fixing clang warnings (which include also two bugs!)

classic/5.0/src/AbsBeamline/Collimator.cpp

@@ -66,8 +66,8 @@ Collimator::Collimator():
     nHolesX_m(0),
     nHolesY_m(0),
     pitch_m(0.0),
-    sphys_m(NULL),
-    lossDs_m(nullptr)
+    lossDs_m(nullptr),
+    sphys_m(NULL)
 {}
 
 
@@ -105,8 +105,8 @@ Collimator::Collimator(const Collimator &right):
     nHolesX_m(right.nHolesX_m),
     nHolesY_m(right.nHolesY_m),
     pitch_m(right.pitch_m),
-    sphys_m(NULL),
-    lossDs_m(nullptr)
+    lossDs_m(nullptr),
+    sphys_m(NULL)
 {
   setGeom();
 }
@@ -146,8 +146,8 @@ Collimator::Collimator(const std::string &name):
     nHolesX_m(0),
     nHolesY_m(0),
     pitch_m(0.0),
-    sphys_m(NULL),
-    lossDs_m(nullptr)
+    lossDs_m(nullptr),
+    sphys_m(NULL)
 {}
 
 

classic/5.0/src/AbsBeamline/Probe.cpp

@@ -213,7 +213,7 @@ bool  Probe::checkProbe(PartBunch &bunch, const int turnnumber, const double t,
     double r_end = sqrt(xend_m * xend_m + yend_m * yend_m);
     double r1 = sqrt(rmax(0) * rmax(0) + rmax(1) * rmax(1));
     double r2 = sqrt(rmin(0) * rmin(0) + rmin(1) * rmin(1));
-   
+
     if( r1 > r_start - 10.0 && r2 < r_end + 10.0 ){
         size_t tempnum = bunch.getLocalNum();
         int pflag = 0;
@@ -260,17 +260,17 @@ bool  Probe::checkProbe(PartBunch &bunch, const int turnnumber, const double t,
 		    if (k1 == 0.0)
 		      tangle = 1.0e12;
 		    else
-		      tangle = abs(1/k1);
+                      tangle = std::abs(1/k1);
 		  }else if (bunch.P[i](0) == 0.0 ){
 		    k2 = -A_m/B_m;
 		    if (k2 == 0.0)
 		      tangle = 1.0e12;
 		    else
-		      tangle = abs(1/k2);
+                      tangle = std::abs(1/k2);
 		  }else {
 		    k1 = bunch.P[i](1)/bunch.P[i](0);
 		    k2 = -A_m/B_m;
-		    tangle = abs(( k1-k2 )/(1 + k1*k2));
+		    tangle = std::abs(( k1-k2 )/(1 + k1*k2));
 		  }
 		  double dist2 = dist1 * sqrt( 1+1/tangle/tangle );
 		  double dt = dist2/(sqrt(1.0-1.0/(1.0 + dot(bunch.P[i], bunch.P[i]))) * Physics::c)*1.0e9;
@@ -313,4 +313,3 @@ const std::string &Probe::getType() const {
     static const std::string type("Probe");
     return type;
 }
-

classic/5.0/src/AbsBeamline/RBend.cpp

@@ -1158,7 +1158,7 @@ bool RBend::InMagnetCentralRegion(Vector_t R, double &deltaX, double &angle) {
 
 bool RBend::InMagnetEntranceRegion(Vector_t R, double &deltaX) {
 
-    if(std::abs(R(0) <= aperture_m / 2.0)) {
+    if(std::abs(R(0)) <= aperture_m / 2.0) {
 
         Vector_t RTransformed(0.0, R(1), 0.0);
         RTransformed(0) = (R(0) - xOriginEngeEntry_m) * cosEntranceAngle_m

classic/5.0/src/AbsBeamline/SBend.cpp

@@ -1127,7 +1127,7 @@ bool SBend::InMagnetCentralRegion(Vector_t R, double &deltaX, double &angle) {
 
 bool SBend::InMagnetEntranceRegion(Vector_t R, double &deltaX) {
 
-    if(std::abs(R(0) <= aperture_m / 2.0)) {
+    if(std::abs(R(0)) <= aperture_m / 2.0) {
 
