replace all pointers to ElementBase with shared and weak pointers resp.

src/AbstractObjects/BeamSequence.h

@@ -20,6 +20,8 @@
 
 #include "AbstractObjects/Element.h"
 
+#include <memory>
+
 class Beamline;
 
 
@@ -48,7 +50,7 @@ public:
 
     /// Return the embedded CLASSIC beam line.
     //  The result it the ideal line.
-    virtual Beamline *fetchLine() const = 0;
+    virtual std::shared_ptr<Beamline> fetchLine() const = 0;
 
 protected:
 
@@ -68,4 +70,4 @@ private:
     void operator=(const BeamSequence &);
 };
 
-#endif // OPAL_BeamSequence_HH
+#endif // OPAL_BeamSequence_HH
\ No newline at end of file

src/AbstractObjects/Table.h

@@ -20,7 +20,9 @@
 
 #include "AbstractObjects/Object.h"
 #include "AbstractObjects/Expressions.h"
+
 #include <vector>
+#include <memory>
 
 class Attribute;
 class Beamline;
@@ -113,7 +115,7 @@ public:
     /// Return embedded CLASSIC beamline.
     //  Returns the CLASSIC beamline representing the table.
     //  The data of the table are attached to each position in the line.
-    virtual const Beamline *getLine() const = 0;
+    virtual std::shared_ptr<const Beamline> getLine() const = 0;
 
     /// Return a table row.
     //  Returns the values stored in the row specified by the first argument,
@@ -165,4 +167,4 @@ private:
     void operator=(const Table &);
 };
 
-#endif // OPAL_Table_HH
+#endif // OPAL_Table_HH
\ No newline at end of file

src/Algorithms/ParallelTTracker.cpp

@@ -605,7 +605,7 @@ void ParallelTTracker::computeExternalFields(OrbitThreader &oth) {
 
 void ParallelTTracker::computeWakefield(IndexMap::value_t &elements) {
     bool hasWake = false;
-    WakeFunction *wfInstance;
+    std::shared_ptr<WakeFunction> wfInstance;
 
     Inform msg("ParallelTTracker ", *gmsg);
 
@@ -640,7 +640,7 @@ void ParallelTTracker::computeWakefield(IndexMap::value_t &elements) {
 
             if (!wakeStatus_m) {
                 msg << level2 << "============== START WAKE CALCULATION =============" << endl;
-                wfInstance->initialize((*it).get());
+                wfInstance->initialize(*it);
                 wakeStatus_m = true;
             }
 
@@ -677,7 +677,7 @@ void ParallelTTracker::computeWakefield(IndexMap::value_t &elements) {
 void ParallelTTracker::computeParticleMatterInteraction(IndexMap::value_t elements, OrbitThreader &oth) {
     Inform msg("ParallelTTracker ", *gmsg);
     std::set<IndexMap::value_t::value_type> elementsWithParticleMatterInteraction;
-    std::set<ParticleMatterInteractionHandler*> particleMatterinteractionHandlers;
+    std::set<ParticleMatterInteractionHandler::SP> particleMatterinteractionHandlers;
     std::pair<double, double> currentRange(0.0, 0.0);
 
     while (elements.size() > 0) {
@@ -698,8 +698,8 @@ void ParallelTTracker::computeParticleMatterInteraction(IndexMap::value_t elemen
     }
 
     if (elementsWithParticleMatterInteraction.size() > 0) {
-        std::set<ParticleMatterInteractionHandler*> oldSPHandlers;
-        std::vector<ParticleMatterInteractionHandler*> leftBehindSPHandlers, newSPHandlers;
+        std::set<ParticleMatterInteractionHandler::SP> oldSPHandlers;
+        std::vector<ParticleMatterInteractionHandler::SP> leftBehindSPHandlers, newSPHandlers;
         for (auto it: activeParticleMatterInteractionHandlers_m) {
             oldSPHandlers.insert(it);
         }
@@ -738,7 +738,7 @@ void ParallelTTracker::computeParticleMatterInteraction(IndexMap::value_t elemen
         do {
             ///all particles in material if max per node is 2 and other degraders have 0 particles
             //check if more than one degrader has particles
-            ParticleMatterInteractionHandler* onlyDegraderWithParticles = NULL;
+            ParticleMatterInteractionHandler::SP onlyDegraderWithParticles = NULL;
             int degradersWithParticlesCount = 0;
             for (auto it: activeParticleMatterInteractionHandlers_m) {
                 it->setFlagAllParticlesIn(false);
@@ -979,7 +979,7 @@ void ParallelTTracker::writePhaseSpace(const long long /*step*/, bool psDump, bo
         FieldList collimators = itsOpalBeamline_m.getElementByType(ElementBase::CCOLLIMATOR);
         if (collimators.size() != 0) {
             for (FieldList::iterator it = collimators.begin(); it != collimators.end(); ++ it) {
-                FlexibleCollimator* coll = static_cast<FlexibleCollimator*>(it->getElement().get());
+                std::shared_ptr<FlexibleCollimator> coll = std::static_pointer_cast<FlexibleCollimator>(it->getElement());
                 std::string name = coll->getName();
                 unsigned int losses = coll->getLosses();
                 collimatorLosses.push_back(std::make_pair(name, losses));
@@ -1216,7 +1216,7 @@ void ParallelTTracker::autophaseCavities(const BorisPusher &pusher) {
     auto elementSet = itsOpalBeamline_m.getElements(nextR);
     for (auto element: elementSet) {
         if (element->getType() == ElementBase::TRAVELINGWAVE) {
-            const TravelingWave *TWelement = static_cast<const TravelingWave *>(element.get());
+            std::shared_ptr<const TravelingWave> TWelement = std::static_pointer_cast<const TravelingWave>(element);
             if (!TWelement->getAutophaseVeto()) {
                 CavityAutophaser ap(itsReference, element);
                 ap.getPhaseAtMaxEnergy(itsOpalBeamline_m.transformToLocalCS(element, itsBunch_m->RefPartR_m),
@@ -1225,7 +1225,7 @@ void ParallelTTracker::autophaseCavities(const BorisPusher &pusher) {
             }
 
