following topics, with the serial, quarter annular harbor test case as a working example. Compiling the code for serial execution, the basic input/output files for ADCIRC, and what to do with the output. Overviews of the main input and output files are also described. This section assumes several things. The user ...
* knows ADCIRC is a finite element model, with linear triangular elements
* has access to a computer on which to run ADCIRC, and that the OS is Unix/Linux
* knows how to edit text files
* is familiar with working on computers via the "command line"
* has the source code
* has a compiler available (see notes below)

=== Compiling ADCIRC ===
The ADCIRC model is written in Fortran and needs to be compiled into executable code for the specific computer. Thus, the user needs a Fortran compiler available to translate the text source code into something the computer can execute. The mechanics of compiling ADCIRC are independent of the specific compiler. The [https://adcirc.org/files/2018/11/ADCIRCDevGuide.pdf ADCIRC Developers Guide] also has useful documentation on compiling, and readers may wish to look to it for further assistance.

==== Do you have a Fortran compiler? ====
If the answer to this question is "Huh?", then read this: [https://en.wikipedia.org/wiki/Fortran Fortran-Wikipedia] and this: [https://en.wikipedia.org/wiki/Compiler Compilers-Wikipedia].

==== Which compiler do I use? ====
If a compiler is not available and you have administrative access to the computer, install the GNU Fortran compiler. Otherwise, have an administrative user install it. The compiler is available [https://gcc.gnu.org/wiki/GFortranBinaries here]. If you are working on a High-Performance Computing (HPC) cluster maintained as a research and applications resource, then the chances are very high that a Fortran compiler exists on the cluster. In fact, there are probably several, typically including the GNU Fortran computer gfortran, and commercial compilers from Intel (ifort) and Portland Group (pgf). Which compiler you actually use depends on how your specific user environment is configured. Large clusters frequently use the "module" approach to add applications to the user's environment, or else just publish a list of compilers and how to add paths to them. Consult your system's documentation or an administrator if you cannot determine what compiler is available.

==== OK, actual compile time ====
The ADCIRC source code is packaged in directories ("folders"). The actual compiling is done in the "work" directory. In a terminal (i.e., on the command-line), go there. In this directory, there is a file called "makefile", which is a system for compiling software into executable code. There is also a file called cmplrflags.mk that contains sections for different compilers. You can either edit this file to specify the compiler or you can specify the compiler at the command line. For instance, assuming that you have the gfortran compiler available somewhere on your environment's PATH, do one of the following:
* Edit the cmplrflags.mk file by uncommenting the line that says <code>compiler=gnu</code>. This will tell the make process to use compiler information as defined in the "gnu" section for a Linux OS. At the command prompt, type <code>make adcirc</code>.
OR
* Skip editing the cmplrflags.mk file and just type <code>make adcirc compiler=gnu</code>.
This will compile the serial ADCIRC model. If compilation is successful, there should be an executable file named "adcirc" in the work directory. If you receive errors when compiling and are unsure how to deal with them, a quick search for the error on the internet may help you identify issues, such as compiler flag(s) or software libraries needed for your system. If you are not successful, you may need to reach out to an administrator for your system or to the ADCIRC listserv.

=== Running the Serial Quarter Annular Harbor Test Case ===
The test case is the so-called serial quarter annular problem. It is described in some detail [https://adcirc.org/home/documentation/example-problems/quarter-annular-harbor-with-tidal-forcing-example/ here]. The ADCIRC grid is only 63 nodes (triangle vertices) and 96 elements. A plot of the grid is shown to the right. The red arc indicates open boundary nodes, and the green lines represent land (i.e., no flow) boundaries. The forcing for this test is a 0.3048 meter M2 tide on the open boundary, run for 5 days with a 180 sec timestep and a 2 day ramp up of the boundary forcing.

