Merge branch 'master' of git.assembla.com:plumed2

configurations/.gitignore

+/*.local

configurations/README

+Configuration files ending with ".local" will not be tracked by git.
+This might be useful to maintain local configurations.

regtest/rt9/COLVAR.reference

-#! FIELDS time uwall.bias lwall.bias uwall.force2 lwall.force2
- 0.000000  0.062  0.797  4.935 127.597
- 0.050000  0.119  0.298  9.505 47.693
- 0.100000  0.131  0.070 10.488 11.261
- 0.150000  0.104  0.007  8.287  1.149
- 0.200000  0.106  0.006  8.463  0.882
+#! FIELDS time ang1 ang2 uwall.bias lwall.bias uwall.force2 lwall.force2
+ 0.000000  0.356  0.059  0.062 16.714  4.935 76827.763
+ 0.050000  0.377  0.114  0.119  5.952  9.505 16326.651
+ 0.100000  0.381  0.158  0.131  2.005 10.488 3191.662
+ 0.150000  0.372  0.187  0.104  0.817  8.287 829.754
+ 0.200000  0.373  0.188  0.106  0.770  8.463 759.514

regtest/rt9/plumed.dat

@@ -6,7 +6,7 @@ LOWER_WALLS ARG=ang2 AT=0.2 KAPPA=40.0 EXP=4 EPS=0.3 OFFSET=0.1 LABEL=lwall
 
 PRINT ...
   STRIDE=10
-  ARG=*.bias,*.force2
+  ARG=ang1,ang2,*.bias,*.force2
   FILE=COLVAR FMT=%6.3f
 ... PRINT
 

user-doc/extract

@@ -65,6 +65,7 @@ awk 'BEGIN{gfile="automatic/GLOSSARY1.list"}{
     } else if ( $2=="INTERNAL" ){
       if(output!="")close(output);
       output="automatic/"$3".txt";
+      lfile="automatic/"$3".txt";
       print "/**" > output
       print "\\page "$3 > output
       print "\\section "$3 > output