Commit 6ec30988 authored by Onur.Kerimoglu's avatar Onur.Kerimoglu
Browse files

merged with github

parents 97344b14 46e9eba2
Please read information and documentation on http://sourceforge.net/projects/fabm/
Please read information and documentation on http://fabm.net
For the brave ones:
cd src; make
The procedure to build FABM depends on the host [hydrodynamic model] you want
to use it with. Please visit the wiki for instructions: http://fabm.net/wiki.
If you encounter errors during compilation please check the WWW-page:
http://sourceforge.net/projects/fabm/
for further information and if that does not
help, send an e-mail to fabm-users@googlegroups.com.
If you encounter any problems, send an e-mail to fabm-users@googlegroups.com.
Good luck, and remember to inform of further developments for inclusion,
Good luck, and remember to inform us of further developments for inclusion,
exciting simulations etc.
The FABM team.
......@@ -2,7 +2,7 @@
FABM is a Fortran 2003 programming framework for biogeochemical models of marine and freshwater systems.
FABM is published in "**A general framework for aquatic biogeochemical models**"*: J. Bruggeman and K. Bolding, Environmental Modelling and Software, [doi](http://www.sciencedirect.com/science/article/pii/S1364815214001066)*
FABM is published in "Bruggeman, J., Bolding, K., 2014. A general framework for aquatic biogeochemical models. Environmental Modelling & Software 61: 249–265. DOI: [10.1016/j.envsoft.2014.04.002](http://dx.doi.org/10.1016/j.envsoft.2014.04.002)"
Further information is provided [here](http://fabm.net/wiki)
Further information is provided on [the FABM wiki](http://fabm.net/wiki)
#
#$Id$
#
Currently, there are three versions of the GOTM documentation with the
names coded as "papertype.filetype". These are:
a4.filetype
letter.filetype
html.filetype
"filetype" can be dvi, ps, or pdf. To produce these files type "make
"papertype_filetype" in this directory. For example,
"make letter_pdf"
will create the documention in US-letter format, which
can be display with
"acroread letter.pdf".
Similarly, the files "a4.pdf" and "html.pdf" can be produced, where
"html.pdf" essentially corresponds to the paper version of the
GOTM web documentation. The web version is produced from the
latex source code by typing
"make html_web".
The html-pages are created by "latex2html" such that your result
depends on the variables you have set in ".latex2html-init" in
your home directory (or their defaults if you don't have this file).
To copy the html-pages to the server type "make html_scp".
This option is available only to those that have the password.
%
%$Id$
%
\documentclass[a4paper,twoside,11pt]{article}
% AMS math and symbols
\usepackage{amsmath,amsfonts,amssymb,amsbsy,latexsym}
% natural science bibliography
\usepackage[round]{natbib}
% definitions used in the GOTM-manual
\input definitions.tex
% graphics
\usepackage{graphics}
% to make pdf files look OK
\usepackage{ae}
% set page margins for print
\setlength{\evensidemargin}{-0.4mm}
\setlength{\oddsidemargin}{4.6mm}
\setlength{\textwidth}{155mm}
\pagestyle{myheadings}
\renewcommand{\baselinestretch}{1.0}
\begin{document}
% the titlepage
\begin{titlepage}
{\sf \bf \LARGE
\begin{center}
Lars Umlauf $\bs \cdot$ Hans Burchard $\bs \cdot$ Karsten Bolding
\end{center}
}
\vspace{14mm}
{\sf \bf \Huge
\begin{center}
GOTM
\end{center}
}
\vspace{6mm}
{\sf \bf \LARGE
\begin{center}
Sourcecode \\
and \\
Test Case Documentation
\end{center}
}
\vspace{5mm}
{\sf \bf \Large
\begin{center}
Version 4.0
\end{center}
}
\vspace{8mm}
\begin{figure}[!h]
\begin{center}
\scalebox{0.6}{\includegraphics{figures/mixerA.eps}}
\end{center}
\end{figure}
\vspace{7mm}
{\sf \bf \Large
\begin{center}
Flow --- Mixing --- Ecosystem dynamics
\end{center}
}
\end{titlepage}
% table of contents
\cleardoublepage
\tableofcontents
% include the section files
% the introduction. All files
% ending with 'Intro.tex' are hand-made,
% all others come from 'ProTeX'
\cleardoublepage
\include{introduction}
\cleardoublepage
\include{mainIntro}
\include{gotm}
\cleardoublepage
\include{meanflowIntro}
\include{meanflow}
\cleardoublepage
\include{turbulenceIntro}
\include{turbulence}
\cleardoublepage
\include{airseaIntro}
\include{airsea}
\cleardoublepage
\include{observationsIntro}
\include{observations}
\cleardoublepage
\include{outputIntro}
\include{output}
\cleardoublepage
\include{utilIntro}
\include{util}
\cleardoublepage
\include{bioIntro}
\include{bio}
\cleardoublepage
\include{extraIntro}
\include{seagrass}
\include{sediment}
\cleardoublepage
\include{guiIntro}
\cleardoublepage
\include{cases}
% Bibliography with BibTeX:
\cleardoublepage
\bibliographystyle{agu}
\addcontentsline{toc}{section}{Bibliography}
\bibliography{gotm}
\end{document}
This diff is collapsed.
