cleanup unused code, some from #62

ippl/test/FFT/SeaborgRes/TestFFT-PPP.cpp

@@ -49,10 +49,6 @@ bool Configure(int argc, char *argv[], InterPolT *interPol,
   Inform msg("Configure ");
   Inform errmsg("Error ");
 
-  string bc_str;
-  string interPol_str;
-  string dist_str;
-
   for (int i=1; i < argc; ++i) {
     string s(argv[i]);
     if (s == "-grid") {

ippl/test/FFT/SeaborgRes/TestFFT-SPP.cpp

@@ -24,10 +24,6 @@ bool Configure(int argc, char *argv[], InterPolT *interPol,
   Inform msg("Configure ");
   Inform errmsg("Error ");
 
-  string bc_str;
-  string interPol_str;
-  string dist_str;
-
   for (int i=1; i < argc; ++i) {
     string s(argv[i]);
     if (s == "-grid") {

ippl/test/FFT/SeaborgRes/TestFFT-SSP.cpp

@@ -49,10 +49,6 @@ bool Configure(int argc, char *argv[], InterPolT *interPol,
   Inform msg("Configure ");
   Inform errmsg("Error ");
 
-  string bc_str;
-  string interPol_str;
-  string dist_str;
-
   for (int i=1; i < argc; ++i) {
     string s(argv[i]);
     if (s == "-grid") {
@@ -247,16 +243,4 @@ int main(int argc, char *argv[])
     testmsg << " nx= " << nx << " ny= " << ny << " nz= " << nz;
     testmsg << " ||d||= " << fabs(realDiff) << endl;
     return 0;
-}
-
+}
\ No newline at end of file
-/***************************************************************************
- * $RCSfile: TestFFT-SSP.cpp,v $   $Author: adelmann $
- * $Revision: 1.1.1.1 $   $Date: 2003/01/23 07:40:36 $
- ***************************************************************************/
-
-/***************************************************************************
- * $RCSfile: addheaderfooter,v $   $Author: adelmann $
- * $Revision: 1.1.1.1 $   $Date: 2003/01/23 07:40:17 $
- * IPPL_VERSION_ID: $Id: addheaderfooter,v 1.1.1.1 2003/01/23 07:40:17 adelmann Exp $ 
- ***************************************************************************/
-

ippl/test/FFT/SeaborgRes/TestFFT.cpp

@@ -49,10 +49,6 @@ bool Configure(int argc, char *argv[], InterPolT *interPol,
   Inform msg("Configure ");
   Inform errmsg("Error ");
 
-  string bc_str;
-  string interPol_str;
-  string dist_str;
-
   for (int i=1; i < argc; ++i) {
     string s(argv[i]);
     if (s == "-grid") {

ippl/test/FFT/TestFFT-XT3.cpp

@@ -51,10 +51,6 @@ bool Configure(int argc, char *argv[], InterPolT *interPol,
   Inform msg("Configure ");
   Inform errmsg("Error ");
 
-  string bc_str;
-  string interPol_str;
-  string dist_str;
-
   for (int i=1; i < argc; ++i) {
     string s(argv[i]);
     if (s == "-grid") {

ippl/test/FFT/TestRCMIC.cpp

@@ -26,9 +26,6 @@ bool Configure(int argc, char *argv[],
   Inform msg("Configure ");
   Inform errmsg("Error ");
 
-  string bc_str;
-  string dist_str;
-
   for (int i=1; i < argc; ++i) {
     string s(argv[i]);
     if (s == "-grid") {
@@ -167,8 +164,8 @@ int main(int argc, char *argv[])
   BareField<double,D>   RFieldSPStan_save(layoutSPStan);
   BareField<std::complex<double>,D> CFieldSPStan0h(layoutSPStan0h);
 
