From d1d97b788aa110f517e4fef305205f0500abfcd3 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Sun, 6 Dec 2015 16:01:56 +0000
Subject: [PATCH] Fixed cluster diameter business and added test
---
regtest/adjmat/rt-dfg2/plumed.dat | 3 ++-
regtest/adjmat/rt-dfg2/size.reference | 4 ++--
src/adjmat/ClusterAnalysisBase.cpp | 6 ------
src/adjmat/ClusterDiameter.cpp | 20 ++++----------------
src/adjmat/ClusterDistribution.cpp | 7 +++++--
src/adjmat/ClusterProperties.cpp | 7 +++++--
src/adjmat/ClusterSize.cpp | 5 ++++-
7 files changed, 22 insertions(+), 30 deletions(-)
diff --git a/regtest/adjmat/rt-dfg2/plumed.dat b/regtest/adjmat/rt-dfg2/plumed.dat
index 7ec486832..8cc97a833 100644
--- a/regtest/adjmat/rt-dfg2/plumed.dat
+++ b/regtest/adjmat/rt-dfg2/plumed.dat
@@ -12,6 +12,7 @@ OUTPUT_CLUSTER CLUSTERS=dfs CLUSTER=1 FILE=dfs.dat
clust2a: CLUSTER_WITHSURFACE CLUSTERS=dfs RCUT_SURF=0.3
size2a: CLUSTER_NATOMS CLUSTERS=clust2a CLUSTER=2
+dia2a: CLUSTER_DIAMETER CLUSTERS=clust2a CLUSTER=2
OUTPUT_CLUSTER CLUSTERS=clust2a CLUSTER=2 FILE=dfs2.dat
-PRINT ARG=size2a FILE=size
+PRINT ARG=size2a,dia2a FILE=size FMT=%8.4f
diff --git a/regtest/adjmat/rt-dfg2/size.reference b/regtest/adjmat/rt-dfg2/size.reference
index 180f9d2e4..0ed52ef58 100644
--- a/regtest/adjmat/rt-dfg2/size.reference
+++ b/regtest/adjmat/rt-dfg2/size.reference
@@ -1,2 +1,2 @@
-#! FIELDS time size2a
- 0.000000 78.000000
+#! FIELDS time size2a dia2a
+ 0.000000 78.0000 2.3294
diff --git a/src/adjmat/ClusterAnalysisBase.cpp b/src/adjmat/ClusterAnalysisBase.cpp
index e92367e92..1b92aca9d 100644
--- a/src/adjmat/ClusterAnalysisBase.cpp
+++ b/src/adjmat/ClusterAnalysisBase.cpp
@@ -41,12 +41,6 @@ myclusters(NULL)
if(!found_cluster) error("unable to interpret input clusters " + matname[0] );
myclusters = dynamic_cast<ClusteringBase*>( mybasemulticolvars[0] );
if( !myclusters ) error("input label is not that of a DFS object");
-
- // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)
- for(unsigned i=0;i<myclusters->getNumberOfNodes();++i) addTaskToList(i);
-
- // And now finish the setup of everything in the base
- setupAtomLists();
}
void ClusterAnalysisBase::turnOnDerivatives(){
diff --git a/src/adjmat/ClusterDiameter.cpp b/src/adjmat/ClusterDiameter.cpp
index f250e0afb..af37292ec 100644
--- a/src/adjmat/ClusterDiameter.cpp
+++ b/src/adjmat/ClusterDiameter.cpp
@@ -72,7 +72,7 @@ ClusterAnalysisBase(ao)
for(unsigned j=0;j<i;++j) addTaskToList( i*getNumberOfNodes() + j );
}
// Now create a higest vessel
- addVessel("HIGHEST", "", -1); readVesselKeywords();
+ addVessel("HIGHEST", "", -1); setupAtomLists();
}
void ClusterDiameter::turnOnDerivatives(){
@@ -93,22 +93,10 @@ void ClusterDiameter::calculate(){
}
void ClusterDiameter::performTask( const unsigned& task_index, const unsigned& current, MultiValue& myvals ) const {
- unsigned iatom=current/getNumberOfNodes(), jatom = current - iatom*getNumberOfNodes();
+ unsigned iatom=std::floor(current/getNumberOfNodes()), jatom = current - iatom*getNumberOfNodes();