%
%$Id$
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% Copyright (2003) by The GOTM Team %
% _______________________________________ %
% %
% LaTeX Definitions %
% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% figures and tables
\newcommand{\fig}[1]{figure {\ref{#1}}}
\newcommand{\tab}[1]{table {\ref{#1}}}
\newcommand{\sect}[1]{section {\ref{#1}}}
\newcommand{\sects}[2]{sections {\ref{#1}}--{\ref{#2}}}
\newcommand{\Fig}[1]{Figure {\ref{#1}}}
\newcommand{\Tab}[1]{Table {\ref{#1}}}
\newcommand{\Sect}[1]{Section {\ref{#1}}}
\newcommand{\Sects}[2]{Sections {\ref{#1}}--{\ref{#2}}}
\newcommand{\eq}[1]{(\ref{#1})}
% displaystyle
\newcommand{\dps}[1]{\displaystyle{#1}}
% symbols
\newcommand{\eps}{\varepsilon}
% boldsymbols
\newcommand{\bs}[1]{{\boldsymbol #1}}
% vectors / tensors
\newcommand{\V}[1]{{\boldsymbol #1}}
\newcommand{\T}[1]{{\boldsymbol #1}}
% partial derivatives with respect to coordinates
\newcommand{\pderh}[4]{\dfrac{\partial {#1}^{#2}}{\partial {#3}^{#4}}}
\newcommand{\pderl}[4]{\dfrac{\partial {#1}_{#2}}{\partial {#3}^{#4}}}
\newcommand{\pder}[2]{\dfrac{\partial}{\partial {#1}^{#2}}}
\newcommand{\frstder}[1]{\dfrac{\partial}{\partial {#1}}}
\newcommand{\dfrstder}[1]{\dfrac{\partial}{\partial {#1}}}
\newcommand{\scndder}[2]{\dfrac{\partial^2 {#1}}{\partial {#2}^2}}
\newcommand{\dscndder}[2]{\dfrac{\partial^2 {#1}}{\partial {#2}^2}}
\newcommand{\partder}[2]{\dfrac{\partial {#1}}{\partial {#2}}}
\newcommand{\dpartder}[2]{\dfrac{\partial {#1}}{\partial {#2}}}
\newcommand{\deriv}[2]{\dfrac{\text{d} {#1}}{\text{d} {#2}}}
\newcommand{\frstderiv}[1]{\dfrac{\text{d} }{\text{d} {#1}}}
% turbulence
\def\mean#1{ {\langle #1 \rangle} }
\def\meandot#1{ \dot{ \rule{0mm}{4mm} \langle #1 \rangle} }
% Christoffel Symbols
\newcommand{\chra}[3]{\left[\; #1#2,#3\; \right]}
\newcommand{\chrb}[3]{\left\{ #1 \atop #2\;#3 \right\}}
%operators
\newcommand{\gradient}{{\, \rm grad}}
\newcommand{\divergence}{{\, \rm div }}
\newcommand{\rotation}{{\, \rm rot}}
%stuff
\def\magn#1{| #1 |}
\newcommand{\comma}{\; , \quad}
\newcommand{\point}{\quad .}
\newcommand{\centigrade}{{\ensuremath{^\circ\text{C }{}}}}
\newcommand{\degree}{{\ensuremath{^\circ{\;}}}}
This diff is collapsed.
