improve includes: only include strictly necessary

ippl/src/AppTypes/Vektor.h

@@ -17,6 +17,7 @@
 #include "PETE/IpplExpressions.h"
 #include "AppTypes/TSVMeta.h"
 
+#include <cmath>
 #include <iostream>
 #include <iomanip>
 
@@ -277,6 +278,17 @@ cross(const Vektor<T1,D> &lhs, const Vektor<T2,D> &rhs)
   return TSV_MetaCross< Vektor<T1,D> , Vektor<T2,D> > :: apply(lhs,rhs);
 }
 
+//----------------------------------------------------------------------
+// euclidean norm
+//----------------------------------------------------------------------
+template < class T, unsigned D >
+inline double
+euclidean_norm(const Vektor<T, D> &a)
+{
+  return std::sqrt(dot(a, a));
+}
+
+
 //----------------------------------------------------------------------
 // I/O
 template<class T, unsigned D>
@@ -296,10 +308,4 @@ inline std::ostream& operator<<(std::ostream& out, const Vektor<T,D>& rhs)
   return out;
 }
 
-#endif // VEKTOR_H
-
-/***************************************************************************
- * $RCSfile: Vektor.h,v $   $Author: adelmann $
- * $Revision: 1.1.1.1 $   $Date: 2003/01/23 07:40:24 $
- * IPPL_VERSION_ID: $Id: Vektor.h,v 1.1.1.1 2003/01/23 07:40:24 adelmann Exp $
- ***************************************************************************/
\ No newline at end of file
+#endif // VEKTOR_H
\ No newline at end of file

ippl/src/FFT/FFT.hpp

@@ -15,7 +15,7 @@
 #include "FFT/FFT.h"
 #include "FieldLayout/FieldLayout.h"
 #include "Field/BareField.h"
-#include "Utility/IpplStats.h"
+//#include "Utility/IpplStats.h"
 
 //=============================================================================
 // FFT CCTransform Constructors

ippl/src/Field/BareField.h

@@ -31,6 +31,7 @@
 #include "Index/SIndex.h"
 #include "SubField/SubBareField.h"
 #include "Utility/IpplInfo.h"
+#include "Utility/IpplStats.h"
 #include "Utility/PAssert.h"
 #include "Utility/Unique.h"
 #include "Utility/my_auto_ptr.h"

ippl/src/Field/BareField.hpp

@@ -33,10 +33,9 @@
 #include "Utility/Inform.h"
 #include "Utility/Unique.h"
 #include "Utility/IpplInfo.h"
-#include "Utility/IpplStats.h"
+//#include "Utility/IpplStats.h"
 
 #include <map>
-#include <utility>
 #include <cstdlib>
 
 

ippl/src/Index/SIndexAssign.hpp

@@ -27,9 +27,9 @@
 #include "Index/SIndexAssign.h"
 #include "Index/SIndex.h"
 #include "Field/BrickIterator.h"
-#include "Field/Field.h"
-#include "Field/IndexedField.h"
-#include "Field/Assign.h"
+// #include "Field/Field.h"
+// #include "Field/IndexedField.h"
+// #include "Field/Assign.h"
 #include "Utility/IpplInfo.h"
 
 

ippl/src/Meshes/UniformCartesian.hpp

@@ -14,7 +14,6 @@
 #include "Field/BareField.h"
 #include "Field/BrickExpression.h"
 #include "Field/LField.h"
-#include "Field/Field.h"
 #include "Field/Assign.h"
 #include "Field/AssignDefs.h"
 

ippl/src/Message/Communicate.cpp

@@ -38,7 +38,6 @@
 
 #include "Utility/IpplInfo.h"
 #include "Utility/IpplStats.h"
-#include "Utility/RandomNumberGen.h"
 #include "Utility/PAssert.h"
 #include <cstdio>
 

ippl/src/Message/Message.h

@@ -31,7 +31,6 @@
  * of resolving who needs to free up the storage used for the Message elements.
  ***************************************************************************/
 
