Merge branch 'v2.2'

CHANGES/v2.2.txt

@@ -5,7 +5,14 @@
 Version 2.2 (Oct 13, 2015)
 ----------------------------
 
-Include all fixes in branch 2.1 indicated in \ref CHANGES-2-1 .
+Version 2.2 contains several improvements with respect to 2.1. Users currently working with 2.1
+should have a look at the section "Changes leading to incompatible behavior" below and
+might need tiny adjustments in their input files. In 2.2 we restored more features of 1.3
+that were missing in 2.1, so users still working with 1.3 could opt for an upgrade.
+A tutorial explaining how to move from PLUMED 1 to PLUMED 2 is available (see \ref moving).
+
+Below you find a list of all the changes with respect to version 2.1.
+Notice that version 2.2 includes already all the fixes in branch 2.1 up to 2.1.4 indicated in \ref CHANGES-2-1 .
 
 Changes from version 2.1 which are relevant for users:
 - Changes leading to incompatible behavior:
@@ -105,7 +112,7 @@ For developers:
 - ./configure is automatically relaunched when changing ./configure or Makefile.conf. This makes it more robust
   to switch between branches.
 
-Unreleased changes (will be included in 2.2.2)
+Version 2.2.2 (Apr 13, 2016)
 ----------------------------------------------
 
 For users:
@@ -119,7 +126,8 @@ For users:
 - Fixed a bug in the normalization of kernel functions (relevant for \ref HISTOGRAM).
 - Fixed a regression introduced in v2.2 that was making \ref METAD with non-MPI multiple walkers crash
   if reading frequently. See \issue{190}
-- Updated patch for gromacs 5.1
+- Updated patch for gromacs 5.x. Patches for gromacs 5.0 and 5.1 have been fixed so as to allow
+  patching in runtime mode.
 - Possibility to control manual generation (including pdf) from ./configure. Pdf manual is now off
   by default. Notice that on travis CI it is still generated.
 

src/bias/External.cpp

@@ -41,7 +41,7 @@ The following is an input for a calculation with an external potential that is
 defined in the file bias.dat and that acts on the distance between atoms 3 and 5.
 \verbatim
 DISTANCE ATOMS=3,5 LABEL=d1
-EXTERNAL ARG=d1 FILENAME=bias.dat LABEL=external 
+EXTERNAL ARG=d1 FILE=bias.dat LABEL=external 
 \endverbatim
 (See also \ref DISTANCE \ref PRINT).
 
@@ -64,7 +64,7 @@ potential acting on two torsional angles:
 \verbatim
 TORSION ATOMS=4,5,6,7 LABEL=t1
 TORSION ATOMS=6,7,8,9 LABEL=t2
-EXTERNAL ARG=t1,t2 FILENAME=bias.dat LABEL=ext
+EXTERNAL ARG=t1,t2 FILE=bias.dat LABEL=ext
 \endverbatim
 
 The header in the file bias.dat for this calculation would read: