Fixed examples for inputs in generic

src/function/Bessel.cpp

@@ -34,7 +34,27 @@ namespace function {
 /*
 Calculate the value of a Bessel function.
 
-\par Examples
+This action can be used to evaluate [Bessel functions](https://en.wikipedia.org/wiki/Bessel_function).
+This was action is needed because the modified Bessel function of the first kind of order 0 is needed in 
+order to calculate the [von-Misses distribution](https://en.wikipedia.org/wiki/Von_Mises_distribution) 
+that is used in the implementation of [KERNEL](KERNEL.md).  You can thus only use this function to evaluate the 
+modified Bessel function of the first kind of order 0.  You can evaluate the value of this Bessel function 
+at $x=1$ by using the following input:
+
+```plumed
+c: CONSTANT VALUE=1
+b: BESSEL ARG=c ORDER=0
+```
+
+Notice that you can also use a vector in the input for this action as illustrated below:
+
+```plumed
+c: CONSTANT VALUES=1,1,5,2
+b: BESSEL ARG=c ORDER=0
+```
+
+The value output by BESSEL in this case is also a vector with three components.  These components give the values
+of the Bessel function at 1.0, 1.5 and 2.0 respectively.
 
 */
 //+ENDPLUMEDOC

src/function/LessThan.cpp

@@ -21,6 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "LessThan.h"
 #include "FunctionShortcut.h"
+#include "FunctionOfScalar.h"
 #include "FunctionOfVector.h"
 #include "FunctionOfMatrix.h"
 #include "core/ActionRegister.h"
@@ -196,6 +197,8 @@ Transform all the elements of a matrix using a switching function that is one wh
 
 typedef FunctionShortcut<LessThan> LessThanShortcut;
 PLUMED_REGISTER_ACTION(LessThanShortcut,"LESS_THAN")
+typedef FunctionOfScalar<LessThan> ScalarLessThan;
+PLUMED_REGISTER_ACTION(ScalarLessThan,"LESS_THAN_SCALAR")
 typedef FunctionOfVector<LessThan> VectorLessThan;
 PLUMED_REGISTER_ACTION(VectorLessThan,"LESS_THAN_VECTOR")
 typedef FunctionOfMatrix<LessThan> MatrixLessThan;

src/function/MoreThan.cpp

@@ -21,6 +21,7 @@
 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
 #include "MoreThan.h"
 #include "FunctionShortcut.h"
+#include "FunctionOfScalar.h"
 #include "FunctionOfVector.h"
 #include "FunctionOfMatrix.h"
 #include "core/ActionRegister.h"
@@ -59,6 +60,8 @@ Transform all the elements of a matrix using a switching function that is one wh
 
 typedef FunctionShortcut<MoreThan> MoreThanShortcut;
 PLUMED_REGISTER_ACTION(MoreThanShortcut,"MORE_THAN")
+typedef FunctionOfScalar<MoreThan> ScalarMoreThan;
+PLUMED_REGISTER_ACTION(ScalarMoreThan,"MORE_THAN_SCALAR")
 typedef FunctionOfVector<MoreThan> VectorMoreThan;
 PLUMED_REGISTER_ACTION(VectorMoreThan,"MORE_THAN_VECTOR")
 typedef FunctionOfMatrix<MoreThan> MatrixMoreThan;

src/generic/Constant.cpp

@@ -70,7 +70,7 @@ PRINT ARG=c1,c2,c3,c4,c5 FILE=five_scalars
 Lastly, if you want to create a constant $2\times 3$ matrix you would use an input like the one below:
 
 ```plumed
-c: CONSTANT VALUE=1,2,3,4,5,6 NROWS=2 NCOLS=3
+c: CONSTANT VALUES=1,2,3,4,5,6 NROWS=2 NCOLS=3
 PRINT ARG=c FILE=matrix
 ```
 

src/generic/DumpAtoms.cpp

@@ -106,7 +106,7 @@ You can also enforce the output file type by using the `TYPE` keyword as shown b
 
 ```plumed
 c1: COM ATOMS=11-20 
-DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1 UNITS=A TYPE=gro
+DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1 TYPE=gro
 FLUSH STRIDE=1
 ```
 
@@ -120,7 +120,7 @@ your input file as shown below:
 ```plumed
 #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
 # this is required to have proper atom names:
-MOLINFO STRUCTURE=regtest/basic/rt32/reference.pdb
+MOLINFO STRUCTURE=regtest/basic/rt32/helix.pdb
 # if omitted, atoms will have "X" name...
 
 c1: COM ATOMS=11-20 

src/generic/GatherReplicas.cpp

@@ -42,6 +42,7 @@ working the vectors of values.  You then use this action to average over replica
 example shown below.
 