         Vector_t RTransformed(0.0, R(1), 0.0);
         RTransformed(0) = (R(0) - xOriginEngeEntry_m) * cosEntranceAngle_m

classic/5.0/src/Solvers/CSRIGFWakeFunction.cpp

@@ -15,8 +15,7 @@ CSRIGFWakeFunction::CSRIGFWakeFunction(const std::string &name, ElementBase *ele
     lineDensity_m(),
     dlineDensitydz_m(),
     bendRadius_m(0.0),
-    totalBendAngle_m(0.0),
-    NBin_m(N)
+    totalBendAngle_m(0.0)
 { }
 
 void CSRIGFWakeFunction::apply(PartBunch &bunch) {

classic/5.0/src/Solvers/CSRIGFWakeFunction.hh

@@ -25,16 +25,16 @@ private:
     void calculateGreenFunction(PartBunch &bunch, double meshSpacing);
     double calcPsi(const double &psiInitial, const double &x, const double &Ds) const;
 
-    LineDensity lineDensity_m;
     std::vector<Filter *> filters_m;
+    LineDensity lineDensity_m;
     LineDensity dlineDensitydz_m;
 
     // Longitudinal CSR field.
     std::vector<double> Ez_m;
-    
+
     // Chi used to calculate the Green's function
     std::vector<double> Chi_m;
-  
+
     // Green's function
     std::vector<double> Grn_m;
 
@@ -58,8 +58,6 @@ private:
 
     double totalBendAngle_m;
 
-    unsigned int NBin_m;
-
 };
 
 #endif //CSRIGFWAKEFUNCTION_HH

classic/5.0/src/Solvers/CSRWakeFunction.cpp

@@ -17,8 +17,7 @@ CSRWakeFunction::CSRWakeFunction(const std::string &name, ElementBase *element,
     dlineDensitydz_m(),
     d2lineDensitydz2_m(),
     bendRadius_m(0.0),
-    totalBendAngle_m(0.0),
-    NBin_m(N)
+    totalBendAngle_m(0.0)
 { }
 
 void CSRWakeFunction::apply(PartBunch &bunch) {

classic/5.0/src/Solvers/CSRWakeFunction.hh

@@ -53,8 +53,6 @@ private:
 
     double totalBendAngle_m;
 
-    unsigned int NBin_m;
-
 };
 
 #endif //CSRWAKEFUNCTION_HH

classic/5.0/src/Solvers/CollimatorPhysics.hh

@@ -74,7 +74,6 @@ private:
     double I_m;
     double n_m;
 
-    unsigned matToBunchStat_m;
     unsigned bunchToMatStat_m;
     unsigned stoppedPartStat_m;
     unsigned redifusedStat_m;
@@ -85,11 +84,6 @@ private:
     double Emax_m;
     double Emin_m;
 
-    double Kmax_m;
-    double Kmin_m;
-
-    double Emean_m;
-
 public:
     double dT_m;
     int N_m;

src/Algorithms/BeamBeam3D.cpp

@@ -358,7 +358,7 @@ void BeamBeam3D::synchroBeamCollision(PartBunch &bunch) const {
 
             double sepx = part.x() + part.px() * s - slice->xstar;
             double sepy = part.y() + part.py() * s - slice->ystar;
-            double bbfx, bbfy, bbgx, bbgy;
+            double bbfx = 0, bbfy = 0, bbgx = 0, bbgy = 0;
 
             if(std::abs(sx - sy) < 1.0e-6 * std::abs(sx + sy)) {
                 double x = sepx * sepx + sepy * sepy;

src/Algorithms/ParallelTTracker.cpp

@@ -80,7 +80,6 @@ ParallelTTracker::ParallelTTracker(const Beamline &beamline,
 Tracker(beamline, reference, revBeam, revTrack),
 itsBunch(NULL),
 itsDataSink_m(NULL),
-specifiedNPart_m(N),
 bgf_m(NULL),
 itsOpalBeamline_m(),
 lineDensity_m(),
@@ -103,6 +102,7 @@ recpGamma_m(1.0),
 rescale_coeff_m(1.0),
 dtTrack_m(0.0),
 surfaceEmissionStop_m(-1),
+specifiedNPart_m(N),
 minStepforReBin_m(-1),
 minBinEmitted_m(std::numeric_limits<size_t>::max()),
 repartFreq_m(-1),
@@ -138,7 +138,6 @@ ParallelTTracker::ParallelTTracker(const Beamline &beamline,
 				   size_t N):
 Tracker(beamline, reference, revBeam, revTrack),
 itsBunch(&bunch),
-specifiedNPart_m(N),
 itsDataSink_m(&ds),
 bgf_m(NULL),
 itsOpalBeamline_m(),
@@ -160,6 +159,7 @@ recpGamma_m(1.0),
 rescale_coeff_m(1.0),
 dtTrack_m(0.0),
 surfaceEmissionStop_m(-1),
+specifiedNPart_m(N),
 minStepforReBin_m(-1),
 minBinEmitted_m(std::numeric_limits<size_t>::max()),
 repartFreq_m(-1),
@@ -200,7 +200,6 @@ ParallelTTracker::ParallelTTracker(const Beamline &beamline,
 				   Amr* amrptr_in):
 Tracker(beamline, reference, revBeam, revTrack),
 itsBunch(&bunch),
-specifiedNPart_m(N),
 itsDataSink_m(&ds),
 bgf_m(NULL),
 itsOpalBeamline_m(),
@@ -222,6 +221,7 @@ recpGamma_m(1.0),
 rescale_coeff_m(1.0),
 dtTrack_m(0.0),
 surfaceEmissionStop_m(-1),
+specifiedNPart_m(N),
 minStepforReBin_m(-1),
 minBinEmitted_m(std::numeric_limits<size_t>::max()),
 repartFreq_m(-1),

