From 08a230aed55250fb4725cca8f8c9e5b6a5887928 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Wed, 14 Jun 2017 15:11:29 +0200
Subject: [PATCH] Fixed missing empty line

After \par Examples there should be an empty line

[makedoc]
---
 src/analysis/Commit.cpp             | 1 +
 src/bias/ABMD.cpp                   | 1 +
 src/bias/External.cpp               | 1 +
 src/bias/LWalls.cpp                 | 1 +
 src/bias/MetaD.cpp                  | 1 +
 src/bias/MovingRestraint.cpp        | 1 +
 src/bias/PBMetaD.cpp                | 1 +
 src/bias/Restraint.cpp              | 1 +
 src/bias/UWalls.cpp                 | 1 +
 src/colvar/Cell.cpp                 | 1 +
 src/colvar/DHEnergy.cpp             | 1 +
 src/colvar/Dipole.cpp               | 1 +
 src/colvar/Energy.cpp               | 1 +
 src/colvar/Jcoupling.cpp            | 1 +
 src/colvar/NOE.cpp                  | 1 +
 src/colvar/PropertyMap.cpp          | 1 +
 src/colvar/RDC.cpp                  | 1 +
 src/colvar/Volume.cpp               | 1 +
 src/function/Combine.cpp            | 1 +
 src/function/Ensemble.cpp           | 1 +
 src/function/LocalEnsemble.cpp      | 1 +
 src/function/Piecewise.cpp          | 1 +
 src/function/Sort.cpp               | 1 +
 src/function/Stats.cpp              | 1 +
 src/generic/DumpDerivatives.cpp     | 1 +
 src/generic/DumpForces.cpp          | 1 +
 src/generic/Flush.cpp               | 1 +
 src/generic/Print.cpp               | 1 +
 src/generic/UpdateIf.cpp            | 1 +
 src/gridtools/FourierTransform.cpp  | 1 +
 src/multicolvar/DumpMultiColvar.cpp | 1 +
 src/setup/Units.cpp                 | 1 +
 src/vatom/Ghost.cpp                 | 1 +
 33 files changed, 33 insertions(+)

diff --git a/src/analysis/Commit.cpp b/src/analysis/Commit.cpp
index 1b7a3ccf6..dab62d8b4 100644
--- a/src/analysis/Commit.cpp
+++ b/src/analysis/Commit.cpp
@@ -33,6 +33,7 @@ namespace analysis {
 Does a committor analysis.
 
 \par Examples
+
 The following input monitors two torsional angles during a simulation,
 defines two basins (A and B) as a function of the two torsions and
 stops the simulation when it falls in one of the two. In the log
diff --git a/src/bias/ABMD.cpp b/src/bias/ABMD.cpp
index 1fdedf324..12aa76eb8 100644
--- a/src/bias/ABMD.cpp
+++ b/src/bias/ABMD.cpp
@@ -67,6 +67,7 @@ molecules, the biasing potential does not exert work on the system. \f$\eta(t)\f
 an additional white noise acting on the minimum position of the bias.
 
 \par Examples
+
 The following input sets up two biases, one on the distance between atoms 3 and 5
 and another on the distance between atoms 2 and 4. The two target values are defined
 using TO and the two strength using KAPPA. The total energy of the bias is printed.
diff --git a/src/bias/External.cpp b/src/bias/External.cpp
index 4a1a6befa..8ff721c09 100644
--- a/src/bias/External.cpp
+++ b/src/bias/External.cpp
@@ -37,6 +37,7 @@ namespace bias {
 Calculate a restraint that is defined on a grid that is read during start up
 
 \par Examples
+
 The following is an input for a calculation with an external potential that is
 defined in the file bias.dat and that acts on the distance between atoms 3 and 5.
 \verbatim
diff --git a/src/bias/LWalls.cpp b/src/bias/LWalls.cpp
index 5f05d124b..592fce668 100644
--- a/src/bias/LWalls.cpp
+++ b/src/bias/LWalls.cpp
@@ -48,6 +48,7 @@ The expression for the bias due to the wall is given by:
 
 
 \par Examples
+
 The following input tells plumed to add both a lower and an upper walls on the distance
 between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
 are defined at different values. The strength of the walls is the same for the four cases.
diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp
index 4be9a8b3f..b4f09a893 100644
--- a/src/bias/MetaD.cpp
+++ b/src/bias/MetaD.cpp
@@ -159,6 +159,7 @@ as done e.g. in Ref. \cite gil2015enhanced . This indeed can be obtained by usin
 action multiple times in the same input file.
 
