Skip to content

Commit

Permalink
Browse files Browse the repository at this point in the history
Merge branch 'master' of https://github.com/espressomd/espresso
  • Loading branch information
dschwoerer committed Jul 2, 2015
2 parents 51f7c53 + dbf3659 commit 3b294aa
Show file tree
Hide file tree
Showing 49 changed files with 1,923 additions and 270 deletions.
10 changes: 5 additions & 5 deletions .cproject
Expand Up @@ -64,6 +64,11 @@
<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
</scannerConfigBuildInfo>
</storageModule>
<storageModule moduleId="refreshScope" versionNumber="2">
<configuration configurationName="Build (GNU)">
<resource resourceType="PROJECT" workspacePath="/espresso"/>
</configuration>
</storageModule>
<storageModule moduleId="org.eclipse.cdt.make.core.buildtargets">
<buildTargets>
<target name="all" path="" targetID="org.eclipse.cdt.build.MakeTargetBuilder">
Expand Down Expand Up @@ -564,9 +569,4 @@
</target>
</buildTargets>
</storageModule>
<storageModule moduleId="refreshScope" versionNumber="2">
<configuration configurationName="Build (GNU)">
<resource resourceType="PROJECT" workspacePath="/espresso"/>
</configuration>
</storageModule>
</cproject>
5 changes: 5 additions & 0 deletions .project
Expand Up @@ -5,6 +5,11 @@
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>net.sourceforge.texlipse.builder.TexlipseBuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.cdt.autotools.core.genmakebuilderV2</name>
<arguments>
Expand Down
6 changes: 4 additions & 2 deletions doc/ug/analysis.tex
Expand Up @@ -22,7 +22,9 @@ \chapter{Analysis in Tcl}
\index{analysis}
\newescommand{analyze}

\todo{Add a comment to the UG that the analysis routines in \es{} with Python currently require the user to `from espressomd import analyze.'}
\todo{Add a comment to the UG that the analysis routines in \es{} with
Python currently require the user to `from espressomd import
analyze.'}

\es has two fundamentally different classes of observables for
analyzing the systems. On the one hand, some observables are
Expand Down Expand Up @@ -182,7 +184,7 @@ \subsection{Cylindrical Average}
\begin{essyntax}
analyze cylindrical_average \var{center} \var{direction}
\var{length} \var{radius} \var{bins\_axial} \var{bins\_radial}
\var{types} \var{xrange} \var{yrange}
\opt{\var{types}}
\end{essyntax}

The command returns a list of lists. The outer list contains all data
Expand Down
55 changes: 44 additions & 11 deletions doc/ug/inter.tex
Expand Up @@ -973,7 +973,6 @@ \subsection{Rigid bonds}
vtol=\arg{double}
]
\end{pysyntax}
\PythonSyntaxOff

\begin{essyntax}
inter \var{bondid}
Expand Down Expand Up @@ -1652,17 +1651,51 @@ \subsection{Debye-H\"uckel potential}
\index{Debye-H\"uckel potential|mainindex}
\index{interactions!Debye-H\"uckel|mainindex}

\begin{essyntax}
\variant{1}
inter coulomb \var{l_B} dh \var{\kappa} \var{r_\mathrm{cut}}
\variant{2}
inter coulomb \var{l_B} dh \var{\kappa} \var{r_{\text{cut}}}
\var{\varepsilon_{\text{int}}} \var{r_0} \var{r_1} \var{\alpha}
\begin{features}
\required{ELECTROSTATICS}
\end{features}
\end{essyntax}
\begin{pysyntax}
\object{
electrostatics
}{
\require{1}{DH}
}{
bjerrum\textunderscore length=\arg{double},
kappa=\arg{double},
r\textunderscore cut=\arg{double}
}
\leavevmode \\
\object{
electrostatics
}{
\require{1,2}{CDH}
}{
bjerrum\textunderscore length=\arg{double},
kappa=\arg{double},
r\textunderscore cut=\arg{double},
eps\textunderscore int=\arg{double},
eps\textunderscore ext=\arg{double},
r0=\arg{double},
r1=\arg{double},
alpha=\arg{double}
}[
]
\end{pysyntax}

