Ran astyle

src/adjmat/TopologyMatrix.cpp

@@ -31,56 +31,56 @@
 /*
 Adjacency matrix in which two atoms are adjacent if they are connected topologically
 
-The functionality in this action was developed as part of a project that attempted to study 
+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 
+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](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 
-determining if the density within a cylinder that is centered on the vector connecting atoms $i$ and $j$ is 
-less than a certain threshold value.  To make this determination we first determine whether any given atom $k$ 
+The criterion that was developed to determine whether atom $i$ and $j$ are connected in this way works by
+determining if the density within a cylinder that is centered on the vector connecting atoms $i$ and $j$ is
+less than a certain threshold value.  To make this determination we first determine whether any given atom $k$
 is within the cylinder centered on the vector connecting atoms $i$ and $j$ by using the following expression
 
 $$
 f(\mathbf{r}_{ik}, \mathbf{r}_{ij}) = s_1\left( \sqrt{ |\mathbf{r}_{ij}|^2 - \left( \frac{\mathbf{r}_{ij} \cdot \mathbf{r}_{ik}}{|\mathbf{r}_{ij} |} \right)^2} \right)s_2\left( -\frac{\mathbf{r}_{ij} \cdot \mathbf{r}_{ik}}{|\mathbf{r}_{ij} |} \right) s_2\left( \frac{\mathbf{r}_{ij} \cdot \mathbf{r}_{ik}}{|\mathbf{r}_{ij} |} - |\mathbf{r}_{ij}| \right)
 $$
 
-In this expression $s_1$ and $s_2$ are switching functions, while $\mathbf{r}_{lm}$ is used to indicate the vector connecting atoms $l$ and $m$. 
+In this expression $s_1$ and $s_2$ are switching functions, while $\mathbf{r}_{lm}$ is used to indicate the vector connecting atoms $l$ and $m$.
 
 We then calculate the density for a grid of $M$ points along the vector connecting atom $i$ and atom $j$ using and find the maximum density on this grid using:
 
 $$
-\rho_{ij} = \max_{m \in M} \left[ \frac{M}{d_\textrm{max}} \right] \sum_k f(r_{ik}, r_{ij}) \int_{(m-1)d_{\textrm{max}}/M}^{ md_{\textrm{max}} /M } \textrm{d}x \quad K\left( \frac{x - r_{ks} \cdot r_{ij} }{ | r_{ks} | }\right) 
+\rho_{ij} = \max_{m \in M} \left[ \frac{M}{d_\textrm{max}} \right] \sum_k f(r_{ik}, r_{ij}) \int_{(m-1)d_{\textrm{max}}/M}^{ md_{\textrm{max}} /M } \textrm{d}x \quad K\left( \frac{x - r_{ks} \cdot r_{ij} }{ | r_{ks} | }\right)
 $$
 
-where $d_\textrm{max}$ is the `D_MAX` parameter of the switching function $s_3$ that appears in the next equation, $K$ is a kernal function and $s$ is used to represent a point in space that is $d_\textrm{max}$ from atom $j$ along the vector connecting atom $j$ to atom $i$.  
+where $d_\textrm{max}$ is the `D_MAX` parameter of the switching function $s_3$ that appears in the next equation, $K$ is a kernal function and $s$ is used to represent a point in space that is $d_\textrm{max}$ from atom $j$ along the vector connecting atom $j$ to atom $i$.
 
 The final value that is stored in the $i, j$ element of the output matrix is:
 
 $$
 T_{ij} = s_3(|\mathbf{r}_{ij}|)s_4(\rho_{ij})
-$$ 
+$$
 
-where $s_3$ and $s_4$ are switching functions.  
+where $s_3$ and $s_4$ are switching functions.
 