[[File:Screenshot 2018-08-13 15.02.38.png|200px|thumb|Quarter Annular Harbor Test Case Grid]]

# Get the test case [https://www.dropbox.com/s/xsv1yk6cxgr9f2t/serial_quarter_annular_v51_52_20.zip?dl=0 here].
# Extract the downloaded file. It will expand into a directory called "serial_quarter_annular_v51_52_20/". Go there and extract the contents.
# There are several files in this directory. The fort.14 and fort.15 files are input files. The rest are output by ADCIRC and contain various parts of the solution.
# Run the previously compiled ADCIRC serial executable by either copying it to this test case directory and executing it by typing <code>./adcirc</code>, or by using the relative or absolute path to the executable (e.g., <code>/home/MyUserName/ADCIRC/work/adcirc</code>).
This serial case is very fast. It will produce these '''output''' files:
*adcirc.log - runtime diagnostic log file
*fort.16 - another runtime diagnostic log file
*fort.33 - iterative solver diagnostic file
*fort.61 - station output file
*fort.67 - alternating hotstart file
*fort.68 - alternating hotstart file
*maxele.63 - maximum water level over duration of simulation
*maxvel.63 - maximum depth-averaged water speed over duration of simulation

If you get this far, then the case ran. Now it's time to [[visualization|visualize]] the results.

Fort.38 file format

2020-03-18T19:36:31Z

Cfulcher: Created page with "The basic file structure is shown below. Each line of input is represented by a line containing the input variable name(s) in bold face type. Blank lines are to enhance readab..."

The basic file structure is shown below. Each line of input is represented by a line containing the input variable name(s) in bold face type. Blank lines are to enhance readability. Loops indicate multiple lines of input.

==BCFLAG_TEMP=1==

for i=1 to [[numberOfDataSets]]

: for k=1 to [[NP]]

:: k, [[q_heat(k)]]

:: end k loop

: end i loop

==BCFLAG_TEMP=2==

for i=1 to numberOfDataSets

:: (K, (TMP(K,J), J=1,6),K=1,NP)

end i loop

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

==BCFLAG_TEMP=3==

for i=1 to numberOfDataSets

:: (K, (TMP(K,J), J=1,4),K=1,NP)

end i loop

where TMP(K,J) is the surface heat flux parameter Jth heat flux component for the Kth horizontal mesh node. The data are read using an implicit Fortran i/o loop, thus the parentheses around the statement.

==Note==
In all the above cases, NP is the number of nodes in the horizontal mesh (i.e., the 2D fulldomain number of nodes). See the [[fort.15 file]] documentation on 3D baroclinic physics (particularly the explanation of various [[BCFLAG_TEMP]] values) for more details.

Fort.38 file

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Cfulcher: Created page with "The surface temperature boundary condition input file (fort.38) is read in when the RES_BC_FLAG is set to -3, 3, -4, or 4 in the fort.15 file (i.e., when a lateral tem..."

Fort.37 file format

2020-03-18T16:05:58Z

The basic file structure is shown below. Each line of input is represented by a line containing the input variable name(s) in bold face type. Blank lines are to enhance readability. Loops indicate multiple lines of input.

for i=1 to [[numberOfDataSets]]

: '''comment line (date)'''

: for k=1 to [[number_of_ocean_boundary_nodes]]

:: k, ([[TEMPBC]](k,m), m=1,[[NFEN]])

:: end k loop

: end i loop

Fort.37 file

2020-03-18T16:00:45Z

Cfulcher: Created page with "The fort.37 file is the Temperature Boundary Condition Input File. It is read in when the RES_BC_FLAG is set to -3, 3, -4, or 4 in the fort.15 file. == File Format ==..."

The fort.37 file is the Temperature Boundary Condition Input File. It is read in when the [[RES_BC_FLAG]] is set to -3, 3, -4, or 4 in the [[fort.15 file]].

== File Format ==
See [[fort.37 file format]] for details. 

[[Category:input files]]

Noff.100 file format

2020-03-18T15:54:11Z

Cfulcher: Created page with "The basic file structure is shown below. Each line of output is represented by a line containing the output variable name(s) in bold face type. Blank lines are to enhance read..."