 \par Examples
+
 The following input is for a standard metadynamics calculation using as
 collective variables the distance between atoms 3 and 5
 and the distance between atoms 2 and 4. The value of the CVs and
diff --git a/src/bias/MovingRestraint.cpp b/src/bias/MovingRestraint.cpp
index ae9f1c5fe..1d8b11dd6 100644
--- a/src/bias/MovingRestraint.cpp
+++ b/src/bias/MovingRestraint.cpp
@@ -50,6 +50,7 @@ the values of \f$\kappa\f$ and \f$\vec{s}_0\f$ are linearly interpolated.
 Additional material and examples can be also found in the tutorial \ref belfast-5
 
 \par Examples
+
 The following input is dragging the distance between atoms 2 and 4
 from 1 to 2 in the first 1000 steps, then back in the next 1000 steps.
 In the following 500 steps the restraint is progressively switched off.
diff --git a/src/bias/PBMetaD.cpp b/src/bias/PBMetaD.cpp
index 5840eee82..a075ecb40 100644
--- a/src/bias/PBMetaD.cpp
+++ b/src/bias/PBMetaD.cpp
@@ -137,6 +137,7 @@ boundaries. Note that:
 Multiple walkers  \cite multiplewalkers can also be used, in the MPI implementation only. See below the examples.
 
 \par Examples
+
 The following input is for PBMetaD calculation using as
 collective variables the distance between atoms 3 and 5
 and the distance between atoms 2 and 4. The value of the CVs and
diff --git a/src/bias/Restraint.cpp b/src/bias/Restraint.cpp
index 76a963fef..84e2303b9 100644
--- a/src/bias/Restraint.cpp
+++ b/src/bias/Restraint.cpp
@@ -46,6 +46,7 @@ of arguments to the action.
 Additional material and examples can be also found in the tutorial \ref belfast-4
 
 \par Examples
+
 The following input tells plumed to restrain the distance between atoms 3 and 5
 and the distance between atoms 2 and 4, at different equilibrium
 values, and to print the energy of the restraint
diff --git a/src/bias/UWalls.cpp b/src/bias/UWalls.cpp
index 172f6bdd9..5eb0dd060 100644
--- a/src/bias/UWalls.cpp
+++ b/src/bias/UWalls.cpp
@@ -48,6 +48,7 @@ The expression for the bias due to the wall is given by:
 
 
 \par Examples
+
 The following input tells plumed to add both a lower and an upper walls on the distance
 between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits
 are defined at different values. The strength of the walls is the same for the four cases.
diff --git a/src/colvar/Cell.cpp b/src/colvar/Cell.cpp
index 266bb0393..53d799a39 100644
--- a/src/colvar/Cell.cpp
+++ b/src/colvar/Cell.cpp
@@ -35,6 +35,7 @@ namespace colvar {
 Calculate the components of the simulation cell
 
 \par Examples
+
 The following input tells plumed to print the squared modulo of each of the three lattice vectors
 \verbatim
 cell: CELL
diff --git a/src/colvar/DHEnergy.cpp b/src/colvar/DHEnergy.cpp
index 29d03589b..aaf0a35d6 100644
--- a/src/colvar/DHEnergy.cpp
+++ b/src/colvar/DHEnergy.cpp
@@ -56,6 +56,7 @@ Notice that if there are common atoms between GROUPA and GROUPB their interactio
 
 
 \par Examples
+
 \verbatim
 # this is printing the electrostatic interaction between two groups of atoms
 dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0
diff --git a/src/colvar/Dipole.cpp b/src/colvar/Dipole.cpp
index 166dbf68f..5f6748db6 100644
--- a/src/colvar/Dipole.cpp
+++ b/src/colvar/Dipole.cpp
@@ -35,6 +35,7 @@ namespace colvar {
 Calculate the dipole moment for a group of atoms.
 
