From c47b855903dbaadba7d59a485336240476e2f34c Mon Sep 17 00:00:00 2001 From: Giovanni Bussi <giovanni.bussi@gmail.com> Date: Thu, 2 Jan 2014 14:53:33 +0100 Subject: [PATCH] Improved manual --- CHANGES/Unreleased.txt | 54 +++++++++++++++++++++++------------------- user-doc/Doxyfile | 2 +- 2 files changed, 31 insertions(+), 25 deletions(-) diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt index bd1d0e34f..a52390e8d 100644 --- a/CHANGES/Unreleased.txt +++ b/CHANGES/Unreleased.txt @@ -6,30 +6,36 @@ Include all fixes in branch 2.0 indicated in \ref CHANGES-2-0 . Changes from version 2.0 which are relevant for users: - New configuration system based on autoconf (use ./configure from root directory). - Optional packaged are detected at compile time and correctly - enabled/disabled. -- Root-mean-square devations with align weights different from displace weights - are now considerably faster. This will affect \ref RMSD calculations plus - other variables based on RMSD. -- Added WALKERS_MPI to \ref METAD, allowing to run multiple walkers in a mpi-based multi-replica framework. -- Added ACCELERATION to \ref METAD, allowing to calculate on the fly the Metadynamics acceleration factor. -- Added option PRECISION to set number of digits in \ref DUMPATOMS. -- Added NDX_FILE and NDX_GROUP to action \ref GROUP, allowing to import atom lists from ndx files. -- Small optimization in \ref WHOLEMOLECULES -- Small optimization in \ref COORDINATION when NN and MM are even and D_0=0 -- Faster atom scattering with domain decomposition. -- \ref SPRINT topological collective variables. -- \ref CH3SHIFTS collective variable. -- Improved multicolvar neighbor lists. -- Maximum colvar as well as minimum colvar is now possible. -- \ref COMMITTOR analysis. -- Added possibility to use negative strides in atom ranges (e.g. 10-1:-3). -- Added possibility to use \ref COORDINATION or \ref DHENERGY with NLIST in replica exchange simulations. -- Added STRETCH flag to \ref switchingfunction. -- Added possibility to read trajectories from \ref driver using VMD molfile - plugin (requires VMD plugins to be compiled and installed). -- Simplified install with the possibility to use an internally compiled - version of lapack and blas (automatically triggered by autoconf). + Optional packages are detected at compile time and correctly + enabled or disabled. An internal version of lapack and blas will be used + if these libraries are not installed. +- New actions: + - \ref SPRINT topological collective variables. + - \ref CH3SHIFTS collective variable. + - \ref COMMITTOR analysis. + - \ref LOCAL_AVERAGE. + - \ref NLINKS. + - Crystallation module, including \ref Q4, \ref Q6, \ref LOCAL_Q4, \ref LOCAL_Q6, \ref MOLECULES, and \ref AVERAGE_VECTOR. +- New flags for existing actions: + - \ref METAD : WALKERS_MPI flag (multiple walkers in a mpi-based multi-replica framework) + and ACCELERATION flag (calculate on the fly the Metadynamics acceleration factor). + - \ref DUMPATOMS : PRECISION option to set number of digits in output file. + - \ref GROUP : NDX_FILE and NDX_GROUP options to import atom lists from ndx (gromacs) files. + - In many multicolvars, MIN and MAX options can be used. +- Other new features: + - \ref driver can now read trajectories in many formats using VMD molfile plugin + (requires VMD plugins to be compiled and installed). + - \ref switchingfunction : added STRETCH flag. + - Negative strides in atom ranges (e.g. 10-1:-3). + - \ref COORDINATION and \ref DHENERGY with NLIST now work correctly in replica exchange simulations. + - Improved multicolvar neighbor lists. +- Optimizations: + - Root-mean-square devations with align weights different from displace weights + are now considerably faster. This will affect \ref RMSD calculations plus + other variables based on RMSD. + - \ref WHOLEMOLECULES is slighlty faster. + - \ref COORDINATION is slighlty faster when NN and MM are even and D_0=0. + - Atom scattering with domain decomposition is slightly faster Changes from version 2.0 which are relevant for developers: - Added regtests for plumed as a library (e.g. basic/rt-make-0). plumed command has an additional diff --git a/user-doc/Doxyfile b/user-doc/Doxyfile index a6adad9f2..9d299b962 100644 --- a/user-doc/Doxyfile +++ b/user-doc/Doxyfile @@ -17,7 +17,7 @@ # The PROJECT_NAME tag is a single word (or a sequence of words surrounded # by quotes) that should identify the project. -PROJECT_NAME = "Plumed 2.0: user manual" +PROJECT_NAME = "Plumed 2.1: user manual" # The PROJECT_NUMBER tag can be used to enter a project or revision number. # This could be handy for archiving the generated documentation or -- GitLab