Reorganization of manual source files

I renamed all files from .txt to .md so that they can be visualized on github. In addition, I renamed all files to have a name consistent with the content. This makes manual portions easier to find. Notice that I left the original labels (e.g. "Syntax" instead of "Getting Started") not to break direct links to manual, though I think we should rationalize these names as well. [makedoc]

Reorganization of manual source files
7b93c5a7 · Giovanni Bussi · 7bbaf9c1 · 7b93c5a7 · 7b93c5a7 · 7b93c5a7
Commit 7b93c5a7 authored 7 years ago by Giovanni Bussi
--- a/user-doc/.gitignore
+++ b/user-doc/.gitignore
@@ -3,6 +3,7 @@
 /*.tmp
 /automatic
 /*PP.txt
+/*PP.md
 /errors
 /modifier_file
 /*aux

--- a/user-doc/Analysis.txt
+++ b/user-doc/Analysis.txt
-/**
-
 \page Analysis Analysis

 PLUMED can be used to analyse trajectories either on the fly during an MD run or via
@@ -90,5 +88,3 @@ the trajectory.  The RUN keyword then tells PLUMED how frequently to do the dime
 described above if RUN is not present and you are analysing trajectories using \ref driver all the data in 
 the traejctory (with the expection of the first frame) will be analysed. 

-*/
-
--- a/user-doc/Bias.txt
+++ b/user-doc/Bias.txt
-/**
-
 \page Bias Bias

 PLUMED allows you to run a number of enhanced sampling algorithms.
@@ -10,5 +8,3 @@ 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

-*/
-
--- a/user-doc/ChangeLog.md
+++ b/user-doc/ChangeLog.md
+\page ChangeLog Change Log
+
+Here you can find a history of changes across different PLUMED versions.
+The future releases are expected to follow more or less the pace
+of the old release. This means:
+- Approximately once per year, after summer, a new release (2.X). These releases
+  typically group together all the features that were contributed during the
+  year.
+- Approximately every three month, we announce a patch (e.g. 2.2.X).
+  This typically contains bug fixes, and could occasionally contain a new feature.
+
+A few months before each new release we provide a beta release.
+We typically maintain release branches until the fifth patch release (2.X.5),
+which should come out approximately 15 month after the original release (2.X).
+After that, branches are not supported anymore.
+
+Notice that occasionally we publish patches on the mailing list.
+These patches are always included in the following release, but we encourage
+users that want to be up to date to follow the mailing list.
+
+Below you can find change logs for all the published releases.
+We mostly add new features without breaking existing ones.
+However, some of the changes lead to incompatible behavior.
+In the Change Log we try to give as much visibility as possible to these changes
+to avoid surprises.
+
+We also log changes that are relevant if you are developing the code. These
+change lists are however not complete, and if you want to put your hands in the code
+and maintain your own collective variables we suggest you to follow the development
+on github.
+
+@CHANGES@
+
--- a/user-doc/Colvar.txt
+++ b/user-doc/Colvar.txt
-/**
-
-\page colvarintro Collective variables
+\page colvarintro Collective Variables

 Chemical systems contain an enormous number atoms, which, in most cases makes it simply impossible for
 us to understand anything by monitoring the atom postions directly.  Consquentially,
@@ -203,5 +201,3 @@ with a set of connected components are listed below:

 @CONCOMP@

-*/
-
--- a/user-doc/Tools.txt
+++ b/user-doc/Tools.txt
-/**
-
 \page tools Command Line Tools

 PLUMED contains a number of simple command line tools.  To use one of these tools 
@@ -15,4 +13,3 @@ The following is a list of the various standalone tools that PLUMED contains.

 For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file.

-*/
--- a/user-doc/Files.txt
+++ b/user-doc/Files.txt
-/**
-
 \page Files Files

 We tried to design PLUMED in such a manner that input/output is done consistently
@@ -62,5 +60,3 @@ PLUMED will write files named COLVAR.0.gz, COLVAR.1.gz, test.0.HILLS, test.1.HIL
 etc. This is useful since the preserved extension makes it easy
 to process the files later.

