From 5081c1f6f6bdd484f1f13ffef1a51caf4ff4ff36 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Wed, 14 Jun 2017 09:31:00 +0200
Subject: [PATCH] txt -> md in dev doc
Notice that before this fix the first sentence of the page was shown in
the summary ("Related Pages" page). Now it is not shown anymore, which is better.
To add a sentence for the summary (sort of subtitle), add a \brief command
(as in mdTemplate.md)
[makedoc]
---
developer-doc/.gitignore | 4 +-
.../{AddingACLTool.txt => AddingACLTool.md} | 6 --
.../{AddingAColvar.txt => AddingAColvar.md} | 70 -------------------
...AddingAFunction.txt => AddingAFunction.md} | 5 --
.../{AddingAMeasure.txt => AddingAMeasure.md} | 4 --
...ngAMultColvar.txt => AddingAMultColvar.md} | 5 --
...sionTests.txt => AddingRegressionTests.md} | 4 --
.../{CodeFormatting.txt => CodeFormatting.md} | 4 --
developer-doc/Doxyfile | 34 ++++-----
...oPlumed.txt => HowToContributeToPlumed.md} | 3 -
...lationLayout.txt => InstallationLayout.md} | 12 ----
developer-doc/{Intro.txt => Intro.md} | 4 --
developer-doc/Makefile | 2 +-
developer-doc/extract | 21 ++----
developer-doc/{intro-git.txt => intro-git.md} | 5 --
.../{mdTemplate.txt => mdTemplate.md} | 7 +-
developer-doc/{parsing.txt => parsing.md} | 4 --
developer-doc/{plmdIntro.txt => plmdIntro.md} | 4 --
.../{usingDoxygen.txt => usingDoxygen.md} | 6 --
19 files changed, 27 insertions(+), 177 deletions(-)
rename developer-doc/{AddingACLTool.txt => AddingACLTool.md} (98%)
rename developer-doc/{AddingAColvar.txt => AddingAColvar.md} (98%)
rename developer-doc/{AddingAFunction.txt => AddingAFunction.md} (99%)
rename developer-doc/{AddingAMeasure.txt => AddingAMeasure.md} (99%)
rename developer-doc/{AddingAMultColvar.txt => AddingAMultColvar.md} (99%)
rename developer-doc/{AddingRegressionTests.txt => AddingRegressionTests.md} (99%)
rename developer-doc/{CodeFormatting.txt => CodeFormatting.md} (98%)
rename developer-doc/{HowToContributeToPlumed.txt => HowToContributeToPlumed.md} (99%)
rename developer-doc/{InstallationLayout.txt => InstallationLayout.md} (99%)
rename developer-doc/{Intro.txt => Intro.md} (99%)
rename developer-doc/{intro-git.txt => intro-git.md} (98%)
rename developer-doc/{mdTemplate.txt => mdTemplate.md} (99%)
rename developer-doc/{parsing.txt => parsing.md} (97%)
rename developer-doc/{plmdIntro.txt => plmdIntro.md} (99%)
rename developer-doc/{usingDoxygen.txt => usingDoxygen.md} (99%)
diff --git a/developer-doc/.gitignore b/developer-doc/.gitignore
index 7c39bad00..975bc156c 100644
--- a/developer-doc/.gitignore
+++ b/developer-doc/.gitignore
@@ -3,7 +3,7 @@
/*.tmp
/automatic
/*PP.txt
-/links-to-user-manual.txt
-/plumedcheck.txt
+/links-to-user-manual.md
+/plumedcheck.md
/coverage
diff --git a/developer-doc/AddingACLTool.txt b/developer-doc/AddingACLTool.md
similarity index 98%
rename from developer-doc/AddingACLTool.txt
rename to developer-doc/AddingACLTool.md
index cf2db38bc..98d0caae2 100644
--- a/developer-doc/AddingACLTool.txt
+++ b/developer-doc/AddingACLTool.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page AddingACLTool How to add a new command-line tool
To implement a command line tool you need to create a single cpp file call CLToolNAME.cpp. You can, in a command line
@@ -137,6 +134,3 @@ delete plumed; delete action;
Please be aware that words should contain everything that would be required in an input
line to make a valid instance of the Action you require.
-*/
-
-
diff --git a/developer-doc/AddingAColvar.txt b/developer-doc/AddingAColvar.md
similarity index 98%
rename from developer-doc/AddingAColvar.txt
rename to developer-doc/AddingAColvar.md
index f49bda933..0428a8fa3 100644
--- a/developer-doc/AddingAColvar.txt
+++ b/developer-doc/AddingAColvar.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page AddingAColvar How to add a new collective variable
To implement a CV you need to create a single cpp file called <i>ColvarName</i>.cpp in the directory src/colvar.