         } else if (element->getType() == ElementBase::RFCAVITY) {
-            const RFCavity *RFelement = static_cast<const RFCavity *>(element.get());
+            std::shared_ptr<const RFCavity> RFelement = std::static_pointer_cast<const RFCavity>(element);
             if (!RFelement->getAutophaseVeto()) {
                 CavityAutophaser ap(itsReference, element);
                 ap.getPhaseAtMaxEnergy(itsOpalBeamline_m.transformToLocalCS(element, itsBunch_m->RefPartR_m),

src/Algorithms/ParallelTTracker.h

@@ -63,6 +63,7 @@
 
 #include <list>
 #include <vector>
+#include <memory>
 
 class ParticleMatterInteractionHandler;
 
@@ -205,7 +206,7 @@ private:
 
     bool deletedParticles_m;
 
-    WakeFunction* wakeFunction_m;
+    std::shared_ptr<WakeFunction> wakeFunction_m;
 
     double pathLength_m;
 
@@ -242,7 +243,7 @@ private:
     IpplTimings::TimerRef BinRepartTimer_m;
     IpplTimings::TimerRef WakeFieldTimer_m;
 
-    std::set<ParticleMatterInteractionHandler*> activeParticleMatterInteractionHandlers_m;
+    std::set<std::shared_ptr<ParticleMatterInteractionHandler>> activeParticleMatterInteractionHandlers_m;
     bool particleMatterStatus_m;
 
     unsigned long totalParticlesInSimulation_m;

src/Classic/AbsBeamline/BeamStripping.cpp

@@ -69,7 +69,7 @@ BeamStripping::BeamStripping(const BeamStripping &right):
     maxr_m(right.maxr_m),
     minz_m(right.minz_m),
     maxz_m(right.maxz_m),
-    parmatint_m(NULL) {
+    parmatint_m(nullptr) {
 }
 
 BeamStripping::BeamStripping(const std::string &name):
@@ -84,7 +84,7 @@ BeamStripping::BeamStripping(const std::string &name):
     maxr_m(0.0),
     minz_m(0.0),
     maxz_m(0.0),
-    parmatint_m(NULL) {
+    parmatint_m(nullptr) {
 }
 
 
@@ -166,7 +166,7 @@ bool BeamStripping::getStop() const {
 }
 
 
-bool BeamStripping::checkBeamStripping(PartBunchBase<double, 3> *bunch, std::shared_ptr<Cyclotron> cycl,
+bool BeamStripping::checkBeamStripping(PartBunchBase<double, 3> *bunch, std::shared_ptr<Cyclotron> const& cycl,
                                        const int /*turnnumber*/, const double /*t*/, const double /*tstep*/) {
 
     bool flagNeedUpdate = false;
@@ -190,7 +190,7 @@ bool BeamStripping::checkBeamStripping(PartBunchBase<double, 3> *bunch, std::sha
     }
     reduce(&flagNeedUpdate, &flagNeedUpdate + 1, &flagNeedUpdate, OpBitwiseOrAssign());
     if (flagNeedUpdate && parmatint_m) {
-        dynamic_cast<BeamStrippingPhysics*>(parmatint_m)->setCyclotron(cycl);
+        std::dynamic_pointer_cast<BeamStrippingPhysics>(parmatint_m)->setCyclotron(cycl);
         parmatint_m->apply(bunch, boundingSphere);
     }
     return flagNeedUpdate;

src/Classic/AbsBeamline/BeamStripping.h

@@ -27,9 +27,11 @@
 
 #include <string>
 #include <vector>
+#include <memory>
 
 class BeamlineVisitor;
 class Cyclotron;
+class ParticleMatterInteractionHandler;
 
 struct PFieldData {
     std::string filename;
@@ -77,7 +79,7 @@ public:
     /// Apply visitor to BeamStripping.
     virtual void accept(BeamlineVisitor &) const;
 
