From 654802acafde6497904a2fdc417769a73f28e649 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Tue, 7 Jul 2015 14:27:44 +0100
Subject: [PATCH] Moved all adjacency matrix stuff to a separate module
---
.../{crystallization => adjmat}/rt-dfg1/Makefile | 0
.../rt-dfg1/colvar.reference | 0
.../{crystallization => adjmat}/rt-dfg1/conf.gro | 0
regtest/{crystallization => adjmat}/rt-dfg1/config | 0
.../{crystallization => adjmat}/rt-dfg1/config.xyz | 0
.../rt-dfg1/deriv.reference | 0
.../{crystallization => adjmat}/rt-dfg1/plumed.dat | 0
.../{crystallization => adjmat}/rt-dfg2/Makefile | 0
.../rt-dfg2/colvar.reference | 0
regtest/{crystallization => adjmat}/rt-dfg2/config | 0
.../{crystallization => adjmat}/rt-dfg2/plumed.dat | 0
.../{crystallization => adjmat}/rt-dfg2/traj.xyz | 0
regtest/{multicolvar => adjmat}/rt-sprint/Makefile | 0
.../rt-sprint/colvar.reference | 0
regtest/{multicolvar => adjmat}/rt-sprint/config | 0
.../rt-sprint/deriv.reference | 0
.../{multicolvar => adjmat}/rt-sprint/isomers.xyz | 0
.../{multicolvar => adjmat}/rt-sprint/plumed.dat | 0
src/.gitignore | 1 +
src/adjmat/.gitignore | 9 +++++++++
.../AdjacencyMatrixAction.cpp | 12 ++++++------
.../AdjacencyMatrixAction.h | 14 +++++++-------
.../AdjacencyMatrixVessel.cpp | 2 +-
.../AdjacencyMatrixVessel.h | 2 +-
src/{crystallization => adjmat}/DFSBasic.cpp | 2 +-
.../DFSClusterRadius.cpp | 2 +-
src/{crystallization => adjmat}/DFSClustering.cpp | 4 ++--
src/{crystallization => adjmat}/DFSClustering.h | 10 +++++-----
src/{crystallization => adjmat}/DFSMaxSize.cpp | 2 +-
.../DFSNumberOfClusters.cpp | 2 +-
src/adjmat/Makefile | 4 ++++
src/{multicolvar => adjmat}/Sprint.cpp | 2 +-
src/adjmat/module.type | 1 +
33 files changed, 42 insertions(+), 27 deletions(-)
rename regtest/{crystallization => adjmat}/rt-dfg1/Makefile (100%)
rename regtest/{crystallization => adjmat}/rt-dfg1/colvar.reference (100%)
rename regtest/{crystallization => adjmat}/rt-dfg1/conf.gro (100%)
rename regtest/{crystallization => adjmat}/rt-dfg1/config (100%)
rename regtest/{crystallization => adjmat}/rt-dfg1/config.xyz (100%)
rename regtest/{crystallization => adjmat}/rt-dfg1/deriv.reference (100%)
rename regtest/{crystallization => adjmat}/rt-dfg1/plumed.dat (100%)
rename regtest/{crystallization => adjmat}/rt-dfg2/Makefile (100%)
rename regtest/{crystallization => adjmat}/rt-dfg2/colvar.reference (100%)
rename regtest/{crystallization => adjmat}/rt-dfg2/config (100%)
rename regtest/{crystallization => adjmat}/rt-dfg2/plumed.dat (100%)
rename regtest/{crystallization => adjmat}/rt-dfg2/traj.xyz (100%)
rename regtest/{multicolvar => adjmat}/rt-sprint/Makefile (100%)
rename regtest/{multicolvar => adjmat}/rt-sprint/colvar.reference (100%)
rename regtest/{multicolvar => adjmat}/rt-sprint/config (100%)
rename regtest/{multicolvar => adjmat}/rt-sprint/deriv.reference (100%)
rename regtest/{multicolvar => adjmat}/rt-sprint/isomers.xyz (100%)
rename regtest/{multicolvar => adjmat}/rt-sprint/plumed.dat (100%)
create mode 100644 src/adjmat/.gitignore
rename src/{multicolvar => adjmat}/AdjacencyMatrixAction.cpp (95%)
rename src/{multicolvar => adjmat}/AdjacencyMatrixAction.h (89%)
rename src/{multicolvar => adjmat}/AdjacencyMatrixVessel.cpp (98%)
rename src/{multicolvar => adjmat}/AdjacencyMatrixVessel.h (98%)
rename src/{crystallization => adjmat}/DFSBasic.cpp (99%)
rename src/{crystallization => adjmat}/DFSClusterRadius.cpp (99%)
rename src/{crystallization => adjmat}/DFSClustering.cpp (98%)
rename src/{crystallization => adjmat}/DFSClustering.h (91%)
