Commit 414399ac authored by snuverink_j's avatar snuverink_j
Browse files

replace filename macro

parent 340fce01
......@@ -129,7 +129,7 @@ The next five logical flags activate or deactivate execution options:
\item[INFO]
\index{OPTION!INFO}
If this option is turned off, \textit{OPAL} suppresses all information messages. It also affects the \filename{gnu.out} and \filename{eb.out} files in case of \textit{OPAL-cycl} simulations.
If this option is turned off, \textit{OPAL} suppresses all information messages. It also affects the \textit{gnu.out} and \textit{eb.out} files in case of \textit{OPAL-cycl} simulations.
%% \item[TRACE]
%% \index{TRACE}
......@@ -217,7 +217,7 @@ The next five logical flags activate or deactivate execution options:
\item[CSRDUMP]
\index{OPTION!CSRDUMP}
If true the electric csr field component, $E_z$, line density and the derivative of the line density is written into the \filename{data} directory.
If true the electric csr field component, $E_z$, line density and the derivative of the line density is written into the \textit{data} directory.
The first line gives the average position of the beam bunch.
Subsequent lines list $z$ position of longitudinal mesh (with respect to the head of the beam bunch),
$E_z$, line density and the derivative of the line density. Note that currently the line density derivative
......@@ -234,7 +234,7 @@ The next five logical flags activate or deactivate execution options:
%% \item track is continued with $\phi_i + LAG$ to the element $i+1$.
%% \item if $i<n$ goto $1$
%% \end{enumerate}
%% For convenience a file (\filename{inputfn.phases}) with the phases corresponding to the maximum energies is written. A \texttt{AUTOPHASE} value of $4$ gives Astra comparable results.
%% For convenience a file (\textit{inputfn.phases}) with the phases corresponding to the maximum energies is written. A \texttt{AUTOPHASE} value of $4$ gives Astra comparable results.
%% An example is given in see~Section~\ref{trackautoph}.
%The range of the phase within which the energy is maximized is refined \texttt{AUTOPHASE} times. For each level of refinement, $i$, the energy is evaluated at $11$ evenly distributed positions between $\phi_{i, \, \mathrm{low}}$ and $\phi_{i, \, \mathrm{high}}$ with spacing $\mathrm{d}\phi_i = \frac{\phi_{i, \, \mathrm{high}} - \phi_{i, \, \mathrm{low}}}{10}$ such that $\phi_{i,j} = \phi_{i, \, \mathrm{low}} + j \cdot \mathrm{d}\phi_i \quad \forall j \in [0 \ldots 10]$. The new search range is then defined by $\phi_{i,\,\mathrm{max}} \pm \mathrm{d}\phi_i$. The final phase after $N$ refinements has an accuracy of $\frac{2\pi}{5^{N}}$ where $N \equiv \mathrm{AUTOPHASE}$.
......@@ -293,7 +293,7 @@ The next five logical flags activate or deactivate execution options:
\item[LOGBENDTRAJECTORY]
\index{OPTION!LOGBENDTRAJECTORY}
Save the reference trajectory inside dipoles in an ASCII file. For each dipole a separate file is written to the directory \filename{data/}. Default is false.
Save the reference trajectory inside dipoles in an ASCII file. For each dipole a separate file is written to the directory \textit{data/}. Default is false.
\item[VERSION]
\index{OPTION!VERSION}
......
......@@ -141,7 +141,7 @@ Table~\ref{distattruniversal,distattrinjected,distattrsemitted}.
\hline
\tabhead{Attribute Name & Default Value & Units & Description }
\hline
\tabline{WRITETOFILE}{\index{WRITETOFILE} \texttt{FALSE} & None & Echo initial distribution to text file \filename{data/\textless basename \textgreater\_ DIST.dat}.}
\tabline{WRITETOFILE}{\index{WRITETOFILE} \texttt{FALSE} & None & Echo initial distribution to text file \textit{data/\textless basename \textgreater\_ DIST.dat}.}
%\hline
\tabline{SCALABLE}{\index{SCALABLE} \texttt{FALSE} & None & Makes the generation scalable with respect of number of particles. The result depends on the number of cores used.}
%
......
......@@ -643,7 +643,7 @@ adjusted so that the reference particle is bent exactly \texttt{ANGLE} radians w
(Lower output.)
