diff --git a/.travis/pushdoc b/.travis/pushdoc
index 504e580bade827b40ebd52baccc2e18676f00d07..712107e7b4012ca3f8f9983004a06f7844d21d3e 100755
--- a/.travis/pushdoc
+++ b/.travis/pushdoc
@@ -3,16 +3,23 @@
set -e
set -x
-if [[ "$TRAVIS_BRANCH" =~ ^v2\.[0-9]+$ ]] ; then
-# TODO: this should be made automatic by reading the CHANGES/*.txt files:
- if [ "$TRAVIS_BRANCH" = v2.0 ] || [ "$TRAVIS_BRANCH" = v2.1 ] || [ "$TRAVIS_BRANCH" = v2.2 ] ; then
- branchtype=unsupported
+GIT_OWNER=$( echo $TRAVIS_REPO_SLUG | sed "s/\/.*$//" )
+GIT_REPO=$( echo $TRAVIS_REPO_SLUG | sed "s/^.*\///" )
+
+if [ "$GIT_OWNER" = plumed ] ; then
+ if [[ "$TRAVIS_BRANCH" =~ ^v2\.[0-9]+$ ]] ; then
+ # TODO: this should be made automatic by reading the CHANGES/*.txt files:
+ if [ "$TRAVIS_BRANCH" = v2.0 ] || [ "$TRAVIS_BRANCH" = v2.1 ] || [ "$TRAVIS_BRANCH" = v2.2 ] ; then
+ branchtype=unsupported
+ else
+ branchtype=official
+ fi
+ elif [ "$TRAVIS_BRANCH" = master ] ; then
+ branchtype=master
else
- branchtype=official
+ branchtype=unofficial
fi
-elif [ "$TRAVIS_BRANCH" = master ] ; then
- branchtype=master
-else
+else
branchtype=unofficial
fi
@@ -47,27 +54,37 @@ This is an auto redirect page.
</html>
EOF
+if test -z "${GIT_BOT}"
+then
+ export GIT_BOT=plumedbot
+fi
+
+if test -z "${GIT_BOT_EMAIL}"
+then
+ export GIT_BOT_EMAIL=giovanni.bussi+plumedbot@gmail.com
+fi
+
git init
-git config user.email "giovanni.bussi+plumedbot@gmail.com"
-git config user.name "plumedbot"
+git config user.email "${GIT_BOT_EMAIL}"
+git config user.name "${GIT_BOT}"
git checkout -b gh-pages
# this is not to show the GIT_TOKEN on Travis log
set +x
-git remote add doc https://plumedbot:$GIT_TOKEN@github.com/plumed/doc-${TRAVIS_BRANCH}.git
+git remote add doc https://${GIT_BOT}:$GIT_TOKEN@github.com/$GIT_OWNER/doc-${TRAVIS_BRANCH}.git
set -x
cat > README.md << EOF
Precompiled manual for PLUMED ${TRAVIS_BRANCH}
-----------------------------
This repository hosts a precompiled manual for [PLUMED](http://www.plumed.org) ${TRAVIS_BRANCH},
-git revision [$hash](https://github.com/plumed/plumed2/commit/$hash).
+git revision [$hash](https://github.com/${GIT_OWNER}/${GIT_REPO}/commit/$hash).
-This manual has been compiled on [travis](http://travis-ci.org/plumed/plumed2) on $(date).
+This manual has been compiled on [travis](http://travis-ci.org/${GIT_OWNER}/${GIT_REPO}) on $(date).
-To browse the manual you should go [here](http://plumed.github.io/doc-${TRAVIS_BRANCH}).
+To browse the manual you should go [here](http://${GIT_OWNER}.github.io/doc-${TRAVIS_BRANCH}).
You can also download a full copy of the manual for offline access
-at [this link](http://github.com/plumed/doc-${TRAVIS_BRANCH}/archive/gh-pages.zip).
+at [this link](http://github.com/${GIT_OWNER}/doc-${TRAVIS_BRANCH}/archive/gh-pages.zip).
EOF
@@ -99,6 +116,6 @@ set -x
esac
git add --all .