rename src/{crystallization => adjmat}/DFSMaxSize.cpp (99%)
rename src/{crystallization => adjmat}/DFSNumberOfClusters.cpp (99%)
create mode 100644 src/adjmat/Makefile
rename src/{multicolvar => adjmat}/Sprint.cpp (99%)
create mode 100644 src/adjmat/module.type
diff --git a/regtest/crystallization/rt-dfg1/Makefile b/regtest/adjmat/rt-dfg1/Makefile
similarity index 100%
rename from regtest/crystallization/rt-dfg1/Makefile
rename to regtest/adjmat/rt-dfg1/Makefile
diff --git a/regtest/crystallization/rt-dfg1/colvar.reference b/regtest/adjmat/rt-dfg1/colvar.reference
similarity index 100%
rename from regtest/crystallization/rt-dfg1/colvar.reference
rename to regtest/adjmat/rt-dfg1/colvar.reference
diff --git a/regtest/crystallization/rt-dfg1/conf.gro b/regtest/adjmat/rt-dfg1/conf.gro
similarity index 100%
rename from regtest/crystallization/rt-dfg1/conf.gro
rename to regtest/adjmat/rt-dfg1/conf.gro
diff --git a/regtest/crystallization/rt-dfg1/config b/regtest/adjmat/rt-dfg1/config
similarity index 100%
rename from regtest/crystallization/rt-dfg1/config
rename to regtest/adjmat/rt-dfg1/config
diff --git a/regtest/crystallization/rt-dfg1/config.xyz b/regtest/adjmat/rt-dfg1/config.xyz
similarity index 100%
rename from regtest/crystallization/rt-dfg1/config.xyz
rename to regtest/adjmat/rt-dfg1/config.xyz
diff --git a/regtest/crystallization/rt-dfg1/deriv.reference b/regtest/adjmat/rt-dfg1/deriv.reference
similarity index 100%
rename from regtest/crystallization/rt-dfg1/deriv.reference
rename to regtest/adjmat/rt-dfg1/deriv.reference
diff --git a/regtest/crystallization/rt-dfg1/plumed.dat b/regtest/adjmat/rt-dfg1/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-dfg1/plumed.dat
rename to regtest/adjmat/rt-dfg1/plumed.dat
diff --git a/regtest/crystallization/rt-dfg2/Makefile b/regtest/adjmat/rt-dfg2/Makefile
similarity index 100%
rename from regtest/crystallization/rt-dfg2/Makefile
rename to regtest/adjmat/rt-dfg2/Makefile
diff --git a/regtest/crystallization/rt-dfg2/colvar.reference b/regtest/adjmat/rt-dfg2/colvar.reference
similarity index 100%
rename from regtest/crystallization/rt-dfg2/colvar.reference
rename to regtest/adjmat/rt-dfg2/colvar.reference
diff --git a/regtest/crystallization/rt-dfg2/config b/regtest/adjmat/rt-dfg2/config
similarity index 100%
rename from regtest/crystallization/rt-dfg2/config
rename to regtest/adjmat/rt-dfg2/config
diff --git a/regtest/crystallization/rt-dfg2/plumed.dat b/regtest/adjmat/rt-dfg2/plumed.dat
similarity index 100%
rename from regtest/crystallization/rt-dfg2/plumed.dat
rename to regtest/adjmat/rt-dfg2/plumed.dat
diff --git a/regtest/crystallization/rt-dfg2/traj.xyz b/regtest/adjmat/rt-dfg2/traj.xyz
similarity index 100%
rename from regtest/crystallization/rt-dfg2/traj.xyz
rename to regtest/adjmat/rt-dfg2/traj.xyz
diff --git a/regtest/multicolvar/rt-sprint/Makefile b/regtest/adjmat/rt-sprint/Makefile
similarity index 100%
rename from regtest/multicolvar/rt-sprint/Makefile
rename to regtest/adjmat/rt-sprint/Makefile
diff --git a/regtest/multicolvar/rt-sprint/colvar.reference b/regtest/adjmat/rt-sprint/colvar.reference
similarity index 100%
rename from regtest/multicolvar/rt-sprint/colvar.reference
rename to regtest/adjmat/rt-sprint/colvar.reference
diff --git a/regtest/multicolvar/rt-sprint/config b/regtest/adjmat/rt-sprint/config
similarity index 100%
rename from regtest/multicolvar/rt-sprint/config
rename to regtest/adjmat/rt-sprint/config
diff --git a/regtest/multicolvar/rt-sprint/deriv.reference b/regtest/adjmat/rt-sprint/deriv.reference
similarity index 100%
rename from regtest/multicolvar/rt-sprint/deriv.reference