Now we will illustrate the case where the magnet length is set by the \texttt{L} attribute and only the fringe
fields are described by the field map. We change the \filename{TEST-MAP.T7} file to:
fields are described by the field map. We change the \textit{TEST-MAP.T7} file to:
\begin{verbatim}
1DProfile1 1 1 2.0
-10.0 0.0 10.0 1
......@@ -738,7 +738,7 @@ The reason is that the path of the reference particle through the real magnet (w
matches the ideal trajectory. (The effective length of the real magnet is not quite the same as the hard
edged magnet for the reference trajectory.)
We can compensate for this by changing the field map file \filename{TEST-MAP.T7} file to:
We can compensate for this by changing the field map file \textit{TEST-MAP.T7} file to:
\begin{verbatim}
1DProfile1 1 1 2.0
-10.0 -0.03026 10.0 1
......@@ -969,7 +969,7 @@ of Gauss, where the \texttt{Dipole} example (Figure~\ref{sbend3d1}) uses meter a
triplet: SBEND3D, FMAPFN="fdf-tosca-field-map.table", LENGTH_UNITS=10., FIELD_UNITS=-1e-4;
\end{verbatim}
The first few links of the field map \filename{fdf-tosca-field-map.table}:
The first few links of the field map \textit{fdf-tosca-field-map.table}:
\begin{verbatim}
422280 422280 422280 1
......@@ -989,7 +989,7 @@ The first few links of the field map \filename{fdf-tosca-field-map.table}:
\begin{verbatim}
Dipole:SBEND3D,FMAPFN="90degree_Dipole_Magnet.out",LENGTH_UNITS=1000.0, FIELD_UNITS=-10.0;
\end{verbatim}
The first few links of the field map \filename{90degree\_Dipole\_Magnet.out}:
The first few links of the field map \textit{90degree\_Dipole\_Magnet.out}:
\begin{verbatim}
4550000 4550000 4550000 1
X [LENGTH_UNITS]
......@@ -1273,7 +1273,7 @@ A \texttt{CYCLOTRON} object includes the main characteristics of a cyclotron, th
\item[MAXR]
Minimal radial extent of the machine (unit: mm, default : 10000.0)
\end{kdescription}
During the tracking, the particle ($r, z, \theta$) will be deleted if MINZ $< z <$ MAXZ or MINR $< r <$ MAXR, and it will be recorded in the ASCII file \filename{\textless inputfilename\textgreater.loss}.
During the tracking, the particle ($r, z, \theta$) will be deleted if MINZ $< z <$ MAXZ or MINR $< r <$ MAXR, and it will be recorded in the ASCII file \textit{\textless inputfilename\textgreater.loss}.
\noindent Example:
\begin{verbatim}
ring: Cyclotron, TYPE="RING", CYHARMON=6, PHIINIT=0.0,
......@@ -1448,7 +1448,7 @@ label:RFCAVITY, APERTURE=real-vector, L=real,
Using a RF Cavity in \textit{OPAL-t} mode, the following additional parameters are defined:
\begin{kdescription}
\item[FMAPFN]
Field maps in the \filename{T7} format can be specified.
Field maps in the \textit{T7} format can be specified.
\item[TYPE]
Type specifies STANDING [default] or SINGLE GAP structures.
\item[FREQ]
......@@ -1668,7 +1668,7 @@ label:TRAVELINGWAVE, APERTURE=real-vector, L=real,
\item[LAG]
The phase lag [{rad}] (default: 0). In \textit{OPAL-t} this phase is in general relative to the phase at which the reference particle gains the most energy. This phase is determined using an auto-phasing algorithm (see~Appendix~\ref{autophasing}). This auto-phasing algorithm can be switched off, see \texttt{APVETO}.
\item[FMAPFN]
Field maps in the \filename{T7} format can be specified.
Field maps in the \textit{T7} format can be specified.
\item[FREQ]
Defines the frequency of the traveling wave structure in units of MHz. A warning is issued when the frequency of
the cavity card does not correspond to the frequency defined in the FMAPFN file. The frequency defined in the FMAPFN
......@@ -1865,7 +1865,7 @@ cma2: CCollimator, XSTART=x3, XEND=x4,YSTART=y3, YEND=y4,
ZSTART=2, ZEND=100, WIDTH=10.0, PARTICLEMATTERINTERACTION=cmphys;
\end{verbatim}
The particles lost on the CCOLLIMATOR are recorded in the ASCII file \filename{\textless inputfilename\textgreater.loss}
The particles lost on the CCOLLIMATOR are recorded in the ASCII file \textit{\textless inputfilename\textgreater.loss}
\index{Collimators|)}
\clearpage
......@@ -1907,7 +1907,7 @@ eec2: Septum, xstart=4100.0, xend=4300.0,
ystart=-1200.0, yend=-150.0, width=0.05;
\end{verbatim}
The particles lost on the SEPTUM are recorded in the ASCII file \filename{\textless input\_file\_name \textgreater.loss}.