-  INFOMSG("RFieldSPStan   layout= " << layoutSPStan << endl;);
-  INFOMSG("CFieldSPStan0h layout= " << layoutSPStan0h << endl;);
+  INFOMSG("RFieldSPStan   layout= " << layoutSPStan << endl);
+  INFOMSG("CFieldSPStan0h layout= " << layoutSPStan0h << endl);
 
   // For calling FieldDebug functions from debugger, set up output format:
   setFormat(4,3);

ippl/test/PwrSpec/PwrSpec.cpp

@@ -195,7 +195,7 @@ void PwrSpec<T,Dim>::CICforward(ChargedParticles<T,Dim> *univ)
 
     rho_m[gDomainL_m]  = rhocic_m[gDomainL_m];
 
-    INFOMSG("rhocic_m= " << sum(rhocic_m) << " sum(M)= " << sum(univ->M) << " rho_m= " << sum(rho_m) << endl;);
+    INFOMSG("rhocic_m= " << sum(rhocic_m) << " sum(M)= " << sum(univ->M) << " rho_m= " << sum(rho_m) << endl);
 }
 
 /***************************************************************************

ippl/test/particle/PIC3d.cpp

@@ -474,7 +474,7 @@ public:
                 smsg->put(tmp[i]);
             bool res = Ippl::Comm->send(smsg, 0, tag);
             if (! res)
-                ERRORMSG("Ippl::Comm->send(smsg, 0, tag) failed " << endl;);
+                ERRORMSG("Ippl::Comm->send(smsg, 0, tag) failed " << endl);
         }
     }
 

ippl/test/toyfdtf/ipplToyFDTD2.cpp

@@ -211,8 +211,6 @@ int main(int argc, char *argv[]){
     Inform msg(argv[0]);
     Inform msg2all(argv[0],INFORM_ALL_NODES);
 
-    // variable declarations
-    int i,j,k;
     // indices of the 3D array of cells
     int nx, ny, nz;
     // total number of cells along the x, y, and z axes, respectively

src/AbstractObjects/OpalData.h

@@ -38,9 +38,6 @@ class BoundaryGeometry;
 // store element name, max phase
 typedef std::pair<std::string, double > MaxPhasesT;
 typedef std::map<double, double> energyEvolution_t;
-typedef energyEvolution_t::value_type energyEvData_t;
-
-
 
 // Class OpalData
 // ------------------------------------------------------------------------

src/Algorithms/ParallelCyclotronTracker.cpp

@@ -899,7 +899,7 @@ void ParallelCyclotronTracker::visitRFCavity(const RFCavity &as) {
     RFCavity *elptr = dynamic_cast<RFCavity *>(as.clone());
     myElements.push_back(elptr);
 
-    if((elptr->getComponentType() != "SINGLEGAP") && (elptr->getComponentType() != "DOUBLEGAP")) {
+    if ( elptr->getComponentType() != "SINGLEGAP" ) {
         *gmsg << (elptr->getComponentType()) << endl;
         throw OpalException("ParallelCyclotronTracker::visitRFCavity",
                             "The ParallelCyclotronTracker can only play with cyclotron type RF system currently ...");
@@ -1633,7 +1633,7 @@ double ParallelCyclotronTracker::getHarmonicNumber() const {
         return elcycl->getCyclHarm();
     throw OpalException("ParallelCyclotronTracker::getHarmonicNumber()",
                         std::string("The first item in the FieldDimensions list does not ")
-                        +std::string("seem to be an Ring or a Cyclotron element"));
+                        +std::string("seem to be a Ring or a Cyclotron element"));
 }
 
 

src/Algorithms/lomb.cpp

@@ -52,8 +52,6 @@ int LOMB_class::period(std::vector<LOMB_TYPE> *indata, std::vector<LOMB_TYPE> *o
     LOMB_TYPE pt;
 
     CI_lt p, q;
-    CI_vd ai;
-
     /*---------------------------------------------------------------------------*/
 
     wi.erase(wi.begin(), wi.end());
@@ -266,10 +264,7 @@ int LOMB_class::moment(std::vector<LOMB_TYPE> *indata, double *ave, double *adev
     int      n;
     double  pnr, s, ep;
 
