Added more links in documentation for these actions

new-manual/actions.md

@@ -37,7 +37,7 @@ PLUMED ignores any text in comments. Consequently, if you provide the input for
 # d1: DISTANCE ATOMS=1,2 COMPONENTS
 ```
 
-a DISTANCE command is not created. Similar behaviour is observed when you use the ENDPLUMED comand. For example, if your 
+a [DISTANCE](DISTANCE.md) command is not created. Similar behaviour is observed when you use the [ENDPLUMED](ENDPLUMED.md) comand. For example, if your 
 input is as follows:
 
 ```plumed
@@ -50,7 +50,7 @@ PLUMED will evaluate the distance between atom 1 and 2 but will not evaluate the
 
 ## Using INCLUDE files
 
-If, for some reason, you want to spread your PLUMED input over a number of files you can use INCLUDE as shown below:
+If, for some reason, you want to spread your PLUMED input over a number of files you can use [INCLUDE](INCLUDE.md) as shown below:
 
 ````
 INCLUDE FILE=filename

new-manual/parsing.md

@@ -53,15 +53,15 @@ The lepton library is able to interpret any of thse following constants:
 | `sqrt1_2 ` | $\sqrt(0.5)$ |
 
 Notice that this functionality cannot be used when the keyword takes integer numbers in input 
-(e.g.: the PACE argument for METAD).
+(e.g.: the PACE argument for [METAD](METAD.md)).
 
 ## Special replica syntax
 
 PLUMED provides a number of ways to prepare the multiple replicas with almost identical PLUMED files that are required to run a multiple replica simulation:
 
 * You can repare input files for such calculation using cut-and-paste but that is is very error prone.
 * You can write a smart bash or python script to generate all the inputs.
-* You can use different inputs for the various replicas that all contain an INCLUDE directive to include a file that contains the parts of the input that are common to all replicas 
+* You can use different inputs for the various replicas that all contain an [INCLUDE](INCLUDE.md) directive to include a file that contains the parts of the input that are common to all replicas 
 
 We think, however, the best option is to use features that have been available from PLUMED 2.4 onwards that allow you 
 manipulate multiple replica inputs that have only tiny differences in the the input. The following example illustrates how the syntax 
@@ -86,7 +86,7 @@ If you prepare a single `plumed.dat` file like this one and feeds it to PLUMED w
 the 3 replicas will see PLUMED input files that are the same except for the `AT` keyword, that sets the position of the restraint.
 Replica 0 will see a restraint centered at 1.0, replica 1 centered at 1.1, and replica 2 centered at 1.2.
 
-The `@replicas:` keyword is not specific to RESTRAINT and the `AT` keyword. Any keyword in PLUMED can accept that syntax.
+The `@replicas:` keyword is not specific to [RESTRAINT](RESTRAINT.md) and the `AT` keyword. Any keyword in PLUMED can accept that syntax.
 For instance, the following single input file can be used to setup a bias exchange metadynamics simulations:
 
 ```plumed

new-manual/shortcuts.md

@@ -66,7 +66,7 @@ d1: DISTANCES ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6 ATOMS4=7,8 ATOMS5=9,10 LESS_THAN=
 PRINT ARG=d1.* FILE=colvar2
 ```
 
-The values `d1_lessthan` and `d1_mean` will be output in the colvar2 file as these are the components of the DISTANCES shortcut that are defined in the manual. `d1_lt` is not output as this is an intermediate value that is not defined in the manual.
+The values `d1_lessthan` and `d1_mean` will be output in the colvar2 file as these are the components of the [DISTANCES](DISTANCES.md) shortcut that are defined in the manual. `d1_lt` is not output as this is an intermediate value that is not defined in the manual.
 
 The same result can be obtained using the following input:
 

new-manual/specifying_arguments.md

@@ -7,8 +7,8 @@ scalars, vectors, matrices or functions evaluated on a grid.
 ## Single component actions
 
 If an action outputs only one value it is referenced later in the input using the label of the action that calculated it.
-For example, in the input below, the DISTANCE action calculates one scalar every MD time step. This scalar is then reused 
-by the PRINT action, which the time-series of scalars to a file called colvar1.
+For example, in the input below, the [DISTANCE](DISTANCE.md) action calculates one scalar every MD time step. This scalar is then reused 
+by the [PRINT](PRINT.md) action, which the time-series of scalars to a file called colvar1.
 
