ippl/test/PwrSpec/testPwrSpec.cpp

@@ -33,8 +33,6 @@ Build:
 #include <iostream>
 #include <set>
 
-using namespace std;
-
 // dimension of our positions
 const unsigned Dim = 3;
 
@@ -289,7 +287,7 @@ public:
                         k2 -= nr_m[2];
 
                     kk=(int)nint(sqrt(ii*ii+jj*jj+k2*k2));
-                    kk = min(kmax_m, (int)kk);
+                    kk = std::min(kmax_m, (int)kk);
                     spectra1D_m[kk] += real(rho_m.localElement(loop));
                     Nk_m[kk]++;
                 }

ippl/test/particle/CMakeLists.txt

@@ -77,7 +77,6 @@ target_link_libraries (
     ${MPI_CXX_LIBRARIES}
     ${H5Hut_LIBRARY}
     ${HDF5_LIBRARIES}
-    z
     boost_timer
 )
 
@@ -91,4 +90,9 @@ add_executable (salman-1 salman-1.cpp)
 target_link_libraries (salman-1 ${IPPL_LIBS} ${MPI_CXX_LIBRARIES} boost_timer)
 
 add_executable (test-scatter-1 test-scatter-1.cpp)
-target_link_libraries (test-scatter-1 ${IPPL_LIBS} ${MPI_CXX_LIBRARIES} boost_timer)
+target_link_libraries (
+    test-scatter-1
+    ${IPPL_LIBS}
+    ${MPI_CXX_LIBRARIES}
+    boost_timer
+)

ippl/test/particle/PIC3d.cpp

@@ -422,7 +422,7 @@ public:
  	    std::ofstream ostr;
             std::string Fn;
             char numbuf[6];
-            sprintf(numbuf, "%05d", idx);
+            snprintf(numbuf, sizeof(numbuf), "%05d", idx);
             Fn = fn  + std::string(numbuf) + ".dat";
             ostr.open(Fn.c_str(), std::ios::out );
             ostr.precision(15);
@@ -682,4 +682,4 @@ int main(int argc, char *argv[]){
  * $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/particle/p3m3dHeating.cpp

@@ -474,9 +474,8 @@ public:
         h5_prop_t props = H5CreateFileProp ();
         MPI_Comm comm = Ippl::getComm();
         h5_err_t h5err = H5SetPropFileMPIOCollective (props, &comm);
-#if defined (NDEBUG)
+        // suppress unused warning if we compile for production
         (void)h5err;
-#endif
         PAssert (h5err != H5_ERR);
         H5f_m = H5OpenFile (fn.c_str(), H5_O_RDONLY, props);
         PAssert (H5f_m != (h5_file_t)H5_ERR);
@@ -705,7 +704,7 @@ int main(int argc, char *argv[]){
     unsigned printid=1;
 
     msg << "Starting iterations ..." << endl;
-    P->compute_temperature();
+    //P->compute_temperature();
     // calculate initial space charge forces
     P->calculateGridForces(interaction_radius,alpha,0,0,0);
     P->calculatePairForces(interaction_radius,eps,alpha);
@@ -726,6 +725,15 @@ int main(int argc, char *argv[]){
     IpplTimings::TimerRef gridTimer = IpplTimings::getTimer("GridTimer");
     IpplTimings::TimerRef particleTimer = IpplTimings::getTimer("ParticleTimer");
 
+    P->calcMoments();
+    P->computeBeamStatistics();
+    writeBeamStatisticsVelocity(P,0);
+
+    P->calc_field_energy();
+    P->calc_kinetic_energy();
+    P->calc_potential_energy();
+    writeEnergy(P,0);
+    
     for (int it=0; it<iterations; it++) {
       /*
         P->calcMoments();
@@ -769,14 +777,15 @@ int main(int argc, char *argv[]){
         P->compute_temperature();
 
         if (it%print_every==0){
-            //dumpConservedQuantities(P,printid);
-            //compute quantities
-            /*
-             P->calc_field_energy();
-             P->calc_kinetic_energy();
-             P->calc_potential_energy();
-             writeEnergy(P,printid);
-             */
+            P->calcMoments();
+            P->computeBeamStatistics();
+            writeBeamStatisticsVelocity(P,it+1);
+
+            P->calc_field_energy();
+            P->calc_kinetic_energy();
+            P->calc_potential_energy();
+            writeEnergy(P,it+1);
+            
             P->compute_temperature();
             writeTemperature(P,it+1);
 
@@ -787,7 +796,7 @@ int main(int argc, char *argv[]){
     }
     Ippl::Comm->barrier();
 
