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No longer passing pointer to action in calculateCV as first step to g…
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…etting this command running on GPU
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Gareth Aneurin Tribello authored and Gareth Aneurin Tribello committed Feb 5, 2025
1 parent 2986098 commit baaa901
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Showing 11 changed files with 66 additions and 80 deletions.
8 changes: 3 additions & 5 deletions src/colvar/Angle.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -110,8 +110,7 @@ class Angle : public Colvar {
static void registerKeywords( Keywords& keys );
static void parseAtomList( const int& num, std::vector<AtomNumber>& t, ActionAtomistic* aa );
static unsigned getModeAndSetupValues( ActionWithValue* av );
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa );
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial );
};

typedef ColvarShortcut<Angle> AngleShortcut;
Expand Down Expand Up @@ -168,14 +167,13 @@ Angle::Angle(const ActionOptions&ao):
void Angle::calculate() {

if(pbc) makeWhole();
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial );
setValue( value[0] );
for(unsigned i=0; i<derivs[0].size(); ++i) setAtomsDerivatives( i, derivs[0][i] );
setBoxDerivatives( virial[0] );
}

void Angle::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa ) {
void Angle::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial ) {
Vector dij,dik;
dij=delta(cvin.pos[2],cvin.pos[3]);
dik=delta(cvin.pos[1],cvin.pos[0]);
Expand Down
8 changes: 3 additions & 5 deletions src/colvar/DihedralCorrelation.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,7 @@ class DihedralCorrelation : public Colvar {
static void parseAtomList( const int& num, std::vector<AtomNumber>& t, ActionAtomistic* aa );
static unsigned getModeAndSetupValues( ActionWithValue* av );
void calculate() override;
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa );
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial );
};

typedef ColvarShortcut<DihedralCorrelation> DihedralCorrelationShortcut;
Expand Down Expand Up @@ -125,14 +124,13 @@ unsigned DihedralCorrelation::getModeAndSetupValues( ActionWithValue* av ) {
void DihedralCorrelation::calculate() {

if(pbc) makeWhole();
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial );
setValue( value[0] );
for(unsigned i=0; i<derivs[0].size(); ++i) setAtomsDerivatives( i, derivs[0][i] );
setBoxDerivatives( virial[0] );
}

void DihedralCorrelation::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa ) {
void DihedralCorrelation::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial ) {
const Vector d10=delta(cvin.pos[1],cvin.pos[0]);
const Vector d11=delta(cvin.pos[2],cvin.pos[1]);
const Vector d12=delta(cvin.pos[3],cvin.pos[2]);
Expand Down
12 changes: 5 additions & 7 deletions src/colvar/Dipole.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -94,8 +94,7 @@ class Dipole : public Colvar {
static unsigned getModeAndSetupValues( ActionWithValue* av );
void calculate() override;
static void registerKeywords(Keywords& keys);
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa );
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial );
};

typedef ColvarShortcut<Dipole> DipoleShortcut;
Expand All @@ -122,7 +121,7 @@ Dipole::Dipole(const ActionOptions&ao):
derivs(1),
virial(1)
{
parseAtomList(-1,ga_lista,this);
parseAtomList(-1,ga_lista,this);
components=(getModeAndSetupValues(this)==1);
if( components ) {
value.resize(3); derivs.resize(3); virial.resize(3);
Expand Down Expand Up @@ -171,12 +170,12 @@ void Dipole::calculate()
unsigned N=getNumberOfAtoms();

if(!components) {
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial );
for(unsigned i=0; i<N; i++) setAtomsDerivatives(i,derivs[0][i]);
setBoxDerivatives(virial[0]);
setValue(value[0]);
} else {
calculateCV( ColvarInput::createColvarInput( 1, getPositions(), this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 1, getPositions(), this ), value, derivs, virial );
for(unsigned i=0; i<N; i++) {
setAtomsDerivatives(valuex,i,derivs[0][i]);
setAtomsDerivatives(valuey,i,derivs[1][i]);
Expand All @@ -191,8 +190,7 @@ void Dipole::calculate()
}
}

void Dipole::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa ) {
void Dipole::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial ) {
unsigned N=cvin.pos.size(); double ctot=0.;
for(unsigned i=0; i<N; ++i) ctot += cvin.charges[i];
ctot/=(double)N;
Expand Down
26 changes: 12 additions & 14 deletions src/colvar/Distance.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -138,8 +138,7 @@ class Distance : public Colvar {
static unsigned getModeAndSetupValues( ActionWithValue* av );
// active methods:
void calculate() override;
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa );
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial );
};

typedef ColvarShortcut<Distance> DistanceShortcut;
Expand Down Expand Up @@ -226,7 +225,7 @@ void Distance::calculate() {
if(pbc) makeWhole();