The particles lost on the SEPTUM are recorded in the ASCII file \textit{\textless input\_file\_name \textgreater.loss}.
\clearpage
\section{Probe (\textit{OPAL-cycl})}
......@@ -1945,7 +1945,7 @@ The y coordinate of the end point. [{\millim}]
prob1: Probe, xstart=4166.16, xend=4250.0,
ystart=-1226.85, yend=-1241.3;
\end{verbatim}
The particles probed on the PROBE are recorded in the ASCII file \filename{\textless inputfilename\textgreater.loss}.
The particles probed on the PROBE are recorded in the ASCII file \textit{\textless inputfilename\textgreater.loss}.
Please note that these particles are not deleted in the simulation, however, they are recorded in the ``loss" file.
......@@ -1987,7 +1987,7 @@ ystart=-1226.85, yend=-1241.3,
opcharge=1, opmass=PMASS, opyield=2, stop=false;
\end{verbatim}
No matter what the value of STOP is, the particles hitting on the STRIPPER are recorded in the ASCII file \filename{\textless inputfilename\textgreater.loss}.
No matter what the value of STOP is, the particles hitting on the STRIPPER are recorded in the ASCII file \textit{\textless inputfilename\textgreater.loss}.
......
......@@ -58,7 +58,7 @@ and Third-Party Library (TPL) support
\item MPI (\texttt{-D TPL\_ENABLE\_MPI:BOOL=ON })
\end{itemize}
To enable a given TPL, the path to this package's header include and library directories should be specified
when building Trilinos. The TPL libraries such as \filename{libparmetis.a libmetis.a libblas.a liblapacke.a liblapack.a} are needed
when building Trilinos. The TPL libraries such as \textit{libparmetis.a libmetis.a libblas.a liblapacke.a liblapack.a} are needed
to use MultiGrid (SAAMG).
\subsection{Environment Variables}
......@@ -203,7 +203,7 @@ An \textit{OPAL}~library can be build by specifying \texttt{-DBUILD\_LIBOPAL} in
optimization package \ref{bib:optpilot1}.
\section{Emacs Mode for \textit{OPAL}}
An opal-mode for emacs is provided to get highlighted input files. To use it the user should make the directory \filename{\$HOME/.emacs.d/opal} and copy the file \filename{opal.el} there. Then the following lines
An opal-mode for emacs is provided to get highlighted input files. To use it the user should make the directory \textit{\$HOME/.emacs.d/opal} and copy the file \textit{opal.el} there. Then the following lines
\begin{footnotesize}
\begin{verbatim}
(add-to-list 'load-path "~/.emacs.d/opal")
......@@ -212,7 +212,7 @@ An opal-mode for emacs is provided to get highlighted input files. To use it the
(setq auto-mode-alist (append '(("\\.in\$" . opal-mode)) auto-mode-alist))
\end{verbatim}
\end{footnotesize}
should be added to the emacs configuration file \filename{\$HOME/.emacs}. In case your input file has the extensions \filename{.opal} or \filename{.in} you will enjoy highlighted
should be added to the emacs configuration file \textit{\$HOME/.emacs}. In case your input file has the extensions \textit{.opal} or \textit{.in} you will enjoy highlighted
keywords, constants etc.
\section{Regression tests}
......
......@@ -136,17 +136,17 @@ To run the parallel plate benchmark simulation, user need to set the option \tex
\section{Post-Processing}
\label{sec:PostProcessing}
\index{Multipacting!PostProcessing}
In the general case (not only in multipacting simulations), \textit{OPAL} will dump the 6D phase space and statistical information of the particles in the simulation domain, into a \filename{h5} file. The dump frequency, i.e., after how many time steps the particle information will be saved can be specified with the option \texttt{PSDUMPFREQ}. Setting \texttt{Option, PSDUMPFREQ=1} dumps the information in each time step.
