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added integrator, lbboundaries and ek stuff to ug #23

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158 changes: 158 additions & 0 deletions doc/ug/electrokinetics.tex
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,37 @@ \section{Setup}

\subsection{\label{ssec:ek-init}Initialization}

\begin{pysyntax}
\object{
espressomd.electrokinetics
}{
Electrokinetics
}{
agrid = \arg{float},
lb_density = \arg{float},
viscosity = \arg{float},
friction = \arg{float},
T = \arg{float},
bjerrum_length = \arg{float}
}[
bulk_viscosity = \arg{float},
gamma_odd = \arg{float},
gamma_even = \arg{float},
stencil = \arg{string},
advection = \arg{bool},
fluid_coupling = \arg{string}
]
% \end{pysyntax}
% \begin{pysyntax}
\attributes{
espressomd.System()
}{
actors
}{
add.(\arg{electrokinetics.EKBoundary})
}
\end{pysyntax}

\begin{essyntax}
\require{1 or 2 or 3}{electrokinetics}
\opt{agrid \var{agrid}}
Expand Down Expand Up @@ -201,6 +232,30 @@ \subsection{\label{ssec:ek-init}Initialization}

\subsection{\label{ssec:ek-diff-species}Diffusive Species}

\begin{pysyntax}
\object{
espressomd.electrokinetics
}{
Species
}{
density = \arg{float},
D = \arg{float},
valency = \arg{float}
}[
ext_force = \arg{array of 3 floats}
]
% \end{pysyntax}
% \begin{pysyntax}
\attributes{
espressomd.electrokinetics
}{
Elektrokinetics()
}{
add_species(\arg{electrokinetics.Species})
}
\end{pysyntax}


\begin{essyntax}
\require{1 or 2 or 3}{electrokinetics}
\var{species\_number}
Expand All @@ -214,6 +269,7 @@ \subsection{\label{ssec:ek-diff-species}Diffusive Species}
\required[3]{EK_REACTIONS}
\end{features}
\end{essyntax}

The \lit{electrokinetics} command followed by an integer \var{species\_number}
(in the range 0 to 10) and several options can be used to initialize the
diffusive species. Here the options specify: the number density
Expand All @@ -231,6 +287,28 @@ \subsection{\label{ssec:ek-diff-species}Diffusive Species}

\subsection{\label{ssec:ek-boundaries}Boundaries}

\begin{pysyntax}
\object{
espressomd.electrokinetics
}{
EKBoundary
}{
shape = \arg{shapes.Shape},
}[
charge_density= \arg{float},
net_charge = \arg{float}
]
\end{pysyntax}
\begin{pysyntax}
\attributes{
espressomd.System()
}{
ekboundaries
}{
add(\arg{electrokinetics.EKBoundary})
}
\end{pysyntax}

\begin{essyntax}
\require{1 or 2 or 3}{electrokinetics}
\require{2}{boundary}
Expand Down Expand Up @@ -260,6 +338,57 @@ \section{\label{ssec:ek-output}Output}

\subsection{\label{ssec:ek-output-fields}Fields}

\begin{pysyntax}
\object{
espressomd.electrokinetics.Electrokinetics()
}{
print_vtk_velocity
}{
path = \arg{file}
}[]

\object{
espressomd.electrokinetics.Electrokinetics()
}{
print_vtk_boundary
}{
path = \arg{file}
}[]

\object{
espressomd.electrokinetics.Electrokinetics()
}{
print_vtk_density
}{
path = \arg{file}
}[]

\object{
espressomd.electrokinetics.Electrokinetics()
}{
print_vtk_potential
}{
path = \arg{file}
}[]

\object{
espressomd.electrokinetics.Electrokinetics()
}{
print_vtk_lbforce
}{
path = \arg{file}
}[]

\object{
espressomd.electrokinetics.Electrokinetics()
}{
print_vtk_particle_potential
}{
path = \arg{file}
}[]
\end{pysyntax}


\begin{essyntax}
\require{1 or 2 or 3}{electrokinetics}
print
Expand All @@ -285,6 +414,24 @@ \subsection{\label{ssec:ek-output-fields}Fields}
and mayavi2\footnote{http://code.enthought.com/projects/mayavi/}. If the
\opt{vtk} option is not specified, a gnuplot readable data file will be exported.

\begin{pysyntax}
\object{
espressomd.electrokinetics.Species()
}{
print_vtk_velocity
}{
path = \arg{file}
}[]