 \par Examples
+
 The following tells plumed to calculate the dipole of the group of atoms containing
 the atoms from 1-10 and print it every 5 steps
 \verbatim
diff --git a/src/colvar/Energy.cpp b/src/colvar/Energy.cpp
index 891285e14..75ef74781 100644
--- a/src/colvar/Energy.cpp
+++ b/src/colvar/Energy.cpp
@@ -47,6 +47,7 @@ potential energy function. This is for instance not true when
 using GROMACS with lambda replica exchange of with plumed-hrex branch.
 
 \par Examples
+
 The following input instructs plumed to print the energy of the system
 \verbatim
 ENERGY LABEL=ene
diff --git a/src/colvar/Jcoupling.cpp b/src/colvar/Jcoupling.cpp
index 94e5b82a0..7e23ce3b1 100644
--- a/src/colvar/Jcoupling.cpp
+++ b/src/colvar/Jcoupling.cpp
@@ -58,6 +58,7 @@ and SHIFT keywords. You will need to make sure you are using the correct dihedra
 - CO-C\f$\gamma\f$: \f$\chi_1\f$
 
 \par Examples
+
 In the following example we calculate the Ha-N J-coupling from a set of atoms involved in
 dihedral \f$\psi\f$ angles in the peptide backbone. We also add the experimental datapoints and compute
 the correlation and other measures and finally print the results.
diff --git a/src/colvar/NOE.cpp b/src/colvar/NOE.cpp
index 69d9a3797..1ad5291b7 100644
--- a/src/colvar/NOE.cpp
+++ b/src/colvar/NOE.cpp
@@ -48,6 +48,7 @@ Intensities can then in principle ensemble averaged using \ref ENSEMBLE and used
 calculate a scoring function for example with \ref METAINFERENCE.
 
 \par Examples
+
 In the following examples three noes are defined, the first is calculated based on the distances
 of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances
 4-15,4-16,8-15,8-16.
diff --git a/src/colvar/PropertyMap.cpp b/src/colvar/PropertyMap.cpp
index 7ecb08b0c..1df4c0d3c 100644
--- a/src/colvar/PropertyMap.cpp
+++ b/src/colvar/PropertyMap.cpp
@@ -46,6 +46,7 @@ where the parameters \f$X_i\f$  and  \f$Y_i\f$ are provided in the input pdb (al
  \f$D_i(x)\f$  is the MSD after optimal alignment calculated on the pdb frames you input (see Kearsley).
 
 \par Examples
+
 \verbatim
 p3: PROPERTYMAP REFERENCE=../../trajectories/path_msd/allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=4
 PRINT ARG=p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
diff --git a/src/colvar/RDC.cpp b/src/colvar/RDC.cpp
index 067ea3f2c..55ede195e 100644
--- a/src/colvar/RDC.cpp
+++ b/src/colvar/RDC.cpp
@@ -89,6 +89,7 @@ Replica-Averaged restrained simulations can be performed with this CV and the fu
 Additional material and examples can be also found in the tutorial \ref belfast-9
 
 \par Examples
+
 In the following example five N-H RDCs are defined and their correlation with
 respect to a set of experimental data is calculated and restrained. In addition,
 and only for analysis purposes, the same RDCs are calculated using a Single Value
diff --git a/src/colvar/Volume.cpp b/src/colvar/Volume.cpp
index 2a388d778..966c3680b 100644
--- a/src/colvar/Volume.cpp
+++ b/src/colvar/Volume.cpp
@@ -35,6 +35,7 @@ namespace colvar {
 Calculate the volume of the simulation box.
 
 \par Examples
+
 The following input tells plumed to print the volume of the system
 \verbatim
 VOLUME LABEL=vol
diff --git a/src/function/Combine.cpp b/src/function/Combine.cpp
index b74e16014..d8f2e7fbb 100644
--- a/src/function/Combine.cpp
+++ b/src/function/Combine.cpp
@@ -49,6 +49,7 @@ is periodic.
 