In the general case (not only in multipacting simulations), \textit{OPAL} will dump the 6D phase space and statistical information of the particles in the simulation domain, into a \textit{h5} file. The dump frequency, i.e., after how many time steps the particle information will be saved can be specified with the option \texttt{PSDUMPFREQ}. Setting \texttt{Option, PSDUMPFREQ=1} dumps the information in each time step.
A utility tool \filename{h5ToVtk} converts the \filename{h5} file to the Visualization Toolkit (VTK) legacy format. The number of VTK files equals to the number of time steps in \filename{h5} file. These VTK files together with a VTK file automatically generated by the geometry class of \textit{OPAL} which contains the geometry of the RF structure under study can be visualized using for example with Paraview \ref{paraview}. The animation and clip feature of Paraview is very useful to visualize the particle motion inside the RF structure.
A utility tool \textit{h5ToVtk} converts the \textit{h5} file to the Visualization Toolkit (VTK) legacy format. The number of VTK files equals to the number of time steps in \textit{h5} file. These VTK files together with a VTK file automatically generated by the geometry class of \textit{OPAL} which contains the geometry of the RF structure under study can be visualized using for example with Paraview \ref{paraview}. The animation and clip feature of Paraview is very useful to visualize the particle motion inside the RF structure.
For simulations involving the geometry (multipacting and field emission), \textit{OPAL} will also dump the position and current of incident particles into another \filename{h5} file with the name \filename{*\_Surface.h5}, where the asterisk stands for the base name of the user's \textit{OPAL} input file. If we need this surface loss data during post processing, we should specify the dump frequency in the option \texttt{SURFDUMPFREQ} with a positive integer in the \textit{OPAL} input file, otherwise, the default value of the option is \texttt{SURFDUMPFREQ=-1}, and the \filename{*\_Surface.h5} will not be generated. Another utility tool \filename{h5SurfaceVtk} convert the \filename{*\_Surface.h5} file to VTK files. For multipacting simulation, these VTK files can be used to visualize the \emph{hot spots} of the RF structure where multipacting happens.
For simulations involving the geometry (multipacting and field emission), \textit{OPAL} will also dump the position and current of incident particles into another \textit{h5} file with the name \textit{*\_Surface.h5}, where the asterisk stands for the base name of the user's \textit{OPAL} input file. If we need this surface loss data during post processing, we should specify the dump frequency in the option \texttt{SURFDUMPFREQ} with a positive integer in the \textit{OPAL} input file, otherwise, the default value of the option is \texttt{SURFDUMPFREQ=-1}, and the \textit{*\_Surface.h5} will not be generated. Another utility tool \textit{h5SurfaceVtk} convert the \textit{*\_Surface.h5} file to VTK files. For multipacting simulation, these VTK files can be used to visualize the \emph{hot spots} of the RF structure where multipacting happens.
The above mentioned utility tools are based on H5hut library, and will soon be available in the distribution.
Some of the boundary geometry related simulations, like the multipacting simulation using re-normalizing particle number approach, or dark current simulations where the current of field emitted particles from a single triangle has been re-normalized as the model predicted current has exceeded the user defined upper limit, the current (weight) of simulation particles varies and each simulation particle stands for more physical particles than the initial simulation particles. In these cases, instead of using simulation particles, we count the number of \emph{effective particles} defined as the ratio of total current in simulation over the current of a single initial particle.
An ASCII file named \filename{Part\_statistics.dat} containing the simulation time, the number of impacts and associated total SEY value as well as the number of \emph{effective particles} in each time step. This makes the analysis of the time evolution of particle density feasible with tools like GNUPLOT.
An ASCII file named \textit{Part\_statistics.dat} containing the simulation time, the number of impacts and associated total SEY value as well as the number of \emph{effective particles} in each time step. This makes the analysis of the time evolution of particle density feasible with tools like GNUPLOT.
\input{footer}
\ No newline at end of file
......@@ -32,7 +32,7 @@ According to the number of particles defined by the argument \texttt{npart} in \
\begin{verbatim}
Dist1: DISTRIBUTION, TYPE=fromfile, FNAME="PartDatabase.dat";
\end{verbatim}
where the file \filename{PartDatabase.dat} should have two lines:
where the file \textit{PartDatabase.dat} should have two lines:
\begin{verbatim}
1
0.001 0.001 0.001 0.001 0.001 0.001
......@@ -256,7 +256,7 @@ rsys,1
finish
\end{verbatim}
By running this in ANSYS, you can get a fields file with the name \filename{cyc100\_ANSYS.data}.