-#include "Utility/Inform.h"
 #include <complex>
 #include <cstddef>
 #include <vector>

ippl/src/Message/Message.hpp

@@ -12,7 +12,6 @@
  ***************************************************************************/
 
 #include "Message/Message.h"
-#include "Utility/Inform.h"
 #include "Utility/IpplInfo.h"
 
 #include <iterator>

ippl/src/Particle/AbstractParticle.h

@@ -22,7 +22,9 @@
 #define ABSTRACT_PARTICLE_H
 
 #include "Particle/ParticleLayout.h"
-#include "Particle/ParticleAttrib.h"
+
+template<class T> class ParticleAttrib;
+class ParticleAttribBase;
 
 template <class T, unsigned Dim>
 class AbstractParticle {

ippl/src/Particle/Interpolator.h

@@ -16,14 +16,13 @@
 #include "Field/LField.h"
 #include "Field/CompressedBrickIterator.h"
 #include "Index/NDIndex.h"
+#include "Meshes/Centering.h"
 #include "AppTypes/Vektor.h"
 #include "Utility/IpplInfo.h"
 #include "Utility/IpplException.h"
 
-#include <iostream>
+#include <ostream>
 #include <vector>
-#include <utility>
-#include <cmath>
 
 // Helper class and functions for finding nearest grid point given centering
 

ippl/src/Particle/IpplParticleBase.h

@@ -95,15 +95,18 @@
 
 // include files
 #include "Particle/AbstractParticle.h"
+#include "Particle/ParticleAttribBase.h"
+#include "Particle/ParticleLayout.h"
 #include "AppTypes/Vektor.h"
 #include "DataSource/DataSource.h"
 #include "DataSource/MakeDataSource.h"
 #include "Message/Formatter.h"
 #include <vector>
-#include <algorithm>  // Include algorithms
 #include <utility>
 #include <iostream>
 
+template <class T, unsigned Dim>
+using PLayout = ParticleLayout<T, Dim>;
 
 // forward declarations
 class Inform;
@@ -120,7 +123,6 @@ template <class T, unsigned D> class ParticleBConds;
 template<class PLayout>
 class IpplParticleBase : public DataSource,
                          public AbstractParticle<typename PLayout::Position_t, PLayout::Dimension> {
-
 public:
     // useful enums
     enum { Dim = PLayout::Dimension };

ippl/src/Particle/PAssignDefs.h

@@ -18,7 +18,8 @@
 // forward declarations
 template<class T> class ParticleAttrib;
 template<class T, unsigned Dim> class ParticleAttribElem;
-
+template<class T> class ParticleAttribIterator;
+template <class T> class ParticleAttribConstIterator;
 
 //////////////////////////////////////////////////////////////////////
 //

ippl/src/Particle/ParticleAttrib.h

@@ -73,6 +73,7 @@
 // include files
 #include "Particle/ParticleAttribBase.h"
 #include "Particle/ParticleAttribElem.h"
+#include "Particle/PAssign.h"
 #include "SubParticle/SubParticleAttrib.h"
 #include "DataSource/DataSource.h"
 #include "DataSource/MakeDataSource.h"

ippl/src/SubParticle/SubParticleAssignDefs.h

@@ -13,7 +13,7 @@
 
 // include files
 #include "SubField/SubFieldAssignDefs.h"
-#include "SubParticle/SubParticleAssign.h"
+#include "SubParticle/SubParticleAttrib.h"
 
 //////////////////////////////////////////////////////////////////////
 //

ippl/src/Utility/DiscField.h

@@ -14,7 +14,6 @@
 // include files
 #include "Index/NDIndex.h"
 #include "Field/BrickExpression.h"
-#include "Field/Field.h"
 #include "Utility/DiscBuffer.h"
 #include "Utility/DiscConfig.h"
 #include "Utility/Inform.h"
@@ -24,8 +23,6 @@
 #include <cstdlib>
 #include <unistd.h>
 #include <fcntl.h>
-#include <sys/stat.h>
-#include <sys/types.h>
 
