From a4b746e8ed1b1bc4a563f1cf699aa93c202bcb04 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Sun, 28 Jul 2019 16:29:34 +0200
Subject: [PATCH] Fixed some further spelling mistakes
---
user-doc/go-spelling | 2 +-
user-doc/spelling_words.dict | 13 +++++++++++++
user-doc/tutorials/belfast-6.txt | 4 ++--
user-doc/tutorials/marvel-2.txt | 6 +++---
user-doc/tutorials/performance-optimization.txt | 2 +-
5 files changed, 20 insertions(+), 7 deletions(-)
diff --git a/user-doc/go-spelling b/user-doc/go-spelling
index e01ae4b2f..3db4f83aa 100755
--- a/user-doc/go-spelling
+++ b/user-doc/go-spelling
@@ -30,7 +30,7 @@ for file in *PP.md automatic/*.txt ../CHANGES/*.md tutorials/*.txt tutorials/*.s
cat $file | grep -v "\\image" | grep -v "anchor" | sed -e 's/psi-1//' | sed -e 's/-#//' | sed -e 's/@//' | sed -e 's/&//' | sed -e 's/\vdots//' |
awk 'BEGIN{inp=0}{
if($1=="\\endplumedfile" || $1=="\\f]" || $1=="\\f}" || $1=="\\endauxfile" || $1=="\\endverbatim" || $1=="\\endcode"){inp=0;}
- else if($1=="\\plumedfile" || $1=="\\f[" || $1=="\\f{eqnarray*}{" || match($1,"\\auxfile") || $1=="\\verbatim" || index($1,"\\code{")!=0 ){inp=1;}
+ else if($1=="\\plumedfile" || $1=="\\f[" || $1=="\\f{eqnarray*}{" || match($1,"auxfile") || $1=="\\verbatim" || index($1,"\\code{")!=0 ){inp=1;}
else if(inp==0){
skip=0;
for(i=1;i<=NF;++i){
diff --git a/user-doc/spelling_words.dict b/user-doc/spelling_words.dict
index 59aa30937..f0b3636e4 100644
--- a/user-doc/spelling_words.dict
+++ b/user-doc/spelling_words.dict
@@ -950,3 +950,16 @@ initio
inp
dinucleotide
monophosphate
+minima
+analytical
+eigenvectors
+paramagnetic
+PDF
+regex
+nanotube
+covalent
+amino
+filename
+covariance
+peptide
+kinase
diff --git a/user-doc/tutorials/belfast-6.txt b/user-doc/tutorials/belfast-6.txt
index 4ccfa23ef..cb414a0c3 100644
--- a/user-doc/tutorials/belfast-6.txt
+++ b/user-doc/tutorials/belfast-6.txt
@@ -24,7 +24,7 @@ V(\vec{s},t) = \sum_{ k \tau < t} W(k \tau)
where \f$ \tau \f$ is the Gaussian deposition stride,
\f$ \sigma_i \f$ the width of the Gaussian for the \f$i\f$th CV, and \f$ W(k \tau) \f$ the
height of the Gaussian. The effect of the metadynamics bias potential is to push the system away
-from local minima into visiting new regions of the phase space. Furthermore, in the long
+from any local minimum and into visiting new regions of the phase space. Furthermore, in the long
time limit, the bias potential converges to minus the free energy as a function of the CVs:
\f[
@@ -301,7 +301,7 @@ The resulting plot should look like the following:
\image html belfast-6-phifest.png "Estimates of the free energy as a function of the dihedral phi calculated every 500 Gaussian kernels deposited along a 5ns-long metadynamics simulation using 2 CVs."
To assess the convergence of the simulation more quantitatively, we can calculate the free-energy difference between the two
-local minima in the one-dimensional free energy along phi as a function of simulation time.
+local minimums in the one-dimensional free energy along phi as a function of simulation time.