 ```plumed
 d1: DISTANCE ATOMS=1,2
@@ -204,10 +204,10 @@ for inputs that use shortcuts to not have regular expressions that match the lab
 There may be cases where it is useful to access a particular element of a vector or matrix or to combine multiple scalars or vectors into a new value. The following
 actions allow you to complete operations of this type:
 
-- SELECT_COMPONENTS - take $n$ of the elements from the input vector/matrix and output an $n$-dimensional vector that contains these components only.
-- CONCATENATE - combine all the input scalar/vectors/matrices into a single output vector/matrix.
-- FLATTEN - vectorise a matrix
-- VSTACK - construct a matrix by stacking multiple input vectors together 
+- [SELECT_COMPONENTS](SELECT_COMPONENTS.md) - take $n$ of the elements from the input vector/matrix and output an $n$-dimensional vector that contains these components only.
+- [CONCATENATE](CONCATENATE.md) - combine all the input scalar/vectors/matrices into a single output vector/matrix.
+- [FLATTEN](FLATTEN.md) - vectorise a matrix
+- [VSTACK](VSTACK.md) - construct a matrix by stacking multiple input vectors together 
 
 You can then use these outputs from these actions in the input to later actions in your input file.
 

new-manual/specifying_atoms.md

@@ -5,7 +5,7 @@ Many of the actions in PLUMED take a list of atom positions in input. Within PL
 atoms are specified using their numerical indices in the molecular dynamics input file.
 
 In PLUMED lists of atoms can be either provided directly inside the definition of each action, or
-predefined as a GROUP that can be reused multiple times. Lists of atoms can be written as:
+predefined as a [GROUP](GROUP.md) that can be reused multiple times. Lists of atoms can be written as:
 
 - comma separated lists of numbers (`g1: GROUP ATOMS=10,11,15,20`)
 - numerical ranges. So `g2: GROUP ATOMS=10-20` is equivalent to `g2: GROUP ATOMS=10,11,12,13,14,15,16,17,18,19,20`
@@ -28,7 +28,7 @@ A few other wasys of using groups in the input to actions are also available:
 
 ## The MOLINFO command
 
-You can access many useful shortcuts for specifying atomic positions to PLUMED by using the MOLINFO, which takes 
+You can access many useful shortcuts for specifying atomic positions to PLUMED by using the [MOLINFO](MOLINFO.md), which takes 
 a PDB structure file in input. This command allows you to access the following list of shortcuts.
 
 {:#browse-table .display}
@@ -54,7 +54,7 @@ d1: DISTANCE ATOMS=11,com1
 ```
 
 If you don't want to calculate CVs from the virtual atom. That is to say you just want to monitor the position of a virtual atom
-(or any set of atoms) over the course of your trajectory you can do this using DUMPATOMS.
+(or any set of atoms) over the course of your trajectory you can do this using [DUMPATOMS](DUMPATOMS.md).
 
 The list of the virtual atoms defined in PLUMED can be obtained by using the command `GROUP ATOMS=@allatoms REMOVE=@mdatoms`.
 
@@ -66,7 +66,7 @@ you are using involve some property of a molecule. These codes allow the atoms
 periodic boundaries, a fact which PLUMED could only deal with if the topology is passed from the MD code to PLUMED. Doing this
 work would involve a lot laborious programming and goes against our original aim of having a general patch that can be implemented
 in a wide variety of MD codes. Consequentially, we have implemented a more pragmatic solution to this problem - the user specifies
-in input any molecules (or parts of molecules) that must be kept in tact throughout the simulation run using the WHOLEMOLECULES command.
+in input any molecules (or parts of molecules) that must be kept in tact throughout the simulation run using the [WHOLEMOLECULES](WHOLEMOLECULES.md) command.
 
 The following input computes the end-to-end distance for a polymer of 100 atoms and keeps it at a value around 5.
 
@@ -76,7 +76,7 @@ e2e: DISTANCE ATOMS=1,100 NOPBC
 RESTRAINT ARG=e2e KAPPA=1 AT=5
 ```
 