-    virtual bool checkBeamStripping(PartBunchBase<double, 3> *bunch, std::shared_ptr<Cyclotron> cycl, const int turnnumber, const double t, const double tstep);
+    virtual bool checkBeamStripping(PartBunchBase<double, 3> *bunch, std::shared_ptr<Cyclotron> const& cycl, const int turnnumber, const double t, const double tstep);
 
     virtual void initialise(PartBunchBase<double, 3> *bunch, double &startField, double &endField);
 
@@ -145,7 +147,7 @@ private:
     double maxz_m;   /// mm
     ///@}
 
-    ParticleMatterInteractionHandler *parmatint_m;
+    std::shared_ptr<ParticleMatterInteractionHandler> parmatint_m;
 
 protected:
     // object of Matrices including pressure field map and its derivates

src/Classic/AbsBeamline/CCollimator.h

@@ -20,6 +20,8 @@
 
 #include "AbsBeamline/PluginElement.h"
 
+#include <memory>
+
 class ParticleMatterInteractionHandler;
 
 class CCollimator: public PluginElement {
@@ -83,7 +85,7 @@ private:
     ///@}
     double rmax_m; ///< maximum extend in r
 
-    ParticleMatterInteractionHandler *parmatint_m = nullptr;
+    std::shared_ptr<ParticleMatterInteractionHandler> parmatint_m = nullptr;
 };
 
 inline
@@ -100,4 +102,4 @@ inline
 double CCollimator::getWidth() {
     return width_m;
 }
-#endif // CLASSIC_CCollimator_HH
+#endif // CLASSIC_CCollimator_HH
\ No newline at end of file

src/Classic/AbsBeamline/ElementBase.cpp

@@ -151,7 +151,7 @@ Channel *ElementBase::getChannel(const std::string &aKey, bool create) {
 const ConstChannel *ElementBase::getConstChannel(const std::string &aKey) const {
     // Use const_cast to allow calling the non-const method GetChannel().
     // The const return value of this method will nevertheless inhibit set().
-    return const_cast<ElementBase *>(this)->getChannel(aKey);
+    return const_cast<ElementBase * >(this)->getChannel(aKey);
 }
 
 
@@ -310,15 +310,15 @@ bool ElementBase::update(const AttributeSet &set) {
     return true;
 }
 
-void ElementBase::setWake(WakeFunction *wk) {
-    wake_m = wk;//->clone(getName() + std::string("_wake")); }
+void ElementBase::setWake(std::shared_ptr<WakeFunction> const& wf) {
+    wake_m = wf;
 }
 
 void ElementBase::setBoundaryGeometry(BoundaryGeometry *geo) {
     bgeometry_m = geo;//->clone(getName() + std::string("_wake")); }
 }
 
-void ElementBase::setParticleMatterInteraction(ParticleMatterInteractionHandler *parmatint) {
+void ElementBase::setParticleMatterInteraction(std::shared_ptr<ParticleMatterInteractionHandler> const& parmatint) {
     parmatint_m = parmatint;
 }
 

src/Classic/AbsBeamline/ElementBase.h

@@ -399,16 +399,16 @@ public:
 
 
     /// attach a wake field to the element
-    virtual void setWake(WakeFunction *wf);
+    virtual void setWake(std::shared_ptr<WakeFunction> const& wf);
 
     /// return the attached wake object if there is any
-    virtual WakeFunction *getWake() const;
+    virtual std::shared_ptr<WakeFunction> getWake() const;
 
     virtual bool hasWake() const;
 
-    virtual void setParticleMatterInteraction(ParticleMatterInteractionHandler *spys);
+    virtual void setParticleMatterInteraction(std::shared_ptr<ParticleMatterInteractionHandler> const& spys);
 
-    virtual ParticleMatterInteractionHandler *getParticleMatterInteraction() const;
+    virtual std::shared_ptr<ParticleMatterInteractionHandler> getParticleMatterInteraction() const;
 
     virtual bool hasParticleMatterInteraction() const;
 
@@ -466,11 +466,11 @@ private:
     // The user-defined set of attributes.
     AttributeSet userAttribs;
 
-    WakeFunction *wake_m;
+    std::shared_ptr<WakeFunction> wake_m;
 
     BoundaryGeometry *bgeometry_m;
 
