Fixes for more of manual

src/clusters/ClusterDiameter.cpp

@@ -24,7 +24,7 @@
 
 //+PLUMEDOC CONCOMP CLUSTER_DIAMETER
 /*
-Print out the diameter of one of the connected components
+Print out the diameter of one of the connected components.
 
 An example input that determines the diameter of the second largest cluster that is identified by 
 analysing the connected components of a CONTACT_MATRIX using DFSCLUSTERING is shown below:

src/clusters/ClusterDistribution.cpp

@@ -47,7 +47,7 @@ An input similar to this one was used to analyze the formation of a polycrystal
 q6: Q6 SPECIES=1-300 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} 
 lq6: LOCAL_Q6 SPECIES=q6 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} 
 flq6: MORE_THAN ARG=lq6 SWITCH={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}
-cc: COORDINATIONNUMBER SPECIES=flq6 SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
+cc: COORDINATIONNUMBER SPECIES=1-300 SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
 fcc: MORE_THAN ARG=cc SWITCH={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}
 mat: CONTACT_MATRIX GROUP=1-300 SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}
 dfs: DFSCLUSTERING ARG=mat

src/clusters/ClusterProperties.cpp

@@ -48,7 +48,7 @@ file.
 lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45  D_MAX=0.55} 
 cm: CONTACT_MATRIX GROUP=lq  SWITCH={CUBIC D_0=0.45  D_MAX=0.55}
 dfs: DFSCLUSTERING ARG=cm
-clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM
+clust1: CLUSTER_PROPERTIES ARG=lq CLUSTERS=dfs CLUSTER=1 SUM
 PRINT ARG=clust1.sum FILE=colvar
 ```
 

src/clusters/ClusterWithSurface.cpp

@@ -24,7 +24,7 @@
 
 //+PLUMEDOC CONCOMP CLUSTER_WITHSURFACE
 /*
-Determine the atoms that are within a certain cutoff of the atoms in a cluster
+Determine the atoms that are within a certain cutoff of the atoms in a cluster.
 
 This shortcut action can be used to identify the atoms within the largest connected cluster in a system as well 
 as the atoms around the cluster as shown in the example input below:

src/clusters/OutputCluster.cpp

@@ -39,7 +39,7 @@ to a ndx file.
 ```plumed
 mat: CONTACT_MATRIX ATOMS=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
 dfs: DFSCLUSTERING ARG=mat
-OUTPUT_CLUSTER CLUSTERS=dfs CLUSTER=1 FILE=dfs.ndx
+OUTPUT_CLUSTER ATOMS=1-1996 CLUSTERS=dfs CLUSTER=1 FILE=dfs.ndx
 ```
 
 */

src/matrixtools/OuterProduct.cpp

@@ -27,7 +27,50 @@
 /*
 Calculate the outer product matrix of two vectors
 
-\par Examples
+This action can be used to calculate the [outer product](https://en.wikipedia.org/wiki/Outer_product) of two 
+vectors.  As a (useless) example of what can be done with this action consider the following simple input:
+
+```plumed
+d1: DISTANCE ATOMS1=1,2 ATOMS2=3,4
+d2: DISTANCE ATOMS1=5,6 ATOMS2=7,8 ATOMS3=9,10
+pp: OUTER_PRODUCT ARG=d1,d2
+PRINT ARG=pp FILE=colvar
+``` 
+
+This input outputs a $2 \times 3$ matrix. If we call the 2 dimensional vector output by the first DISTANCE action
+$d$ and the 3 dimensional vector output by the second DISTANCE action $h$ then the $(i,j)$ element of the matrix 
+output by the action with the label `pp` is given by:
+
+$$
+p_{ij} = d_i h_j
+$$
+
+These outer product matrices are useful if you are trying to calculate an adjacency matrix that says atoms are 
+connected if they are within a certain distance of each other and if they satisfy a certain criterion.  For example,
+consider the following input:
+
+```plumed
+# Determine if atoms are within 5.3 nm of each other
+c1: CONTACT_MATRIX GROUP=1-100 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3}
+# Calculate the coordination numbers
+ones: ONES SIZE=100
+cc: MATRIX_VECTOR PRODUCT ARG=c1,ones
+# Now use MORE_THAN to work out which atoms have a coordination number that is bigger than six
+cf: MORE_THAN ARG=cc SWITCH={RATIONAL D_0=5.5 R_0=0.5}
+# Now make a matrix in which element i,j is one if atom i and atom j both have a coordination number that is greater than 6
+cfm: OUTER_PRODUCT ARG=cf,cf
+# And multiply this by our contact matrix to determine the desired adjacency matrix
+m: CUSTOM ARG=c1,cfm FUNC=x*y PERIODIC=NO
+PRINT ARG=m FILE=colvar
+```
+
+This input calculates a adjacency matrix which has element $(i,j)$ equal to one if atoms $i$ and $j$ have coordination numbers
+that are greater than 6 and if they are within 5.3 nm of each other.
+
+Notice that you can specify the function of the two input vectors that is to be calculated by using the `FUNC` keyword which accepts 
+mathematical expressions of $x$ and $y$.  In other words, the elements of the outer product are calculated using the lepton library 
+that is used in the CUSTOM action.  In addition, you can set `FUNC=min` or `FUNC=max` to set the elements of the outer product equal to
+the minimum of the two input variables or the maximum respectively.
 
 */
 //+ENDPLUMEDOC