-    std::vector<double> xvec;
-
     CI_lt p, q;
-    CI_vd xp;
     /*---------------------------------------------------------------------------*/
 
     p = indata->begin();

src/Amr/AmrYtWriter.cpp

@@ -496,9 +496,9 @@ void AmrYtWriter::writeBunch(const AmrPartBunch* bunch_p,
         std::string filePrefix(LevelDir);
         filePrefix += '/';
         filePrefix += "DATA_";
-        bool groupSets(false), setBuf(true);
 
         if (gotsome) {
+            bool groupSets(false), setBuf(true);
             for(amrex::NFilesIter nfi(nOutFiles, filePrefix, groupSets, setBuf); nfi.ReadyToWrite(); ++nfi) {
                 std::ofstream& myStream = (std::ofstream&) nfi.Stream();
                 //

src/Amr/AmrYtWriter.h

@@ -39,7 +39,7 @@ public:
      * @param step we write
      * @param bin energy bin we write (multi-bunch simulation)
      */
-    AmrYtWriter(int step, int bin = 0);
+    explicit AmrYtWriter(int step, int bin = 0);
     
     /*!
      * Write yt files to the simulation subdirectory

src/Classic/AbsBeamline/RFCavity.cpp

@@ -534,7 +534,7 @@ double RFCavity::getAutoPhaseEstimateFallback(double E0, double t0, double q, do
 }
 
 double RFCavity::getAutoPhaseEstimate(const double &E0, const double &t0, const double &q, const double &mass) {
-	std::vector<double> t, E, t2, E2;
+    std::vector<double> t, E, t2, E2;
     std::vector<double> F;
     std::vector< std::pair< double, double > > G;
     gsl_spline *onAxisInterpolants;
@@ -543,6 +543,7 @@ double RFCavity::getAutoPhaseEstimate(const double &E0, const double &t0, const
     double phi = 0.0, tmp_phi, dphi = 0.5 * Physics::pi / 180.;
     double dz = 1.0, length = 0.0;
     fieldmap_m->getOnaxisEz(G);
+    if (G.size() == 0) return 0.0;
     double begin = (G.front()).first;
     double end   = (G.back()).first;
     std::unique_ptr<double[]> zvals(      new double[G.size()]);
@@ -628,9 +629,9 @@ double RFCavity::getAutoPhaseEstimate(const double &E0, const double &t0, const
             t[i] = t[i - 1] + getdT(i, E, dz, mass);
             t2[i] = t2[i - 1] + getdT(i, E2, dz, mass);
 
-            E[i] = E[i - 1];
+            E[i]  = E [i - 1];
             E2[i] = E2[i - 1];
-            E[i] += q * scale_m * getdE(i, t, dz, phi, frequency_m, F) ;
+            E[i]  += q * scale_m * getdE(i, t, dz, phi, frequency_m, F) ;
             E2[i] += q * scale_m * getdE(i, t2, dz, phi + dphi, frequency_m, F);
         }
 

src/Classic/AbsBeamline/TravelingWave.cpp

@@ -199,7 +199,6 @@ void TravelingWave::initialise(PartBunchBase<double, 3> *bunch, double &startFie
     }
 
     Inform msg("TravelingWave ", *gmsg);
-    std::stringstream errormsg;
 
     RefPartBunch_m = bunch;
     double zBegin = 0.0, zEnd = 0.0;

src/Classic/Algorithms/PartBunch.cpp

@@ -345,7 +345,7 @@ void PartBunch::resizeMesh() {
                R[n](1) < ymin || R[n](1) > ymax) {
 
                 // delete the particle
-                INFOMSG(level2 << "destroyed particle with id=" << ID[n] << endl;);
+                INFOMSG(level2 << "destroyed particle with id=" << ID[n] << endl);
                 destroy(1, n);
             }
 