By running this in ANSYS, you can get a fields file with the name \textit{cyc100\_ANSYS.data}.
You need to put 6 parameters at the header of the file, namely,
$r_{min}$ [{\millim}], $\Delta r$ [{\millim}], $\theta_{min}$[{^{\circ}}], $\Delta \theta$[{^{\circ}}],
$N_\theta$(total data number in each arc path of azimuthal direction) and $N_r$(total path number along radial direction).
......@@ -299,7 +299,7 @@ But with \texttt{BANDRF} type, the program can also read in the 3D electric fiel
For the detail about its usage, please see Section~\ref{cyclotron}.
\subsection{Default PSI format}
If the value of \texttt{TYPE} is other string rather than above mentioned, the program requires the data format like PSI format field file \filename{ZYKL9Z.NAR} and \filename{SO3AV.NAR}, which was given by the measurement.
If the value of \texttt{TYPE} is other string rather than above mentioned, the program requires the data format like PSI format field file \textit{ZYKL9Z.NAR} and \textit{SO3AV.NAR}, which was given by the measurement.
We add 4 parameters at the header of the file, namely,
$r_{min}$ [{\millim}], $\Delta r$ [{\millim}], $\theta_{min}$[{^{\circ}}], $\Delta \theta$[{^{\circ}}],
If $\Delta r$ or $\Delta \theta$ is decimal,one can set its negative opposite number. This is useful is the decimal is unlimited.
......@@ -346,7 +346,7 @@ triplet: SBEND3D, FMAPFN="fdf-tosca-field-map.table", LENGTH_UNITS=10., FIELD_UN
l1: Line = (ringdef, triplet, triplet);
\end{verbatim}
The field-map with file name \filename{fdf-tosca-field-map.table} is loaded, which is a
The field-map with file name \textit{fdf-tosca-field-map.table} is loaded, which is a
file like
\begin{verbatim}
422280 422280 422280 1
......@@ -470,10 +470,10 @@ For the {\bfseries Tune Calculation mode}, one additional auxiliary file with t
In each line the three values represent energy $E$, radius $r$ and $P_r$ for the SEO (Static Equilibrium Orbit)
at starting point respectively and their units are {MeV}, {\millim} and {\millirad}.
A bash script \filename{tuning.sh} is shown on the next page, to execute \textit{OPAL-cycl} for tune calculations.
A bash script \textit{tuning.sh} is shown on the next page, to execute \textit{OPAL-cycl} for tune calculations.
\examplefromfile{examples/tuning.sh}
To start execution, just run \filename{tuning.sh} which uses the input file \filename{testcycl.in} and the auxiliary file \filename{FIXPO\_ SEO}.
The output file is \filename{plotdata} from which one can plot the tune diagram.
To start execution, just run \textit{tuning.sh} which uses the input file \textit{testcycl.in} and the auxiliary file \textit{FIXPO\_ SEO}.
The output file is \textit{plotdata} from which one can plot the tune diagram.
% -- -- -- -- -- -- Section -- -- -- -- -- --
......@@ -481,23 +481,23 @@ The output file is \filename{plotdata} from which one can plot the tune diagram.
\subsubsection{Single Particle Tracking mode}
The intermediate phase space data is stored in an ASCII file which can be used to
the plot the orbit. The file's name is combined by input file name (without extension) and \filename{-trackOrbit.dat}.
the plot the orbit. The file's name is combined by input file name (without extension) and \textit{-trackOrbit.dat}.
The data are stored in the global Cartesian coordinates.
The frequency of the data output can be set using the option \texttt{SPTDUMPFREQ} of \texttt{OPTION} statement see~Section~\ref{option}
The phase space data per \texttt{STEPSPERTURN} (a parameter in the \texttt{TRACK} command) steps is stored in an ASCII file.
The file's name is a combination of input file name (without extension) and \filename{-afterEachTurn.dat}.
The file's name is a combination of input file name (without extension) and \textit{-afterEachTurn.dat}.
The data is stored in the global cylindrical coordinate system.
Please note that if the field map is ideally isochronous, the reference particle of a given energy take exactly one revolution in \texttt{STEPPERTURN} steps;
Otherwise, the particle may not go through a full {360}{^{\circ}} in \texttt{STEPPERTURN} steps.
There are 3 ASCII files which store the phase space data around $0$, $\pi/8$ and $\pi/4$ azimuths.
