From add153e22d9322a8ba66ee7b5f96da0be367638b Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Fri, 20 Jan 2017 20:16:26 +0100
Subject: [PATCH] A few fixes in manual
addresses #213
[makedoc]
---
CHANGES/v2.1.txt | 2 +-
src/analysis/PCA.cpp | 2 +-
src/cltools/Driver.cpp | 2 ++
src/multicolvar/FilterBetween.cpp | 2 +-
user-doc/Bias.txt | 3 ---
5 files changed, 5 insertions(+), 6 deletions(-)
diff --git a/CHANGES/v2.1.txt b/CHANGES/v2.1.txt
index 5ee2efb83..320e3745f 100644
--- a/CHANGES/v2.1.txt
+++ b/CHANGES/v2.1.txt
@@ -30,7 +30,7 @@ character now has a special usage in component names.
if these libraries are not installed.
- New actions:
- \ref SPRINT topological collective variables.
- - \ref CH3SHIFTS collective variable.
+ - CH3SHIFTS collective variable.
- \ref POSITION collective variable.
- \ref FIT_TO_TEMPLATE.
- \ref COMMITTOR analysis.
diff --git a/src/analysis/PCA.cpp b/src/analysis/PCA.cpp
index d2d690fcd..000e1cfa8 100644
--- a/src/analysis/PCA.cpp
+++ b/src/analysis/PCA.cpp
@@ -73,7 +73,7 @@ elements of the covariance matrix from the input vectors. In this calculation t
Trajectory frames will be collected every five steps and the PCA calculation is performed every 1000 steps. Consequently, if you run a 2000 step simulation the
PCA analysis will be performed twice. The REWEIGHT_BIAS keyword in this input tells PLUMED that rather that ascribing a weight of one to each of the frames
when calculating averages and covariances a reweighting should be performed based and each frames' weight in these calculations should be determined based on
-the current value of the instantaneous bias (see \ref reweighting).
+the current value of the instantaneous bias (see \ref REWEIGHT_BIAS).
\verbatim
d1: DISTANCE ATOMS=1,2
diff --git a/src/cltools/Driver.cpp b/src/cltools/Driver.cpp
index b48fbfc69..922936021 100644
--- a/src/cltools/Driver.cpp
+++ b/src/cltools/Driver.cpp
@@ -77,6 +77,8 @@ plumed driver-float --plumed plumed.dat --ixyz trajectory.xyz
See also examples in \ref driver
*/
+//+ENDPLUMEDOC
+//
//+PLUMEDOC TOOLS driver
diff --git a/src/multicolvar/FilterBetween.cpp b/src/multicolvar/FilterBetween.cpp
index 29a163a5e..07f52c475 100644
--- a/src/multicolvar/FilterBetween.cpp
+++ b/src/multicolvar/FilterBetween.cpp
@@ -45,7 +45,7 @@ MEAN for \ref MFILTER_BETWEEN one is thus calculating:
\mu = \frac{ \sum_i f_i s_i }{ \sum_i f_i}
\f]
-In this action by contrast the colvar is being transformed by the \ref histogram bead. If one thus calculates a MEAN for
+In this action by contrast the colvar is being transformed by the \ref histogrambead. If one thus calculates a MEAN for
thia action one computes:
\f[
diff --git a/user-doc/Bias.txt b/user-doc/Bias.txt
index 0f1b8cb33..94eb105e3 100644
--- a/user-doc/Bias.txt
+++ b/user-doc/Bias.txt
@@ -10,8 +10,5 @@ The list of enhanced sampling algorithms contained in PLUMED is as follows:
Methods, such as \ref METAD or \ref PBMETAD, that work by introducing a history dependent bias can be restarted
using the \subpage RESTART keyword
-You can also use PLUMED in conjunction with VMD's interactive MD module by taking
-advantage of the \subpage IMD action.
-
*/
--
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