if( components ) {
calculateCV( ColvarInput::createColvarInput( 1, getPositions(), this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 1, getPositions(), this ), value, derivs, virial );
Value* valuex=getPntrToComponent("x");
Value* valuey=getPntrToComponent("y");
Value* valuez=getPntrToComponent("z");
Expand All @@ -243,7 +242,7 @@ void Distance::calculate() {
setBoxDerivatives(valuez,virial[2]);
valuez->set(value[2]);
} else if( scaled_components ) {
calculateCV( ColvarInput::createColvarInput( 2, getPositions(), this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 2, getPositions(), this ), value, derivs, virial );

Value* valuea=getPntrToComponent("a");
Value* valueb=getPntrToComponent("b");
Expand All @@ -255,15 +254,14 @@ void Distance::calculate() {
for(unsigned i=0; i<2; ++i) setAtomsDerivatives(valuec,i,derivs[2][i] );
valuec->set(value[2]);
} else {
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial );
for(unsigned i=0; i<2; ++i) setAtomsDerivatives(i,derivs[0][i] );
setBoxDerivatives(virial[0]);
setValue (value[0]);
}
}

void Distance::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa ) {
void Distance::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial ) {
Vector distance=delta(cvin.pos[0],cvin.pos[1]);
const double value=distance.modulo();
const double invvalue=1.0/value;
Expand All @@ -282,15 +280,15 @@ void Distance::calculateCV( const ColvarInput& cvin, std::vector<double>& vals,
vals[2] = distance[2];
setBoxDerivativesNoPbc( cvin.pos, derivs, virial );
} else if(cvin.mode==2) {
Vector d=aa->getPbc().realToScaled(distance);
derivs[0][0] = matmul(aa->getPbc().getInvBox(),Vector(-1,0,0));
derivs[0][1] = matmul(aa->getPbc().getInvBox(),Vector(+1,0,0));
Vector d=cvin.pbc.realToScaled(distance);
derivs[0][0] = matmul(cvin.pbc.getInvBox(),Vector(-1,0,0));
derivs[0][1] = matmul(cvin.pbc.getInvBox(),Vector(+1,0,0));
vals[0] = Tools::pbc(d[0]);
derivs[1][0] = matmul(aa->getPbc().getInvBox(),Vector(0,-1,0));
derivs[1][1] = matmul(aa->getPbc().getInvBox(),Vector(0,+1,0));
derivs[1][0] = matmul(cvin.pbc.getInvBox(),Vector(0,-1,0));
derivs[1][1] = matmul(cvin.pbc.getInvBox(),Vector(0,+1,0));
vals[1] = Tools::pbc(d[1]);
derivs[2][0] = matmul(aa->getPbc().getInvBox(),Vector(0,0,-1));
derivs[2][1] = matmul(aa->getPbc().getInvBox(),Vector(0,0,+1));
derivs[2][0] = matmul(cvin.pbc.getInvBox(),Vector(0,0,-1));
derivs[2][1] = matmul(cvin.pbc.getInvBox(),Vector(0,0,+1));
vals[2] = Tools::pbc(d[2]);
} else {
derivs[0][0] = -invvalue*distance;
Expand Down
13 changes: 7 additions & 6 deletions src/colvar/MultiColvarTemplate.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -25,16 +25,17 @@
namespace PLMD {
namespace colvar {

ColvarInput::ColvarInput( const unsigned& m, const std::vector<Vector>& p, const std::vector<double>& w, const std::vector<double>& q ) :
mode(m),
pos(p),
mass(w),
charges(q)
ColvarInput::ColvarInput( const unsigned& m, const std::vector<Vector>& p, const std::vector<double>& w, const std::vector<double>& q, const Pbc& box ) :
mode(m),
pbc(box),
pos(p),
mass(w),
charges(q)
{
}

ColvarInput ColvarInput::createColvarInput( const unsigned& m, const std::vector<Vector>& p, const Colvar* colv ) {
return ColvarInput( m, p, colv->getMasses(), colv->getCharges(true) );
return ColvarInput( m, p, colv->getMasses(), colv->getCharges(true), colv->getPbc() );
}

}
Expand Down
5 changes: 3 additions & 2 deletions src/colvar/MultiColvarTemplate.h
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Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,11 @@ namespace colvar {
class ColvarInput {
public:
unsigned mode;
const Pbc& pbc;
const std::vector<Vector>& pos;
const std::vector<double>& mass;
const std::vector<double>& charges;
ColvarInput( const unsigned& m, const std::vector<Vector>& p, const std::vector<double>& w, const std::vector<double>& q );
ColvarInput( const unsigned& m, const std::vector<Vector>& p, const std::vector<double>& w, const std::vector<double>& q, const Pbc& box );
static ColvarInput createColvarInput( const unsigned& m, const std::vector<Vector>& p, const Colvar* colv );
};