Vector distance=getSeparation( getPosition(iatom), getPosition(jatom) );
- double dd = distance.modulo(), inv = 1.0/dd ; myvals.setValue( 1, dd );
- if( !doNotCalculateDerivatives() ){
- myvals.addDerivative( 1, 3*iatom + 0, -inv*distance[0] );
- myvals.addDerivative( 1, 3*iatom + 1, -inv*distance[1] );
- myvals.addDerivative( 1, 3*iatom + 2, -inv*distance[2] );
- myvals.addDerivative( 1, 3*jatom + 0, +inv*distance[0] );
- myvals.addDerivative( 1, 3*jatom + 1, +inv*distance[1] );
- myvals.addDerivative( 1, 3*jatom + 2, +inv*distance[2] );
- Tensor vir = -inv*Tensor(distance,distance);
- unsigned vbase = myvals.getNumberOfDerivatives() - 9;
- for(unsigned i=0;i<3;++i){
- for(unsigned j=0;j<3;++j) myvals.addDerivative( 1, vbase+3*i+j, vir(i,j) );
- }
- }
+ double dd = distance.modulo(), inv = 1.0/dd ;
+ myvals.setValue( 0, 1.0 ); myvals.setValue( 1, dd );
}
}
diff --git a/src/adjmat/ClusterDistribution.cpp b/src/adjmat/ClusterDistribution.cpp
index 14810ede9..38f487095 100644
--- a/src/adjmat/ClusterDistribution.cpp
+++ b/src/adjmat/ClusterDistribution.cpp
@@ -78,8 +78,11 @@ nderivatives(0)
parseFlag("INVERSE_TRANSFORM",inverse);
if( inverse && !use_switch ) error("INVERSE_TRANSFORM option was specified but no TRANSOFRM switching function was given");
- // Setup the various things this will calculate
- readVesselKeywords();
+ // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)
+ for(unsigned i=0;i<getNumberOfNodes();++i) addTaskToList(i);
+
+ // And now finish the setup of everything in the base
+ setupAtomLists();
}
void ClusterDistribution::calculate(){
diff --git a/src/adjmat/ClusterProperties.cpp b/src/adjmat/ClusterProperties.cpp
index c7a7f7c5c..5e8a889bb 100644
--- a/src/adjmat/ClusterProperties.cpp
+++ b/src/adjmat/ClusterProperties.cpp
@@ -165,8 +165,11 @@ ClusterAnalysisBase(ao)
if( clustr<1 ) error("cannot look for a cluster larger than the largest cluster");
if( clustr>getNumberOfNodes() ) error("cluster selected is invalid - too few atoms in system");
- // Setup the various things this will calculate
- readVesselKeywords();
+ // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)
+ for(unsigned i=0;i<getNumberOfNodes();++i) addTaskToList(i);
+
+ // And now finish the setup of everything in the base
+ setupAtomLists();
}
void ClusterProperties::calculate(){
diff --git a/src/adjmat/ClusterSize.cpp b/src/adjmat/ClusterSize.cpp
index 5ae3eb1f4..a636dce71 100644
--- a/src/adjmat/ClusterSize.cpp
+++ b/src/adjmat/ClusterSize.cpp
@@ -68,7 +68,10 @@ ClusterAnalysisBase(ao)
if( clustr<1 ) error("cannot look for a cluster larger than the largest cluster");
if( clustr>getNumberOfNodes() ) error("cluster selected is invalid - too few atoms in system");
- addValue(); setNotPeriodic();
+ // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)
+ for(unsigned i=0;i<getNumberOfNodes();++i) addTaskToList(i);
+ // And now finish the setup of everything in the base
+ setupAtomLists(); addValue(); setNotPeriodic();
}
void ClusterSize::turnOnDerivatives(){
--
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