-We ended up abandoning this method and the project (if you want drive bubble formation you are probably better off adding a bias on the volume of the simulation cell). 
+We ended up abandoning this method and the project (if you want drive bubble formation you are probably better off adding a bias on the volume of the simulation cell).
 However, if you would like to try this method an example input that uses this action would look like this:
 
 ```plumed
 mat: TOPOLOGY_MATRIX ...
-    GROUP=1-85 BACKGROUND_ATOMS=86-210 
+    GROUP=1-85 BACKGROUND_ATOMS=86-210
     BIN_SIZE=1.02 SIGMA=0.17 KERNEL=triangular
-    CYLINDER_SWITCH={RATIONAL R_0=0.5 D_MAX=1.0} 
-    SWITCH={RATIONAL D_0=30 R_0=0.5 D_MAX=32} 
-    RADIUS={RATIONAL D_0=0.375 R_0=0.1 D_MAX=0.43} 
+    CYLINDER_SWITCH={RATIONAL R_0=0.5 D_MAX=1.0}
+    SWITCH={RATIONAL D_0=30 R_0=0.5 D_MAX=32}
+    RADIUS={RATIONAL D_0=0.375 R_0=0.1 D_MAX=0.43}
     DENSITY_THRESHOLD={RATIONAL R_0=0.1 D_MAX=0.5}
 ...
 ```
 
-The switching functions $s_1$, $s_2$, $s_3$ and $s_4$ are specified using the `RADIUS`, `CYLINDER_SWITCH`, `SWITCH` and `DENSITY_THRESHOLD` keywords respectively.  
-We loop over the atoms in the group specified using the `BACKGROUND_ATOMS` keyword when looping over $k$ in the formulas above.  An $85 \times 85$ matrix is output 
-from the method as we are determining the connectivity between the atoms specified via the `GROUP` keyword.  
+The switching functions $s_1$, $s_2$, $s_3$ and $s_4$ are specified using the `RADIUS`, `CYLINDER_SWITCH`, `SWITCH` and `DENSITY_THRESHOLD` keywords respectively.
+We loop over the atoms in the group specified using the `BACKGROUND_ATOMS` keyword when looping over $k$ in the formulas above.  An $85 \times 85$ matrix is output
+from the method as we are determining the connectivity between the atoms specified via the `GROUP` keyword.
 
 */
 //+ENDPLUMEDOC

src/wham/Wham.cpp

@@ -46,7 +46,7 @@ wham: WHAM ARG=col TEMP=300
 DUMPVECTOR ARG=wham FILE=wham_data
 ```
 
-As illustrated in the example above this command is used when you have run $N$ trajectories each of which was computed by integrating a different biased Hamiltonian. The input above calculates 
+As illustrated in the example above this command is used when you have run $N$ trajectories each of which was computed by integrating a different biased Hamiltonian. The input above calculates
 the probability of observing the set of configurations during the $N$ trajectories that we ran using the product of multinomial distributions using the formula shown below:
 
 $$

src/wham/WhamHistogram.cpp

@@ -58,7 +58,7 @@ The script above must be run with multiple replicas using the following command:
 mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4
 ````
 
-For more details on how the weights for configurations are determined using the wham method see the documentation 
+For more details on how the weights for configurations are determined using the wham method see the documentation
 for the [WHAM](WHAM.md) action.
 
 */

src/wham/WhamWeights.cpp

@@ -30,7 +30,7 @@ namespace wham {
 Calculate and output weights for configurations using the weighted histogram analysis method.
 
 This shortcut action allows you to calculate and output weights computed using the weighted histogram
-analysis technique.  The following input demonstrates how this works in practise by showing you how this 
+analysis technique.  The following input demonstrates how this works in practise by showing you how this
 action can be used to analyze the output from a series of umbrella sampling calculations.
 The trajectory from each of the simulations run with the different biases should be concatenated into a
 single trajectory before running the following analysis script on the concatenated trajectory using PLUMED
@@ -52,7 +52,7 @@ The script above must be run with multiple replicas using the following command:
 mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4
 ````
 
-For more details on how the weights for configurations are determined using the wham method see the documentation 
+For more details on how the weights for configurations are determined using the wham method see the documentation
 for the [WHAM](WHAM.md) action.
 
 */