@@ -831,38 +831,6 @@ void PartBunch::updateFields(const Vector_t& /*hr*/, const Vector_t& origin) {
                     vbc_m);
 }
 
-
-/**
- * Here we emit particles from the cathode. All particles in a new simulation (not a restart) initially reside in the bin
- container "pbin_m" and are not part of the beam bunch (so they cannot "see" fields, space charge etc.). In pbin_m, particles
- are sorted into the bins of a time histogram that describes the longitudinal time distribution of the beam, where the number
- of bins is given by \f$NBIN \times SBIN\f$. \f$NBIN\f$ and \f$SBIN\f$ are parameters given when defining the initial beam
- distribution. During emission, the time step of the simulation is set so that an integral number of these bins are emitted each step.
- Once all of the particles have been emitted, the simulation time step is reset to the value defined in the input file.
-
- A typical integration time step, \f$\Delta t\f$, is broken down into 3 sub-steps:
-
- 1) Drift particles for \f$\frac{\Delta t}{2}\f$.
-
- 2) Calculate fields and advance momentum.
-
- 3) Drift particles for \f$\frac{\Delta t}{2}\f$ at the new momentum to complete the
- full time step.
-
- The difficulty for emission is that at the cathode position there is a step function discontinuity in the  fields. If we
- apply the typical integration time step across this boundary, we get an artificial numerical bunching of the beam, especially
- at very high accelerating fields. This function takes the cathode position boundary into account in order to achieve
- smoother particle emission.
-
- During an emission step, an integral number of time bins from the distribution histogram are emitted. However, each particle
- contained in those time bins will actually be emitted from the cathode at a different time, so will only spend some fraction
- of the total time step, \f$\Delta t_{full-timestep}\f$, in the simulation. The trick to emission is to give each particle
- a unique time step, \f$Delta t_{temp}\f$, that is equal to the actual time during the emission step that the particle
- exists in the simulation. For the next integration time step, the particle's time step is set back to the global time step,
- \f$\Delta t_{full-timestep}\f$.
-  */
-
-
 inline
 PartBunch::VectorPair_t PartBunch::getEExtrema() {
     const Vector_t maxE = max(eg_m);

src/Classic/Fields/Fieldmap.cpp

@@ -290,6 +290,10 @@ MapType Fieldmap::readHeader(std::string Filename) {
     if (Filename == "1DPROFILE1-DEFAULT")
         return T1DProfile1;
 
+    if (Filename.empty())
+        throw GeneralClassicException("Fieldmap::readHeader()",
+                                      "No field map file specified");
+
     if (!fs::exists(Filename))
         throw GeneralClassicException("Fieldmap::readHeader()",
                                       "File \"" + Filename + "\" doesn't exist");

src/Classic/Fields/Interpolation/MMatrix.cpp

@@ -374,17 +374,6 @@ template <class Tmplt> std::istream& operator>>(std::istream& in, MMatrix<Tmplt>
 
 
 ///////////////// INTERFACES
-const gsl_matrix*         MMatrix_to_gsl(const MMatrix<double>&    m)
-{
-  if(m._matrix == NULL) throw(GeneralClassicException("MMatrix_to_gsl", "Attempt to reference uninitialised matrix"));
-  return (gsl_matrix*)m._matrix;
-}
-
-const gsl_matrix_complex* MMatrix_to_gsl(const MMatrix<m_complex>& m)
-{
-  if(m._matrix == NULL) throw(GeneralClassicException("MMatrix_to_gsl", "Attempt to reference uninitialised matrix"));
-  return (gsl_matrix_complex*)m._matrix;
-}
 