@@ -139,70 +136,3 @@ setValue(nvalue,ncv_val);
\endverbatim
Please only use this functionality for CVs that are VERY similar.
-
-*/
-
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diff --git a/developer-doc/AddingAFunction.txt b/developer-doc/AddingAFunction.md
similarity index 99%
rename from developer-doc/AddingAFunction.txt
rename to developer-doc/AddingAFunction.md
index 1aa062d59..c1307e100 100644
--- a/developer-doc/AddingAFunction.txt
+++ b/developer-doc/AddingAFunction.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page AddingAFunction How to add a new function
Many collective variables are a function of a number of some set of simpler collective variables.
@@ -146,5 +143,3 @@ setValue(nvalue,ncv_val);
Please only use this functionality for functions that are VERY similar.
-*/
-
diff --git a/developer-doc/AddingAMeasure.txt b/developer-doc/AddingAMeasure.md
similarity index 99%
rename from developer-doc/AddingAMeasure.txt
rename to developer-doc/AddingAMeasure.md
index bc472886e..62fe58614 100644
--- a/developer-doc/AddingAMeasure.txt
+++ b/developer-doc/AddingAMeasure.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page AddingAMetric Implementing methods for calculating the distances between pairs of configurations
To implement a new method for calculating the distance between a pair of trajectory frames you will need to work with the
@@ -121,4 +118,3 @@ module's functionality to provide multiple methods for calculating the distance
that you implement should thus have one of these wrapper actions associated with it and the documentation for the measure
should be included in the wrapper code's source code file.
-*/
diff --git a/developer-doc/AddingAMultColvar.txt b/developer-doc/AddingAMultColvar.md
similarity index 99%
rename from developer-doc/AddingAMultColvar.txt
rename to developer-doc/AddingAMultColvar.md
index f6f3ca8b9..7e1f80e76 100644
--- a/developer-doc/AddingAMultColvar.txt
+++ b/developer-doc/AddingAMultColvar.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page AddingAMultiColvar How to add a new MultiColvar
As you are no doubt aware within plumed 2 you can calculate multiple
@@ -265,5 +262,3 @@ PLMD::multicolvar::AtomValuePack by using the methods PLMD::multicolvar::AtomVal
Once you have written all the above function you will need to write regression tests for your new feature if you would like
us to incorporate it in the release version of PLUMED. Details on how to write regression tests are provided here: \ref regtests
-
-*/
diff --git a/developer-doc/AddingRegressionTests.txt b/developer-doc/AddingRegressionTests.md
similarity index 99%
rename from developer-doc/AddingRegressionTests.txt
rename to developer-doc/AddingRegressionTests.md
index d73907de1..f64f5bb4c 100644
--- a/developer-doc/AddingRegressionTests.txt
+++ b/developer-doc/AddingRegressionTests.md
@@ -1,6 +1,3 @@
-e/ This document is formatted for Doxygen
-/**
-
\page regtests Adding regressions tests
When you write new functionality for PLUMED it is important that you document these features AND that you provide suitable
@@ -204,4 +201,3 @@ Notice, however, that with both these commands, even thought there are only forc
and the cell vectors, the forces with respect to all the atomic positions are output. In other words, the output files produced usig --debug-forces and
-dump-foces will contain a lot of zeros.
-*/
diff --git a/developer-doc/CodeFormatting.txt b/developer-doc/CodeFormatting.md
similarity index 98%
rename from developer-doc/CodeFormatting.txt
rename to developer-doc/CodeFormatting.md
index 4d6348976..b5e2d6149 100644
--- a/developer-doc/CodeFormatting.txt
+++ b/developer-doc/CodeFormatting.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page CodeFormatting How to format code properly
Since version 2.3.2, we format code using <a href="http://astyle.sourceforge.net/"> astyle </a>.
@@ -56,4 +53,3 @@ Notice that you cannot work it in the opposite direction (that is, unformat an a
formatted branch). Finally, consider that rebasing might be more complicated.
When all branches will be formatted this will not be an issue anymore.