-
-*/
--- a/user-doc/Functions.txt
+++ b/user-doc/Functions.txt
-/**
 \page Function Functions

 When performing biased dynamics or analysing a trajectory you may wish to analyse/bias the value of
@@ -43,5 +42,3 @@ dz: COMBINE ARG=d.z PERIODIC=-10,10

 @FUNCTION@

-*/
-
--- a/user-doc/Syntax.txt
+++ b/user-doc/Syntax.txt
-/**
-\page Syntax Getting started 
+\page Syntax Getting Started 

 To run PLUMED you need to provide one input file.  In this file you specify what it
 is that PLUMED should do during the course of the run.  Typically this will involve calculating 
@@ -74,5 +73,3 @@ By default the PLUMED inputs and outputs quantities in the following units:
 Unlike PLUMED 1 the units used are independent of the MD engine you are using.  If you want to change these units you can do this using the 
 \subpage UNITS keyword. 

-*/
-
--- a/user-doc/Glossary.txt
+++ b/user-doc/Glossary.txt
-/**
-
-@page glossary Index of Actions 
+\page glossary Index of Actions 

 The following page contains an alphabetically ordered list of all the Actions and command line tools 
 that are available in PLUMED 2. For lists of Actions classified in accordance with the 
@@ -14,4 +12,3 @@ particular tasks that are being performed see:

 @GLOSSARY@

-*/
--- a/user-doc/Group.txt
+++ b/user-doc/Group.txt
-/**
-
 \page Group Groups and Virtual Atoms 

 \section atomSpecs Specifying Atoms
@@ -124,6 +122,3 @@ DISTANCE ATOMS=11,com1
 If you don't want to calculate CVs from the virtual atom.  That is to say you just want to monitor the position of a virtual atom 
 (or any set of atoms) over the course of your trajectory you can do this using \ref DUMPATOMS.

-
-*/
-
--- a/user-doc/Installation.txt
+++ b/user-doc/Installation.txt
-/**
-
 \page Installation Installation

 In this page you can learn how to
@@ -601,8 +599,3 @@ Notice that MD codes with native PLUMED support are not listed here.

 @CODES@

-
-
- 
-*/
-
--- a/user-doc/Intro.txt
+++ b/user-doc/Intro.txt
-/**
 \mainpage Introduction

 PLUMED is a plugin that works with a large number of molecular dynamics codes (\ref codes). 
@@ -7,7 +6,7 @@ PLUMED can also work as a \ref tools to perform analysis on trajectories saved i
 existing formats. If PLUMED is useful for your work please read and cite \cite plumed2, if you are interested in 
 the PLUMED 1 original publication please read and cite \cite plumed1 .

-To follow the development of PLUMED 2, you can look at the detailed \ref Changelog .
+To follow the development of PLUMED 2, you can look at the detailed \ref ChangeLog .

 To install PLUMED, see this page: \ref Installation , while in \ref Syntax you can find a brief introduction on how to write your first PLUMED input file.

@@ -52,38 +51,3 @@ also from the following packages:
 - [PLUMED-GUI](http://github.com/tonigi/vmd_plumed) is a [VMD](http://www.ks.uiuc.edu/Research/vmd/) plugin that computes PLUMED collective variables.
 - [HTMD](http://www.htmd.org/) can use PLUMED collective variables for analysis.

-\page Changelog Change Log
-
-Here you can find a history of changes across different PLUMED versions.
-The future releases are expected to follow more or less the pace
-of the old release. This means:
- Approximately once per year, after summer, a new release (2.X). These releases
-  typically group together all the features that were contributed during the
-  year.
- Approximately every three month, we announce a patch (e.g. 2.2.X).
-  This typically contains bug fixes, and could occasionally contain a new feature.
-
-A few months before each new release we provide a beta release.
-We typically maintain release branches until the fifth patch release (2.X.5),
-which should come out approximately 15 month after the original release (2.X).
-After that, branches are not supported anymore.
-
-Notice that occasionally we publish patches on the mailing list.
-These patches are always included in the following release, but we encourage
-users that want to be up to date to follow the mailing list.
-
-Below you can find change logs for all the published releases.
-We mostly add new features without breaking existing ones.
-However, some of the changes lead to incompatible behavior.
-In the Change Log we try to give as much visibility as possible to these changes
-to avoid surprises.
-
-We also log changes that are relevant if you are developing the code. These
-change lists are however not complete, and if you want to put your hands in the code
-and maintain your own collective variables we suggest you to follow the development
-on github.
-
-@CHANGES@
-
-*/
-
--- a/user-doc/Makefile
+++ b/user-doc/Makefile
@@ -24,4 +24,4 @@ endif
 endif