-Notice that NOPBC is used to in the DISTANCE action so as to ensure that if the end-to-end distance is larger than half the simulation box the distance
+Notice that NOPBC is used to in the [DISTANCE](DISTANCE.md) action so as to ensure that if the end-to-end distance is larger than half the simulation box the distance
 is compute properly. Also notice that, since many MD codes break molecules across cell boundary, it might be necessary to use the
 WHOLEMOLECULES keyword (also notice that it should be before distance).
 
@@ -93,9 +93,9 @@ DUMPATOMS FILE=dump.xyz ATOMS=1-20
 
 Notice that there are other ways to manipulate the coordinates stored within PLUMED:
 
-- FIT_TO_TEMPLATE aligns atoms to a template structure.
-- WRAPAROUND brings a set of atom as close as possible to another set of atoms.
-- RESET_CELL rotates the periodic cell.
+- [FIT_TO_TEMPLATE](FIT_TO_TEMPLATE.md) aligns atoms to a template structure.
+- [WRAPAROUND](WRAPAROUND.md) brings a set of atom as close as possible to another set of atoms.
+- [RESET_CELL](RESET_CELL.md) rotates the periodic cell.
 
 <script>
 $(document).ready(function() {

src/adjmat/BridgeMatrix.cpp

@@ -33,15 +33,15 @@ namespace adjmat {
 /*
 Calculate a matrix with elements equal to one if there is a bridging atom between the two atoms
 
-This adjacency matrix is used to implement the BRIDGE shortcut. The action outputs a adjacency matrix
-in the same way as CONTACT_MATRIX. However, the $j,k$ element of the adjacency matrix is calculated
+This adjacency matrix is used to implement the [BRIDGE](BRIDGE.md) shortcut. The action outputs a adjacency matrix
+in the same way as [CONTACT_MATRIX](CONTACT_MATRIX.md). However, the $j,k$ element of the adjacency matrix is calculated
 using:
 
 $$
 M_{jk} = \sum_i s_A(r_{ij})s_B(r_{ik})
 $$
 
-In this expression, the sum runs over all the atoms that were specified using the BRIDGING_ATOMS keyword, $s_A$ and 
+In this expression, the sum runs over all the atoms that were specified using the `BRIDGING_ATOMS` keyword, $s_A$ and 
 $s_B$ are switching functions, and $r_{ij}$ and $r_{ik}$ are the distances between atom $i$ and $j$ and between atoms
 $i$ and $k$. Less formally, this formula ensures that $j,k$ element of the output matrix is one if there is a bridging 
 atom between atom $j$ and $k$. 

src/adjmat/ContactMatrixShortcut.cpp

@@ -79,9 +79,9 @@ PRINT ARG=cc FILE=colvar
 Implmenting the coordination number this way is useful as there are many different ways to define whether two atoms/molecules and to construct a "contact" matrix based on
 the result. For example:
 
-* You could say that two molecules are connected if they are within a certain distance of each other and if they have the same orientation (see TORSIONS_MATRIX).
-* You could say that two water molecules are connected if they are hydrogen bonded to each other (see HBOND_MATRIX).
-* You could say that two atoms are connected if they are within a certain distance of each other and if they have similar values for a CV (see OUTER_PRODUCT).
+* You could say that two molecules are connected if they are within a certain distance of each other and if they have the same orientation (see [TORSIONS_MATRIX](TORSIONS_MATRIX.md)).
+* You could say that two water molecules are connected if they are hydrogen bonded to each other (see [HBOND_MATRIX](HBOND_MATRIX.md)).
+* You could say that two atoms are connected if they are within a certain distance of each other and if they have similar values for a CV (see [OUTER_PRODUCT](OUTER_PRODUCT.md)).
 
