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Commit 17cffaae authored by Giovanni Bussi's avatar Giovanni Bussi
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Small cleaning on documentation

I removed the claim that I am the only author and cleaned a bit
the introduction
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// This document is formatted for Doxygen // This document is formatted for Doxygen
/** /**
\mainpage A Plumed Clone \mainpage Plumed 2
\author Giovanni Bussi (as of now) Roadmap:
\date 2011 - Cloning most PLUMED1 features (to be defined)
\version 1.9.x - Public beta release (to be defined)
\warning Very, very unstable - 2.0 public release (to be defined)
As it can be guessed from the version number, this is a candidate for PLUMED2
which should be reviewed by a reasonable number the PLUMED developers.
If it is not accepted as a full package, it can be considered as a repository
of a few ideas which can be stolen and used in real PLUMED2 development.
If accepted, a possible road map is:
- 1.99 public release before end of 2011, cloning most PLUMED1 features.
It should be usable by (and useful for) developers and people
in the community willing to try it.
- 2.0 public release before mid of 2012, possibly able to superseed completely PLUMED1.
\section Motivation Motivation
- Simpler interface with MD codes. PLUMED should compile by itself as a library,
using a proper configure/make procedure, so as to avoid learning all the compilation
details of each MD code. Patching a new code should just consist in the insertion of
proper function calls and minimal modification to Makefile (to link plumed library),
without the need of further hacking inside PLUMED.
- PLUMED should be easy to extend. Adding a new method/CV should be possible
without touching the rest.
- Other issues:
- More friendly units.
- More flexible CVs (such as function of other CVs).
- Possibility to re-read input.
\section FeaturesAndChanges Features and changes \section FeaturesAndChanges Features and changes
This are some comments about the structure of the code:
- Re-designed from scratch, hopefully better. - Re-designed from scratch, hopefully better.
- Input is conceptually similar but NON compatible. It is difficult to automatically - Input is conceptually similar but NON compatible. It is difficult to automatically
convert old input files, but we could provide a short transition guide. convert old input files, but we could provide a short transition guide.
...@@ -176,37 +152,6 @@ INCLUDE anotherplumed.dat ...@@ -176,37 +152,6 @@ INCLUDE anotherplumed.dat
LOAD share-object.so LOAD share-object.so
\endverbatim \endverbatim
\section SharingPolicy Sharing Policy
- I think that Plumed should become fully open, with a public-access shared repository.
I would like to switch from cvs to git, which allows for easier branch manipulation.
On the central repository, we should have a public master branch where we can
publish our work, but for which we do not provide support (developer version).
From time to time, as usual, we can provide a supported release (2.0, 2.1 ,...)
- If it is necessary to work privately, it can be done on a local branch
(maybe shared among a few collaborators). Git easily allows to merge multiple times, so it should
be relatively easy to stay up do date with the master branch. Finally, when the work
is ready, we can merge it into the master branch.
This sort of private working should be discouraged for the development of PLUMED kernel.
However, it would be perfect to implement new CVs or new methods, since they are
completely decoupled from the rest.
\section ToDo To Do
\todo Pbc on COLVARs (possibly with some smart trick for functions-of-functions).
\todo Optimize atoms sharing. "Calc" should be divided in more steps:
* Finding list of atoms needed and requesting them (on NAMD, this goes at the
end of the previous step).
* Sending the atoms
* Receiving the atoms and computing everything
* Sending the forces back
Moreover, it would be nice to allow PLUMED to be run only on a subset of
the available processors.
\todo Replica exchange.
\todo Interfaces with other codes
\todo Implementation of CVs
\todo Implementation of free energy methods
\section Install Install \section Install Install
- Configure and compile your MD code - Configure and compile your MD code
......
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