%
%$Id$
%
%@String{OMOD = "Ocean Modelling"}
%@String{APM = "App. Math. Modelling"}
%@String{IJNMF = "Int. J. Numer. Meth. Fluids"}
%@String{MWR = "Monthly Weather Review"}
%@String{Franzius = "Mitteilungen des Franzius-Institutes"}
%@STRING{JGR = "J. Geophys. Res."}
%@String{ECSS = "Estuarine, Coastal and Shelf Science"}
%@String{OD = "Ocean Dynamics"}
%@STRING{UNESCO = "Unesco technical papers in marine sciences"}
%@String{EFM = "Environmental Fluid Mechanics"}
%@String{SR = "Journal of Sea Research"}
%@String{QJR = "Q. J. R. Meteorol. Soc."}
%@String{JAOT = "Journal of Atmospheric and Oceanic Technology"}
%@String{JMR = "Journal of Marine Research"}
@String{CSR = "Continental Shelf Research"}
@String{DSR = "Deep Sea Research II"}
@String{JMS = "Journal of Marine Systems"}
@STRING{JPO = "Journal of Physical Oceanography"}
@String{JSR = "Journal of Sea Research"}
@STRING{OD = "Ocean Dynamics"}
@String{OM = "Ocean Modelling"}
@String{LO = "Limnology and Oceanography"}
@String{MEPS = "Marine Ecology Progress Series"}
@String{CE = "Chemistry and Ecology"}
@String{acc = "Accepted for publication"}
@String{sub = "Submitted"}
@String{inp = "In Press"}
@article(carnieletal_2007,
author = "Sandro Carniel and Marcello Vichi and Mauro Sclavo",
title = "Sensitivity of a coupled physical-biological model to turbulence:
high frequency simulations in a northern {A}diratic station.",
journal = CE,
year = "2007",
volume = "23(2)",
pages = "157--175")
@article(bruggemannkooijman_2007,
author = "J. Bruggemann and A. L. M. Kooijman",
title = "A biodiversity-inspire approach to aquatic ecosystem modeling.",
journal = LO,
year = "2007",
volume = "52(4)",
pages = "1533--1544")
@article(maaretall_2007,
author = "Marie Maar and Torkel Gissel Nielsen and Karsten Bolding and
Hans Burchard and Andre W. Visser",
title = "Grazing effects of blue mussel Mytilus edulis on the pelagic
food web under different turbulence conditions",
journal = MEPS,
year = "2007",
volume = "339",
pages = "199--213")
@Article{steineretal_2006,
author = {Nadja Steiner and Ken Denman and Norm McFarlane and
Larry Solheim},
title = {Simulating the Atmosphere-Ocean Physical Conditions and
Effects on the Planktonic Ecosystem Response During {SERIES}},
journal = DSR,
year = {2006},
volume = {53},
pages = {2434-2454},
note = {doi:10.1016/j.dsr2.2006.05.030}
}
@article(ralstonstacey_2004,
author = "D. K. Ralston and M. T. Stacey",
title = "Shear and turbulence production across subtidal channels",
journal = JMS,
year = "2006",
volume = "64",
pages = "147--171")
@article(torresetal_2006,
author = "R. Torres and J. I. Allen and F. G. Figueiras",
title = "Sequential data assimilation in an upwelling influenced estuary",
journal = JMS,
volume = "60",
year = "2006",
pages = "317--329")
@article(allenetal_2006,
author = "J.I. Allen and S. D. Archer and J. C. Blackford and F. J.
Gilbert and A. H. Taylor",
title = "Changes in DMS production and flux in relation to decadal shifts
in ocean circulation",
journal = "Tellus B",
year = "2006",
volume = "58",
pages = "242--254")
@article(allenetal_2004,
author = "J.I. Allen and J. D. Siddorn and J. C. Blackford and F. J.
Gilbert",
title = "Turbulence as a control on the microbial loop in a temperate
seasonally stratified marine systems model",
journal = JSR,
year = "2004",
volume = "52",
pages = "1--20")
@article(archeretal_2004,
author = "S. D. Archer and F. J. Gilbert and J.I. Allen and
J. C. Blackford and P. D. Nightingale",
title = "Modelling of the seasonal patterns of dimethyl sulphide production
and fate during 1989 at a site in the {N}orth {S}ea",
journal = "Canadian Journal of Fisheries Research",
year = "2004",
volume = "61",
pages = "765--787")
@article(blackfordetal_2004,
author = "J. C. Blackford and J.I. Allen and F. J. Gilbert J.I. Allen",
title = "Ecosystem dynamics at six contrasting sites: a generic
modelling study",
journal = JMS,
year = "2004",
volume = "52",
pages = "191--215")
@article{burchardetal_2005,
author = {Hans Burchard and H.U. Lass and V. Mohrholz and L. Umlauf
and J. Sellschopp and V. Fiekas and K. Bolding and
L. Arneborg},
title = {Dynamics of medium-intensity dense water plumes in the
