From b7f6d083810a526ecf8780e08ea08e479e213d91 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Tue, 23 Jul 2019 11:24:13 +0200
Subject: [PATCH] Fixed some wrong references in tutorials

---
 src/ves/Opt_BachAveragedSGD.cpp    |  4 ++--
 user-doc/tutorials/a-trieste-5.txt | 16 ++++++++--------
 user-doc/tutorials/aa-lugano-4.txt |  2 +-
 user-doc/tutorials/lyon.txt        |  6 +++---
 4 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/src/ves/Opt_BachAveragedSGD.cpp b/src/ves/Opt_BachAveragedSGD.cpp
index 99e489bd6..34151444f 100644
--- a/src/ves/Opt_BachAveragedSGD.cpp
+++ b/src/ves/Opt_BachAveragedSGD.cpp
@@ -138,7 +138,7 @@ is updated every 500 iterations (e.g. every 1000 ps). The target distribution is
 also output to a file every 2000 iterations (the TARGETDIST_OUTPUT keyword).
 Here we also employ MULTIPLE_WALKERS flag to enable the usage of
 multiple walkers.
-\plumedmultireplicasfile{2}
+\plumedmultireplicafile{2}
 phi:   TORSION ATOMS=5,7,9,15
 psi:   TORSION ATOMS=7,9,15,17
 
@@ -172,7 +172,7 @@ OPT_AVERAGED_SGD ...
   TARGETDIST_STRIDE=500
   TARGETDIST_OUTPUT=2000
 ... OPT_AVERAGED_SGD
-\endplumedmultireplicasfile
+\endplumedmultireplicafile
 
 
 
diff --git a/user-doc/tutorials/a-trieste-5.txt b/user-doc/tutorials/a-trieste-5.txt
index 086f3c2fa..17d39dec9 100644
--- a/user-doc/tutorials/a-trieste-5.txt
+++ b/user-doc/tutorials/a-trieste-5.txt
@@ -103,7 +103,7 @@ file with common definitions and specific input files with replica-dependent key
 However, as of PLUMED 2.4, we introduced a simpler manner to manipulate multiple replica
 inputs with tiny differences. Look at the following example:
 
-\plumedmultiplereplicasfile{3}
+\plumedmultireplicafile{3}
 # Compute a distance
 d: DISTANCE ATOMS=1,2
 
@@ -115,7 +115,7 @@ RESTRAINT ARG=d AT=@replicas:1.0,1.1,1.2 KAPPA=1.0
 #   RESTRAINT ARG=d AT=1.1 KAPPA=1.0
 # On replica 2, this means:
 #   RESTRAINT ARG=d AT=1.2 KAPPA=1.0
-\endplumedmultiplereplicasfile
+\endplumedmultireplicafile
 
 If you prepare a single `plumed.dat` file like this one and feeds it to PLUMED while using 3 replicas,
 the 3 replicas will see the very same input except for the `AT` keyword, that sets the position of the restraint.
@@ -123,7 +123,7 @@ Replica 0 will see a restraint centered at 1.0, replica 1 centered at 1.1, and r
 
 The `@replicas:` keyword is not special for \ref RESTRAINT or for 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 \cite piana simulations:
-\plumedmultiplereplicasfile{2}
+\plumedmultireplicafile{2}
 # Compute distance between atoms 1 and 2
 d: DISTANCE ATOMS=1,2
 
@@ -143,7 +143,7 @@ METAD ...
 #  METAD ARG=d HEIGHT=1.0 PACE=100 SIGMA=0.1 GRID_MIN=0.0 GRID_MAX=2.0
 # On replica 1, this means:
 #  METAD ARG=t HEIGHT=1.0 PACE=100 SIGMA=0.3 GRID_MIN=-pi GRID_MAX=+pi
-\endplumedmultiplereplicasfile
+\endplumedmultireplicafile
 
 This would be a typical setup for a bias exchange simulation.
 Notice that even though variables `d` and `t` are both read in both replicas,
@@ -153,7 +153,7 @@ This is because variables that are defined but not used are never actually calcu
 If the value that should be provided for each replica is a vector, you should use curly braces as delimiters.
 For instance, if the restraint acts on two variables, you can use the following input:
 
-\plumedmultiplereplicasfile{3}
+\plumedmultireplicafile{3}
 # Compute distance between atoms 1 and 2
 d: DISTANCE ATOMS=10,20
 
@@ -172,13 +172,13 @@ RESTRAINT ...
 #  RESTRAINT ARG=d AT=3.0,4.0 KAPPA=1.0,3.0
 # On replica 2 this means:
 #  RESTRAINT ARG=d AT=5.0,6.0 KAPPA=1.0,3.0
-\endplumedmultiplereplicasfile
+\endplumedmultireplicafile
 