Their names are the combinations of input file name (without extension) and \filename{-Angle0.dat}, \filename{-Angle1.dat} and \filename{-Angle2.dat} respectively.
Their names are the combinations of input file name (without extension) and \textit{-Angle0.dat}, \textit{-Angle1.dat} and \textit{-Angle2.dat} respectively.
The data is stored in the global cylindrical coordinate system, which can be used to check the property of the closed orbit.
\subsubsection{Tune calculation mode}
The tunes $\nu_r$ and $\nu_z$ of each energy are stored in a ASCII file with name \filename{tuningresult}.
The tunes $\nu_r$ and $\nu_z$ of each energy are stored in a ASCII file with name \textit{tuningresult}.
\subsubsection{Multi-particle tracking mode}
......@@ -506,10 +506,10 @@ including RMS envelop size, RMS emittance, external field, time, energy, length
tracking step, are stored in the H5hut file-format \ref{bib:howison2010} and can be analyzed
using the H5root \ref{bib:schietinger}.
The frequency of the data output can be set using the \texttt{PSDUMPFREQ} option of \texttt{OPTION} statement see~Section~\ref{option}.
The file is named like the input file but the extension is \filename{.h5}.
The file is named like the input file but the extension is \textit{.h5}.
The intermediate phase space data of central particle (with ID of 0) and an off-centering particle (with ID of 1)
are stored in an ASCII file. The file's name is combined by the input file name (without extension) and \filename{-trackOrbit.dat}.
are stored in an ASCII file. The file's name is combined by the input file name (without extension) and \textit{-trackOrbit.dat}.
The frequency of the data output can be set using the \texttt{SPTDUMPFREQ} option of \texttt{OPTION} statement see~Section~\ref{option}.
......
......@@ -59,7 +59,7 @@ where $\gamma$ is the relativistic factor, $q$ is the charge, and $m$ is the res
\section{Positioning of Elements}
Since \textit{OPAL} version 2.0 of \textit{OPAL} elements can be placed in space using 3D coordinates \texttt{X}, \texttt{Y}, \texttt{Z}, \texttt{THETA}, \texttt{PHI} and \texttt{PSI}, see Section~\ref{Element:common}. The old notation using \texttt{ELEMEDGE} is still supported. \textit{OPAL-t} then computes the position in 3D using \texttt{ELEMDGE}, \texttt{ANGLE} and \texttt{DESIGNENERGY}. It assumes that the trajectory consists of straight lines and segments of circles. Fringe fields are ignored. For cases where these simplifications aren't justifiable the user should use 3D positioning. For a simple switchover \textit{OPAL} writes a file \filename{\_3D.opal} where all elements are placed in 3D.
Since \textit{OPAL} version 2.0 of \textit{OPAL} elements can be placed in space using 3D coordinates \texttt{X}, \texttt{Y}, \texttt{Z}, \texttt{THETA}, \texttt{PHI} and \texttt{PSI}, see Section~\ref{Element:common}. The old notation using \texttt{ELEMEDGE} is still supported. \textit{OPAL-t} then computes the position in 3D using \texttt{ELEMDGE}, \texttt{ANGLE} and \texttt{DESIGNENERGY}. It assumes that the trajectory consists of straight lines and segments of circles. Fringe fields are ignored. For cases where these simplifications aren't justifiable the user should use 3D positioning. For a simple switchover \textit{OPAL} writes a file \textit{\_3D.opal} where all elements are placed in 3D.
Beamlines containing guns should be supplemented with the element \texttt{SOURCE}. This allows \textit{OPAL} to distinguish the cases and adjust the initial energy of the reference particle.
......@@ -195,12 +195,12 @@ As can be seen from Figure~\ref{OPALTSchemeSimple} the integration of the trajec
\section{Output}
In addition to the progress report that \textit{OPAL-t} writes to the standard output (stdout) it also writes different files for various purposes.