 When the coordination numbers is implemented in the way described above (by doing the matrix-vector multiplication) you have the flexibility to define the contact matrix that
 is used in the multiplication in whatever way you choose. In other words, this implementation of the coordination number is much more flexible. For example, suppose you want 

src/adjmat/DistanceMatrix.cpp

@@ -39,7 +39,7 @@ If you would like to calculate the matrix of distances between the atoms in two
 d2: DISTANCE_MATRIX GROUPA=1-7 GROUPB=8-20
 ```
 
-Once you have calculated your distance matrix in this way you can do many of the operations that were discussed for CONTACT_MATRIX with the output.
+Once you have calculated your distance matrix in this way you can do many of the operations that were discussed for [CONTACT_MATRIX](CONTACT_MATRIX.md) with the output.
 For example, you can use the COMPONENTS flag to calcuate the $x$, $y$ and $z$ components of the vectors connecting the atoms in your two groups by using 
 an input like that shown below:
 
@@ -57,7 +57,7 @@ d3: DISTANCE_MATRIX GROUP=1-7 CUTOFF=1.0
 
 This command will only store those distances that are less than 1 nm. Notice, however, that the cutoff implemented here is __not__ a continuous function.
 You should thus be careful when commands such as this one above to ensure that any quantities that are forced have continuous derivatives. If you use 
-the CUTOFF keyword, however, many of the features that are used to optimise CONTACT_MATRIX are used for this action.
+the CUTOFF keyword, however, many of the features that are used to optimise [CONTACT_MATRIX](CONTACT_MATRIX.md) are used for this action.
 
 
 */

src/adjmat/HbondMatrix.cpp

@@ -34,7 +34,7 @@ Adjacency matrix in which two atoms are adjacent if there is a hydrogen bond bet
 A useful tool for developing complex collective variables is the notion of the
 so called adjacency matrix. An adjacency matrix is an $N \times N$ matrix in which the $i$th, $j$th element tells you whether
 or not the $i$th and $j$th atoms/molecules from a set of $N$ atoms/molecules are adjacent or not. As detailed in the documentation
-for CONTACT_MATRIX there are then a range of further analyses that you can perform on these matrices. 
+for [CONTACT_MATRIX](CONTACT_MATRIX.md) there are then a range of further analyses that you can perform on these matrices. 
 
 For this action the elements of the adjacency matrix are calculated using:
 
@@ -53,7 +53,7 @@ is a switching function that acts on the angle between the vector connecting ato
 
 It is important to note that hydrogen bonds, unlike regular bonds, are asymmetric. In other words, the hydrogen atom does not sit at the
 mid point between the two other atoms in this three-center bond. As a result of this adjacency matrices calculated using HBOND_MATRIX are not
-symmetric like those calculated by CONTACT_MATRIX. 
+symmetric like those calculated by [CONTACT_MATRIX](CONTACT_MATRIX.md). 
 
 The following input can be used to analyze the number of hydrogen bonds each of the oxygen atoms in a box of water participates in. Each
 water molecule can participate in a hydrogen bond in one of two ways. It can either donate one of its hydrogen atom to the neighboring oxygen or

src/adjmat/Neighbors.cpp

@@ -26,23 +26,23 @@
 /*
 Build a matrix with ones in for the N nearest neighbours of an atom
 
-The following input illustrates how to use this action in tandem with DISTANCE_MATRIX to find the six
+The following input illustrates how to use this action in tandem with [DISTANCE_MATRIX](DISTANCE_MATRIX.md) to find the six
 nearest atoms to each of the first 100 atoms in the input file:
 
 ```plumed
 d1: DISTANCE_MATRIX GROUP=1-100
 n: NEIGHBORS ARG=d1 NLOWEST=6
 ```
 
-Alternatively, if you would like to use a CONTACT_MATRIX to do something similar you would do the following:
+Alternatively, if you would like to use a [CONTACT_MATRIX](CONTACT_MATRIX.md) to do something similar you would do the following:
 