 clean:
-	rm -fr html latex automatic *~ *PP.txt errors manual.pdf regtests
+	rm -fr html latex automatic *~ *PP.txt *PP.md errors manual.pdf regtests
--- a/user-doc/Misc.txt
+++ b/user-doc/Misc.txt
-/**
-
 \page Miscelaneous Miscelaneous

 - \subpage comments
@@ -437,6 +435,3 @@ chosen replicas. This is useful e.g. for bias exchange metadynamics \cite piana.
 </TR>
 </TABLE>

-
-
-*/
--- a/user-doc/Modules.txt
+++ b/user-doc/Modules.txt
-/**
-
-@page mymodules List of modules
+\page mymodules List of modules

 The functionality in PLUMED 2 is divided into a small number of modules.  Some
 users may only wish to use a subset of the functionality available within the 
@@ -54,4 +52,3 @@ Until PLUMED 2.2, it was also possible to switch on or off modules by adding fil
 in the plumed2/src directory. Since PLUMED 2.3 this is discouraged, since any choice made
 in this manner will be overwritten next time `./configure` is used.

-*/
--- a/user-doc/Performances.txt
+++ b/user-doc/Performances.txt
-/**
-
 \page Performances Performances 

 In this page we collect hints on how to use the features available in PLUMED to speed
@@ -218,5 +216,3 @@ or just use somenthing else)

 To have an accurate timing of your input you can use the \ref DEBUG DETAILED_TIMERS.
  
-
-*/
--- a/user-doc/Regex.txt
+++ b/user-doc/Regex.txt
-/**
-
 \page Regex Regular Expressions

 When you use need to pass many arguments to a PLUMED action, being them
@@ -82,5 +80,3 @@ You can check the log to see whether or not your regular expression is picking t

 For more information on regular expressions visit http://www.regular-expressions.info/reference.html.

-*/
-
--- a/user-doc/Tutorials.txt
+++ b/user-doc/Tutorials.txt
-/**
-
-@page tutorials Tutorials 
+\page tutorials Tutorials 

 The following pages describe how to perform a variety of tasks using PLUMED

@@ -10,4 +8,3 @@ In addition, the following websites contain resources that might be helpful

 @WEBSITES@

-*/
--- a/user-doc/extract
+++ b/user-doc/extract
@@ -262,16 +262,20 @@ done
 sed -ie 's/<b> --/<b> \\c \\-\\-/g' automatic/*.txt
 rm automatic/*.txte

-rm -f *PP.txt
-for f in *.txt
+rm -f *PP.txt *PP.md
+for f in *.txt *.md
 do

-file=${f%.txt}
+test -f $f || continue
+
+extension=${f##*.}
+
+file=${f%.$extension}

 # first replace with the content of the files
 # then grep out the special strings

-cat $file.txt |
+cat $f |
  sed "
    /^ *@COLVAR@ *$/r     automatic/COLVAR.list
    /^ *@MCOLVAR@ *$/r    automatic/MCOLVAR.list
@@ -304,5 +308,5 @@ cat $file.txt |
    /^ *@VERSION@ *$/r    automatic/version.tmp
    /^ *@CHANGES@ *$/r    automatic/changes.tmp
    /^ *@PDFMANUAL@ *$/r  automatic/pdfmanual.tmp
-" | grep -Ev '^ *@[A-Z]*@ *$' > ${file}PP.txt
+" | grep -Ev '^ *@[A-Z]*@ *$' > ${file}PP.$extension
 done