 Notice the double curly braces. The outer ones are used by PLUMED to know there the argument of the `AT` keyword ends,
 whereas the inner ones are used to group the values corresponding to each replica.
 Also notice that the last example can be split in multiple lines exploiting the fact that
 within multi-line statements (enclosed by pairs of `...`) newlines are replaced with simple spaces:
-\plumedmultiplereplicasfile{3}
+\plumedmultireplicafile{3}
 d: DISTANCE ATOMS=10,20
 t: TORSION ATOMS=30,31,32,33
 RESTRAINT ...
@@ -192,7 +192,7 @@ RESTRAINT ...
   }
   KAPPA=1.0
 ...
-\endplumedmultiplereplicasfile
+\endplumedmultireplicafile
 
 In short, whenever there are keywords that should vary across replicas, you should set them using the `@replicas:` keyword.
 As mentioned above, you can always use the old syntax with separate input file, and this is recommended when the
diff --git a/user-doc/tutorials/aa-lugano-4.txt b/user-doc/tutorials/aa-lugano-4.txt
index 5e5ec3b4f..bc343abfd 100644
--- a/user-doc/tutorials/aa-lugano-4.txt
+++ b/user-doc/tutorials/aa-lugano-4.txt
@@ -136,7 +136,7 @@ To prevent the cluster from evaporating you need to lower the temperature in the
 <b> 
 Now try to think how we can use a bias potential to stop the cluster from evaporating. Why might using a bias potential be preferable to the method that you have just employed? 
 N.B. The next exercise is in the hidden section below so you need to expand it.  Please try to come up with your own answer to the question of what bias potential we should be using 
-before expanding this section by thinking about the material that was covered in \ref a-lugano-2.
+before expanding this section by thinking about the material that was covered in \ref lugano-2.
 </b>
 
 \hidden{The bias potential}
diff --git a/user-doc/tutorials/lyon.txt b/user-doc/tutorials/lyon.txt
index 8df3e819d..7ccfc0f0c 100644
--- a/user-doc/tutorials/lyon.txt
+++ b/user-doc/tutorials/lyon.txt
@@ -225,7 +225,7 @@ gnuplot or some other plotting package. </b>
 \hidden{Example time series}
 
 \anchor lyon-time-series
-\image html lyon-time-series.png "Time series for the second and third moments of the distribution of coordination numbers for two trajectories of Lennard Jones 7.  The time series on the left was computed from a trajectory that was performed at \f$k_B T = 0.2 \epsilon\f$, while the two time series on the right were computed at a temperature of \f$k_B T = 0.1 \epsilon\f$.  You can see that at the higher temperature there are jumps between distinct minima in the energy landscape.  At the lower temperature, however, the system remains trapped in a single basin in the energy lanscape"
+\image html lyon-time-series.png "Time series for the second and third moments of the distribution of coordination numbers for two trajectories of Lennard Jones 7.  The time series on the left was computed from a trajectory that was performed at a temperature of 0.2, while the two time series on the right were computed at a temperature of 0.1.  You can see that at the higher temperature there are jumps between distinct minima in the energy landscape.  At the lower temperature, however, the system remains trapped in a single basin in the energy lanscape"
 
 \endhidden
 
@@ -264,7 +264,7 @@ you are going to have to use many more time steps than you did in previous exerc
 configuration space is explored at this lower temperature
 
 \anchor lyon-lj7-fes
-\image html lyon-histograms-highT.png "The free energy for Lennard Jones seven calculated by computing a histogram based on an MD trajectory at \f$k_B T = 0.2 \epsilon\f$ (left) and \f$k_B T = 0.1 \epsilon\f$."
+\image html lyon-histograms-highT.png "The free energy for Lennard Jones seven calculated by computing a histogram based on an MD trajectory at a temperature of 0.2 (left) and at a temperature of 0.1."
 
 \endhidden
 
@@ -278,7 +278,7 @@ in a lower temperature simulation.  The fact that the histogram shows that the p
 is not converged.  The free energy will thus look like the one shown below instead of looking like the one in the previous hidden section:
 
 \anchor lyon-lj7-fes2
-\image html lyon-histograms-lowT.png "The free energy for Lennard Jones seven calculated by computing a histogram based on an MD trajectory at \f$k_B T = 0.2 \epsilon\f$ (left) and \f$k_B T = 0.1 \epsilon\f$."
+\image html lyon-histograms-lowT.png "The free energy for Lennard Jones seven calculated by computing a histogram based on an MD trajectory at a temperature of 0.2 (left) and at a temperature of 0.1."
   
 \endhidden
 
-- 
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