 MMatrix<double>    re(MMatrix<m_complex> mc)
 {

src/Classic/Fields/Interpolation/MMatrix.h

@@ -172,10 +172,7 @@ public:
   friend MMatrix<m_complex>& operator +=(MMatrix<m_complex>& m1, const MMatrix<m_complex>& m2);
   friend MMatrix<double>&    operator +=(MMatrix<double>&    m1, const MMatrix<double>&    m2);
   template <class Tmplt2> friend MMatrix<Tmplt2>      operator + (MMatrix<Tmplt2>      m1, const MMatrix<Tmplt2>      m2);
- 
-  friend const gsl_matrix*         MMatrix_to_gsl(const MMatrix<double>& m);
-  friend const gsl_matrix_complex* MMatrix_to_gsl(const MMatrix<gsl_complex>& m);
- 
+
   friend class MMatrix<double>; //To do the eigenvector problem, MMatrix<double> needs to see MMatrix<complex>'s _matrix
 
 
@@ -233,10 +230,6 @@ MMatrix<double>    im(MMatrix<m_complex> m);
 MMatrix<m_complex> complex(MMatrix<double> real);
 MMatrix<m_complex> complex(MMatrix<double> real, MMatrix<double> imaginary);
 
-//return pointer to gsl_matrix objects that store matrix data in m
-const gsl_matrix*         MMatrix_to_gsl(const MMatrix<double>&      m);
-const gsl_matrix_complex* MMatrix_to_gsl(const MMatrix<gsl_complex>& m);
-
 //////////////////////////// MMatrix declaration end ///////////////
 
 

src/Classic/Fields/Interpolation/MVector.cpp

@@ -188,11 +188,6 @@ template <class Tmplt> std::istream& operator>>(std::istream& in, MVector<Tmplt>
   return in;
 }
 
-const gsl_vector*         MVector_to_gsl(const MVector<double>&      vd)
-{return vd.get_vector(vd);}
-const gsl_vector_complex* MVector_to_gsl(const MVector<gsl_complex>& vc)
-{return vc.get_vector(vc);}
-
 template <class Tmplt>
 MVector<Tmplt> MVector<Tmplt>::sub(size_t n1, size_t n2) const
 {

src/Classic/Fields/Interpolation/MVector.h

@@ -150,11 +150,6 @@ public:
   friend class MMatrix<Tmplt>;
   friend class MMatrix<double>;
 
-//  friend gsl_vector*         MVectorToGSL(MVector<double>&     );
-//  friend gsl_vector_complex* MVectorToGSL(MVector<gsl_complex>&);
-  friend const gsl_vector*         MVector_to_gsl(const MVector<double>&     );
-  friend const gsl_vector_complex* MVector_to_gsl(const MVector<gsl_complex>&);
-
 private:
   void build_vector ( size_t size ); //copy from data and put it in the vector
   void build_vector ( const Tmplt* data_start, const Tmplt* data_end ); //copy from data and put it in the vector
@@ -204,10 +199,6 @@ MVector<m_complex> complex(MVector<double> real, MVector<double> imaginary);
 MVector<double>    re     (MVector<m_complex> mv);
 MVector<double>    im     (MVector<m_complex> mv);
 
-//Interface to gsl
-const gsl_vector*         MVector_to_gsl(const MVector<double>&      vd);
-const gsl_vector_complex* MVector_to_gsl(const MVector<gsl_complex>& vc);
-
 ///////////////// MVector End ///////////////// Nb: some inlined functions below...
 
 //////////////////////////// MVector Inlined Functions //////////////

src/Classic/Fields/SectorField.h

@@ -79,8 +79,8 @@ class SectorField {
      *         Overwrites any existing data
      *  \returns true if any field value is non-zero
      */
-    virtual bool getFieldstrengthPolar
-                  (const Vector_t &R_p, Vector_t &E_p, Vector_t &B_p) const = 0;
+    /* virtual bool getFieldstrengthPolar */
+    /*               (const Vector_t &R_p, Vector_t &E_p, Vector_t &B_p) const = 0; */
 
