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Fixed a bug that appears when you try to sum all the elements in a ma…
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…trix
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Gareth Aneurin Tribello authored and Gareth Aneurin Tribello committed Apr 12, 2024
1 parent e7e3445 commit 9b64405
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1 change: 1 addition & 0 deletions regtest/adjmat/rt-matrixsum/Makefile
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include ../../scripts/test.make
18 changes: 18 additions & 0 deletions regtest/adjmat/rt-matrixsum/colvar.reference
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#! FIELDS time s
0.000000 0.1870
1.000000 0.1453
2.000000 0.5477
3.000000 -0.6148
4.000000 -0.7783
5.000000 -4.3542
6.000000 2.8148
7.000000 0.1168
8.000000 2.1041
9.000000 1.6821
10.000000 -2.4892
11.000000 -1.7454
12.000000 4.1613
13.000000 4.8999
14.000000 4.9588
15.000000 0.0031
16.000000 0.5671
5 changes: 5 additions & 0 deletions regtest/adjmat/rt-matrixsum/config
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type=driver
plumed_modules=adjmat
# this is to test a different name
arg="--plumed plumed.dat --ixyz isomers.xyz --dump-forces forces --dump-forces-fmt=%8.4f" # --debug-forces forces.num"
extra_files="../../trajectories/isomers.xyz"
272 changes: 272 additions & 0 deletions regtest/adjmat/rt-matrixsum/forces.reference
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14
0.0551 0.1000 0.0318
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X -1.0000 -1.0000 -1.0000
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0.0891 0.0179 0.0383
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1.2470 1.6980 -0.8409
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1.2582 1.0255 -0.6016
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6 changes: 6 additions & 0 deletions regtest/adjmat/rt-matrixsum/plumed.dat
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d1: DISTANCE COMPONENTS ATOMS1=1,2 ATOMS2=3,4 ATOMS3=5,6
v: VSTACK ARG=d1.x,d1.y,d1.z
vT: TRANSPOSE ARG=v
s: SUM ARG=vT PERIODIC=NO
PRINT ARG=s FILE=colvar FMT=%8.4f
BIASVALUE ARG=s
4 changes: 2 additions & 2 deletions regtest/symfunc/rt-smac/forces.reference
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Expand Up @@ -167398,8 +167398,8 @@ X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X -0.0028 -0.0064 -0.0065
X -0.0006 0.0000 0.0054
X -0.0028 0.0150 -0.0065
X -0.0006 -0.0214 0.0054
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
X 0.0000 0.0000 0.0000
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5 changes: 2 additions & 3 deletions src/adjmat/ActionWithMatrix.cpp
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Expand Up @@ -20,7 +20,6 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "ActionWithMatrix.h"
#include "AdjacencyMatrixBase.h"