Noff.100 file

2020-03-18T15:49:36Z

Cfulcher: Created page with "The noff.100 file records the wet/dry state of elements where 1 indicates an element is categorized as wet on the time step that the dataset was written while a value of 0 ind..."

The noff.100 file records the wet/dry state of elements where 1 indicates an element is categorized as wet on the time step that the dataset was written while a value of 0 indicates that an element is categorized as dry. The name of the elemental wet/dry array in ADCIRC is [[NOFF]].

These data are generally only valuable to ADCIRC developers who are working on experimental wet/dry algorithms.

The writing of the noff.100 output file is activated when the [[outputNOFF]] parameter is set to .true. in the optional [[wetDryContol namelist]] at the bottom of the [[fort.15 file]].

== File Format ==
See [[noff.100 file format]] for details. 

[[Category:output files]]

Fort.93 file format

2020-03-18T14:33:30Z

Fort.93 file

2020-03-18T13:37:13Z

Cfulcher: Created page with "Output ice field files are written to a fort.93 file that has the same format as the fort.73 pressure file or fort.63 elevation file. This fi..."

Output ice field files are written to a fort.93 file that has the same format as the [[fort.73 file|fort.73 pressure file]] or [[fort.63 file|fort.63 elevation file]]. This file is only generated when ice fields are used and when global meteorology output is specified for outputting. The settings for global meteorology output are ([[NOUTGW]], [[TOUTSGW]], [[TOUTFGW]], [[NSPOOLGW]]) in the [[fort.15 file]].

== File Format ==
See [[fort.93 file format]] for details. 

[[Category:output files]]

Fort.91 file format

2020-03-17T13:09:28Z

Fort.91 file

2020-03-17T13:06:44Z

Cfulcher: Created page with "If the ice coverage input feature of ADCIRC has been activated, the fort.91 output file will be produced according to the output control specifications for specified meteorolo..."

If the ice coverage input feature of ADCIRC has been activated, the fort.91 output file will be produced according to the output control specifications for specified meteorological recording stations ([[NOUTM]], etc) specified in the [[fort.15 file]].

== File Format ==
See [[fort.91 file format]] for details. 

[[Category:output files]]

Fort.90 file format

2020-03-16T18:24:44Z

Fort.90 file

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Cfulcher: Created page with "The fort.90 file contains primitive weighting in continuity equation time series output at all nodes in the model grid as specified fort.15 file. This output file (fort.90..."

The fort.90 file contains primitive weighting in continuity equation time series output at all nodes in the model grid as specified [[fort.15 file]]. This output file (fort.90) uses the output specifiers for the [[fort.63 file]] to determine its format, output frequency, etc.

== File Format ==
See [[fort.90 file format]] for details. 

[[Category:output files]]

Fort.83 file format

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Fort.83 file

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Cfulcher: Created page with "The fort.83 file contains scalar concentration time series output at all nodes in the model grid file as specified in the fort.15 file. == File Format == See fort.83 fi..."

The fort.83 file contains scalar concentration time series output at all nodes in the model grid file as specified in the [[fort.15 file]].

== File Format ==
See [[fort.83 file format]] for details. 

[[Category:output files]]

Fort.81 file format

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Fort.81 file

2020-03-16T12:55:09Z

Cfulcher: Created page with "The fort.81 file contains scalar concentration time series output at the concentration recording stations as specified in the fort.15 file. == File Format == See fort.8..."

The fort.81 file contains scalar concentration time series output at the concentration recording stations as specified in the [[fort.15 file]].

== File Format ==
See [[fort.81 file format]] for details. 

[[Category:output files]]

Fort.77 file format

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The basic file structure is shown below. Each line of output is represented by a line containing the output variable name(s) in bold face type. Blank lines are to enhance readability. Loops indicate multiple lines of output.