\subsection*{\filename{\textless input\_file\_name \textgreater.stat}}
\subsection*{\textit{\textless input\_file\_name \textgreater.stat}}
This file is used to log the statistical properties of the bunch in the ASCII variant of the SDDS format \ref{bib:borland1995}. It can be viewed with the SDDS Tools \ref{bib:borland2016} or GNUPLOT. The frequency with which the statistics are computed and written to file can be controlled With the option \texttt{STATDUMPFREQ}. The information that is stored are found in the following table.
\begin{center}
\begin{tabular}{}
\caption{Information stored in the file \filename{\textless input\_file\_name \textgreater.stat}}\\
\caption{Information stored in the file \textit{\textless input\_file\_name \textgreater.stat}}\\
\hline
\tabhead{Column Nr. & Name & Units & Meaning}
\hline
......@@ -267,11 +267,11 @@ This file is used to log the statistical properties of the bunch in the ASCII va
\end{longtable}
\end{center}
\subsection*{\filename{data/\textless input\_file\_name \textgreater\_Monitors.stat}}
\subsection*{\textit{data/\textless input\_file\_name \textgreater\_Monitors.stat}}
\textit{OPAL-t} computes the statistics of the bunch for every \texttt{MONITOR} that it passes. The information that is written can be found in the following table.
\begin{center}
\begin{longtable}{p{1.2cm}p{1.9cm}p{1.3cm}p{9.5cm}}
\caption{Information stored in the file \filename{\textless input\_file\_name \textgreater\_Monitors.stat}}\\
\caption{Information stored in the file \textit{\textless input\_file\_name \textgreater\_Monitors.stat}}\\
\hline
\tabhead{Column Nr. & Name & Units & Meaning}
\hline
......@@ -320,13 +320,13 @@ This file is used to log the statistical properties of the bunch in the ASCII va
\end{longtable}
\end{center}
\subsection*{\filename{data/\textless input\_file\_name \textgreater\_3D.opal}}
\subsection*{\textit{data/\textless input\_file\_name \textgreater\_3D.opal}}
\textit{OPAL-t} copies the input file into this file and replaces all occurrences of \texttt{ELEMEDGE} with the corresponding position using \texttt{X}, \texttt{Y}, \texttt{Z}, \texttt{THETA}, \texttt{PHI} and \texttt{PSI}.
\subsection*{\filename{data/\textless input\_file\_name \textgreater\_ElementPositions.txt}}
\subsection*{\textit{data/\textless input\_file\_name \textgreater\_ElementPositions.txt}}
\textit{OPAL-t} stores for every element the position of the entrance and the exit. Additionally the reference trajectory inside dipoles is stored. On the first column the name of the element is written prefixed with ``BEGIN: '', ``END: '' and ``MID: '' respectively. The remaining columns store the z-component then the x-component and finally the y-component of the position in floor coordinates.
\subsection*{\filename{data/\textless input\_file\_name \textgreater\_ElementPositions.py}}
\subsection*{\textit{data/\textless input\_file\_name \textgreater\_ElementPositions.py}}
This Python script can be used to generate visualizations of the beam line in different formats. Beside an ASCII file that can be printed using GNUPLOT a VTK file and an HTML file can be generated. The VTK file can then be opened in e.g. ParaView \ref{paraview,bib:paraview} or VisIt \ref{bib:visit}. The HTML file can be opened in any modern web browser. Both the VTK and the HTML output are three-dimensional. For the ASCII format on the other hand you have provide the normal of a plane onto which the beam line is projected.
The script is not directly executable. Instead one has to pass it as argument to \texttt{python}:
......@@ -341,11 +341,11 @@ The following arguments can be passed
\item \texttt{-{}-export-web} to export for the web
\item \texttt{-{}-project-to-plane x y z} to project the beam line to the plane with the normal with the components \texttt{x}, \texttt{y} and \texttt{z}
\end{itemize}
\subsection*{\filename{data/\textless input\_file\_name \textgreater\_ElementPositions.stat}}
\subsection*{\textit{data/\textless input\_file\_name \textgreater\_ElementPositions.stat}}
This file can be used when plotting the statistics of the bunch to indicate the positions of the magnets. It is written in the SDDS format. The information that is written can be found in the following table.
\begin{center}
\begin{longtable}{p{1.2cm}p{2.2cm}p{1.3cm}p{9.2cm}}
\caption{Information stored in the file \filename{\textless input\_file\_name \textgreater\_ElementPositions.stat}}\\
\caption{Information stored in the file \textit{\textless input\_file\_name \textgreater\_ElementPositions.stat}}\\
\hline
\tabhead{Column Nr. & Name & Units & Meaning}
\hline
......@@ -375,12 +375,12 @@ This file can be used when plotting the statistics of the bunch to indicate the
\end{longtable}
\end{center}
\subsection*{\filename{data/\textless input\_file\_name \textgreater\_DesignPath.dat}}
\subsection*{\textit{data/\textless input\_file\_name \textgreater\_DesignPath.dat}}
The trajectory of the reference particle is stored in this ASCII file. The content of the columns are listed in the following table.
\begin{center}
\begin{longtable}{p{1.2cm}p{1.3cm}p{11.2cm}}
\caption{Information stored in the file \filename{\textless input\_file\_name \textgreater\_DesignPath.dat}}\\
\caption{Information stored in the file \textit{\textless input\_file\_name \textgreater\_DesignPath.dat}}\\
\hline
\tabhead{Column Nr. & Units & Meaning}
\hline
......