{A}rkona {S}ea, {W}estern {B}altic {S}ea},
journal = OD,
volume = {55},
pages = {391-402},
year = {2005},
}
@article{burchardetal_2004,
author = {Hans Burchard and Karsten Bolding and Wilfried K\"uhn and
Andreas Meister and Thomas Neumann and Lars Umlauf},
title = {Description of a flexible and extendable
physical-biogeochemical model system for the water column},
journal = JMS,
volume = {61},
pages = {180-211},
year = {2006},
note = {},
}
@article{stipsetal_2005,
author = {Adolf Stips and Hans Burchard and Karsten Bolding and
Hartmut Prandke and A. W\"uest},
title = {Measurement and simulation of viscous dissipation rates
in the wave affected surface layer},
journal = DSR,
volume = 52,
pages = {1133-1155},
year = {2005},
}
@article{stipsetal_2002,
author = {Adolf Stips and Hans Burchard and Karsten Bolding and
Walter Eifler},
title = {Modelling of convective turbulence with a two-equation
$k$-$\epsilon$ turbulence closure scheme},
journal = OD,
volume = 52,
pages = {153-168},
year = {2002},
}
@article{burchardetal_2002,
author = {Hans Burchard and Karsten Bolding and Tom P. Rippeth
and Adolf Stips and John H. Simpson
and J\"urgen S\"undermann},
title = {Microstructure of turbulence in the Northern North Sea:
comparative study of observations and model simulations},
journal = JSR,
volume = 47,
pages = {223-238},
year = {2002},
}
@article{burchardbolding_2000,
author = {Hans Burchard and Karsten Bolding},
title = {Comparitive analysis of four second-moment turbulence closure
for the oceanic mixed layer.},
journal = JPO,
year = {2000},
}
@article{burchardetal_1998,
author = {Hans Burchard and Adolf Stips and Walter Eifler
and Karsten Bolding and Manuel Villarreal},
title = {Numerical simulation of dissipation measurements in
non-stratified and strongly stratified estuaries.},
journal = {Interactions between Estuaries, Coastal Seas and Shelf Sea},
pages = {1-18},
year = {2000}
}
@article(umlaufetal_2003,
author = "L. Umlauf and H. Burchard and K. Hutter",
title = "Extending the $k$-$\omega$ turbulence model towards oceanic
applications",
journal = OM,
volume = "5",
pages = "195-218",
year = "2003" )
@article(umlaufburchard_2003,
author = "L. Umlauf and H. Burchard",
title = "A generic length-scale equation for geophysical turbulence models",
journal =JMR,
volume = "61",
pages = "235--265",
year = "2003" )
@article(umlaufburchard_2005,
author = "L. Umlauf and H. Burchard",
title = "Second-order turbulence closure models for gephysical boundary
layers. {A} review of recent work",
journal =CSR,
volume = "25",
pages = "795--827",
year = "2005" )
@article(umlauf_2005,
author = "Lars Umlauf",
title = "Modelling the effects of horizontal and vertical shear in
stratified turbulent flows",
journal =DSR,
volume = "52",
pages = "1181--1201",
year = "2005" )
@article(arneborgetall_2005,
author = "Lars Arneborg and Volker Fiekas and Lars Umlauf and Hans Burchard",
title = "Gravity current dynamics and entrainment - {A} process study based
on observations in the {A}rkona {B}asin",
journal =JPO,
year = "2005",
note = sub )
%
%$Id$
%
\documentclass[a4paper,twoside]{article}
% AMS math and symbols
\usepackage{amsmath,amsfonts,amssymb,amsbsy,latexsym}
% natural science bibliography
\usepackage[round]{natbib}
% definitions used in the GOTM-manual
\input definitions.tex
% graphics
\usepackage{graphics}
% center it on a4-format
\setlength{\evensidemargin}{4.6mm}
\setlength{\oddsidemargin}{4.6mm}
\setlength{\textwidth}{150mm}
\begin{document}
% the titlepage
\begin{titlepage}
{\sf \bf \LARGE
\begin{center}
Lars Umlauf $\bs \cdot$ Hans Burchard $\bs \cdot$ Karsten Bolding
\end{center}
}
\vspace{14mm}
{\sf \bf \Huge
\begin{center}
GOTM
\end{center}
}
\vspace{6mm}
{\sf \bf \LARGE
\begin{center}
Sourcecode \\
and \\
Test Case Documentation
\end{center}
}
\vspace{5mm}
{\sf \bf \Large
\begin{center}
Version 4.0
\end{center}
}
\vspace{8mm}
\begin{figure}[!h]
\begin{center}
\scalebox{0.6}{\includegraphics{figures/mixerA.eps}}
\end{center}
\end{figure}
\vspace{7mm}
{\sf \bf \Large
\begin{center}
Flow --- Mixing --- Sediment Transport
\end{center}
}
\end{titlepage}
% table of contents
\tableofcontents