-git commit -m "Update to plumed/plumed2@$hash"
+git commit -m "Update to ${GIT_OWNER}/${GIT_REPO}@$hash"
# -q and 2> is not to show the GIT_TOKEN on Travis log
git push -q -f doc gh-pages 2> /dev/null
diff --git a/developer-doc/usingDoxygen.md b/developer-doc/usingDoxygen.md
index b5df9683204c730c4df5d143b6feaf2625b7fdee..0708548f1102a21fb3bb493e22009d67ea2e8e26 100644
--- a/developer-doc/usingDoxygen.md
+++ b/developer-doc/usingDoxygen.md
@@ -501,5 +501,21 @@ unofficial or unsupported branch (see .travis/pushdoc script).
Bottom line: when you make a commit where you modified the manual and you want the online manual to be updated,
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!
-
+and to revert the commit if there are errors!
+
+It is possible to generate PLUMED manuals for your own personal forks
+using a similar procedure as described above.
+For this to work you need to enable Travis CI for your forked repository
+and define appropriately the environment variables on Travis CI.
+The github account used to automatically push the generated manuals
+should be defined using the GIT_BOT variable,
+preferably this should be a dummy account. A github token
+enabling html access for that account should be defined using the GIT_TOKEN variable.
+Furthermore, you need to define an email address associated to the account using the GIT_BOT_EMAIL variable.
+It is better to make all these environment variable hidden such that they are
+not shown in the public logs on travis-ci.org.
+To generate a manual for a specific branch you need to create a repository
+USERNAME/doc-NAMEOFTHEBRANCH and give write access to the account given in
+GIT_BOT. The generated manuals will be accessible on
+https://USERNAME.github.io/doc-NAMEOFTHEBRANCH. Note that manuals generated in
+this way will always be labeled as unofficial and not shown in search engine results.
diff --git a/regtest/basic/rt-dimer-1/plumed.dat b/regtest/basic/rt-dimer-1/plumed.dat
index 10dce80499b695a07f7e3ea8f98bede1b866c878..da50311efcae7859d573180c60cd7eceb6810791 100644
--- a/regtest/basic/rt-dimer-1/plumed.dat
+++ b/regtest/basic/rt-dimer-1/plumed.dat
@@ -1,4 +1,7 @@
-dim: DIMER NATOMS=22 ATOMS=1,3,14,17 Q=0.5 TEMP=300 DSIGMA=0.002
+GROUP ATOMS=1,3,14,17 LABEL=d1g1
+GROUP ATOMS=23,25,36,39 LABEL=d1g2
+
+dim: DIMER ATOMS1=d1g1 ATOMS2=d1g2 Q=0.5 TEMP=300 DSIGMA=0.002
DUMPDERIVATIVES ARG=dim STRIDE=1 FILE=deriv FMT=%8.4f
PRINT ARG=dim FILE=colvar FMT=%8.4f
diff --git a/src/colvar/Dimer.cpp b/src/colvar/Dimer.cpp
index baead008e84b7b611fc71e5aed2f5cfa8f139417..378cf8c855c270a19019b6efa89894433d925288 100644
--- a/src/colvar/Dimer.cpp
+++ b/src/colvar/Dimer.cpp
@@ -96,21 +96,24 @@ the total number of atoms:
dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002 NOVSITES
\endplumedfile
-The NOVSITES flag is not required if one provides the atom serial of each Dimer. This is
-defined as the atom serial of the first bead of the dimer and is thus a number between 1 and N.
-Along with the ATOMS list also the number N of lines describing the first beads has to be given.
-For example, the Dimer interaction energy of dimers 1,5,7 is:
+The NOVSITES flag is not required if one provides the atom serials of each Dimer. These are
+defined through two atomlists provided __instead__ of the ALLATOMS keyword.
+For example, the Dimer interaction energy of dimers specified by beads (1;23),(5;27),(7;29) is:
\plumedfile
-dim: DIMER TEMP=300 Q=0.5 NATOMS=N ATOMS=1,5,7 DSIGMA=0.002
+dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002
\endplumedfile
+Note that the ATOMS1,ATOMS2 keywords can support atom groups and
+interval notation as defined in \ref GROUP.
+
+
In a Replica Exchange simulation the keyword DSIGMA can be used in two ways:
if a plumed.n.dat file is provided for each replica, then DSIGMA is passed as a single value,
like in the previous examples, and each replica will read its own DSIGMA value. If
a unique plumed.dat is given, DSIGMA has to be a list containing a value for each replica.