src/Algorithms/bet/EnvelopeBunch.cpp

@@ -93,7 +93,7 @@ void EnvelopeBunch::calcBeamParameters() {
     Inform msg("calcBeamParameters");
     IpplTimings::startTimer(statParamTimer_m);
     double ex, ey, nex, ney, b0, bRms, bMax, bMin, g0, dgdt, gInc;
-    double RxRms, RyRms, Px, PxRms, PxMax, PxMin, Py, PyRms, PyMax, PyMin;
+    double RxRms = 0.0, RyRms = 0.0, Px = 0.0, PxRms = 0.0, PxMax = 0.0, PxMin = 0.0, Py = 0.0, PyRms = 0.0, PyMax = 0.0, PyMin = 0.0;
     double Pz, PzMax, PzMin, PzRms;
     double x0Rms, y0Rms, zRms, zMax, zMin, I0, IRms, IMax, IMin;
 
@@ -625,7 +625,7 @@ void EnvelopeBunch::setBinnedLShape(EnvelopeBunchShape shape, double z0, double
     reduce(gz0, gz0, OpAddAssign());
     reduce(gzN, gzN, OpAddAssign());
 
-    double hbin_m = (gzN - gz0) / nebin_m;
+    hbin_m = (gzN - gz0) / nebin_m;
 
     // initialize all bins with an empty vector
     for(int i = 0; i < nebin_m; i++) {
@@ -1568,4 +1568,3 @@ Inform &EnvelopeBunch::slprint(Inform &os) {
     }
     return os;
 }
-

src/Distribution/Distribution.cpp

@@ -198,6 +198,7 @@ Distribution::Distribution():
     cathodeFermiEnergy_m(0.0),
     cathodeTemp_m(0.0),
     emitEnergyUpperLimit_m(0.0),
+    avrgpz_m(0.0),
     inputMoUnits_m(InputMomentumUnitsT::NONE),
     sigmaTRise_m(0.0),
     sigmaTFall_m(0.0),
@@ -220,8 +221,7 @@ Distribution::Distribution():
     paraFNVYZe_m(0.0),
     secondaryFlag_m(0),
     ppVw_m(0.0),
-    vVThermal_m(0.0),
-    avrgpz_m(0.0) {
+    vVThermal_m(0.0) {
 
     SetAttributes();
 
@@ -280,6 +280,7 @@ Distribution::Distribution(const std::string &name, Distribution *parent):
     pyWrite_m(parent->pyWrite_m),
     tOrZWrite_m(parent->tOrZWrite_m),
     pzWrite_m(parent->pzWrite_m),
+    avrgpz_m(parent->avrgpz_m),
     inputMoUnits_m(parent->inputMoUnits_m),
     sigmaTRise_m(parent->sigmaTRise_m),
     sigmaTFall_m(parent->sigmaTFall_m),
@@ -312,8 +313,7 @@ Distribution::Distribution(const std::string &name, Distribution *parent):
     tFall_m(parent->tFall_m),
     sigmaRise_m(parent->sigmaRise_m),
     sigmaFall_m(parent->sigmaFall_m),
-    cutoff_m(parent->cutoff_m),
-    avrgpz_m(parent->avrgpz_m){
+    cutoff_m(parent->cutoff_m){
 }
 