namespace PLMD {
namespace adjmat {
Expand Down Expand Up @@ -72,7 +71,7 @@ void ActionWithMatrix::finishChainBuild( ActionWithVector* act ) {
else {
next_action_in_chain=am;
// Build the list of things we are going to loop over in runTask
AdjacencyMatrixBase* aa=dynamic_cast<AdjacencyMatrixBase*>(act); if( aa || act->getName()=="VSTACK" ) return ;
if( am->isAdjacencyMatrix() || act->getName()=="VSTACK" ) return ;
plumed_massert( !matrix_to_do_after, "cannot add " + act->getLabel() + " in " + getLabel() + " as have already added " + matrix_to_do_after->getLabel() );
matrix_to_do_after=am; am->matrix_to_do_before=this;
}
Expand Down Expand Up @@ -134,7 +133,7 @@ void ActionWithMatrix::performTask( const unsigned& task_index, MultiValue& myva
void ActionWithMatrix::runTask( const std::string& controller, const unsigned& current, const unsigned colno, MultiValue& myvals ) const {
double outval=0; myvals.setTaskIndex(current); myvals.setSecondTaskIndex( colno );
if( isActive() ) performTask( controller, current, colno, myvals );
bool hasval=false;
bool hasval = !isAdjacencyMatrix();
for(int i=0; i<getNumberOfComponents(); ++i) {
if( fabs(myvals.get( getConstPntrToComponent(i)->getPositionInStream()) )>0 ) { hasval=true; break; }
}
Expand Down
2 changes: 2 additions & 0 deletions src/adjmat/ActionWithMatrix.h
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Expand Up @@ -59,6 +59,8 @@ class ActionWithMatrix : public ActionWithVector {
static void registerKeywords( Keywords& keys );
explicit ActionWithMatrix(const ActionOptions&);
virtual ~ActionWithMatrix();
///
virtual bool isAdjacencyMatrix() const { return false; }
///
void getAllActionLabelsInMatrixChain( std::vector<std::string>& mylabels ) const override ;
/// Get the first matrix in this chain
Expand Down
1 change: 1 addition & 0 deletions src/adjmat/AdjacencyMatrixBase.h
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Expand Up @@ -49,6 +49,7 @@ class AdjacencyMatrixBase : public ActionWithMatrix {
public:
static void registerKeywords( Keywords& keys );
explicit AdjacencyMatrixBase(const ActionOptions&);
bool isAdjacencyMatrix() const override { return true; }
unsigned getNumberOfDerivatives() override ;
unsigned getNumberOfColumns() const override;
void prepare() override;
Expand Down
8 changes: 6 additions & 2 deletions src/adjmat/FunctionOfMatrix.h
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Expand Up @@ -324,12 +324,16 @@ void FunctionOfMatrix<T>::performTask( const std::string& controller, const unsi
}
} else {
unsigned base=0; ind2 = index2;
if( index2>=getConstPntrToComponent(0)->getShape()[0] ) ind2 = index2 - getConstPntrToComponent(0)->getShape()[0];
for(unsigned j=argstart; j<getNumberOfArguments(); ++j) {
if( getPntrToArgument(j)->getRank()!=2 ) continue ;
if( index2>=getPntrToArgument(j)->getShape()[0] ) ind2 = index2 - getPntrToArgument(j)->getShape()[0];
break;
}
for(unsigned j=argstart; j<getNumberOfArguments(); ++j) {
if( getPntrToArgument(j)->getRank()==2 ) {
for(int i=0; i<getNumberOfComponents(); ++i) {
unsigned ostrn=getConstPntrToComponent(i)->getPositionInStream();
unsigned myind = base + getConstPntrToComponent(i)->getShape()[1]*index1 + ind2;
unsigned myind = base + getPntrToArgument(j)->getShape()[1]*index1 + ind2;
myvals.addDerivative( ostrn, myind, derivatives(i,j) );
myvals.updateIndex( ostrn, myind );
}
Expand Down
5 changes: 2 additions & 3 deletions src/adjmat/MatrixTimesMatrix.cpp
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Expand Up @@ -20,7 +20,6 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "ActionWithMatrix.h"
#include "AdjacencyMatrixBase.h"
#include "core/ActionRegister.h"

//+PLUMEDOC MCOLVAR MATRIX_PRODUCT
Expand Down Expand Up @@ -101,8 +100,8 @@ void MatrixTimesMatrix::prepare() {

void MatrixTimesMatrix::getAdditionalTasksRequired( ActionWithVector* action, std::vector<unsigned>& atasks ) {

AdjacencyMatrixBase* adj=dynamic_cast<AdjacencyMatrixBase*>( getPntrToArgument(0)->getPntrToAction() );
if( !adj ) return;
ActionWithMatrix* adj=dynamic_cast<ActionWithMatrix*>( getPntrToArgument(0)->getPntrToAction() );
if( !adj->isAdjacencyMatrix() ) return;
adj->retrieveAtoms(); adj->getAdditionalTasksRequired( action, atasks );
}

Expand Down
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2 comments on commit 9b64405