     /** Return the field value in cartesian coordinates
      *

src/Classic/Fields/SectorMagneticFieldMap.cpp

@@ -189,8 +189,9 @@ std::string SectorMagneticFieldMap::SymmetryToString
           ));
 }
 
-bool SectorMagneticFieldMap::getFieldstrengthPolar (
-        const Vector_t &R_p, Vector_t &/*E_p*/, Vector_t &B_p) const {
+/*
+bool SectorMagneticFieldMap::getFieldstrengthPolar
+                    (const Vector_t &R_p, Vector_t &, Vector_t &B_p) const {
     // vector_t::operator[i] const returns by value, not by const reference
     // so we need to make an array here
     double R_temp[3] = {R_p[0], R_p[1], R_p[2]};
@@ -202,13 +203,14 @@ bool SectorMagneticFieldMap::getFieldstrengthPolar (
     SectorField::convertToPolar(R_temp, &(B_p[0]));
     return false;
 }
+*/
 
 bool SectorMagneticFieldMap::getFieldstrength (
         const Vector_t &R_c, Vector_t &/*E_c*/, Vector_t &B_c) const {
     // coordinate transform; field is in the x-z plane but OPAL-CYCL assumes
     // x-y plane; rotate to the start of the bend and into polar coordinates;
     // apply mirror symmetry about the midplane
-    double radius = (getPolarBoundingBoxMin()[0]+getPolarBoundingBoxMax()[0])/2;
+    double radius   = (getPolarBoundingBoxMin()[0]+getPolarBoundingBoxMax()[0])/2;
     double midplane = (getPolarBoundingBoxMin()[1]+getPolarBoundingBoxMax()[1])/2;
     double R_temp[3] = {R_c(0)+radius, R_c(1), R_c(2)};
     double B_temp[3] = {0., 0., 0.};

src/Classic/Fields/SectorMagneticFieldMap.h

@@ -114,8 +114,8 @@ class SectorMagneticFieldMap : public SectorField {
      *         Overwrites any existing data
      *  \returns false if R_p is inside the bounding box
      */
-    bool getFieldstrengthPolar
-                  (const Vector_t &R_p, Vector_t &E_p, Vector_t &B_p) const;
+    /* bool getFieldstrengthPolar */
+    /*               (const Vector_t &R_p, Vector_t &E_p, Vector_t &B_p) const; */
 
     /** Get the field value in cartesian coordinates
      *

src/Classic/FixedAlgebra/FTpsData.h

@@ -25,8 +25,6 @@
 #include "FixedAlgebra/FArray1D.h"
 #include "FixedAlgebra/FMonomial.h"
 
-#define DEBUG_FTpsData_H
-
 // Template class FTpsData<N>
 // ------------------------------------------------------------------------
 /// Internal utility class for FTps<T,N> class.

src/Distribution/Distribution.cpp

@@ -304,7 +304,7 @@ void Distribution::create(size_t &numberOfParticles, double massIneV, double cha
         createDistributionMultiGauss(numberOfLocalParticles, massIneV);
         break;
     default:
-        INFOMSG("Distribution unknown." << endl;);
+        INFOMSG("Distribution unknown." << endl);
         break;
     }
 
@@ -1194,15 +1194,15 @@ void Distribution::createMatchedGaussDistribution(size_t numberOfParticles,
     int Nsectors = (int)Attributes::getReal(itsAttr[Attrib::Distribution::NSECTORS]);
 
     if ( Nint < 0 )
-        throw OpalException("Distribution::CreateMatchedGaussDistribution()",
+        throw OpalException("Distribution::createMatchedGaussDistribution()",
                             "Negative number of integration steps");
 
     if ( Nsectors < 0 )
-        throw OpalException("Distribution::CreateMatchedGaussDistribution()",
+        throw OpalException("Distribution::createMatchedGaussDistribution()",
                             "Negative number of sectors");
 
     if ( Nsectors > 1 && full == false )
-        throw OpalException("Distribution::CreateMatchedGaussDistribution()",
+