 Distribution::~Distribution() {

src/Distribution/LaserProfile.h

 #ifndef OPAL_LASERPROFILE_HH
-#define OPAL_LaserProfile_HH
+#define OPAL_LASERPROFILE_HH
 // ------------------------------------------------------------------------
 // $RCSfile: LaserProfile.h,v $
 // ------------------------------------------------------------------------
@@ -47,14 +47,11 @@ public:
     void GetProfileMax(unsigned short int *profileMax_m, unsigned short int   *image);
 
 private:
-    double X, Y;
     //unsigned short int profileMax_m;
     hsize_t sizeX_m, sizeY_m;
     gsl_histogram2d *hist2d_m;
-    const gsl_rng_type *rngT_m;
     gsl_rng *r_m;
     gsl_histogram2d_pdf *pdf_m;
 
 };
 #endif
-

src/Solvers/FFTBoxPoissonSolver.cpp

@@ -110,7 +110,6 @@ FFTBoxPoissonSolver::FFTBoxPoissonSolver(PartBunch &beam, std::string greensFunc
     layout_m(&beam.getFieldLayout()),
     mesh2_m(0),
     layout2_m(0),
-    itsBunch_m(&beam),
     greensFunction_m(greensFunction) {
     int i;
     domain_m = layout_m->getDomain();

src/Solvers/FFTBoxPoissonSolver.h

@@ -100,8 +100,6 @@ private:
     Vector_t hr_m;
     Vektor<int, 3> nr_m;
 
-    PartBunch *itsBunch_m;
-
     std::string greensFunction_m;
 
     double a_m; // the box size

src/Solvers/FFTPoissonSolver.cpp

@@ -200,7 +200,6 @@ FFTPoissonSolver::FFTPoissonSolver(PartBunch &beam, std::string greensFunction):
     layout3_m(nullptr),
     mesh4_m(nullptr),
     layout4_m(nullptr),
-    itsBunch_m(&beam),
     greensFunction_m(greensFunction) {
     int i;
     domain_m = layout_m->getDomain();

src/Solvers/FFTPoissonSolver.h

@@ -136,8 +136,6 @@ private:
     BConds<double, 3, Mesh_t, Center_t> bc_m;
     BConds<Vector_t, 3, Mesh_t, Center_t> vbc_m;
 
-    PartBunch *itsBunch_m;
-
     std::string greensFunction_m;
 
     bool bcz_m;

src/Structure/LossDataSink.h

@@ -34,8 +34,8 @@ class LossDataSink {
     void save();
 
     void addParticle(const Vector_t x, const Vector_t p, const size_t id);
-    
-    void addParticle(const Vector_t x, const Vector_t p, const size_t  id, const double time, const size_t turn); 
+
+    void addParticle(const Vector_t x, const Vector_t p, const size_t  id, const double time, const size_t turn);
 
 private:
 
@@ -50,12 +50,12 @@ private:
             os_m.open(fn_m.c_str(), std::ios::app);
         }
     }
-    
+
     void close() {
         if(Ippl::myNode() == 0)
             os_m.close();
     }
-    
+
     void writeHeaderASCII() {
         if(Ippl::myNode() == 0) {
             if (time_m.size() != 0)
@@ -86,13 +86,11 @@ private:
 
     // used to write out the data
     std::ofstream os_m;
-    
+
     std::string element_m;
 
     bool h5hut_mode_m;
 
-    bool hdf5FileIsOpen_m;
-
     /// %Pointer to H5 file for particle data.
     h5_file_t *H5file_m;
 
@@ -106,11 +104,8 @@ private:
     std::vector<double> px_m;
     std::vector<double> py_m;
     std::vector<double> pz_m;
-    
+
     std::vector<size_t> turn_m;
     std::vector<double> time_m;
 };
 #endif
-
-
-

src/Tables/Survey.cpp

@@ -652,14 +652,14 @@ double Survey::getPhi(const Survey::Row &row, int, int) const {
 
 double Survey::getTheta(const Survey::Row &row, int, int) const {
     const Rotation3D &rot = row.getMap().getRotation();
-    double arg = abs(rot(0, 2)) + abs(rot(2, 2));
+    double arg = std::abs(rot(0, 2)) + std::abs(rot(2, 2));
     return (arg > 1.0e-10) ? atan2(rot(0, 2), rot(2, 2)) : 0.0;
 }
 
 
 double Survey::getPsi(const Survey::Row &row, int, int) const {
     const Rotation3D &rot = row.getMap().getRotation();
-    double arg = abs(rot(1, 0)) + abs(rot(1, 1));
+    double arg = std::abs(rot(1, 0)) + std::abs(rot(1, 1));
     return (arg > 1.0e-10) ? atan2(rot(1, 0), rot(1, 1)) : 0.0;
 }