\object{
espressomd.electrokinetics.Species()
}{
print_vtk_density
}{
path = \arg{file}
}[]
\end{pysyntax}

\begin{essyntax}
\require{1 or 2 or 3}{electrokinetics}
\var{species\_number}
Expand All @@ -305,6 +452,17 @@ \subsection{\label{ssec:ek-output-fields}Fields}

\subsection{\label{ssec:ek-local-quantities}Local Quantities}

\begin{pysyntax}
\attributes{
espressomd.electrokinetics
}{
Species[node]
}{
density = \arg{float},
flux = \arg{float}
}
\end{pysyntax}

\begin{essyntax}
\require{1 or 2 or 3}{electrokinetics}
node \var{x} \var{y} \var{z}
Expand Down
116 changes: 116 additions & 0 deletions doc/ug/lb.tex
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,15 @@ \section{Setting up a LB fluid}
gamma_odd = \arg{float},
gamma_even = \arg{float}
]
% \end{pysyntax}
% \begin{pysyntax}
\attributes{
espressomd.System()
}{
actors
}{
add.(\arg{lb.LBFluid | LBFluid_GPU})
}
\begin{features}
\required[1]{LB}
\required[2]{LB_GPU}
Expand Down Expand Up @@ -179,6 +188,17 @@ \section{Setting up a LB fluid}
This causes the old forces to be reused and thus conserves momentum.

\section{LB as a thermostat}
\begin{pysyntax}
\object{
espressomd.System().thermostat
}{
set_lb
}{
kT = \arg{float}
}[]
\end{pysyntax}


\begin{essyntax}
thermostat \require{1 or 2 or 3}{lb} \var{T}
\begin{features}
Expand Down Expand Up @@ -341,6 +361,24 @@ \section{SC component-dependent interactions between particles}
information see \ref{sec:LennardJones} and \ref{sec:affinity}.

\section{Reading and setting single lattice nodes}

\begin{pysyntax}
\attributes{
espressomd.lb
}{
LBFluid | LBFluid_GPU[node]
}{
velocity,
density,
pi,
pi_neq,
population,
boundary
}

\end{pysyntax}


\begin{essyntax}
lbnode \var{x} \var{y} \var{z} \alt{print \asep set} \var{args}
\begin{features}
Expand Down Expand Up @@ -395,6 +433,61 @@ \section{Removing total fluid momentum}

\section{Visualization}
\label{ssec:LBvisualization}

\begin{pysyntax}
\object{
espressomd.lb.LBFluid | LBFluid_GPU()
}{
print_vtk_velocity
}{
path = \arg{file}
}[]

\object{
espressomd.lb.LBFluid | LBFluid_GPU()
}{
print_vtk_boundary
}{
path = \arg{file}
}[]

\object{
espressomd.lb.LBFluid | LBFluid_GPU()
}{
print_velocity
}{
path = \arg{file}
}[]

\object{
espressomd.lb.LBFluid | LBFluid_GPU()
}{
print_velocity
}{
path = \arg{file}
}[]

\object{
espressomd.lb.LBFluid | LBFluid_GPU()
}{
save_checkpoint
}{
path = \arg{file}
}[
binary = \arg{bool}
]

\object{
espressomd.lb.LBFluid | LBFluid_GPU()
}{
load_checkpoint
}{
path = \arg{file}
}[
binary = \arg{bool}
]
\end{pysyntax}

\begin{essyntax}
\variant{1} lbfluid print \opt{vtk} \var{property} \var{filename}
\variant{2} lbfluid print vtk velocity \opt{bb1_x bb1_y bb1_z bb2_x bb2_y bb2_z} \var{filename}
Expand All @@ -420,6 +513,29 @@ \section{Visualization}
have to be supplied when exporting the density field, to save both components.

\section{Setting up boundary conditions}

\begin{pysyntax}
\object{
espressomd.lbboundaries
}{
LBBoundary
}{
shape = \arg{shapes.Shape}
}[
velocity = \arg{array of 3 floats},
force = \arg{array of 3 floats}
]
% \end{pysyntax}
% \begin{pysyntax}
\attributes{
espressomd.System()
}{
lbboundaries
}{
add.(\arg{lbboundaries.LBBoundary})
}
\end{pysyntax}

\begin{essyntax}
\variant{1} lbboundary \var{shape} \var{shape\_args} \opt{velocity
\var{vx} \var{vy} \var{vz}}
Expand Down
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