-*/
diff --git a/developer-doc/Doxyfile b/developer-doc/Doxyfile
index 9e917ee1f..2f45cfe10 100644
--- a/developer-doc/Doxyfile
+++ b/developer-doc/Doxyfile
@@ -754,23 +754,23 @@ WARN_LOGFILE =
# spaces.
# Note: If this tag is empty the current directory is searched.
-INPUT = ./Intro.txt \
- ./mdTemplate.txt \
- ./plmdIntro.txt \
- ./usingDoxygen.txt \
- ./parsing.txt \
- ./links-to-user-manual.txt \
- ./AddingAColvar.txt \
- ./AddingAFunction.txt \
- ./AddingACLTool.txt \
- ./AddingAMeasure.txt \
- ./AddingAMultColvar.txt \
- ./InstallationLayout.txt \
- ./AddingRegressionTests.txt \
- ./HowToContributeToPlumed.txt \
- ./intro-git.txt \
- ./plumedcheck.txt \
- ./CodeFormatting.txt
+INPUT = ./Intro.md \
+ ./mdTemplate.md \
+ ./plmdIntro.md \
+ ./usingDoxygen.md \
+ ./parsing.md \
+ ./links-to-user-manual.md \
+ ./AddingAColvar.md \
+ ./AddingAFunction.md \
+ ./AddingACLTool.md \
+ ./AddingAMeasure.md \
+ ./AddingAMultColvar.md \
+ ./InstallationLayout.md \
+ ./AddingRegressionTests.md \
+ ./HowToContributeToPlumed.md \
+ ./intro-git.md \
+ ./plumedcheck.md \
+ ./CodeFormatting.md
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
diff --git a/developer-doc/HowToContributeToPlumed.txt b/developer-doc/HowToContributeToPlumed.md
similarity index 99%
rename from developer-doc/HowToContributeToPlumed.txt
rename to developer-doc/HowToContributeToPlumed.md
index ed259b614..b9873be5c 100644
--- a/developer-doc/HowToContributeToPlumed.txt
+++ b/developer-doc/HowToContributeToPlumed.md
@@ -1,5 +1,3 @@
-// This document is formatted for Doxygen
-/**
\page HowToContributeToPlumed How to contribute new functionality to PLUMED
We welcome researchers to contribute new functionality to the PLUMED code. In fact, we would
@@ -195,4 +193,3 @@ will still be able to download it from your fork, but obviosuly your module won'
enhancement we will add to the main PLUMED repository.
As always this fix should be done on your fork of the repository first and then merged into the release version of PLUMED using a pull request.
-*/
diff --git a/developer-doc/InstallationLayout.txt b/developer-doc/InstallationLayout.md
similarity index 99%
rename from developer-doc/InstallationLayout.txt
rename to developer-doc/InstallationLayout.md
index 3f52d4291..0d80e5b06 100644
--- a/developer-doc/InstallationLayout.txt
+++ b/developer-doc/InstallationLayout.md
@@ -1,5 +1,3 @@
-// This document is formatted for Doxygen
-/**
\page InstallationLayout Installation Layout
I write here some notes related to how plumed is installed.
@@ -150,13 +148,3 @@ Using the standard behavior explained in the autoconf documentation, it is possi
for plumed install either during configure (with `--prefix`) or by setting `prefix` during `make install`.
-
-
-
-
-
-
-
-
-
-*/
diff --git a/developer-doc/Intro.txt b/developer-doc/Intro.md
similarity index 99%
rename from developer-doc/Intro.txt
rename to developer-doc/Intro.md
index a32d71471..ff136d152 100644
--- a/developer-doc/Intro.txt
+++ b/developer-doc/Intro.md
@@ -1,5 +1,3 @@
-// This document is formatted for Doxygen
-/**
\mainpage Introduction
This is the developer manual. Please first have a look at the <a href="../../user-doc/html/index.html"> user manual </a>.
@@ -102,5 +100,3 @@ This list is built automatically based on the PLUMED_REGISTER_ACTION macro.
