# Changeset 1205

Ignore:
Timestamp:
Jul 15, 2013 10:55:47 AM (8 years ago)
Message:

added additional hint for palm installation at hlrn and removed some typos

Location:
palm/trunk/TUTORIAL/SOURCE
Files:
2 edited

### Legend:

Unmodified
 r1080 \frametitle{Overview} \begin{itemize} \item<1->{The canopy model embedded in PALM can be used to study the effect of a plant canopy on:} \item<1->{The canopy model embedded in PALM can be used to study the effect of a plant canopy on e.g.:} \begin{itemize} \item<2->{mean flow field,} \item<4->{scalar exchange processes between canopy and atmosphere.} \end{itemize} \item<5->{Within the canopy model, the plant canopy acts as a sink for momentum and as a source/sink for active (temperature) and passive (e.g. tracer) scalars.} \item<5->{Within the canopy model, the plant canopy acts as a sink for momentum and as a source/sink for active (e.g. temperature) and passive (e.g. tracer) scalars.} \item<6->{The canopy model does not account for each plant element, but rather accounts for a volume averaged effect on the flow and scalar concentration, depending on:} \begin{itemize} \item<7->{leaf area distribution,} \item<7->{leaf area density,} \item<8->{drag coefficient.} \end{itemize} \item<1->{A plant canopy affects the flow by acting as a momentum sink due to form and viscous drag forces.} \item<2->{The effectiveness of momentum absorption depends on the amount of leaf area per unit volume and the aerodynamic drag.} \item<3->{Due to the aerodynamic drag the flow is decelerated within the canopy, leading to an inflection point in the vertical profile of the horizontal velocity at the canopy top. \item<3->{Due to the aerodynamic drag, the flow is decelerated within the canopy, leading to an inflection point in the vertical profile of the horizontal velocity at the canopy top. \begin{center} \includegraphics[width=0.5\textwidth]{canopy_model_figures/abb1.png} \begin{footnotesize} \begin{itemize} \item<1->{The inflection point in the velocity profile introduces instabilities to the flow, leading to the formation of Kelvin-Helmholtz waves near the canopy top (\textcircled{{\tiny 1}})} \item<2->{Wave breaking induces further instabilities, whereby a longitudinal component is added to the developing turbulence structures (\textcircled{{\tiny 2}} \& \textcircled{{\tiny 3}})} \item<3->{Due to the persistent instabilities the turbulence structures develop a distinct three-dimensionality (\textcircled{{\tiny 4}})} \item<1->{The inflection point in the velocity profile introduces instabilities to the flow, leading to the formation of Kelvin-Helmholtz waves near the canopy top (\textcircled{{\tiny 1}}).} \item<2->{Wave breaking induces further instabilities, whereby a longitudinal component is added to the developing turbulence structures (\textcircled{{\tiny 2}} \& \textcircled{{\tiny 3}}).} \item<3->{Due to the persistent instabilities the turbulence structures develop a distinct three-dimensionality (\textcircled{{\tiny 4}}).} \item<4->{The large turbulence structures developing due to the inflection point instability significantly contribute to the vertical mixing of in-canopy and above-canopy air. \begin{center} } \item<2->{It is assumed that the foliage is warmed by the penetrating solar radiation and, in turn, warms the surrounding air.} \item<3->{The source strength $S_{\theta}$ is defined as the vertical derivative of the upward kinematic vertical heat flux given by (Shaw and Schumann, 1992):\\ \item<3->{The source strength $S_{\theta}$ is defined as the vertical derivative of the upward kinematic vertical heat flux $Q_{\theta}$, given by (Shaw and Schumann, 1992):\\ \begin{align*} Q_{\theta}(z) = Q_{\theta}(h) exp(-\alpha F) \text{ , } Q_{\theta}(h) \text{ : Heat flux at canopy top} (http://palm.muk.uni-hannover.de) } \item<3->{The following slides will describe how to set up a simulation with a simple horizontally homogeneous canopy block covering the entire model domain surface. In this case, {\small \texttt{plant\_canopy = 'block'}} must be set in \&inipar {\small \texttt{NAMELIST}}.} \item<3->{The following slides will describe how to set up a simulation with a simple horizontally homogeneous canopy block covering the entire model domain surface. In this case, {\small \texttt{canopy\_mode = 'block'}} must be set in \&inipar {\small \texttt{NAMELIST}}.