 #include <vector>
 #include <iostream>

ippl/src/Utility/DiscField.hpp

@@ -27,7 +27,6 @@
 #include "Utility/DiscField.h"
 #include "Utility/DiscConfig.h"
 #include "Utility/DiscMeta.h"
-#include "Field/BrickIterator.h"
 #include "Message/Tags.h"
 
 #include "Utility/PAssert.h"

ippl/src/Utility/DiscParticle.h

@@ -15,9 +15,9 @@
 #include "Utility/DiscConfig.h"
 #include "Utility/IpplInfo.h"
 #include "Utility/PAssert.h"
+#include "Message/Communicate.h"
 #include "Message/Message.h"
-
-
+#include "Message/Tags.h"
 
 #include <vector>
 #include <iostream>
@@ -26,7 +26,6 @@
 // forward declarations
 template<class T> class IpplParticleBase;
 template<class T> class ParticleAttrib;
-class Message;
 
 class DiscParticle {
 

ippl/src/Utility/Inform.h

@@ -34,6 +34,7 @@
 #include <iostream>
 #include <iomanip>
 #include <sstream>
+#include <string>
 
 #define INFORM_ALL_NODES        (-1)
 

ippl/src/Utility/IpplInfo.cpp

@@ -25,6 +25,7 @@
 
 // include files
 #include "Utility/IpplInfo.h"
+#include "Utility/Inform.h"
 #include "Utility/IpplStats.h"
 #include "Utility/PAssert.h"
 #include "Utility/RandomNumberGen.h"

ippl/src/Utility/IpplInfo.h

@@ -43,9 +43,8 @@
  */
 
 // include files
-#include "Utility/Inform.h"
-#include "Message/Communicate.h"
 #include "Utility/StaticIpplInfo.h"
+#include "Utility/Inform.h"
 
 #include <iostream>
 #include <stack>
@@ -56,6 +55,8 @@
 #include <mpi.h>
 
 // forward declarations
+class Communicate;
+class Inform;
 class IpplStats;
 class IpplInfo;
 std::ostream& operator<<(std::ostream&, const IpplInfo&);

ippl/src/Utility/IpplMemoryUsage.cpp

@@ -40,6 +40,9 @@
 //
 #include "Utility/IpplMemoryUsage.h"
 
+#include "Message/GlobalComm.h"
+#include "Utility/IpplInfo.h"
+
 //////////////////////////////////////////////////////////////////////
 IpplMemoryUsage::IpplMemoryUsage()
 { }

ippl/src/Utility/IpplMemoryUsage.h

@@ -38,11 +38,11 @@
 // You should have received a copy of the GNU General Public License
 // along with OPAL. If not, see <https://www.gnu.org/licenses/>.
 //
-#ifndef IPPL_MEMPRYUSAGE_H
-#define IPPL_MEMPRYUSAGE_H
+#ifndef IPPL_MEMORYUSAGE_H
+#define IPPL_MEMORYUSAGE_H
 
-#include "Ippl.h"
 #include <memory>
+#include <string>
 
 #include <sys/resource.h>
 #include <sys/time.h> // not required but increases portability

ippl/src/Utility/IpplStats.h

@@ -38,10 +38,11 @@
 // include files
 #include "Utility/IpplInfo.h"
 #include "Utility/Timer.h"
-#include "Utility/Inform.h"
 
 #include <vector>
 
+class Inform;
+
 class IpplStats {
 
 public:

ippl/src/Utility/IpplTimings.cpp

@@ -7,7 +7,6 @@
 
 #include "Utility/IpplTimings.h"
 #include "Utility/Inform.h"
-#include "Utility/IpplInfo.h"
 #include "Message/GlobalComm.h"
 #include "PETE/IpplExpressions.h"
 

ippl/src/Utility/PAssert.h

@@ -6,7 +6,6 @@
 
 #ifndef PASSERT_H
 #define PASSERT_H
-#include "Utility/IpplInfo.h"
 