......@@ -145,7 +145,7 @@ For a thickness of $\Delta s=1e-4$ $m$, $\theta=0.5349 \alpha$ (in degree).
Small step is needed in the routine of CollimatorPhysics.
If a large step is given in the main input file, in the file \filename{CollimatorPhysics.cpp},
If a large step is given in the main input file, in the file \textit{CollimatorPhysics.cpp},
it is divided by a integer number $n$ to make the step size using for the calculation of collimator physics less than 1.01e-12 s. As shown
by Figure~\ref{diagram,diagram2} in the previous section, first we track one step for the particles already in the
collimator and the newcomers, then another (n-1) steps to make sure the particles in the collimator experience the same time as the ones
......
......@@ -265,7 +265,7 @@ Its attributes are:
This argument is only available for \texttt{AUTO} mode multi-bunch run in \textit{OPAL-cycl}.
\item[MULTIPACTING] see~Chapter~\ref{multpact}\TODO{Describe attribute}
\item[OBJECTIVES] An array of column names from the \filename{.stat} file used in \texttt{STATISTICAL-ERRORS} to compute mean value and standard deviation across all runs.
\item[OBJECTIVES] An array of column names from the \textit{.stat} file used in \texttt{STATISTICAL-ERRORS} to compute mean value and standard deviation across all runs.
\end{kdescription}
Example:
\begin{verbatim}
......@@ -287,7 +287,7 @@ To use this method one has to specify the \texttt{METHOD} using the following fo
\end{center}
\noindent where \texttt{<track{\textunderscore}method>} is the method that should track the particles, \texttt{<ncores>} is the number of cores used for a run and \texttt{<nruns>} is the number of individual runs that should be performed. \textbf{It should be noted that the total number of cores available has to be greater or equal to \texttt{ncores} + 1.} One core is needed to manage the distribution of tasks and to collect the results. The other cores are used to perform the simulations. If in total $N \times \texttt{ncores} + 1$ cores are available then $N$ individual runs are processed in parallel each using \texttt{ncores}.
\sloppy For each run of the method \texttt{STATISTICAL-ERRORS} a unique base name is generated of the form \filename{foo}. Each individual run is then performed in a directory \filename{foo{\textunderscore}run{\textunderscore}ddddd}. The files that are produced by the \texttt{<track{\textunderscore}method>} are kept. \textbf{This can lead to a large amount of data especially when snapshots of the phase space are stored frequently. The user should make sure that the file system can handle the amount of data or set the option \texttt{PSDUMPFREQ} to a big number.}
\sloppy For each run of the method \texttt{STATISTICAL-ERRORS} a unique base name is generated of the form \textit{foo}. Each individual run is then performed in a directory \textit{foo{\textunderscore}run{\textunderscore}ddddd}. The files that are produced by the \texttt{<track{\textunderscore}method>} are kept. \textbf{This can lead to a large amount of data especially when snapshots of the phase space are stored frequently. The user should make sure that the file system can handle the amount of data or set the option \texttt{PSDUMPFREQ} to a big number.}
In the end the method \texttt{STATISTICAL-ERRORS} computes the mean and the standard deviation for each variable in the array \texttt{OBJECTIVES} along the machine and stores this information in to the \filename{.stat} file.
In the end the method \texttt{STATISTICAL-ERRORS} computes the mean and the standard deviation for each variable in the array \texttt{OBJECTIVES} along the machine and stores this information in to the \textit{.stat} file.
\input{footer}
\ No newline at end of file
......@@ -176,7 +176,7 @@ To run opal on N nodes in parallel environment interactively, use this command i
# mpirun -np N opal testinj2-2.in
\end{verbatim}
If restart a job from the last step of an existing \filename{.h5} file, add a new argument like this:
If restart a job from the last step of an existing \textit{.h5} file, add a new argument like this:
\begin{verbatim}
# mpirun -np N opal testinj2-2.in --restart -1
\end{verbatim}
......
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