} \end{itemize} \end{frame} Do you want to simulate a more customized canopy, which e.g. covers only half the model surface?\\ \begin{itemize} \item<2->{Step I: Copy the file \texttt{user\_init\_plant\_canopy.f90} from {\small \texttt{trunk/SOURCE}} to the directory {\small \texttt{USER\_CODE (\$Home/palm/current\_version)}} of the specific job and make the desired changes for {\small \texttt{CASE ('user\_defined\_canopy\_1')}}.} \item<2->{Step I: Copy the file \texttt{user\_init\_plant\_canopy.f90} from {\small \texttt{trunk/SOURCE}} to the directory {\small \texttt{\$Home/palm/current\_version/USER\_CODE/}} and make the desired changes for {\small \texttt{CASE ('user\_defined\_canopy\_1')}}.} \item<3->{Step II: In your parameter file set: {\scriptsize \texttt{canopy\_mode = 'user\_defined\_canopy\_1'}}} \end{itemize} \end{footnotesize} \vspace{7pt} \tikzstyle{background} = [rectangle, fill=gray!10, text width=1\textwidth, text centered, rounded corners, minimum height=10em] \tikzstyle{Key1} = [rectangle, draw, fill=gray!70, text width=0.05, minimum size=0.05, font=\tiny]
 r1105 % Folie 6 \begin{frame} \frametitle{PALM - Installation / General Requirements} \frametitle{PALM - Installation / General Requirements (I)} \footnotesize \item<4->[4.]{The Message Passing Interface (MPI),  if the parallel version of PALM shall be used.} \item<5->[5.]{On the \textcolor{green}{local} computer, the revision control system subversion (see subversion.tigris.org). This is already included in many Linux distributions (e.g. SuSe). Subversion requires port 3690 to be open for tcp/udp. If there are firewall restrictions concerning this port, the PALM code cannot be accessed. The user needs a permit to access the PALM repository. For getting a permit please contact the PALM group (raasch@muk.uni-hannover.de) and define a username and a password under which you like to access the repository. This username and password also gives you access to advanced features of the online documentation. (trac-server)} \item<6->[6.]{All participants of this seminar are already permitted to access the repository. Use \dq seminar2012\dq as username and \dq palm2012\dq as password.} \end{itemize} \end{frame} % Folie 6a \begin{frame} \frametitle{PALM - Installation / General Requirements (II)} \footnotesize \begin{itemize} \item<1->[6.]{All participants of this seminar are already permitted to access the repository. Use \dq seminar2012\dq as username and \dq palm2012\dq as password.} \item<2->[7.]{For the installation of the PALM code on the \textcolor{red}{remote} computer (at HLRN), a sufficient virtual memory has to be allocated on the \textcolor{red}{remote} computer. The value of 256 MByte that is set by \texttt{ulimit -S -v 256000} in the users profile under {\tt $\sim$/.profile} is not sufficient.  Please remove this line in your user profile in order to disable the virtual memory limitation.} \end{itemize} \end{frame} This has to be done in file {\tt $\sim$/.bashrc} or  in file {\tt $\sim$/.profile}, depending on your default shell. You can get your default shell via command: \\ \par\medskip \qquad{\tt echo \$SHELL}} \item<3->[3.]{Please also remove the line \texttt{ulimit -S -v 256000} in file {\tt$\sim$/.profile} to disable the virtual memory limitation of 256 MByte that is set for your seminar user account.} \end{itemize} \end{frame} \footnotesize \begin{itemize} \item<1->[3.]{On the \textcolor{green}{local} host, edit your configuration file ({\tt .mrun.config}), and replace in the lcsgih-block \textless replace by your HLRN username\textgreater with your HLRN-username.}\\ \par\medskip \item<2->[4.]{Create directory {\tt job\_queue} on the \textcolor{green}{local} and the \textcolor{red}{remote} host:\\ \par\medskip \item<1->[4.]{On the \textcolor{green}{local} host, edit your configuration file ({\tt .mrun.config}), and replace in the lcsgih-block \textless replace by your HLRN username\textgreater with your HLRN-username.}\\ \par\medskip \item<2->[5.]{Create directory {\tt job\_queue} on the \textcolor{green}{local} and the \textcolor{red}{remote} host:\\ \par\medskip \qquad{\tt mkdir$\sim\$/job\_queue}} \end{itemize}