 #include <exception>
 #include <stdexcept>

optimizer/Comm/types.h

@@ -21,8 +21,6 @@
 #ifndef __COMM_TYPES__
 #define __COMM_TYPES__
 
-#include <vector>
-
 #include "mpi.h"
 
 namespace Comm {

optimizer/Util/CmdArguments.cpp

@@ -27,6 +27,8 @@
 //
 #include "Util/CmdArguments.h"
 
+#include "boost/algorithm/string.hpp"
+
 void CmdArguments::addArguments(int argc, char **argv) {
 
     for(int i=1; i<argc; i++) {

optimizer/Util/CmdArguments.h

@@ -35,7 +35,6 @@
 #include <set>
 
 #include "boost/smart_ptr.hpp"
-#include "boost/algorithm/string.hpp"
 #include "boost/utility/value_init.hpp"
 
 #include "Util/OptPilotException.h"

optimizer/Util/MPIHelper.cpp

@@ -22,6 +22,7 @@
 
 #include <boost/static_assert.hpp>
 #include <boost/serialization/map.hpp>
+#include <boost/serialization/vector.hpp>
 
 #include <boost/archive/text_oarchive.hpp>
 #include <boost/archive/text_iarchive.hpp>

optimizer/Util/Types.h

@@ -21,17 +21,12 @@
 #ifndef __TYPES_H__
 #define __TYPES_H__
 
-#include <vector>
 #include <map>
+#include <utility>
+#include <vector>
 
-#include <boost/serialization/map.hpp>
-#include "boost/serialization/vector.hpp"
 #include "boost/tuple/tuple.hpp"
 
-#include "boost/variant.hpp"
-#include "boost/fusion/adapted/struct/adapt_struct.hpp"
-#include "boost/fusion/include/adapt_struct.hpp"
-
 #include "Expression/Expression.h"
 
 //FIXME: add namespaces

src/AbstractObjects/Attribute.cpp

@@ -20,6 +20,8 @@
 #include "AbstractObjects/AttributeBase.h"
 #include "Utilities/Options.h"
 
+#include "Utility/Inform.h"
+
 #include <set>
 #include <iostream>
 

src/AbstractObjects/Attribute.h

@@ -24,9 +24,6 @@
 #include <iosfwd>
 #include <string>
 
-// #include <Ippl.h>
-#include <Utility/Inform.h>
-
 class Statement;
 
 // Class Attribute

src/Algorithms/ParallelTTracker.cpp

@@ -22,19 +22,18 @@
 #include "Algorithms/ParallelTTracker.h"
 
 #include <cfloat>
-#include <iostream>
+#include <cmath>
 #include <fstream>
+#include <limits>
 #include <iomanip>
+#include <iostream>
 #include <sstream>
 #include <string>
-#include <limits>
-#include <cmath>
 
 #include "Algorithms/OrbitThreader.h"
 #include "Algorithms/CavityAutophaser.h"
 #include "Beamlines/Beamline.h"
 #include "Beamlines/FlaggedBeamline.h"
-#include "Lines/Sequence.h"
 
 #include "Solvers/CSRWakeFunction.hh"
 

src/Algorithms/ThickTracker.h

@@ -24,42 +24,27 @@
 #define OPAL_ThickTracker_HH
 
 #include "Algorithms/Tracker.h"
-#include "Structure/DataSink.h"
 
 #include "Hamiltonian.h"
 
