From 38a84d2df2290091931be6f8e5f9d586b33392d4 Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Mon, 29 Jul 2019 14:27:34 +0200
Subject: [PATCH] fixed a number of clang warnings
---
src/bias/MaxEnt.cpp | 1 -
src/dimred/PCA.cpp | 4 ++--
src/multicolvar/MultiColvarCombine.cpp | 2 +-
src/multicolvar/MultiColvarProduct.cpp | 2 +-
src/pamm/PAMM.cpp | 1 +
src/reference/OptimalRMSD.cpp | 2 +-
src/reference/SimpleRMSD.cpp | 2 +-
src/tools/ConjugateGradient.h | 2 +-
src/vesselbase/ActionWithAveraging.h | 1 +
src/vesselbase/BridgeVessel.cpp | 2 +-
10 files changed, 10 insertions(+), 9 deletions(-)
diff --git a/src/bias/MaxEnt.cpp b/src/bias/MaxEnt.cpp
index 31e022d6d..a0b4a0f03 100644
--- a/src/bias/MaxEnt.cpp
+++ b/src/bias/MaxEnt.cpp
@@ -142,7 +142,6 @@ class MaxEnt : public Bias {
double totalWork;
double BetaReweightBias;
double simtemp;
- double reweight_bias2;
vector<ActionWithValue*> biases;
std::string type;
std::string error_type;
diff --git a/src/dimred/PCA.cpp b/src/dimred/PCA.cpp
index c343f0ef6..2b0acbc1f 100644
--- a/src/dimred/PCA.cpp
+++ b/src/dimred/PCA.cpp
@@ -183,7 +183,7 @@ void PCA::performAnalysis() {
for(unsigned i=1; i<getNumberOfDataPoints(); ++i) {
my_input_data->getStoredData( i, false ).transferDataToPDB( mypdb );
for(unsigned j=0; j<getArguments().size(); ++j) mypdb.getArgumentValue( getArguments()[j]->getName(), args[j] );
- double d = myconf0->calc( mypdb.getPositions(), getPbc(), getArguments(), args, mypack, true );
+ myconf0->calc( mypdb.getPositions(), getPbc(), getArguments(), args, mypack, true );
// Accumulate average displacement of arguments (Here PBC could do fucked up things - really needs Berry Phase ) GAT
for(unsigned j=0; j<myconf0->getNumberOfReferenceArguments(); ++j) sarg[j] += 0.5*getWeight(i)*mypack.getArgumentDerivative(j);
// Accumulate average displacement of position
@@ -200,7 +200,7 @@ void PCA::performAnalysis() {
for(unsigned i=0; i<getNumberOfDataPoints(); ++i) {
my_input_data->getStoredData( i, false ).transferDataToPDB( mypdb );
for(unsigned j=0; j<getArguments().size(); ++j) mypdb.getArgumentValue( getArguments()[j]->getName(), args[j] );
- double d = myconf0->calc( mypdb.getPositions(), getPbc(), getArguments(), args, mypack, true );
+ myconf0->calc( mypdb.getPositions(), getPbc(), getArguments(), args, mypack, true );
for(unsigned jarg=0; jarg<narg; ++jarg) {
// Need sorting for PBC with GAT
double jarg_d = 0.5*mypack.getArgumentDerivative(jarg) + myconf0->getReferenceArguments()[jarg] - sarg[jarg];
diff --git a/src/multicolvar/MultiColvarCombine.cpp b/src/multicolvar/MultiColvarCombine.cpp
index 1ea5e0afc..ee7c5ddcf 100644
--- a/src/multicolvar/MultiColvarCombine.cpp
+++ b/src/multicolvar/MultiColvarCombine.cpp
@@ -82,7 +82,7 @@ double MultiColvarCombine::compute( const unsigned& tindex, AtomValuePack& myato
dot += coeff[i]*tval[1];
}
if( !doNotCalculateDerivatives() ) {
- MultiValue& myvals = myatoms.getUnderlyingMultiValue(); std::vector<double> cc(2);
+ myatoms.getUnderlyingMultiValue(); std::vector<double> cc(2);
for(unsigned i=0; i<coeff.size(); ++i) {
cc[1]=coeff[i]; MultiValue& myder=getInputDerivatives( i, false, myatoms );
splitInputDerivatives( 1, 1, 2, i, cc, myder, myatoms );
diff --git a/src/multicolvar/MultiColvarProduct.cpp b/src/multicolvar/MultiColvarProduct.cpp
index 32748fed6..6868b4ef6 100644
--- a/src/multicolvar/MultiColvarProduct.cpp
+++ b/src/multicolvar/MultiColvarProduct.cpp
@@ -75,7 +75,7 @@ double MultiColvarProduct::compute( const unsigned& tindex, AtomValuePack& myato
dot *= tval[1];
}
if( !doNotCalculateDerivatives() ) {
- MultiValue& myvals = myatoms.getUnderlyingMultiValue(); std::vector<double> cc(2);
+ myatoms.getUnderlyingMultiValue(); std::vector<double> cc(2);
for(unsigned i=0; i<getNumberOfBaseMultiColvars(); ++i) {
getInputData( i, false, myatoms, cc ); cc[1] = dot / cc[1];
MultiValue& myder=getInputDerivatives( i, false, myatoms );
diff --git a/src/pamm/PAMM.cpp b/src/pamm/PAMM.cpp