\begin{essyntax}
\require{1}{\variant{1}
inter coulomb \var{l_\mathrm{B}} dh \var{\kappa} \var{r_\mathrm{cut}}}
\variant{2}
inter coulomb \var{l_\mathrm{B}} dh \var{\kappa} \var{r_{\text{cut}}}
\var{\varepsilon_{\text{int}}} \var{\varepsilon_{ext}} \var{r_0} \var{r_1}
\require{1,2}{\var{\alpha}}
\begin{features}
\required[1]{ELECTROSTATICS}
\required[2]{COULOMB_DEBYE_HUECKEL}
\end{features}
\end{essyntax}\leavevmode
\\
\fbox{\parbox{\textwidth}{NOTE: the two variants are mutually exclusive. If
``COULOMB_DEBYE_HUECKEL'' is defined in the configuration file, variant \variant{1}
would not work.}}\\
\\
Defines the electrostatic potential by
\begin{equation}
U^{C-DH} = l_B k_B T \frac{q_1 q_2 exp(-\kappa r)}{r}\quad \mathrm{for}\quad r<r_{\mathrm{cut}}
Expand Down
17 changes: 12 additions & 5 deletions doc/ug/part.tex
Expand Up @@ -26,7 +26,6 @@ \section{\keyword{part}: Creating single particles}
\subsection{Defining particle properties}
\label{ssec:particleproperties}

\PythonSyntaxOn
\begin{pysyntax}
\property{
espressomd.System()
Expand Down Expand Up @@ -66,7 +65,6 @@ \subsection{Defining particle properties}
`rotational_friction':\arg{float}\}}
}
\end{pysyntax}
\PythonSyntaxOff
\begin{essyntax}
part
\var{pid}
Expand Down Expand Up @@ -298,8 +296,8 @@ \subsection{Defining particle properties}
\noindent
\fbox{\parbox{\linewidth-2\fboxsep-2\fboxrule}{%
Please note that even though swimming is interoperable with the
CPU version of LB it is only supported on \emph{less than three}
Open MPI nodes, i.e.\ $\text{\keyword{n_nodes}} \leq 1$.%
CPU version of LB it is only supported on \emph{one} Open MPI
node, i.e.\ $\text{\keyword{n_nodes}} = 1$.%
}}
\end{arguments}

Expand Down Expand Up @@ -770,7 +768,16 @@ \subsection{\texttt{copy\_particles}: copying a set of particles}
copy_particles set {1 2} set {3 4}
copy_particles range 1 4
\end{tclcode}
All these examples do the same - making exact copies of particles 1 through 4.
All these examples do the same---making exact copies of particles 1 through 4.

\noindent
\fbox{\parbox{\linewidth-2\fboxsep-2\fboxrule}{%
Please note that \keyword{copy_particles} only works if only
fundamental particle properties are used, such as \keyword{pos},
\keyword{type}, etc.\ as the \keyword{copy_particles} procedure
only possesses parsers for these. Other properties, such as
\keyword{quatu} cannot be parsed and will thus lead to an error.%
}}

\section{\texttt{constraint}: Setting up constraints}\label{sec:constraint}
\newescommand{constraint}
Expand Down
18 changes: 9 additions & 9 deletions doc/ug/pypresso.tex
Expand Up @@ -14,15 +14,15 @@
\bool_new:N \l_pypresso_enable_bool
\bool_set_false:N \l_pypresso_enable_bool

\NewDocumentCommand \PythonSyntaxOn { }
{
\bool_set_true:N \l_pypresso_enable_bool
}

\NewDocumentCommand \PythonSyntaxOff { }
{
\bool_set_false:N \l_pypresso_enable_bool
}
% \NewDocumentCommand \PythonSyntaxOn { }
% {
% \bool_set_true:N \l_pypresso_enable_bool
% }
%
% \NewDocumentCommand \PythonSyntaxOff { }
% {
% \bool_set_false:N \l_pypresso_enable_bool
% }

\cs_new_protected:Npn \pypresso_object:nnnnn #1#2#3#4#5
{
Expand Down

0 comments on commit 3b294aa

Please sign in to comment.