-#include "MapAnalyser.h"
-
 #include "Algorithms/IndexMap.h"
 #include "AbsBeamline/BeamStripping.h"
-#include "AbsBeamline/CCollimator.h"
-#include "AbsBeamline/Corrector.h"
-#include "AbsBeamline/Degrader.h"
 #include "AbsBeamline/Drift.h"
-#include "AbsBeamline/FlexibleCollimator.h"
 #include "AbsBeamline/ElementBase.h"
-#include "AbsBeamline/Marker.h"
-#include "AbsBeamline/Monitor.h"
 #include "AbsBeamline/Multipole.h"
-#include "AbsBeamline/Probe.h"
-#include "AbsBeamline/RFCavity.h"
-#include "AbsBeamline/RBend.h"
 #include "AbsBeamline/RBend3D.h"
 #include "AbsBeamline/SBend.h"
-#include "AbsBeamline/Septum.h"
-#include "AbsBeamline/Solenoid.h"
-#include "AbsBeamline/TravelingWave.h"
 
 #include "Elements/OpalBeamline.h"
 
-#include "Structure/Beam.h"
-
-//#include <array>
 #include <cmath>
-
+#include <list>
+#include <string>
 #include <tuple>
+#include <vector>
 
 class BMultipoleField;
+class DataSink;
 
 template <class T, unsigned Dim>
 class PartBunchBase;
@@ -101,14 +86,13 @@ class PartBunchBase;
 
 class ThickTracker: public Tracker {
 
-public:
+private:
     typedef Hamiltonian::series_t                       series_t;
-    typedef MapAnalyser::fMatrix_t                      fMatrix_t;
-    typedef MapAnalyser::cfMatrix_t                     cfMatrix_t;
     typedef FVps<double, 6>                             map_t;
     typedef FVector<double, 6>                          particle_t;
     typedef std::tuple<series_t, std::size_t, double>   tuple_t;
     typedef std::list<tuple_t>                          beamline_t;
+    typedef FMatrix<double, 6, 6>                       fMatrix_t;
 
 public:
 
@@ -331,7 +315,6 @@ private:
 
 
     Hamiltonian hamiltonian_m;
-    MapAnalyser mapAnalyser_m;
 
 
     Vector_t RefPartR_m;

src/BasicActions/Option.cpp

@@ -20,13 +20,13 @@
 #include "BasicActions/Option.h"
 #include "Attributes/Attributes.h"
 #include "Parser/FileStream.h"
+#include "Utilities/OpalException.h"
 #include "Utilities/Options.h"
 #include "Utilities/OptionTypes.h"
 #include "Utilities/ClassicRandom.h"
-#include "Utility/IpplInfo.h"
-
-#include "Utilities/OpalException.h"
 
+#include "Utility/Inform.h"
+#include "Utility/IpplInfo.h"
 #include "Utility/IpplMemoryUsage.h"
 
 #include <ctime>

src/BasicActions/PSystem.cpp

@@ -18,9 +18,10 @@
 
 #include "BasicActions/PSystem.h"
 
-#include "Ippl.h"
 #include "Attributes/Attributes.h"
 
+#include "Utility/IpplInfo.h"
+
 #include <cstdlib>
 // Class PSystem
 // ------------------------------------------------------------------------

src/BasicActions/System.cpp

@@ -18,9 +18,10 @@
 
 #include "BasicActions/System.h"
 
-#include "Ippl.h"
 #include "Attributes/Attributes.h"
 
+#include "Utility/IpplInfo.h"
+
 #include <cstdlib>
 // Class System
 // ------------------------------------------------------------------------

src/Classic/AbsBeamline/BeamStripping.cpp

@@ -38,10 +38,7 @@
 #include <cmath>
 #include <cstdio>
 
-#include "Ippl.h"
-
-#include "gsl/gsl_spline.h"
-#include "gsl/gsl_interp.h"
+#include "Utility/Inform.h"
 