rename to regtest/adjmat/rt-sprint/deriv.reference
diff --git a/regtest/multicolvar/rt-sprint/isomers.xyz b/regtest/adjmat/rt-sprint/isomers.xyz
similarity index 100%
rename from regtest/multicolvar/rt-sprint/isomers.xyz
rename to regtest/adjmat/rt-sprint/isomers.xyz
diff --git a/regtest/multicolvar/rt-sprint/plumed.dat b/regtest/adjmat/rt-sprint/plumed.dat
similarity index 100%
rename from regtest/multicolvar/rt-sprint/plumed.dat
rename to regtest/adjmat/rt-sprint/plumed.dat
diff --git a/src/.gitignore b/src/.gitignore
index 838ba6a71..be04342c3 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -3,6 +3,7 @@
# Only track modules that are part of the plumed core
!/Makefile
!/README
+!/adjmat
!/analysis
!/bias
!/blas
diff --git a/src/adjmat/.gitignore b/src/adjmat/.gitignore
new file mode 100644
index 000000000..488855233
--- /dev/null
+++ b/src/adjmat/.gitignore
@@ -0,0 +1,9 @@
+/*
+# in this directory, only accept source, Makefile and README
+!/.gitignore
+!/*.c
+!/*.cpp
+!/*.h
+!/Makefile
+!/README
+!/module.type
diff --git a/src/multicolvar/AdjacencyMatrixAction.cpp b/src/adjmat/AdjacencyMatrixAction.cpp
similarity index 95%
rename from src/multicolvar/AdjacencyMatrixAction.cpp
rename to src/adjmat/AdjacencyMatrixAction.cpp
index b409cbc07..9a017c01f 100644
--- a/src/multicolvar/AdjacencyMatrixAction.cpp
+++ b/src/adjmat/AdjacencyMatrixAction.cpp
@@ -22,10 +22,10 @@
#include "AdjacencyMatrixAction.h"
namespace PLMD {
-namespace multicolvar {
+namespace adjmat {
void AdjacencyMatrixAction::registerKeywords( Keywords& keys ){
- MultiColvarFunction::registerKeywords( keys );
+ multicolvar::MultiColvarFunction::registerKeywords( keys );
keys.reserveFlag("USE_ORIENTATION",false,"When computing whether two atoms/molecules are adjacent also take their orientations into account");
keys.add("numbered","SWITCH","This keyword is used if you want to employ an alternative to the continuous swiching function defined above. "
"The following provides information on the \\ref switchingfunction that are available. "
@@ -117,13 +117,13 @@ void AdjacencyMatrixAction::doJobsRequiredBeforeTaskList(){
else dertime=true;
}
-void AdjacencyMatrixAction::calculateWeight( AtomValuePack& myatoms ) const {
+void AdjacencyMatrixAction::calculateWeight( multicolvar::AtomValuePack& myatoms ) const {
Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
double dfunc, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ),getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( distance.modulo(), dfunc );
myatoms.setValue(0,sw);
}
-double AdjacencyMatrixAction::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
+double AdjacencyMatrixAction::compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const {
// active_elements.activate( tindex );
double f_dot, dot_df;
@@ -148,9 +148,9 @@ double AdjacencyMatrixAction::compute( const unsigned& tindex, AtomValuePack& my
// Add contribution due to separation between atoms
Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
double dfunc, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(0) ) ).calculate( distance.modulo(), dfunc );
- CatomPack atom0=getCentralAtomPackFromInput( myatoms.getIndex(0) );
+ multicolvar::CatomPack atom0=getCentralAtomPackFromInput( myatoms.getIndex(0) );
myatoms.addComDerivatives( 1, (-dfunc)*f_dot*distance, atom0 );
- CatomPack atom1=getCentralAtomPackFromInput( myatoms.getIndex(1) );
+ multicolvar::CatomPack atom1=getCentralAtomPackFromInput( myatoms.getIndex(1) );
myatoms.addComDerivatives( 1, (dfunc)*f_dot*distance, atom1 );