[[RUNDES]], [[RUNID]], [[AGRID]]

[[NDSETSE]], [[NP]], [[DTDP]]*[[NSPOOL_TVW]], [[NSPOOL_TVW]], [[IRTYPE]]

for j=1, [[NDSETSE]]
: [[TIME]], [[IT]]
: for k=1, [[NP]]
:: k, [[DP(k)]]
:end k loop
end j loop

== Notes ==
The basic file structure is shown below. Each line of output is represented by a line containing the output variable name(s) in bold face type. Blank lines are to enhance readability. Loops indicate multiple lines of output.

[[RUNDES]], [[RUNID]], [[AGRID]]

[[NDSETGE]], [[NP]], [[DTDP]]*[[NSPOOLGE]], [[NSPOOLGE]], [[IRTYPE]]

for j=1, [[NDSETGE]]
: [[TIME]], [[IT]]
: for k=1, [[NP]]
:: k, [[DP(k)]]
:end k loop
end j loop

== Notes ==
When this file is written in sparse format and therefore only receiving data for a small portion of the nodes (the weirs) the numbering will be referenced to the global node number. Only the change in elevation from the original fort.14 specified elevation will be written to the file.

Fort.77 file

2020-03-16T12:17:33Z

Cfulcher: Created page with "When time varying weirs are activated and output is requested, ADCIRC will create the fort.77 output file. == File Format == See fort.77 file format for details. ..."

When time varying weirs are activated and output is requested, ADCIRC will create the fort.77 output file.

== File Format ==
See [[fort.77 file format]] for details. 

[[Category:output files]]

Fort.76 file format

2020-03-10T17:59:15Z

Fort.76 file

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Cfulcher: Created page with "If the time varying bathymetry feature of ADCIRC has been activated, the fort.76 output file will be produced according to the output control specifications for full domain ti..."

If the time varying bathymetry feature of ADCIRC has been activated, the fort.76 output file will be produced according to the output control specifications for full domain time varying water surface elevation output ([[NOUTGE]], etc) as specified in the [[fort.15 file]].

== File Format ==
See [[fort.76 file format]] for details. 

[[Category:output files]]

Fort.75 file format

2020-03-10T17:53:11Z

Fort.75 file

2020-03-10T17:51:36Z

Cfulcher: Created page with "If the time varying bathymetry feature of ADCIRC has been activated, the fort.75 output file will be produced according to the output control specifications for water surface..."

If the time varying bathymetry feature of ADCIRC has been activated, the fort.75 output file will be produced according to the output control specifications for water surface elevation recording stations (NOUTE, etc) as specified in the [[fort.15 file]].

== File Format ==
See [[fort.75 file format]] for details. 

[[Category:output files]]

Fort.73 file format

2020-03-10T17:49:48Z

Fort.73 file

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Cfulcher: Created page with "The fort.73 file contains atmospheric pressure (m of water) time series output at all nodes in the model grid as specified in the fort.15 file. == File Format == See fo..."

The fort.73 file contains atmospheric pressure (m of water) time series output at all nodes in the model grid as specified in the [[fort.15 file]].

== File Format ==
See [[fort.73 file format]] for details. 

[[Category:output files]]

Fort.72 file format

2020-03-09T14:19:52Z

Fort.72 file

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Cfulcher: Created page with "The fort.72 file contains wind velocity or stress time series output at the meteorological recording stations in the model grid as specified in the fort.15 file. == File..."

The fort.72 file contains wind velocity or stress time series output at the meteorological recording stations in the model grid as specified in the [[fort.15 file]].

== File Format ==
See [[fort.72 file format]] for details. 

[[Category:output files]]

Fort.71 file format

2020-03-09T14:00:31Z

Fort.71 file

2020-03-09T13:58:26Z

Cfulcher: Created page with "The fort.71 file contains atmospheric pressure time series output at the meteorological recording stations specified in the fort.15 file. == File Format == See fort.71..."

The fort.71 file contains atmospheric pressure time series output at the meteorological recording stations specified in the [[fort.15 file]].

== File Format ==
See [[fort.71 file format]] for details. 

[[Category:output files]]