Expand Down Expand Up @@ -177,7 +178,7 @@ void MultiColvarTemplate<T>::performTask( const unsigned& task_index, MultiValue
std::vector<Tensor> & virial( myvals.getFirstAtomVirialVector() );
std::vector<std::vector<Vector> > & derivs( myvals.getFirstAtomDerivativeVector() );
// Calculate the CVs using the method in the Colvar
T::calculateCV( ColvarInput(mode, fpositions, mass, charge), values, derivs, virial, this );
T::calculateCV( ColvarInput(mode, fpositions, mass, charge, getPbc() ), values, derivs, virial );
for(unsigned i=0; i<values.size(); ++i) myvals.setValue( i, values[i] );
// Finish if there are no derivatives
if( doNotCalculateDerivatives() ) return;
Expand Down
8 changes: 3 additions & 5 deletions src/colvar/Plane.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -72,8 +72,7 @@ class Plane : public Colvar {
static unsigned getModeAndSetupValues( ActionWithValue* av );
// active methods:
void calculate() override;
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa );
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial );
};

typedef ColvarShortcut<Plane> PlaneShortcut;
Expand Down Expand Up @@ -134,14 +133,13 @@ Plane::Plane(const ActionOptions&ao):
void Plane::calculate() {

if(pbc) makeWhole();
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial );
setValue( value[0] );
for(unsigned i=0; i<derivs[0].size(); ++i) setAtomsDerivatives( i, derivs[0][i] );
setBoxDerivatives( virial[0] );
}

void Plane::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa ) {
void Plane::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial ) {
Vector d1=delta( cvin.pos[1], cvin.pos[0] );
Vector d2=delta( cvin.pos[2], cvin.pos[3] );
Vector cp = crossProduct( d1, d2 );
Expand Down
18 changes: 8 additions & 10 deletions src/colvar/Position.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -103,8 +103,7 @@ class Position : public Colvar {
static unsigned getModeAndSetupValues( ActionWithValue* av );
// active methods:
void calculate() override;
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa );
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial );
};

typedef ColvarShortcut<Position> PositionShortcut;
Expand Down Expand Up @@ -184,7 +183,7 @@ void Position::calculate() {
}

if(scaled_components) {
calculateCV( ColvarInput::createColvarInput( 1, distance, this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 1, distance, this ), value, derivs, virial );
Value* valuea=getPntrToComponent("a");
Value* valueb=getPntrToComponent("b");
Value* valuec=getPntrToComponent("c");
Expand All @@ -195,7 +194,7 @@ void Position::calculate() {
setAtomsDerivatives (valuec,0,derivs[2][0]);
valuec->set(value[2]);
} else {
calculateCV( ColvarInput::createColvarInput( 0, distance, this ), value, derivs, virial, this );
calculateCV( ColvarInput::createColvarInput( 0, distance, this ), value, derivs, virial );
Value* valuex=getPntrToComponent("x");
Value* valuey=getPntrToComponent("y");
Value* valuez=getPntrToComponent("z");
Expand All @@ -214,14 +213,13 @@ void Position::calculate() {
}
}

void Position::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa ) {
void Position::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial ) {
if( cvin.mode==1 ) {
Vector d=aa->getPbc().realToScaled(cvin.pos[0]);
Vector d=cvin.pbc.realToScaled(cvin.pos[0]);
vals[0]=Tools::pbc(d[0]); vals[1]=Tools::pbc(d[1]); vals[2]=Tools::pbc(d[2]);
derivs[0][0]=matmul(aa->getPbc().getInvBox(),Vector(+1,0,0));
derivs[1][0]=matmul(aa->getPbc().getInvBox(),Vector(0,+1,0));
derivs[2][0]=matmul(aa->getPbc().getInvBox(),Vector(0,0,+1));
derivs[0][0]=matmul(cvin.pbc.getInvBox(),Vector(+1,0,0));
derivs[1][0]=matmul(cvin.pbc.getInvBox(),Vector(0,+1,0));
derivs[2][0]=matmul(cvin.pbc.getInvBox(),Vector(0,0,+1));
} else {
for(unsigned i=0; i<3; ++i) vals[i]=cvin.pos[0][i];
derivs[0][0]=Vector(+1,0,0); derivs[1][0]=Vector(0,+1,0); derivs[2][0]=Vector(0,0,+1);
Expand Down
30 changes: 15 additions & 15 deletions src/colvar/SelectMassCharge.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -80,9 +80,9 @@ Get the mass of one or multiple atoms
namespace PLMD {
namespace colvar {