 ```plumed
+#SETTINGS NREPLICAS=2
 # Calculate distance between atoms 1 and 2 on for all 2 replicas
 d: DISTANCE ATOMS=1,2
 # Now gather the values of this distance on all the replicas:
@@ -55,6 +56,7 @@ PRINT ARG=s FILE=colvar
 Now suppose that we wanted to calculate a time average of the distance and an average over the replicas.  We could use an input like this:
 
 ```plumed
+#SETTINGS NREPLICAS=2
 d: DISTANCE ATOMS=1,2
 g: GATHER_REPLICAS ARG=d
 s: COMBINE ARG=g.rep-0,g.rep-1 COEFFICIENTS=0.5,0.5 PERIODIC=NO

src/generic/MassChargeInput.cpp

@@ -49,7 +49,7 @@ The first column of numbers is a numerical index, the second column is the masse
 You can read masses and charges from a PDB file instead by using an input like the one shown below:
 
 ```plumed
-#SETTINGS INPUTFILES=regtest/basic/rt-readmasscharge/test.pdb
+#SETTINGS NATOMS=108 INPUTFILES=regtest/basic/rt-readmasscharge/test.pdb
 mq: READMASSCHARGE PDBFILE=regtest/basic/rt-readmasscharge/test.pdb
 ```
 

src/generic/MolInfo.cpp

@@ -33,7 +33,7 @@ are in the backbone of a protein to the [ALPHARMSD](ALPHARMSD.md) action is show
 
 ```plumed
 #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
-MOLINFO STRUCTURE=reference.pdb
+MOLINFO STRUCTURE=regtest/basic/rt32/helix.pdb
 ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a
 ```
 
@@ -42,7 +42,7 @@ in a GC Watson-Crick pair.
 
 ```plumed
 #SETTINGS MOLFILE=regtest/basic/rt-ermsd/ref.pdb
-MOLINFO STRUCTURE=reference.pdb MOLTYPE=dna
+MOLINFO STRUCTURE=regtest/basic/rt-ermsd/ref.pdb MOLTYPE=dna
 hb1: DISTANCE ATOMS=@N2-2,@O2-15
 hb2: DISTANCE ATOMS=@N1-2,@N3-15
 hb3: DISTANCE ATOMS=@O6-2,@N4-15
@@ -53,7 +53,7 @@ The last example shows you how you can use MOLINFO to calculate torsion angles
 
 ```plumed
 #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
-MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
+MOLINFO MOLTYPE=protein STRUCTURE=regtest/basic/rt32/helix.pdb
 t1: TORSION ATOMS=@phi-3
 t2: TORSION ATOMS=@psi-4
 PRINT ARG=t1,t2 FILE=colvar STRIDE=10
@@ -205,7 +205,8 @@ Finally, notice that some shortcuts are available even when you not using the MO
 Since PLUMED 2.6 it is possible to use the expressive selection syntax of [mdtraj](http://mdtraj.org/latest/atom_selection.html) and/or [MDAnalysis](https://www.mdanalysis.org/docs/documentation_pages/selections.html):
 
 ```plumed
-MOLINFO STRUCTURE=helix.pdb PYTHON_BIN=python
+#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
+MOLINFO STRUCTURE=regtest/basic/rt32/helix.pdb PYTHON_BIN=python
 g1: GROUP ATOMS=@mda:backbone
 g2: GROUP ATOMS={@mda:{resnum 1 or resid 3:5}}
 #g3: GROUP ATOMS={@mda:{resid 3:5} @mda:{resnum 1}}

src/generic/Ones.cpp

@@ -33,7 +33,7 @@ The following input creates and outputs a constant vector with 10 elements that
 
 ```plumed
 ones: ONES SIZE=10
-PRINT ARG=ones FILES=onesfile
+PRINT ARG=ones FILE=onesfile
 ```
 