myatoms.addBoxDerivatives( 1, (-dfunc)*f_dot*Tensor(distance,distance) );
diff --git a/src/multicolvar/AdjacencyMatrixAction.h b/src/adjmat/AdjacencyMatrixAction.h
similarity index 89%
rename from src/multicolvar/AdjacencyMatrixAction.h
rename to src/adjmat/AdjacencyMatrixAction.h
index 6cf1b667d..0b92ba656 100644
--- a/src/multicolvar/AdjacencyMatrixAction.h
+++ b/src/adjmat/AdjacencyMatrixAction.h
@@ -19,18 +19,18 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_multicolvar_AdjacencyMatrixAction_h
-#define __PLUMED_multicolvar_AdjacencyMatrixAction_h
+#ifndef __PLUMED_adjmat_AdjacencyMatrixAction_h
+#define __PLUMED_adjmat_AdjacencyMatrixAction_h
-#include "MultiColvarFunction.h"
+#include "multicolvar/MultiColvarFunction.h"
#include "tools/SwitchingFunction.h"
#include "tools/Matrix.h"
#include "AdjacencyMatrixVessel.h"
namespace PLMD {
-namespace multicolvar {
+namespace adjmat {
-class AdjacencyMatrixAction : public MultiColvarFunction {
+class AdjacencyMatrixAction : public multicolvar::MultiColvarFunction {
friend class AdjacencyMatrixVessel;
private:
/// Are we including the orientation in our measure of adjacency
@@ -64,8 +64,8 @@ protected:
public:
static void registerKeywords( Keywords& keys );
explicit AdjacencyMatrixAction(const ActionOptions&);
- double compute( const unsigned& tindex, AtomValuePack& myatoms ) const ;
- void calculateWeight( AtomValuePack& myatoms ) const ;
+ double compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const ;
+ void calculateWeight( multicolvar::AtomValuePack& myatoms ) const ;
void doJobsRequiredBeforeTaskList();
/// Finish the calculation
virtual void completeCalculation()=0;
diff --git a/src/multicolvar/AdjacencyMatrixVessel.cpp b/src/adjmat/AdjacencyMatrixVessel.cpp
similarity index 98%
rename from src/multicolvar/AdjacencyMatrixVessel.cpp
rename to src/adjmat/AdjacencyMatrixVessel.cpp
index 56d0938e7..92bbd4a25 100644
--- a/src/multicolvar/AdjacencyMatrixVessel.cpp
+++ b/src/adjmat/AdjacencyMatrixVessel.cpp
@@ -24,7 +24,7 @@
#include "AdjacencyMatrixAction.h"
namespace PLMD {
-namespace multicolvar {
+namespace adjmat {
void AdjacencyMatrixVessel::registerKeywords( Keywords& keys ){
StoreDataVessel::registerKeywords(keys);
diff --git a/src/multicolvar/AdjacencyMatrixVessel.h b/src/adjmat/AdjacencyMatrixVessel.h
similarity index 98%
rename from src/multicolvar/AdjacencyMatrixVessel.h
rename to src/adjmat/AdjacencyMatrixVessel.h
index 373d390d8..dc35a7cf1 100644
--- a/src/multicolvar/AdjacencyMatrixVessel.h
+++ b/src/adjmat/AdjacencyMatrixVessel.h
@@ -25,7 +25,7 @@
#include "vesselbase/StoreDataVessel.h"
namespace PLMD {
-namespace multicolvar {
+namespace adjmat {
class AdjacencyMatrixAction;
diff --git a/src/crystallization/DFSBasic.cpp b/src/adjmat/DFSBasic.cpp
similarity index 99%
rename from src/crystallization/DFSBasic.cpp
rename to src/adjmat/DFSBasic.cpp
index 58f9d053b..f5d062be7 100644
--- a/src/crystallization/DFSBasic.cpp
+++ b/src/adjmat/DFSBasic.cpp
@@ -125,7 +125,7 @@ clust: DFSCLUSTERING DATA=cf WTOL=0.03 CLUSTER=1 SWITCH={CUBIC D_0=0.4 D_MAX=0
//+ENDPLUMEDOC
namespace PLMD {
-namespace crystallization {
+namespace adjmat {
class DFSBasic : public DFSClustering {
private:
diff --git a/src/crystallization/DFSClusterRadius.cpp b/src/adjmat/DFSClusterRadius.cpp
similarity index 99%
rename from src/crystallization/DFSClusterRadius.cpp
rename to src/adjmat/DFSClusterRadius.cpp
index d72bf626a..64d95feb5 100644
--- a/src/crystallization/DFSClusterRadius.cpp
+++ b/src/adjmat/DFSClusterRadius.cpp
@@ -38,7 +38,7 @@ done by this action.
