Merge branch 'small-fixes' into 'master'

Small fixes

See merge request !441

CMakeLists.txt

@@ -41,6 +41,7 @@ set (CMAKE_CXX_STANDARD 11)
 set (CMAKE_CXX_STANDARD_REQUIRED ON)
 set (CMAKE_CXX_EXTENSIONS OFF)
 
+# Disable compile time assert (used by IPPL)
 add_definitions (-DNOCTAssert)
 
 add_compile_options (-Wall)
@@ -171,7 +172,7 @@ if (ENABLE_AMR)
 endif ()
 
 option (ENABLE_AMR_MG_SOLVER "Enable AMR MG solver" OFF)
-option (ENABLE_SAAMG_SOLVER "Enable iteartive SA-AMG-PCG self field solver" OFF)
+option (ENABLE_SAAMG_SOLVER "Enable iterative SA-AMG-PCG self field solver" OFF)
 if (ENABLE_SAAMG_SOLVER OR ENABLE_AMR_MG_SOLVER)
     #
     # :FIXME: We have to add checks whether the required Trilinos modules

CMakeModules/FindGTest.cmake

 #
 # Find gtest Google Test includes and library
 #
-# gtest
-# It can be found at:
-#     http://amas.web.psi.ch/tools/GSL/index.html
-#
 # GTEST_INCLUDE_DIR - where to find gtest/gtest.h
 # GTEST_LIBRARY     - libgtest.a path
 # GTEST_MAIN_LIBRARY     - libgtest_main.a path

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/CMakeLists.txt

@@ -7,6 +7,7 @@ set (_HDRS
     FFTBase.h
     FFT.hpp
     FFT.h
+    fftpack.h
     fftpack_FFT.h
     )
 

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/Field/CMakeLists.txt

@@ -3,10 +3,10 @@ set (_SRCS
 
 set (_HDRS
     Assign.hpp
+    Assign.h
     AssignDefs.h
     AssignGeneralBF.hpp
     AssignGeneralIBF.hpp
-    Assign.h
     AssignTags.h
     BareField.hpp
     BareField.h

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/CMakeLists.txt

@@ -2,6 +2,7 @@ set (_SRCS
     )
 
 set (_HDRS
+    AbstractParticle.h
     BoxParticleCachingPolicy.h
     CellParticleCachingPolicy.h
     GenArrayParticle.h
@@ -9,8 +10,8 @@ set (_HDRS
     IntCIC.h
     Interpolator.h
     IntNGP.h
-    IntTSC.h
     IntSUDS.h
+    IntTSC.h
     NoParticleCachingPolicy.h
     PairBuilder/BasicPairBuilder.h
     PairBuilder/HashPairBuilder.h

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 +55,7 @@
 #include <mpi.h>
 
 // forward declarations
+class Communicate;
 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>

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;
-}
-
-/***************************************************************************
- * $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 $ 
- ***************************************************************************/
-
+}
\ No newline at end of file

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

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/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"));
 }