changelog

brought the "changes after alpha" up together with other changes

CHANGES/v2.4.md

@@ -9,10 +9,6 @@ should have a look at the section "Changes leading to incompatible behavior" bel
 might need tiny adjustments in their input files.
 Notice that version 2.4 includes already all the fixes in branch 2.3 up to 2.3.2 indicated in \ref CHANGES-2-3 .
 
-\warning This is an alpha release!
-
-\warning Notice that this list is not complete yet
-
 Changes from version 2.3 which are relevant for users:
 - Changes leading to incompatible behavior:
   - A c++11 compliant compiler is required (see \issue{212}). This should mean:
@@ -20,14 +16,16 @@ Changes from version 2.3 which are relevant for users:
     - clang 3.3
     - intel 15
     Since the number of c++11 features that we use is limited, older compilers might work as well.
-- The meaning of BIASFACTOR=1 in \ref METAD has been modified and can now be used to indicate unbiased
-  simulations. Non-well-tempered metadynamics is BIASFACTOR=-1, which is the new default value.
-  Notice that this has an implication on the biasfactor written in the HILLS file when doing
-  non-well-tempered metadynamics.
-- Due to a change in \ref COMMITTOR, the format of its output file has been slightly changed.
-- \ref HISTOGRAM : When using weights default is now to output histogram divided by number of frames from which data was taken.  In addition the 
-  UNORMALIZED flag has been replaced with the keyword NORMALIZATION, which can be set equal to true, false or ndata.
-- Sharing coordinates and applying force is now faster (in some cases these can result in much better scaling of the performances in parallel).
+  - The meaning of BIASFACTOR=1 in \ref METAD has been modified and can now be used to indicate unbiased
+    simulations. Non-well-tempered metadynamics is BIASFACTOR=-1, which is the new default value.
+    Notice that this has an implication on the biasfactor written in the HILLS file when doing
+    non-well-tempered metadynamics.
+  - Due to a change in \ref COMMITTOR, the format of its output file has been slightly changed.
+  - \ref HISTOGRAM : When using weights default is now to output histogram divided by number of frames from which data was taken.  In addition the 
+    UNORMALIZED flag has been replaced with the keyword NORMALIZATION, which can be set equal to true, false or ndata.
+  - All switching functions are now stretched by default, also when using the "simple syntax" (e.g. `COORDINATION NN=6`).
+    Switching functions were already stretched by default when using the advanced syntax (e.g. `COORDINATION SWITCH={}`)
+    since version 2.2.  Notice that this will introduce small numerical differences in the computed switching functions.
 - New modules:
   - A new PLUMED-ISDB module have been included, this module includes a number of CVs to calculate experimental data with the internal ability
     to also calculate a \ref METAINFERENCE score.
@@ -73,6 +71,7 @@ Changes from version 2.3 which are relevant for users:
   - \ref pesmd : Tool for performing Langevin dynamics on an energy landscape that is specified using a PLUMED input file
   - \ref pathtools 
 - Other changes:
+  - Sharing coordinates and applying force is now faster (in some cases these can result in much better scaling of the performances in parallel).
   - \ref COMMITTOR : new flag to use committor to keep track of the visited basins without stopping the simulation
   - \ref PBMETAD : multiple walkers using files (thanks to Marco De La Pierre).
   - \ref PBMETAD : adaptive gaussians
@@ -82,6 +81,11 @@ Changes from version 2.3 which are relevant for users:
   - \ref METAD : added options to perform Transition Tempered Metadynamics (thanks to James Dama)
   - PDB files with more than 100k atoms can now be read using [hybrid 36](http://cci.lbl.gov/hybrid_36/) format,
     see \issue{226}.
+  - Added experimental lepton support. Set env var `export PLUMED_USE_LEPTON=yes` to activate lepton as a matheval replacement.
+    Notice that this is an experimental feature and is not fully validated yet. See \issue{244}.
+  - When parsing constants, PLUMED uses lepton library. This allows to pass
+    arguments such as `HEIGHT=exp(0.5)`.
+  - \ref CUSTOM function has been added as an alias to \ref MATHEVAL .
   - Trajectories read in \ref driver also support the usual replica convention, that is if
     trajectory with replica suffix is not found the driver will look for a trajectory without the replica suffix.
   - A new syntax (`@replicas:`) can be used to specify different arguments for different replicas.
@@ -89,6 +93,7 @@ Changes from version 2.3 which are relevant for users:
   - Examples in the documentation now have syntax highlighting and links to the documentation of used actions.
   - \ref COORDINATIONNUMBER : Added option to have pairwise distance moments of coordination number in the multicolvar module
   - GROMACS patch updated to gromacs-2016.4
+  - Fixed a bug in \ref LOCAL_AVERAGE which appears when you use SPECIESA and SPECIESB keywords instead of just SPECIES
 
 Changes from version 2.3 which are relevant for developers:
   - A few fixes has been made to improve exception safety. Although we still cannot declare
@@ -104,17 +109,7 @@ Changes from version 2.3 which are relevant for developers:
   - Added `--enable-rpath` option for autoconf (off by default).
   - Files related to changelog are now stored as `.md` files. This makes
     it possible to navigate them from github.
+  - `configure.ac` has been simplified and improved in order to more easily probe C++ libraries.
+  - added `plumed_custom_skip` function to regtests in order to skip specific tests based on specific conditions (e.g. OS).
+  - environment variable `LDSO` has been renamed to `LDSHARED`, which is standard in the python community.
 
-Fixes after alpha release:
-  - Fixed a bug in \ref LOCAL_AVERAGE which appears when you use SPECIESA and SPECIESB keywords instead of just SPECIES
-  - All switching functions are now stretched by default, also when using the "simple syntax" (e.g. `COORDINATION NN=6`).
-    Switching functions were already stretched by default when using the advanced syntax (e.g. `COORDINATION SWITCH={}`)
-    since version 2.2.  Notice that this will introduce small numerical differences in the computed switching functions.
-  - Added experimental lepton support. Set env var `export PLUMED_USE_LEPTON=yes` to activate lepton as a matheval replacement.
-    Notice that this is an experimental feature and is not fully validated yet. See \issue{244}.
-  - When parsing constants, PLUMED uses lepton library. This allows to pass
-    arguments such as `HEIGHT=exp(0.5)`.
-  - \ref CUSTOM function has been added as an alias to \ref MATHEVAL .
-  - (developers): `configure.ac` has been simplified and improved in order to more easily probe C++ libraries.
-  - (developers): added `plumed_custom_skip` function to regtests in order to skip specific tests based on specific conditions (e.g. OS).
-  - (developers): environment variable `LDSO` has been renamed to `LDSHARED`, which is standard in the python community.