-    P->closeH5();
+    //P->closeH5();
     Ippl::Comm->barrier();
 
     IpplTimings::stopTimer(allTimer);

ippl/test/particle/p3m3dMicrobunching.cpp

@@ -465,6 +465,8 @@ class ChargedParticles : public IpplParticleBase<PL> {
                     MPI_Comm comm = Ippl::getComm();
                     h5_err_t h5err = H5SetPropFileMPIOCollective (props, &comm);
                     PAssert (h5err != H5_ERR);
+                    // suppress unused warning if we compile for production
+		    (void) h5err;
                     H5f_m = H5OpenFile(fn.c_str(), H5_O_WRONLY, props);
                 }
 

ippl/test/particle/pbconds3D.cpp

@@ -33,7 +33,6 @@ typedef ParticleSpatialLayout<Real,Dim> playout_t;
 int main(int argc, char *argv[])
 {
 
-  unsigned int i, j;
   Ippl ippl(argc, argv);
   Inform testmsg(argv[0]);
 
@@ -59,6 +58,8 @@ int main(int argc, char *argv[])
 
   testmsg << "Start of initialization ..." << endl;
   if (P.singleInitNode()) {
+    unsigned int j;
+
     P.create(20); // makes new particles at end of current array
     // put ten particles near right edge, and ten near left edge
     for (j=0; j < 10; j++) { // initialize new values
@@ -74,13 +75,12 @@ int main(int argc, char *argv[])
   }
   testmsg << "Performing initial update ..." << endl;
   P.update();         // do update to move particles to proper loc
-  testmsg << "End of initialization" << i << ": localnum=";
   testmsg << P.getLocalNum() << ", totalnum=";
   testmsg << P.getTotalNum() << endl;
 
   // Just print out the contents of node 0's data
   testmsg << "------------------" << endl;
-  for (i=0; i < P.getLocalNum(); i++) {
+  for (unsigned int i=0; i < P.getLocalNum(); i++) {
     testmsg << "LID=" << i << ", GID=" << P.ID[i] << ", data[0]=";
     testmsg << P.data[0][i] << ", data[1]=" << P.data[1][i] << ", R=";
     testmsg << P.R[i] << endl;
@@ -93,14 +93,14 @@ int main(int argc, char *argv[])
   //
 
   testmsg << "Testing open boundary conditions ... moving by (5,-1,10):" << endl;
-  for (i=0; i < 2*Dim; ++i)
+  for (unsigned int i=0; i < 2*Dim; ++i)
     P.getBConds()[i] = ParticleNoBCond;
 
   Vektor<Real,Dim> offset1(5,-1,10);
   assign(P.R, P.R + offset1);
   P.update();
   testmsg << "------------------" << endl;
-  for (i=0; i < P.getLocalNum(); i++) {
+  for (unsigned int i=0; i < P.getLocalNum(); i++) {
     testmsg << "LID=" << i << ", GID=" << P.ID[i] << ", data[0]=";
     testmsg << P.data[0][i] << ", data[1]=" << P.data[1][i] << ", R=";
     testmsg << P.R[i] << endl;
@@ -121,7 +121,7 @@ int main(int argc, char *argv[])
   assign(P.R, P.R + offset2);
   P.update();
   testmsg << "------------------" << endl;
-  for (i=0; i < P.getLocalNum(); i++) {
+  for (unsigned int i=0; i < P.getLocalNum(); i++) {
     testmsg << "LID=" << i << ", GID=" << P.ID[i] << ", data[0]=";
     testmsg << P.data[0][i] << ", data[1]=" << P.data[1][i] << ", R=";
     testmsg << P.R[i] << endl;

optimizer/CMakeLists.txt

-#-----------------------------------------------------------------------------
-# options
-
-option (ARCH_BG "Set architecture to BlueGene" OFF)
-
 #-----------------------------------------------------------------------------
 # Common sources and libs
 
@@ -55,19 +50,3 @@ if (BUILD_OPAL_UNIT_TESTS)
     enable_testing()
     add_subdirectory(Tests)
 endif ()
-
-#-----------------------------------------------------------------------------
-# Doxygen
-if (ENABLE_DOXYDOC)
-    find_package(Doxygen)
-    if (DOXYGEN_FOUND)
-        configure_file (${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile
-            ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY
-	    )
-        add_custom_target (optpilot-doc
-            ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
-            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-            COMMENT "Generating API documentation with Doxygen" VERBATIM
-            )
-    endif ()
-endif ()

optimizer/Expression/GlobalFunctions.h

@@ -50,7 +50,7 @@ struct _stat_sum {
         double step      = boost::get<double>(args[2]);
         std::string name = boost::get<std::string>(args[3]);
 