For 4 replicas:
\plumedfile
-dim: DIMER TEMP=300 Q=0.5 NATOMS=N ATOMS=1,5,7 DSIGMA=0.002,0.002,0.004,0.01
+dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002,0.002,0.004,0.01
\endplumedfile
@@ -136,12 +139,14 @@ public:
virtual void calculate();
protected:
bool trimer,useall;
- int myrank, nranks, natoms;
+ int myrank, nranks;
double qexp,temperature,beta,dsigma;
vector<double> dsigmas;
private:
void consistencyCheck();
- vector<int> usedatoms;
+ vector<AtomNumber> usedatoms1;
+ vector<AtomNumber> usedatoms2;
+
};
PLUMED_REGISTER_ACTION(Dimer, "DIMER")
@@ -154,8 +159,8 @@ void Dimer::registerKeywords( Keywords& keys) {
keys.add("compulsory","DSIGMA","The interaction strength of the dimer bond.");
keys.add("compulsory", "Q", "The exponent of the dimer potential.");
keys.add("compulsory", "TEMP", "The temperature (in Kelvin) of the simulation.");
- keys.add("atoms", "ATOMS", "The list of atoms being considered by this CV. Used if ALLATOMS flag is missing");
- keys.add("atoms","NATOMS","The number of dimerized atoms. Used in combination with ATOMS list");
+ keys.add("atoms", "ATOMS1", "The list of atoms representing the first bead of each Dimer being considered by this CV. Used if ALLATOMS flag is missing");
+ keys.add("atoms", "ATOMS2", "The list of atoms representing the second bead of each Dimer being considered by this CV. Used if ALLATOMS flag is missing");
keys.addFlag("ALLATOMS", false, "Use EVERY atom of the system. Overrides ATOMS keyword.");
keys.addFlag("NOVSITES", false, "If present the configuration is without virtual sites at the centroids.");
@@ -193,6 +198,7 @@ Dimer::Dimer(const ActionOptions& ao):
if(useall)
{
// go with every atom in the system but not the virtuals...
+ int natoms;
if(trimer)
natoms= 2*getTotAtoms()/3;
else
@@ -207,27 +213,23 @@ Dimer::Dimer(const ActionOptions& ao):
}
else // serials for the first beads of each dimer are given
{
- parseVector("ATOMS",usedatoms);
- double ntm;
- parse("NATOMS",ntm);
- natoms=ntm;
+ parseAtomList("ATOMS1",usedatoms1);
+ parseAtomList("ATOMS2",usedatoms2);
- int isz = usedatoms.size();
+ int isz1 = usedatoms1.size();
- for(unsigned int i=0; i<isz; i++)
+ for(unsigned int i=0; i<isz1; i++)
{
AtomNumber ati;
- ati.setIndex(usedatoms[i]-1);
+ ati.setIndex(usedatoms1[i].index());
atoms.push_back(ati);
-
}
- for(unsigned int i=0; i<isz; i++)
+ int isz2 = usedatoms2.size();
+ for(unsigned int i=0; i<isz2; i++)
{
AtomNumber atip2;
- atip2.setIndex(usedatoms[i]+natoms-1);
- if(usedatoms[i]>natoms)
- error("The Dimer CV requires that when choosing atoms you refere only to the first beads.");
+ atip2.setIndex(usedatoms2[i].index());
atoms.push_back(atip2);
}
@@ -237,11 +239,8 @@ Dimer::Dimer(const ActionOptions& ao):
beta = 1./(kBoltzmann*temperature);
addValueWithDerivatives(); // allocate
-
requestAtoms(atoms);
-
setNotPeriodic();
-
}
void Dimer::calculate()
@@ -302,13 +301,15 @@ These are checked here and PLUMED error handlers are (eventually) called.
******************/
void Dimer::consistencyCheck()
{
- if(useall==false && natoms==0)
- error("Either NATOMS or ATOMS are required to specify the number of dimerized atoms.");
+ if(!useall && usedatoms1.size()!=usedatoms2.size())
+ error("The provided atom lists are of different sizes.");
if(qexp<0.5 || qexp>1)
warning("Dimer CV is meant to be used with q-exponents between 0.5 and 1. We are not responsible for any black hole. :-)");
+
if(dsigma<0)
error("Please use positive sigma values for the Dimer strength constant");
+
if(temperature<0)
error("Please, use a positive value for the temperature...");