We can use the bash script analyze_FES.sh to integrate the multiple free-energy profiles in the two basins defined
by the following intervals in phi space: basin A, -3<phi<-1, basin B, 0.5<phi<1.5.
diff --git a/user-doc/tutorials/marvel-2.txt b/user-doc/tutorials/marvel-2.txt
index 534cc46af..d10b2795e 100644
--- a/user-doc/tutorials/marvel-2.txt
+++ b/user-doc/tutorials/marvel-2.txt
@@ -326,7 +326,7 @@ must pass them in a particular order in order to pass between these two conforma
S(X)=\frac{\sum_{i=1}^{N} i\ \exp^{-\lambda \vert X-X_i \vert }}{ \sum_{i=1}^{N} \exp^{-\lambda \vert X-X_i \vert } }
\f]
-In this expression \f$\vert X-X_i \vert\f$ is the distance between the instantaneous coordinate of the system, \f$X\f$, in the high-dimensional space and
+In this expression \f$\vertX-X_i\vert\f$ is the distance between the instantaneous coordinate of the system, \f$X\f$, in the high-dimensional space and
\f$X_i\f$ is the coordinate of the \f$i\f$th way mark in the path. The largest exponential in the sum that appears in the numerator and the denominator
will thus be the one that corresponds to the point that is closest to where the system currently lies. In other words, \f$S(X)\f$, measures the position
on a (curvilinear) path that connects two states of interest as shown in red in the figure below:
@@ -387,7 +387,7 @@ In the \ref PATH case, however, we can use the value of \f$Z(X)\f$ to measure ho
These two coordinates, \f$S(X)\f$ and \f$Z(X)\f$, are very flexible. They are thus been used widely in the literature on modelling conformational changes of biomolecules.
A part of this flexibility comes because one can use any set of way markers to define the \ref PATH. Another flexibility comes, however, when you
-recognize that you can also change the way in which the distance, \f$ \vert X- X_i \vert \f$, is calculated in the two formulas above. For example
+recognize that you can also change the way in which the distance, \f$\vertX- X_i\vert\f$, is calculated in the two formulas above. For example
this distance can be calculated using the \ref RMSD distance or it can be calculated by measuring the sum of the squares of a set of displacements
in collective variable values (see \ref TARGET). Changing the manner in which the distance between path way points is calculated thus provides a
way to control the level of detail that is incorporated in the description of the reaction \ref PATH.
@@ -402,7 +402,7 @@ and even using \ref PATH collective variables that change adaptively as the simu
for solving your particular problem. Having said that, however, there is some general guidance on setting up \ref PATH collective variable and it is
this that we will focus on in this section. The first thing that you will need to double check is the spacing between the frames in your
\ref PATH. Lets suppose that your \ref PATH has \f$N\f$ of these way markers upon it you will need to calculate is the \f$N \times N\f$ matrix of
-distances between way markers. That is to say you will have to calculate the distance \f$\vert X_j - X_i \vert\f$ between each pair of frames.
+distances between way markers. That is to say you will have to calculate the distance \f$\vertX_j-X_i\vert\f$ between each pair of frames.
The values of the distance in this matrix for a good \ref PATH are shown in the figure below:
\anchor marvel-2-good-matrix-fig
diff --git a/user-doc/tutorials/performance-optimization.txt b/user-doc/tutorials/performance-optimization.txt
index b2e94cd79..45a1370c6 100644
--- a/user-doc/tutorials/performance-optimization.txt
+++ b/user-doc/tutorials/performance-optimization.txt
@@ -269,7 +269,7 @@ Run your simulation and check the timing. Which is the most expensive action now
The standard solution to the problem above is to use a grid to store the Gaussian functions.
In this manner, at the first step PLUMED will take some time to put all the Gaussian functions
on the grid, but subsequent calculations of the force will be much faster, since they will just
-require a grid lookup (rather than a sum over the history).
+require that the action look up the value on the grid (rather than a sum over the history).
Time the simulation using the following lines to perform METAD:
\plumedfile
--
GitLab