-    ParticleMatterInteractionHandler *parmatint_m;
+    std::shared_ptr<ParticleMatterInteractionHandler> parmatint_m;
 
     bool positionIsFixed;
     ///@{ ELEMEDGE attribute
@@ -541,12 +541,12 @@ bool ElementBase::isSharable() const
 { return shareFlag; }
 
 inline
-WakeFunction *ElementBase::getWake() const
+std::shared_ptr<WakeFunction> ElementBase::getWake() const
 { return wake_m; }
 
 inline
 bool ElementBase::hasWake() const
-{ return wake_m != NULL; }
+{ return wake_m != nullptr; }
 
 inline
 BoundaryGeometry *ElementBase::getBoundaryGeometry() const
@@ -557,12 +557,12 @@ bool ElementBase::hasBoundaryGeometry() const
 { return bgeometry_m != NULL; }
 
 inline
-ParticleMatterInteractionHandler *ElementBase::getParticleMatterInteraction() const
+std::shared_ptr<ParticleMatterInteractionHandler> ElementBase::getParticleMatterInteraction() const
 { return parmatint_m; }
 
 inline
 bool ElementBase::hasParticleMatterInteraction() const
-{ return parmatint_m != NULL; }
+{ return parmatint_m != nullptr; }
 
 inline
 void ElementBase::setCSTrafoGlobal2Local(const CoordinateSystemTrafo &trafo)

src/Classic/AbsBeamline/FlexibleCollimator.h

@@ -80,7 +80,7 @@ private:
     unsigned int losses_m;
     std::unique_ptr<LossDataSink> lossDs_m;
 
-    ParticleMatterInteractionHandler *parmatint_m;
+    std::shared_ptr<ParticleMatterInteractionHandler> parmatint_m;
 };
 
 inline
@@ -108,4 +108,4 @@ std::string FlexibleCollimator::getDescription() const {
     return description_m;
 }
 
-#endif // CLASSIC_FlexibleCollimator_HH
+#endif // CLASSIC_FlexibleCollimator_HH
\ No newline at end of file

src/Classic/AbsBeamline/Integrator.cpp

@@ -25,7 +25,7 @@
 // Class Integrator
 // ------------------------------------------------------------------------
 
-Integrator::Integrator(ElementBase *elem):
+Integrator::Integrator(ElementBase::SP const& elem):
     ElementBase(elem->getName()), itsElement(elem)
 {}
 
@@ -42,4 +42,4 @@ Integrator::~Integrator()
 void Integrator::makeSharable() {
     shareFlag = true;
     itsElement->makeSharable();
-}
+}
\ No newline at end of file

src/Classic/AbsBeamline/Integrator.h

@@ -42,12 +42,12 @@ class Integrator: public ElementBase {
 
 public:
 
-    explicit Integrator(ElementBase *);
+    explicit Integrator(ElementBase::SP const& );
     Integrator(const Integrator &rhs);
     virtual ~Integrator();
 
     /// Return the embedded element.
-    inline ElementBase *getElement() const;
+    inline ElementBase::SP getElement() const;
 
     /// Set sharable flag.
     //  The whole structure depending on [b]this[/b] is marked as sharable.
@@ -81,7 +81,7 @@ public:
 protected:
 
     /// Pointer to the replaced element.
-    Pointer<ElementBase> itsElement;
+    ElementBase::SP itsElement;
 
 private:
 
@@ -94,8 +94,8 @@ private:
 // Implementation.
 // ------------------------------------------------------------------------
 
-inline ElementBase *Integrator::getElement() const {
-    return &*itsElement;
+inline ElementBase::SP Integrator::getElement() const {
+    return itsElement;
 }
 
-#endif // CLASSIC_Integrator_HH
+#endif // CLASSIC_Integrator_HH
\ No newline at end of file

src/Classic/Beamlines/ElmPtr.cpp

@@ -33,7 +33,7 @@ ElmPtr::ElmPtr(const ElmPtr &rhs):
 {}
 
 
-ElmPtr::ElmPtr(ElementBase *elem):
+ElmPtr::ElmPtr(ElementBase::SP const& elem):
     itsElement(elem)
 {}
 
@@ -44,4 +44,4 @@ ElmPtr::~ElmPtr()
 
 void ElmPtr::accept(BeamlineVisitor &visitor) const {
     itsElement->accept(visitor);
-}
+}
\ No newline at end of file

src/Classic/Beamlines/ElmPtr.h

@@ -35,7 +35,7 @@ public:
 
     ElmPtr();
     ElmPtr(const ElmPtr &);
-    ElmPtr(ElementBase *);
+    ElmPtr(ElementBase::SP const& );
     virtual ~ElmPtr();
 
     /// Apply visitor.

src/Classic/Construction/Factory.h

@@ -20,10 +20,11 @@
 //
 // ------------------------------------------------------------------------
 
+#include "AbsBeamline/Definition.h"
+
 #include <string>
 #include <memory>
 
-class ElementBase;
 class AttributeSet;