 #define CHECK_BSTP_FSCANF_EOF(arg) if (arg == EOF)\
 throw GeneralClassicException("BeamStripping::getPressureFromFile",\

src/Classic/AbsBeamline/Component.h

@@ -25,7 +25,6 @@
 
 #include "AbsBeamline/ElementBase.h"
 #include "Fields/EMField.h"
-#include "Algorithms/Vektor.h"
 
 class PartData;
 

src/Classic/AbsBeamline/Degrader.cpp

@@ -21,13 +21,12 @@
 #include "AbsBeamline/Degrader.h"
 #include "Algorithms/PartBunchBase.h"
 #include "AbsBeamline/BeamlineVisitor.h"
-#include "Fields/Fieldmap.h"
 #include "Structure/LossDataSink.h"
 #include "Utilities/Options.h"
 #include "Solvers/ParticleMatterInteractionHandler.hh"
 #include "Physics/Physics.h"
-#include "Utilities/Util.h"
 #include <memory>
+#include <string>
 
 extern Inform *gmsg;
 

src/Classic/AbsBeamline/Degrader.h

@@ -25,6 +25,8 @@
 #include "AbsBeamline/Component.h"
 #include "AbsBeamline/BeamlineVisitor.h"
 #include "BeamlineGeometry/StraightGeometry.h"
+
+#include <string>
 #include <vector>
 
 class LossDataSink;

src/Classic/AbsBeamline/ElementBase.h

@@ -65,8 +65,8 @@
 
 #include "AbsBeamline/AttributeSet.h"
 #include "BeamlineGeometry/Geometry.h"
+#include "BeamlineGeometry/Euclid3D.h"
 #include "MemoryManagement/RCObject.h"
-#include "Algorithms/Vektor.h"
 #include "Algorithms/Quaternion.h"
 #include "Algorithms/CoordinateSystemTrafo.h"
 #include "Utilities/GeneralClassicException.h"
@@ -328,7 +328,6 @@ public:
 
     virtual bool isInside(const Vector_t &r) const;
 
-    void setMisalignment(double x, double y, double s);
     void setMisalignment(const CoordinateSystemTrafo &cst);
 
     void getMisalignment(double &x, double &y, double &s) const;

src/Classic/AbsBeamline/SBend.cpp

@@ -19,13 +19,10 @@
 // ------------------------------------------------------------------------
 
 #include "AbsBeamline/SBend.h"
-#include "Algorithms/PartBunchBase.h"
 #include "AbsBeamline/BeamlineVisitor.h"
-#include "Utilities/Options.h"
 #include "Fields/Fieldmap.h"
-#include "AbstractObjects/OpalData.h"
-#include <iostream>
-#include <fstream>
+
+#include <string>
 
 extern Inform *gmsg;
 

src/Classic/Algorithms/PBunchDefs.h

@@ -3,17 +3,10 @@
 
 #include "Algorithms/Vektor.h"
 #include "Particle/IntCIC.h"
-#include "Particle/IntNGP.h"
-#include "Particle/IntSUDS.h"
-#include "Particle/IntTSC.h"
 #include "Particle/ParticleSpatialLayout.h"
-#include "Particle/ParticleUniformLayout.h"
-#include "Particle/ParticleAttrib.h"
 #include "Meshes/UniformCartesian.h"
-#include "Meshes/Centering.h"
 #include "FieldLayout/CenteredFieldLayout.h"
 #include "Field/Field.h"
-#include "FFT/FFT.h"
 
 #ifdef ENABLE_AMR
     #include "Amr/AmrDefs.h"
@@ -22,37 +15,21 @@
 #endif
 
 typedef IntCIC  IntrplCIC_t;
-typedef IntNGP  IntrplNGP_t;
-typedef IntSUDS IntrplSUDS_t;
-typedef IntTSC  IntrplTSC_t;
 
 typedef ParticleSpatialLayout<double, 3>::ParticlePos_t Ppos_t;
 typedef ParticleSpatialLayout<double, 3>::ParticleIndex_t PID_t;
 
-typedef ParticleUniformLayout<double, 3>::ParticlePos_t UPpos_t;
-typedef ParticleUniformLayout<double, 3>::ParticleIndex_t UPID_t;
-
-typedef ParticleAttrib<double> Pscalar_t;
-
-typedef InterpolatorTraits<double, 3, IntrplCIC_t>::Cache_t Pcache_t;
-
 typedef UniformCartesian<3, double> Mesh_t;