From 3f18899030a1c6f8b3254a4b27d4ad54773b7ee4 Mon Sep 17 00:00:00 2001 From: Carlo Camilloni <carlo.camilloni@gmail.com> Date: Wed, 4 Jun 2014 20:25:04 +0200 Subject: [PATCH] Documentation: a couple of links to the tutorials --- src/analysis/Histogram.cpp | 2 ++ src/bias/MetaD.cpp | 6 ++++++ src/colvar/CS2Backbone.cpp | 2 ++ src/colvar/RDC.cpp | 2 ++ user-doc/Group.txt | 2 ++ user-doc/Syntax.txt | 2 ++ 6 files changed, 16 insertions(+) diff --git a/src/analysis/Histogram.cpp b/src/analysis/Histogram.cpp index 394cedbfd..ee9efed09 100644 --- a/src/analysis/Histogram.cpp +++ b/src/analysis/Histogram.cpp @@ -39,6 +39,8 @@ In case a kernel density estimation is used the probability density is estimated continuos function on the grid with a BANDWIDTH defined by the user. In this case the normalisation is such that the INTEGRAL over the grid is 1. In case a discrete density estimation is used the probabilty density is estimated as a discrete function on the grid. In this case the normalisation is such that the SUM of over the grid is 1. + +Additional material and examples can be also found in the tutorial \ref belfast-1. \par Examples diff --git a/src/bias/MetaD.cpp b/src/bias/MetaD.cpp index be05b2b7e..dc87ce287 100644 --- a/src/bias/MetaD.cpp +++ b/src/bias/MetaD.cpp @@ -128,6 +128,12 @@ for replica exchange methods to be computed correctly. Multiple walkers \cite multiplewalkers can also be used. See below the examples. +Additional material and examples can be also found in the tutorials: + +- \ref belfast-6 +- \ref belfast-7 +- \ref belfast-8 + \par Examples The following input is for a standard metadynamics calculation using as collective variables the distance between atoms 3 and 5 diff --git a/src/colvar/CS2Backbone.cpp b/src/colvar/CS2Backbone.cpp index 637488514..93acd2357 100644 --- a/src/colvar/CS2Backbone.cpp +++ b/src/colvar/CS2Backbone.cpp @@ -94,6 +94,8 @@ both these files can be copied from almost/branches/almost-2.1/toppar. All the above files must be in a single folder that must be specified with the keyword DATA. +Additional material and examples can be also found in the tutorial \ref belfast-9 + \par Examples case 1: diff --git a/src/colvar/RDC.cpp b/src/colvar/RDC.cpp index e21fa65f2..d9594589c 100644 --- a/src/colvar/RDC.cpp +++ b/src/colvar/RDC.cpp @@ -84,6 +84,8 @@ a set of function from the GNU Scientific Library (GSL). (With SVD forces are no Replica-Averaged restrained simulations can be performed with this CV using the ENSEMBLE flag. +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. diff --git a/user-doc/Group.txt b/user-doc/Group.txt index cae30d8ed..0e322baec 100644 --- a/user-doc/Group.txt +++ b/user-doc/Group.txt @@ -19,6 +19,8 @@ predefined as \ref GROUP that can be reused multiple times. Atoms' list can be d Note that some collective variable can only accept a fixed number of atoms, for example a \ref DISTANCE is calculated using two atoms only, an \ref ANGLE is calcuated using either 3 or 4 atoms and \ref TORSION is calculated using 4 atoms. +Additional material and examples can be also found in the tutorial \ref belfast-1. + \subsection mols Molecules In addition, for certain colvars, pdb files can be read in using the following keywords and used to select ATOMS: diff --git a/user-doc/Syntax.txt b/user-doc/Syntax.txt index 6658d9b73..c07a45f96 100644 --- a/user-doc/Syntax.txt +++ b/user-doc/Syntax.txt @@ -8,6 +8,8 @@ one or more collective variables, perhaps calculating a function of these CVs some free energy method. A very brief introduction to the syntax used in the PLUMED input file is provided in this <a href="http://www.youtube.com/watch?v=PxJP16qNCYs"> 10-minute video </a>. +Additional material and examples can be also found in the tutorial \ref belfast-1. + Within this input file every line is an instruction for PLUMED to perform some particular action. This could be the calculation of a colvar, an occasional analysis of the trajectory or a biassing of the dynamics. The first word in these lines specify what particular action is to be performed. This is then followed by a number of keywords -- GitLab