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Found broken examples in automatic/ANGLES.tmp
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/CAVITY.tmp
Found broken examples in automatic/CLASSICAL_MDS.tmp
Found broken examples in automatic/CLUSTER_DIAMETER.tmp
Found broken examples in automatic/CLUSTER_DISTRIBUTION.tmp
Found broken examples in automatic/CLUSTER_PROPERTIES.tmp
Found broken examples in automatic/CONSTANT.tmp
Found broken examples in automatic/CONTACT_MATRIX.tmp
Found broken examples in automatic/CONTACT_MATRIX_PROPER.tmp
Found broken examples in automatic/COORDINATIONNUMBER.tmp
Found broken examples in automatic/DFSCLUSTERING.tmp
Found broken examples in automatic/DISTANCE_FROM_CONTOUR.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FIND_CONTOUR.tmp
Found broken examples in automatic/FIND_CONTOUR_SURFACE.tmp
Found broken examples in automatic/FIND_SPHERICAL_CONTOUR.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
Found broken examples in automatic/FUNCPATHMSD.tmp
Found broken examples in automatic/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GHBFIX.tmp
Found broken examples in automatic/GPROPERTYMAP.tmp
Found broken examples in automatic/HBOND_MATRIX.tmp
Found broken examples in automatic/INCLUDE.tmp
Found broken examples in automatic/INCYLINDER.tmp
Found broken examples in automatic/INENVELOPE.tmp
Found broken examples in automatic/INTERPOLATE_GRID.tmp
Found broken examples in automatic/LOCAL_AVERAGE.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/MULTICOLVARDENS.tmp
Found broken examples in automatic/OUTPUT_CLUSTER.tmp
Found broken examples in automatic/PAMM.tmp
Found broken examples in automatic/PCA.tmp
Found broken examples in automatic/PCAVARS.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PLUMED.tmp
Found broken examples in automatic/PYCVINTERFACE.tmp
Found broken examples in automatic/PYTHONFUNCTION.tmp
Found broken examples in automatic/Q3.tmp
Found broken examples in automatic/Q4.tmp
Found broken examples in automatic/Q6.tmp
Found broken examples in automatic/QUATERNION.tmp
Found broken examples in automatic/SPRINT.tmp
Found broken examples in automatic/TETRAHEDRALPORE.tmp
Found broken examples in automatic/TORSIONS.tmp
Found broken examples in automatic/WHAM_WEIGHTS.tmp
Found broken examples in AnalysisPP.md
Found broken examples in CollectiveVariablesPP.md
Found broken examples in MiscelaneousPP.md

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Found broken examples in automatic/ANGLES.tmp
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/CAVITY.tmp
Found broken examples in automatic/CLASSICAL_MDS.tmp
Found broken examples in automatic/CLUSTER_DIAMETER.tmp
Found broken examples in automatic/CLUSTER_DISTRIBUTION.tmp
Found broken examples in automatic/CLUSTER_PROPERTIES.tmp
Found broken examples in automatic/CONSTANT.tmp
Found broken examples in automatic/CONTACT_MATRIX.tmp
Found broken examples in automatic/CONTACT_MATRIX_PROPER.tmp
Found broken examples in automatic/COORDINATIONNUMBER.tmp
Found broken examples in automatic/DFSCLUSTERING.tmp
Found broken examples in automatic/DISTANCE_FROM_CONTOUR.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FIND_CONTOUR.tmp
Found broken examples in automatic/FIND_CONTOUR_SURFACE.tmp
Found broken examples in automatic/FIND_SPHERICAL_CONTOUR.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
Found broken examples in automatic/FUNCPATHMSD.tmp
Found broken examples in automatic/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GHBFIX.tmp
Found broken examples in automatic/GPROPERTYMAP.tmp
Found broken examples in automatic/HBOND_MATRIX.tmp
Found broken examples in automatic/INCLUDE.tmp
Found broken examples in automatic/INCYLINDER.tmp
Found broken examples in automatic/INENVELOPE.tmp
Found broken examples in automatic/INTERPOLATE_GRID.tmp
Found broken examples in automatic/LOCAL_AVERAGE.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/MULTICOLVARDENS.tmp
Found broken examples in automatic/OUTPUT_CLUSTER.tmp
Found broken examples in automatic/PAMM.tmp
Found broken examples in automatic/PCA.tmp
Found broken examples in automatic/PCAVARS.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PLUMED.tmp
Found broken examples in automatic/PYCVINTERFACE.tmp
Found broken examples in automatic/PYTHONFUNCTION.tmp
Found broken examples in automatic/Q3.tmp
Found broken examples in automatic/Q4.tmp
Found broken examples in automatic/Q6.tmp
Found broken examples in automatic/QUATERNION.tmp
Found broken examples in automatic/SPRINT.tmp
Found broken examples in automatic/TETRAHEDRALPORE.tmp
Found broken examples in automatic/TORSIONS.tmp
Found broken examples in automatic/WHAM_WEIGHTS.tmp
Found broken examples in AnalysisPP.md
Found broken examples in CollectiveVariablesPP.md
Found broken examples in MiscelaneousPP.md

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