Improved manual

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

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