class SelectMassCharge :
public ActionAtomistic,
public ActionWithValue {
class SelectMassCharge :
public ActionAtomistic,
public ActionWithValue {
public:
static void registerKeywords( Keywords& keys );
explicit SelectMassCharge(const ActionOptions&);
Expand Down Expand Up @@ -112,13 +112,13 @@ SelectMassCharge::SelectMassCharge(const ActionOptions&ao):
std::vector<AtomNumber> atoms; parseAtomList("ATOMS",atoms);
log.printf(" getting %s of atoms : ", getName().c_str() );
for(unsigned i=0; i<atoms.size(); ++i) {
std::pair<std::size_t,std::size_t> p = getValueIndices( atoms[i] );
if( getName()=="MASS" && !masv[p.first]->isConstant() ) error("cannot deal with non-constant " + getName() + " values");
if( getName()=="CHARGE" && !chargev[p.first]->isConstant() ) error("cannot deal with non-constant " + getName() + " values");
log.printf("%d ", atoms[i].serial() );
std::pair<std::size_t,std::size_t> p = getValueIndices( atoms[i] );
if( getName()=="MASS" && !masv[p.first]->isConstant() ) error("cannot deal with non-constant " + getName() + " values");
if( getName()=="CHARGE" && !chargev[p.first]->isConstant() ) error("cannot deal with non-constant " + getName() + " values");
log.printf("%d ", atoms[i].serial() );
}
log.printf("\n"); requestAtoms(atoms);
std::vector<unsigned> shape(1);
std::vector<unsigned> shape(1);
if(atoms.size()==1) shape.resize(0);
else shape[0] = atoms.size();
addValue( shape ); setNotPeriodic();
Expand All @@ -127,13 +127,13 @@ SelectMassCharge::SelectMassCharge(const ActionOptions&ao):

// calculator
void SelectMassCharge::calculate() {
Value* myval = getPntrToComponent(0);
if( getName()=="CHARGES" ) {
if( !chargesWereSet ) error("cannot determine charges are charges were not set");
for(unsigned i=0; i<getNumberOfAtoms(); ++i) myval->set( i, getCharge(i) );
} else {
for(unsigned i=0; i<getNumberOfAtoms(); ++i) myval->set( i, getMass(i) );
}
Value* myval = getPntrToComponent(0);
if( getName()=="CHARGES" ) {
if( !chargesWereSet ) error("cannot determine charges are charges were not set");
for(unsigned i=0; i<getNumberOfAtoms(); ++i) myval->set( i, getCharge(i) );
} else {
for(unsigned i=0; i<getNumberOfAtoms(); ++i) myval->set( i, getMass(i) );
}
}

}
Expand Down
10 changes: 4 additions & 6 deletions src/colvar/Torsion.cpp
View file
Original file line number Diff line number Diff line change
Expand Up @@ -119,8 +119,7 @@ class Torsion : public Colvar {
static unsigned getModeAndSetupValues( ActionWithValue* av );
// active methods:
void calculate() override;
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa );
static void calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial );
static void registerKeywords(Keywords& keys);
};

Expand Down Expand Up @@ -224,14 +223,13 @@ unsigned Torsion::getModeAndSetupValues( ActionWithValue* av ) {
// calculator
void Torsion::calculate() {
if(pbc) makeWhole();
if(do_cosine) calculateCV( ColvarInput::createColvarInput( 1, getPositions(), this ), value, derivs, virial, this );
else calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial, this );
if(do_cosine) calculateCV( ColvarInput::createColvarInput( 1, getPositions(), this ), value, derivs, virial );
else calculateCV( ColvarInput::createColvarInput( 0, getPositions(), this ), value, derivs, virial );
for(unsigned i=0; i<6; ++i) setAtomsDerivatives(i,derivs[0][i] );
setValue(value[0]); setBoxDerivatives( virial[0] );
}

void Torsion::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs,
std::vector<Tensor>& virial, const ActionAtomistic* aa ) {
void Torsion::calculateCV( const ColvarInput& cvin, std::vector<double>& vals, std::vector<std::vector<Vector> >& derivs, std::vector<Tensor>& virial ) {
Vector d0=delta(cvin.pos[1],cvin.pos[0]);
Vector d1=delta(cvin.pos[3],cvin.pos[2]);
Vector d2=delta(cvin.pos[5],cvin.pos[4]);
Expand Down
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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/METATENSOR.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/SIZESHAPE_POSITION_LINEAR_PROJ.tmp
Found broken examples in automatic/SIZESHAPE_POSITION_MAHA_DIST.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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