@}
-
-*/
diff --git a/developer-doc/Makefile b/developer-doc/Makefile
index e06ef46d0..61e4e9e96 100644
--- a/developer-doc/Makefile
+++ b/developer-doc/Makefile
@@ -13,7 +13,7 @@ ifeq ($(make_doc),yes)
endif
clean:
- rm -fr automatic html latex *~ links-to-user-manual.txt plumedcheck.txt coverage coverage.info
+ rm -fr automatic html latex *~ links-to-user-manual.md plumedcheck.md coverage coverage.info
coverage:
lcov -c -d ../src/ --output-file coverage.info
diff --git a/developer-doc/extract b/developer-doc/extract
index ffad04846..d31fd9f58 100755
--- a/developer-doc/extract
+++ b/developer-doc/extract
@@ -21,29 +21,22 @@ awk '
next;
}
{
- printf("%s","/// \\class PLMD::"namespace""$1"\n");
- printf("%s","/// \\ingroup INPUTDIRECTIVES\n");
+ printf("%s","\\class PLMD::"namespace""$1"\n");
+ printf("%s","\\ingroup INPUTDIRECTIVES\n");
action=tolower($2);
firstchar=substr($2,1,1);
n=split(action,actionarray,"");
lowercase=0;
if(firstchar==actionarray[1]) lowercase=1;
- printf("%s","/// Provides the keyword <a href=\"../../user-doc/html/");
+ printf("%s","\\brief Provides the keyword <a href=\"../../user-doc/html/");
for(i=1;i<=n;i++){
if(actionarray[i]!="_") printf("_");
printf("%s",actionarray[i]);
};
printf("%s",".html\"> "$2" </a>\n");
-}' > links-to-user-manual.txt
+}' > links-to-user-manual.md
cat ../src/maketools/plumedcheck | grep "# DOC:" |
-{
-cat << \EOF
-// This document is formatted for Doxygen
-/**
-
-EOF
-
awk '
{
sub("# DOC:","");
@@ -53,11 +46,7 @@ awk '
print
print ""
} else print $0
-
-}END{
- printf("%s\n","*/");
-}'
-} > plumedcheck.txt
+}' > plumedcheck.md
# Create a directory to put all the files in
diff --git a/developer-doc/intro-git.txt b/developer-doc/intro-git.md
similarity index 98%
rename from developer-doc/intro-git.txt
rename to developer-doc/intro-git.md
index 1a2cdd864..e3bcc17a5 100644
--- a/developer-doc/intro-git.txt
+++ b/developer-doc/intro-git.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page intro-git A brief introduction to git
Clone the github repository:
@@ -118,5 +115,3 @@ All these things can be done with a GUI:
> git gui
\endverbatim
-
-*/
diff --git a/developer-doc/mdTemplate.txt b/developer-doc/mdTemplate.md
similarity index 99%
rename from developer-doc/mdTemplate.txt
rename to developer-doc/mdTemplate.md
index 2a3afe66b..b93de9029 100644
--- a/developer-doc/mdTemplate.txt
+++ b/developer-doc/mdTemplate.md
@@ -1,8 +1,7 @@
-// This document is formatted for Doxygen
-/**
-
\page HowToPlumedYourMD How to add plumed to an MD code
+\brief Learn how to use plumed in a not yet supported MD code
+
Plumed ships with scripts that can be used to add it to many of the standard MD packages. Obviously though, if no patch is provided for the MD code you use then you will have to write one yourself. Plumed has been designed so that it can be added to an MD code
either statically (i.e. as a collection of objects) or as a dynamic library.
For technical reasons it
@@ -468,5 +467,3 @@ The two files `energy1` and `energy2` should be virtually identical.
In case you were able to have the virial properly working (see previous section), then you can try the same with a constant temperarure-constant pressure
simulation. In this case, please also monitor the volume of the resulting trajectory.
-
-*/
diff --git a/developer-doc/parsing.txt b/developer-doc/parsing.md
similarity index 97%
rename from developer-doc/parsing.txt
rename to developer-doc/parsing.md
index 212b36d5d..2edcdf6b3 100644
--- a/developer-doc/parsing.txt
+++ b/developer-doc/parsing.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page parsing Parsing functionality
By now you are probably familiar with the way that plumed2 input looks:
@@ -27,4 +24,3 @@ This routine will then read the list of action objects you passed to the constru
Please note when you are implementing functionality to read the plumed input that you never need to implement anything to read ARGS and LABEL as these keywords are read elsewhere in the code.
-*/
diff --git a/developer-doc/plmdIntro.txt b/developer-doc/plmdIntro.md
similarity index 99%
rename from developer-doc/plmdIntro.txt
rename to developer-doc/plmdIntro.md
index e39f29aef..40266de9b 100644
--- a/developer-doc/plmdIntro.txt
+++ b/developer-doc/plmdIntro.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page ABriefIntroduction A brief introduction to the plumed core
Plumed 2, unlike its predecessor plumed 1, which was written in plain C, is written in C++.
@@ -514,4 +511,3 @@ autoconf
and the necessary changes will be made to the configure script. <b>You should never edit the configure script directly</b>
-*/
diff --git a/developer-doc/usingDoxygen.txt b/developer-doc/usingDoxygen.md
similarity index 99%
rename from developer-doc/usingDoxygen.txt
rename to developer-doc/usingDoxygen.md
index 5328babe4..b5df96832 100644
--- a/developer-doc/usingDoxygen.txt
+++ b/developer-doc/usingDoxygen.md
@@ -1,6 +1,3 @@
-// This document is formatted for Doxygen
-/**
-
\page usingDoxygen Creating plumed documentation
<b> Whenever you make a change to the documentation for PLUMED and you want the
@@ -506,6 +503,3 @@ Bottom line: when you make a commit where you modified the manual and you want t
add [makedoc] in the commit log. After ten minutes or so the manual should be up to date, remember to double check on the web
and to revert the commit if there are errors!
-
-
-*/
--
GitLab