//+ENDPLUMEDOC
namespace PLMD {
-namespace crystallization {
+namespace adjmat {
class DFSClusterDiameter : public DFSClustering {
private:
diff --git a/src/crystallization/DFSClustering.cpp b/src/adjmat/DFSClustering.cpp
similarity index 98%
rename from src/crystallization/DFSClustering.cpp
rename to src/adjmat/DFSClustering.cpp
index 295ed4e9e..b5aad90a8 100644
--- a/src/crystallization/DFSClustering.cpp
+++ b/src/adjmat/DFSClustering.cpp
@@ -23,10 +23,10 @@
namespace PLMD {
-namespace crystallization {
+namespace adjmat {
void DFSClustering::registerKeywords( Keywords& keys ){
- multicolvar::AdjacencyMatrixAction::registerKeywords( keys );
+ AdjacencyMatrixAction::registerKeywords( keys );
}
DFSClustering::DFSClustering(const ActionOptions&ao):
diff --git a/src/crystallization/DFSClustering.h b/src/adjmat/DFSClustering.h
similarity index 91%
rename from src/crystallization/DFSClustering.h
rename to src/adjmat/DFSClustering.h
index 3ad613abe..9d28d26c8 100644
--- a/src/crystallization/DFSClustering.h
+++ b/src/adjmat/DFSClustering.h
@@ -19,15 +19,15 @@
You should have received a copy of the GNU Lesser General Public License
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
-#ifndef __PLUMED_crystallization_DFSClustering_h
-#define __PLUMED_crystallization_DFSClustering_h
+#ifndef __PLUMED_adjmat_DFSClustering_h
+#define __PLUMED_adjmat_DFSClustering_h
-#include "multicolvar/AdjacencyMatrixAction.h"
+#include "AdjacencyMatrixAction.h"
namespace PLMD {
-namespace crystallization {
+namespace adjmat {
-class DFSClustering : public multicolvar::AdjacencyMatrixAction {
+class DFSClustering : public AdjacencyMatrixAction {
private:
/// Used to identify the cluster we are working on
int number_of_cluster;
diff --git a/src/crystallization/DFSMaxSize.cpp b/src/adjmat/DFSMaxSize.cpp
similarity index 99%
rename from src/crystallization/DFSMaxSize.cpp
rename to src/adjmat/DFSMaxSize.cpp
index 93e59f1d3..5843d5f09 100644
--- a/src/crystallization/DFSMaxSize.cpp
+++ b/src/adjmat/DFSMaxSize.cpp
@@ -65,7 +65,7 @@ clust: DFSMAXCLUSTER DATA=cf BETA=0.5 SWITCH={CUBIC D_0=0.4 D_MAX=0.5} TRANSFO
//+ENDPLUMEDOC
namespace PLMD {
-namespace crystallization {
+namespace adjmat {
class DFSMaxCluster : public DFSClustering {
private:
diff --git a/src/crystallization/DFSNumberOfClusters.cpp b/src/adjmat/DFSNumberOfClusters.cpp
similarity index 99%
rename from src/crystallization/DFSNumberOfClusters.cpp
rename to src/adjmat/DFSNumberOfClusters.cpp
index 6db6912e0..3c592611c 100644
--- a/src/crystallization/DFSNumberOfClusters.cpp
+++ b/src/adjmat/DFSNumberOfClusters.cpp
@@ -32,7 +32,7 @@ Find the number of clusters that have a size larger than a certain cutoff
//+ENDPLUMEDOC
namespace PLMD {
-namespace crystallization {
+namespace adjmat {
class DFSNumberOfClusters : public DFSClustering {
private:
diff --git a/src/adjmat/Makefile b/src/adjmat/Makefile
new file mode 100644
index 000000000..f68246671
--- /dev/null
+++ b/src/adjmat/Makefile
@@ -0,0 +1,4 @@
+USE=core tools vesselbase multicolvar
+
+# generic makefile
+include ../maketools/make.module
diff --git a/src/multicolvar/Sprint.cpp b/src/adjmat/Sprint.cpp
similarity index 99%
rename from src/multicolvar/Sprint.cpp
rename to src/adjmat/Sprint.cpp
index f4ceaab18..e3f827799 100644
--- a/src/multicolvar/Sprint.cpp
+++ b/src/adjmat/Sprint.cpp
@@ -74,7 +74,7 @@ PRINT ARG=ss.* FILE=colvar
namespace PLMD {
-namespace multicolvar {
+namespace adjmat {
class Sprint : public AdjacencyMatrixAction {
private:
diff --git a/src/adjmat/module.type b/src/adjmat/module.type
new file mode 100644
index 000000000..de8327303
--- /dev/null
+++ b/src/adjmat/module.type
@@ -0,0 +1 @@
+default-off
--
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