 Notice that the ONES action is a shortcut to [CONSTANT](CONSTANT.md).

src/generic/PDB2Constant.cpp

@@ -43,7 +43,7 @@ The following example illustrates how this action can be used to read a set of r
 
 ```plumed
 #SETTINGS INPUTFILES=regtest/basic/rt19/test0.pdb
-ref: PDB2CONSTANT FILE=regtest/basic/rt19/test0.pdb
+ref: PDB2CONSTANT REFERENCE=regtest/basic/rt19/test0.pdb
 ```
 
 You can see how the reference positions are converted to [CONSTANT](CONSTANT.md) action that outputs a vector by expanding the shortcut.
@@ -52,7 +52,7 @@ You can also use this command to read in multiple reference positions as illustr
 
 ```plumed
 #SETTINGS INPUTFILES=regtest/mapping/rt-pathtools-3/all.pdb
-ref: PDB2CONSTANT FILE=regtest/mapping/rt-pathtools-3/all.pdb
+ref: PDB2CONSTANT REFERENCE=regtest/mapping/rt-pathtools-3/all.pdb
 ```
 
 The [CONSTANT](CONSTANT.md) that is created by this action is a matrix. Each row of the output matrix contains one set of reference positions.
@@ -61,7 +61,7 @@ keyword to specify the particular configuration that you would like to read in a
 
 ```plumed
 #SETTINGS INPUTFILES=regtest/mapping/rt-pathtools-3/all.pdb
-ref: PDB2CONSTANT FILE=regtest/mapping/rt-pathtools-3/all.pdb NUMBER=4
+ref: PDB2CONSTANT REFERENCE=regtest/mapping/rt-pathtools-3/all.pdb NUMBER=4
 ```
 
 The input above will reads in the fourth configuration in the input PDB file only.
@@ -123,8 +123,8 @@ You can read in these reference values by using the PDB2CONSTANT command as foll
 
 ```plumed
 #SETTINGS INPUTFILES=regtest/mapping/rt-pathtools-4/epath.pdb
-t1_ref: PDB2CONSTANT FILE=regtest/mapping/rt-pathtools-4/epath.pdb ARG=t1
-t2_ref: PDB2CONSTANT FILE=regtest/mapping/rt-pathtools-4/epath.pdb ARG=t2
+t1_ref: PDB2CONSTANT REFERENCE=regtest/mapping/rt-pathtools-4/epath.pdb ARG=t1
+t2_ref: PDB2CONSTANT REFERENCE=regtest/mapping/rt-pathtools-4/epath.pdb ARG=t2
 ``` 
 
 Notice that separate PDB2CONSTANT commands are required for reading in `t1` and `t2`.  Furthermore, because the 

src/generic/ResetCell.cpp

@@ -70,24 +70,14 @@ arbitrary.
 Reset cell to be triangular after a rototranslational fit
 
 ```plumed
+#SETTINGS INPUTFILES=regtest/basic/rt63/align.pdb
 DUMPATOMS FILE=dump-original.xyz ATOMS=1-20
-FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=OPTIMAL
+FIT_TO_TEMPLATE STRIDE=1 REFERENCE=regtest/basic/rt63/align.pdb TYPE=OPTIMAL
 DUMPATOMS FILE=dump-fit.xyz ATOMS=1-20
 RESET_CELL TYPE=TRIANGULAR
 DUMPATOMS FILE=dump-reset.xyz ATOMS=1-20
 ```
 
-The reference file for the FIT_TO_TEMPLATE is just a normal pdb file with the format shown below:
-
-\auxfile{ref.pdb}
-ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H
-ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C
-ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H
-ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H
-ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O
-END
-\endauxfile
-
 */
 //+ENDPLUMEDOC
 

src/multicolvar/DumpMultiColvar.cpp

@@ -30,7 +30,7 @@ This action has been depracated as the same result can be be achieved using [DUM
 at the expanded version of the shortct in the example input below:
 
 ```plumed
-c1: COORDINATION SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}
+c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}
 DUMPMULTICOLVAR DATA=dd FILE=coords.xyz
 ```