index 7e847bc5f..bde0ce38d 100644
--- a/src/pamm/PAMM.cpp
+++ b/src/pamm/PAMM.cpp
@@ -118,6 +118,7 @@ public:
/// We have to overwrite this here
unsigned getNumberOfQuantities() const ;
/// Calculate the weight of this object ( average of input weights )
+ using PLMD::multicolvar::MultiColvarBase::calculateWeight;
void calculateWeight( multicolvar::AtomValuePack& myatoms );
/// Actually do the calculation
double compute( const unsigned& tindex, multicolvar::AtomValuePack& myatoms ) const ;
diff --git a/src/reference/OptimalRMSD.cpp b/src/reference/OptimalRMSD.cpp
index 88194f45f..922c255c6 100644
--- a/src/reference/OptimalRMSD.cpp
+++ b/src/reference/OptimalRMSD.cpp
@@ -81,7 +81,7 @@ double OptimalRMSD::calc( const std::vector<Vector>& pos, ReferenceValuePack& my
void OptimalRMSD::extractAtomicDisplacement( const std::vector<Vector>& pos, std::vector<Vector>& direction ) const {
std::vector<Tensor> rot(1); Matrix<std::vector<Vector> > DRotDPos( 3, 3 );
std::vector<Vector> centeredreference( getNumberOfAtoms() ), centeredpos( getNumberOfAtoms() ), avector( getNumberOfAtoms() );
- double d=myrmsd.calc_PCAelements(pos,avector,rot[0],DRotDPos,direction,centeredpos,centeredreference,true);
+ myrmsd.calc_PCAelements(pos,avector,rot[0],DRotDPos,direction,centeredpos,centeredreference,true);
unsigned nat = pos.size(); for(unsigned i=0; i<nat; ++i) direction[i] = getDisplace()[i]*( direction[i] - getReferencePosition(i) );
}
diff --git a/src/reference/SimpleRMSD.cpp b/src/reference/SimpleRMSD.cpp
index 5edc34d6f..2273a00cd 100644
--- a/src/reference/SimpleRMSD.cpp
+++ b/src/reference/SimpleRMSD.cpp
@@ -62,7 +62,7 @@ double SimpleRMSD::calc( const std::vector<Vector>& pos, ReferenceValuePack& myd
void SimpleRMSD::extractAtomicDisplacement( const std::vector<Vector>& pos, std::vector<Vector>& direction ) const {
std::vector<Vector> tder( getNumberOfAtoms() );
- double d=myrmsd.simpleAlignment( getAlign(), getDisplace(), pos, getReferencePositions(), tder, direction, true );
+ myrmsd.simpleAlignment( getAlign(), getDisplace(), pos, getReferencePositions(), tder, direction, true );
for(unsigned i=0; i<pos.size(); ++i) direction[i] = getDisplace()[i]*direction[i];
}
diff --git a/src/tools/ConjugateGradient.h b/src/tools/ConjugateGradient.h
index 28fae1019..399a2958c 100644
--- a/src/tools/ConjugateGradient.h
+++ b/src/tools/ConjugateGradient.h
@@ -49,7 +49,7 @@ void ConjugateGradient<FCLASS>::minimise( const double& ftol, std::vector<double
double fret=this->linemin( xi, p, myfunc );
// The exit condition
if( 2.0*fabs(fret-fp) <= ftol*(fabs(fret)+fabs(fp)+EPS)) { return; }
- fp = fret; double igeng = this->calcDerivatives( p, xi, myfunc );
+ fp = fret; this->calcDerivatives( p, xi, myfunc );
double ddg=0., gg=0.;
for(unsigned j=0; j<p.size(); ++j) { gg += g[j]*g[j]; ddg += (xi[j]+g[j])*xi[j]; }
diff --git a/src/vesselbase/ActionWithAveraging.h b/src/vesselbase/ActionWithAveraging.h
index 397fd00e0..42e351d6e 100644
--- a/src/vesselbase/ActionWithAveraging.h
+++ b/src/vesselbase/ActionWithAveraging.h
@@ -85,6 +85,7 @@ public:
virtual unsigned getNumberOfQuantities() const ;
unsigned getNumberOfArguments() const ;
/// Overwrite ActionWithArguments getArguments() so that we don't return the bias
+ using ActionWithArguments::getArguments;
std::vector<Value*> getArguments();
void update();
/// This does the clearing of the action
diff --git a/src/vesselbase/BridgeVessel.cpp b/src/vesselbase/BridgeVessel.cpp
index e9c0d672f..c960fd652 100644
--- a/src/vesselbase/BridgeVessel.cpp
+++ b/src/vesselbase/BridgeVessel.cpp
@@ -70,7 +70,7 @@ void BridgeVessel::prepare() {
}
void BridgeVessel::setBufferStart( unsigned& start ) {
- unsigned tmp=myOutputAction->getSizeOfBuffer( start );
+ myOutputAction->getSizeOfBuffer( start );
}
MultiValue& BridgeVessel::transformDerivatives( const unsigned& current, MultiValue& invals, MultiValue& outvals ) {
--
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