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[ESPResSo-devel] Suggestions for ESPResSo++

From: Olaf Lenz
Subject: [ESPResSo-devel] Suggestions for ESPResSo++
Date: Wed, 23 Jan 2008 17:29:08 +0100
User-agent: Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv: Gecko/20071022 Thunderbird/ Mnenhy/

Dear users and developers of ESPResSo!
Dear possible users of ESPResSo++!

As many of you might already have heard, we are currently planning a
complete rewrite of the ESPResSo software.  With the experience gained
in ESPResSo, we want to make "ESPResSo++" a flexible, powerful,
user-friendly software for simulations in soft-matter research.
ESPResSo++ should - of course - be able to do all the simulations that
could be performed with ESPResSo, and more.

We already have a number of ideas concerning this new program.  To
make sure that we did not forget any crucial feature for the new
software, we want to ask you to help us!

What we need is descriptions of typical simulation scenarios that
people want to tackle with the new software. On the one hand, we want
to collect scenarios that were successfully tackled with ESPResSo or
that are to be tackled in the future.  On the other hand, however, we
also want to know of scenarios that could NOT successfully be solved
with ESPResSo: Have you ever had a problem that you thought ESPResSo
should be able to solve, but it wasn't? Have you ever tried to solve a
problem with ESPResSo and found out that ESPResSo is suboptimally
suited or inefficient?

Attached, you will find a template file for a use case scenario.  It
would be nice if you could fill in one or more of these templates to
describe scenarios that you think should be solvable in ESPResSo++!

Detailed instructions on how to fill in the template are found in the
template file. It is written in LaTeX, but even if you don't know
LaTeX, you should still be able to edit it. The file contains a simple
example scenario.

Furthermore, if you know of somebody who intended to use ESPResSo to
solve a problem at some time but he couldn't use it and put ESPResSo
aside, please send him this template!

Best regards

     The ESPResSo++ team

%% This is a template for a use case for ESPResSo++.
%% General hints:
%% * Try to be as specific as you can.
%% * If you do specify magnitudes without any units, reduced units are
%%   assumed.
%% * If a section/subsection/minisec does not apply to your use case,
%%   skip it and/or remove it.

% Give the use case a name.
\section{Use Case: Ion distribution around a charged rod}

\minisec{Short description}
% Please provide a short description of the simulated system and the
% purpose of the simulation.
Simulation of a charged cylinder in a salt solution to determine the
distribution of the ions around the cylinder.

% Please provide your name.
Olaf Lenz

% If available, can you provide references to articles where the
% system is used?
\item M.~Deserno. {\em Counterion condensation for rigid linear
    polyelectrolytes}.  PhD thesis, Universit{\"a}t Mainz, February

\subsection*{Description of the physical system}
% In this subsection, the physical system of the use case should be
% specified.

\minisec{Statistical Ensemble}
% In what physical ensemble does the system live?  
% Examples: NVT, NVE, NpT, \mu pT

\minisec{Periodic directions}
% In which directions is the system periodic?
% Examples: all, none, x and y

\minisec{Unit cell geometry}
% If any of the directions is periodic, please specify the geometry
% and size of the unit cell
% Examples: cubic ($L=100$), rectangular ($L_x=L_y=100$, $L_z=50$)
cubic ($L=100$)

\minisec{Fixed objects and external fields}
% Are there any fixed objects in the system ("constraints" in
% ESPResSo)? Please specify all properties of the object (position,
% direction, charge, ...)!
% Are there any external fields actig in the system?
% Examples: cylinder in z-direction, cylindrical pore in z
% direction, electric field ($E=0.1$) in z-direction
1 charged cylinder (charge: -300), parallel to the z-axis in the
center of the unit cell in x and y, that stretches the whole box

\minisec{Number and types of particles}
% What types of particles do exist in the system?
% How many particles of each type exist?
% Example: 100 ions, 1000 dipoles, 10000 ellipsoids
400 counterions, 100 coions

\minisec{Constant properties of the particles} 
% What properties do the different types of particles have, that do
% not change during the simulation? Please specify their values, if
% possible.  
% Example: dipoles: dipole moment $\mu=1.0$
counterions: charge $q=+1$; coions: charge $q=-1$

\minisec{Variable properties of the particles}
% What properties of the different particle types are variable?
% By default, we assume that the 3D position is variable, please
% specify, if the particles are fixed in any direction.
% Example: direction of the dipole moment, particles are fixed in z

% What interactions act between the different objects (particles and
% fixed objects) in the system? Please give the type and the
% parameters of the interactions!
% Please specify explicitly, if there is no interaction between some
% particle types. If the system contains bonds with a fixed length (as
% implemented by Rattle/Shake/LINC), specify them here.
\item purely repulsive core of a LJ interaction ($\sigma=2.0$,
  $\epsilon=1.0$, $r_\mathrm{cut}=1.0$) between all particles and
  between the cylinder and the particles
\item electrostatic interactions between all particles and between
  the cylinder and the particles 

\minisec{Non-equilibrium process}
% In the case of an out-of-equilibrium simulation, please describe the
% underlying physical process, i.e. which changes are expected in the
% system.

\minisec{Other comments}
% Are there any additional comments on the physical system?

\subsection*{Description of the simulation}
% In this subsection, the simulation process should be described.
% If you do not feel it is necessary to specify some of the items,
% just skip the section. For example, the setup of some systems might
% be trivial, or the type of analysis is not important.
% Any MD, any thermostat, any barostat, MC single particle moves

\minisec{Molecular dynamics or Monte-Carlo}
% Please specify whether a molecular dynamics (MD) or a Monte-Carlo
% (MC) type of simulation is to be performed.  
% Examples: MD, MC, hybrid (MD plus MC volume moves for contant pressure)

\minisec{System setup and warming up}
% Specify, how the system can can be set up (including "warming up"),
% i.e. how an initial configuration of the system can be created.
% If necessary, specify in which geometry the particles should be
% located initially.
% Example: 
\item Randomly place the ions in the whole system.
\item Warm up by doing a simulation without electrostatic interactions
  and with capped LJ interactions.

\minisec{Required simulation algorithms}
% If any specific algorithms are required for the simulation, please
% specify them here.  
% Examples: Lattice-Boltzmann for hydrodynamic interactions

\minisec{Suggested simulation algorithms}
% If you want to suggest algorithms that can be effectively used in
% the simulation, please specify them here. These can encompass:
% thermostats, barostats, algorithms for long-ranged algorithms, etc.
\item P3M for electrostatic interactions
\item Verlet lists for the short-ranged interactions

% Describe, what analysis are to be done in the system, and, if
% possible, the expected values. If you do averages, specify exactly
% what you average over (e.g. time average, ensemble average, ...). Also,
% specify the statistical methods you use (e.g. histograms).
Compute the radial distribution function of the ion types with respect to
the cylinder:
\item In each timestep, compute density histograms of the ion types
  over the distance to the cylinder.
\item At the end, average the histograms.
\item Compute the radial distribution function by normalising the

\subsection*{Further information}

\minisec{Did the use case work with the old ESPResSo program?}
% If this use case did not work with the old ESPResSo code, or only
% insatisfactorily, please specify why it did not work!

\minisec{Bottlenecks and expected problems}
% If you do know of specific problems connected to this use case
% (extensive memory consumption, performance bottlenecks) or things
% that require special attention, please list them here.

\minisec{Expected hardware requirements}
% How many processors do you expect should typically suffice to
% perform a simulation?
One processor.


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