 ```plumed
 c1: CONTACT_MATRIX GROUP=1-100 SWITCH={RATIONAL R_0=0.5}
 n: NEIGHBORS ARG=c1 NHIGHEST=6
 ```
 
 This command is useful for implementing alternatives to the symmatry functions that are defined by the shortcuts
-in the module symfunc. For example, suppose that you want to calculate a variant on the TETRAHEDRAL symmetry function.
+in the module symfunc. For example, suppose that you want to calculate a variant on the [TETRAHEDRAL](TETRAHEDRAL.md) symmetry function.
 In this variant on the CV the coordination sphere around each central atom is not defined using a switching function. Instad
 this coordination sphere contains only the four nearest atoms. You can implement this CV by using the following input:
 

src/adjmat/TopologyMatrix.cpp

@@ -34,7 +34,7 @@ Adjacency matrix in which two atoms are adjacent if they are connected topologic
 The functionality in this action was developed as part of a project that attempted to study 
 the nucleation of bubbles. The idea was to develop a criterion that would allow one to determine
 if two gas atoms $i$ and $j$ are part of the same bubble or not. This criterion would then be used 
-to construct a adjacency matrix, which could be used in the same way that CONTACT_MATRIX is used in other
+to construct a adjacency matrix, which could be used in the same way that [CONTACT_MATRIX](CONTACT_MATRIX.md) is used in other
 methods.
 
 The criterion that was developed to determine whether atom $i$ and $j$ are connected in this way works by 

src/adjmat/TorsionsMatrix.cpp

@@ -27,11 +27,11 @@
 /*
 Calculate the matrix of torsions between two vectors of molecules
 
-This action was implemented to ensure that we can calculate the SMAC collective variable that is discussed in 
+This action was implemented to ensure that we can calculate the [SMAC](SMAC.md) collective variable that is discussed in 
 [this paper](https://www.sciencedirect.com/science/article/abs/pii/S0009250914004503?via%3Dihub). This particular action 
 tracks the relative orientations for all the pairs of molecules in a set much like the variables described in the crystdistrib module. 
 
-The orientations of molecules can be specified using either PLANE or DISTANCE. The example below shows how you can use 
+The orientations of molecules can be specified using either [PLANE](PLANE.md) or [DISTANCE](DISTANCE.md). The example below shows how you can use 
 internal vectors connecting two atoms in the molecules to define the orientation of that molecule. Three of these internal
 vectors are calculated using a DISTANCE command in the input below. The matrix of torsional angles between these various
 vectors is then computed:
@@ -46,7 +46,7 @@ PRINT ARG=m FILE=matrix
 
 In this example, the torsional angle in element $(1,2)$ of the matrix with label `m` is the angle between the plane containing atoms 1,5 and 10 and the plane
 connecting atoms 1,10 and 15. In other words, the elements in this matrix are the torsional angles between the vectors in the input matrices
-around the vector connecting the corresponding atomic positions that are specified using the POSTIONS keyword.
+around the vector connecting the corresponding atomic positions that are specified using the `POSTIONS` keyword.
 
 You can also calculate a matrix of torsional angles between two different groups of molecules by using an input like the one below:
 
@@ -60,7 +60,7 @@ m: TORSIONS_MATRIX ARG=sA,sBT POSITIONS1=1,11 POSITIONS2=21,31,41
 PRINT ARG=m FILE=matrix
 ```
 
-In this example, the orientations of the molecules are specified using the PLANE action and is given by a normal to the plane containing the three atoms from the molecule
+In this example, the orientations of the molecules are specified using the [PLANE](PLANE.md) action and is given by a normal to the plane containing the three atoms from the molecule
 that was specified. The final output is $2 \times 3$ matrix that contains all the torsional angles between the molecules defined by the two PLANE actions.
 
 */

src/clusters/ClusterDiameter.cpp

@@ -27,7 +27,7 @@
 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:
+analysing the connected components of a [CONTACT_MATRIX](CONTACT_MATRIX.md) using [DFSCLUSTERING](DFSCLUSTERING.md) is shown below:
 
 ```plumed
 # Calculate a contact matrix between the first 100 atoms in the configuration