 
 \par Examples
+
 The following input tells plumed to print the distance between atoms 3 and 5
 its square (as computed from the x,y,z components) and the distance
 again as computed from the square root of the square.
diff --git a/src/function/Ensemble.cpp b/src/function/Ensemble.cpp
index b6b26b1c3..f74e1aa67 100644
--- a/src/function/Ensemble.cpp
+++ b/src/function/Ensemble.cpp
@@ -36,6 +36,7 @@ Calculates the replica averaging of a collective variable over multiple replicas
 Each collective variable is averaged separately and stored in a component labelled <em>label</em>.cvlabel.
 
 \par Examples
+
 The following input tells plumed to calculate the distance between atoms 3 and 5
 and the average it over the available replicas.
 \verbatim
diff --git a/src/function/LocalEnsemble.cpp b/src/function/LocalEnsemble.cpp
index e623be76a..a17e9112e 100644
--- a/src/function/LocalEnsemble.cpp
+++ b/src/function/LocalEnsemble.cpp
@@ -36,6 +36,7 @@ If more than one collective variable is given for each argument then they
 are averaged separately. The average is stored in a component labelled <em>label</em>.cvlabel.
 
 \par Examples
+
 The following input tells plumed to calculate the chemical shifts for four
 different proteins in the same simulation box then average them, calcualated
 the sum of the squared deviation with respect to the experiemntal values and
diff --git a/src/function/Piecewise.cpp b/src/function/Piecewise.cpp
index e3e147b69..14b80e52c 100644
--- a/src/function/Piecewise.cpp
+++ b/src/function/Piecewise.cpp
@@ -55,6 +55,7 @@ in a vector of values. Each value will be named as the name of the original
 argument with suffix _pfunc.
 
 \par Examples
+
 \verbatim
 dist1: DISTANCE ATOMS=1,10
 dist2: DISTANCE ATOMS=2,11
diff --git a/src/function/Sort.cpp b/src/function/Sort.cpp
index 4636f3ad2..86c7c0fb0 100644
--- a/src/function/Sort.cpp
+++ b/src/function/Sort.cpp
@@ -41,6 +41,7 @@ This function sorts its arguments according to their magnitudes. The lowest argu
 labelled <em>label</em>.1, the second lowest will be labelled <em>label</em>.2 and so on.
 
 \par Examples
+
 The following input tells plumed to print the distance of the closest and of
 the farthest atoms to atom 1, chosen among atoms from 2 to 5
 \verbatim
diff --git a/src/function/Stats.cpp b/src/function/Stats.cpp
index 3513c9dcb..45b9f0026 100644
--- a/src/function/Stats.cpp
+++ b/src/function/Stats.cpp
@@ -38,6 +38,7 @@ from other actions using PARARG (for example using experimental values from coll
 \ref CS2BACKBONE, \ref RDC, \ref NOE, \ref PRE).
 
 \par Examples
+
 The following input tells plumed to print the distance between three couple of atoms
 and compare them with three reference distances.
 
diff --git a/src/generic/DumpDerivatives.cpp b/src/generic/DumpDerivatives.cpp
index 7c1075cf1..5b49081a7 100644
--- a/src/generic/DumpDerivatives.cpp
+++ b/src/generic/DumpDerivatives.cpp
@@ -40,6 +40,7 @@ will be output.  This command is most often used to test whether or not analytic
 can be done by outputting the derivatives calculated analytically and numerically.  You can control the buffering of output using the \ref FLUSH keyword.
 
 \par Examples
+
 The following input instructs plumed to write a file called deriv that contains both the
 analytical and numerical derivatives of the distance between atoms 1 and 2.
 \verbatim
diff --git a/src/generic/DumpForces.cpp b/src/generic/DumpForces.cpp
index 4a6aa3efb..a5ae199e6 100644
--- a/src/generic/DumpForces.cpp
+++ b/src/generic/DumpForces.cpp
@@ -41,6 +41,7 @@ by specifying more than one argument. You can control the buffering of output us
 
 
 \par Examples
+
 The following input instructs plumed to write a file called forces that contains
 the force acting on the distance between atoms 1 and 2.
 \verbatim
diff --git a/src/generic/Flush.cpp b/src/generic/Flush.cpp
index e05159a03..8b1be153a 100644
--- a/src/generic/Flush.cpp
+++ b/src/generic/Flush.cpp
@@ -40,6 +40,7 @@ storing data for printing in the buffers. Notice that wherever it is written in
 plumed input file, it will flush all the open files.
 
