fixed examples in new documentation for actions

new-manual/index.ndx

@@ -0,0 +1,6 @@
+[ Protein ]
+1 3 5 7 9
+2 4 6 8 10
+[ Group2 ]
+30 31 32 33 34 35 36 37 38 39 40
+5

src/core/ActionToPutData.cpp

@@ -68,7 +68,7 @@ tstep: PUT CONSTANT UNIT=time PERIODIC=NO
 # This is how you create a value to hold a 10 x 10 matrix in plumed whose elements are unitless
 matrix: PUT SHAPE=10,10 UNIT=number PERIODIC=NO
 # Lastly, if you want to pass a value that has a periodic domain you can do so as follows
-tor: PUT PERIODIC=-pi,pi
+tor: PUT UNIT=number PERIODIC=-pi,pi
 ```
 
 */

src/core/PbcAction.cpp

@@ -46,7 +46,7 @@ pbc: PBC
 
 Instead this command would be called from python like this:
 
-```plumed
+```python
 import plumed
 
 # Create a PLUMED object

src/refdist/Difference.cpp

@@ -159,7 +159,7 @@ void Difference::read( ActionWithArguments* action ) {
     } else action->getPntrToArgument(1)->setDomain( min0, max0 );
   } else if( action->getPntrToArgument(1)->isPeriodic() ) {
     periodic=true; action->getPntrToArgument(1)->getDomain( min0, max0 );
-    if( !action->getPntrToArgument(1)->isConstant() ) {
+    if( !action->getPntrToArgument(0)->isConstant() ) {
       action->error("period for input variables " + action->getPntrToArgument(0)->getName() + " and " + action->getPntrToArgument(1)->getName() + " should be the same 1");
     } else action->getPntrToArgument(0)->setDomain( min0, max0 );
   }

src/refdist/Kernel.cpp

@@ -75,17 +75,17 @@ distance as is done in the following example:
 
 ```plumed
 d1: DISTANCE ATOMS=1,2
-d2: DISTANCEE ATOMS=3,4
+d2: DISTANCE ATOMS=3,4
 k: KERNEL ARG=d1,d2 TYPE=gaussian CENTER=1,1 SIGMA=0.1,0.1
 ```
 
 or you can use the [MAHALANOBIS_DISTANCE](MAHALANOBIS_DISTANCE.md) as is done here:
 
 ```plumed
-t1: TORSION ATOMS=1,2,3,4
-t2: TORSION ATOMS=5,6,7,8
+phi: TORSION ATOMS=1,2,3,4
+psi: TORSION ATOMS=5,6,7,8
 k: KERNEL ...
-   ARG=t1,t2 TYPE=von-misses
+   ARG=phi,psi TYPE=von-misses
    CENTER=-1.09648066E+0000,-7.17867907E-0001 
    COVAR=1.40523052E-0001,-1.05385552E-0001,-1.05385552E-0001,1.63290557E-0001
 ...
@@ -98,9 +98,9 @@ Notice that you specify the Kernel function in a separate PLUMED input file by u
 
 ```plumed
 #SETTINGS INPUTFILES=regtest/pamm/rt-pamm-periodic/2D-testc-0.75.pammp
-t1: TORSION ATOMS=1,2,3,4
-t2: TORSION ATOMS=5,6,7,8
-k: KERNEL ARG=t1,t2 REFERENCE=regtest/pamm/rt-pamm-periodic/2D-testc-0.75.pammp NUMBER=3
+phi: TORSION ATOMS=1,2,3,4
+psi: TORSION ATOMS=5,6,7,8
+k: KERNEL ARG=phi,psi REFERENCE=regtest/pamm/rt-pamm-periodic/2D-testc-0.75.pammp NUMBER=3
 ```
 
 This command computes the same Kernel that was computed in the previous input.  The keyword `REFERENCE` specifies that the parameters are to be read
@@ -110,9 +110,9 @@ Lastly, note that you can use vectors in the input to this shortcut as shown her
 
 ```plumed
 #SETTINGS INPUTFILES=regtest/pamm/rt-pamm-periodic/2D-testc-0.75.pammp
-t1: TORSION ATOMS1=1,2,3,4 ATOMS2=9,10,11,12 ATOMS3=17,18,19,20
-t2: TORSION ATOMS1=5,6,7,8 ATOMS2=13,14,15,16 ATOMS3=21,22,23,24
-k: KERNEL ARG=t1,t2 REFERENCE=regtest/pamm/rt-pamm-periodic/2D-testc-0.75.pammp NUMBER=3
+phi: TORSION ATOMS1=1,2,3,4 ATOMS2=9,10,11,12 ATOMS3=17,18,19,20
+psi: TORSION ATOMS1=5,6,7,8 ATOMS2=13,14,15,16 ATOMS3=21,22,23,24
+k: KERNEL ARG=phi,psi REFERENCE=regtest/pamm/rt-pamm-periodic/2D-testc-0.75.pammp NUMBER=3
 ```
 
 The output `k` here is a vector with three components. The first component is the kernel evaluated with the torsion involving atoms 1, 2, 3 and 4 and the 
@@ -136,7 +136,7 @@ PLUMED_REGISTER_ACTION(Kernel,"KERNEL")
 
 void Kernel::registerKeywords(Keywords& keys) {
   ActionShortcut::registerKeywords( keys );
-  keys.add("numbered","ARG","the arguments that should be used as input to this method");
+  keys.addInputKeyword("numbered","ARG","scalar/vector","the arguments that should be used as input to this method");
   keys.add("compulsory","TYPE","gaussian","the type of kernel to use");
   keys.add("compulsory","CENTER","the position of the center of the kernel");
   keys.add("optional","SIGMA","square root of variance of the cluster");