 \par Examples
+
 A command like this in the input will instruct plumed to flush all the output files every 100 steps
 \verbatim
 d1: DISTANCE ATOMS=1,10
diff --git a/src/generic/Print.cpp b/src/generic/Print.cpp
index 8542a978c..36a469023 100644
--- a/src/generic/Print.cpp
+++ b/src/generic/Print.cpp
@@ -37,6 +37,7 @@ in the input so you can print files with different strides or print different qu
 to different files.  You can control the buffering of output using the \subpage FLUSH keyword.
 
 \par Examples
+
 The following input instructs plumed to print the distance between atoms 3 and 5 on a file
 called COLVAR every 10 steps, and the distance and total energy on a file called COLVAR_ALL
 every 1000 steps.
diff --git a/src/generic/UpdateIf.cpp b/src/generic/UpdateIf.cpp
index 086007f0c..3f794dc37 100644
--- a/src/generic/UpdateIf.cpp
+++ b/src/generic/UpdateIf.cpp
@@ -60,6 +60,7 @@ particular sense. For example, conditionally updating a \ref METAD keyword
 can lead to unexpected results.
 
 \par Examples
+
 The following input instructs plumed dump all the snapshots where an atom is in touch with
 the solute.
 \verbatim
diff --git a/src/gridtools/FourierTransform.cpp b/src/gridtools/FourierTransform.cpp
index d8509b27d..38e4a1c0f 100644
--- a/src/gridtools/FourierTransform.cpp
+++ b/src/gridtools/FourierTransform.cpp
@@ -55,6 +55,7 @@ The keyword "FOURIER_PARAMETERS" deserves just a note on the usage. This keyword
 The default values of these parameters are: \f$a=1\f$ and \f$b=1\f$.
 
 \par Examples
+
 The following example tells Plumed to compute the complex 2D 'backward' Discrete Fourier Transform by taking the data saved on a grid called 'density', and normalizing the output by \f$ \frac{1}{\sqrt{N_x\, N_y}}\f$, where \f$N_x\f$ and \f$N_y\f$ are the number of data on the grid (it can be the case that \f$N_x \neq N_y\f$):
 
 \verbatim
diff --git a/src/multicolvar/DumpMultiColvar.cpp b/src/multicolvar/DumpMultiColvar.cpp
index 9a12d79d0..2a3b6a65c 100644
--- a/src/multicolvar/DumpMultiColvar.cpp
+++ b/src/multicolvar/DumpMultiColvar.cpp
@@ -45,6 +45,7 @@ namespace multicolvar {
 Dump atom positions and multicolvar on a file.
 
 \par Examples
+
 In this examples we calculate the distances between the  atoms of the first and the second
 group and we write them in the file MULTICOLVAR.xyz. For each couple it writes the
 coordinates of their geometric center and their distance.
diff --git a/src/setup/Units.cpp b/src/setup/Units.cpp
index 0be6e9737..890cecdae 100644
--- a/src/setup/Units.cpp
+++ b/src/setup/Units.cpp
@@ -44,6 +44,7 @@ the units. For example, trajectories written in .gro format (with \ref DUMPATOMS
 are going to be always in nm.
 
 \par Examples
+
 \verbatim
 # this is using nm - kj/mol - fs
 UNITS LENGTH=nm TIME=fs
diff --git a/src/vatom/Ghost.cpp b/src/vatom/Ghost.cpp
index 3fa8c674e..0e9b73301 100644
--- a/src/vatom/Ghost.cpp
+++ b/src/vatom/Ghost.cpp
@@ -37,6 +37,7 @@ The computed ghost atom is stored as a virtual atom that can be accessed in
 an atom list through the the label for the GHOST action that creates it.
 
 \par Examples
+
 The following input instructs plumed to print the distance between the
 ghost atom and the center of mass for atoms 15,20:
 \verbatim
-- 
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