-        boost::scoped_ptr<SDDSReader> sim_stats(new SDDSReader(stat_filename_));
+        const std::unique_ptr<SDDSReader> sim_stats(new SDDSReader(stat_filename_));
         try {
             sim_stats->parseFile();
         } catch (OptPilotException &ex) {

optimizer/Expression/MaxNormRadialPeak.h

@@ -60,8 +60,8 @@ struct MaxNormRadialPeak {
 
         bool is_valid = true;
 
-        boost::scoped_ptr<PeakReader> meas_peaks(new PeakReader(meas_filename_));
-        boost::scoped_ptr<PeakReader> sim_peaks(new PeakReader(sim_filename_));
+        const std::unique_ptr<PeakReader> meas_peaks(new PeakReader(meas_filename_));
+        const std::unique_ptr<PeakReader> sim_peaks(new PeakReader(sim_filename_));
         try {
             sim_peaks->parseFile();
             meas_peaks->parseFile();

optimizer/Expression/NumberOfPeaks.h

@@ -52,7 +52,7 @@ struct NumberOfPeaks {
 
         bool is_valid = true;
 
-        boost::scoped_ptr<PeakReader> sim_peaks(new PeakReader(sim_filename_));
+        const std::unique_ptr<PeakReader> sim_peaks(new PeakReader(sim_filename_));
         std::size_t nPeaks = 0;
 
         try {

optimizer/Expression/Parser/ast.hpp

@@ -100,13 +100,13 @@ namespace client { namespace ast
         operand first;
         std::list<operation> rest;
     };
-
+#if 0
     // print functions for debugging
     inline std::ostream& operator<<(std::ostream& out, nil)
     {
         out << "nil"; return out;
     }
-
+#endif
     inline std::ostream& operator<<(std::ostream& out, identifier const& id)
     {
         out << id.name; return out;

optimizer/Expression/Parser/evaluator.hpp

@@ -14,9 +14,9 @@
 #include <boost/assert.hpp>
 #include <boost/variant/get.hpp>
 #include <boost/variant/variant.hpp>
-#include <boost/spirit/include/phoenix_core.hpp>
-#include <boost/spirit/include/phoenix_function.hpp>
-#include <boost/spirit/include/phoenix_operator.hpp>
+#include <boost/phoenix/core.hpp>
+#include <boost/phoenix/function.hpp>
+#include <boost/phoenix/operator.hpp>
 
 #include "ast.hpp"
 #include "function.hpp"

optimizer/Expression/Parser/expression_def.hpp

@@ -4,11 +4,21 @@
     Distributed under the Boost Software License, Version 1.0. (See accompanying
     file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
 =============================================================================*/
+
+/*
+  with boost 1.81 and newer we get multiple definition of
+  `boost::phoenix::placeholders::uargX` errors. A solution
+  suggested in https://github.com/boostorg/phoenix/issues/111
+  is to define BOOST_PHOENIX_STL_TUPLE_H_ so that
+  boost/stl/tuple.h is not included in boost/phoenix.hpp
+*/
+#define BOOST_PHOENIX_STL_TUPLE_H_
+
 #include "expression.hpp"
 #include "error_handler.hpp"
 #include "annotation.hpp"
-#include <boost/spirit/include/phoenix_function.hpp>
-#include <boost/spirit/include/phoenix.hpp>
+#include <boost/phoenix/function.hpp>
+#include <boost/phoenix.hpp>
 #include <boost/fusion/adapted.hpp>
 //#include <boost/spirit/include/qi_lit.hpp>
 
@@ -190,4 +200,4 @@ namespace client { namespace parser
         on_success(primary_expr,
             annotation_function(error_handler.iters)(_val, _1));
     }
-}}
\ No newline at end of file
+}}

optimizer/Expression/Parser/requirements.hpp

@@ -11,10 +11,9 @@
 #include "error_handler.hpp"
 #include <set>
 #include <boost/function.hpp>
-#include <boost/shared_ptr.hpp>
-#include <boost/spirit/include/phoenix_core.hpp>
-#include <boost/spirit/include/phoenix_function.hpp>
-#include <boost/spirit/include/phoenix_operator.hpp>
+#include <boost/phoenix/core.hpp>
+#include <boost/phoenix/function.hpp>
+#include <boost/phoenix/operator.hpp>
 
 namespace client { namespace code_gen
 {

optimizer/Expression/ProbeVariable.h

@@ -47,7 +47,7 @@ struct ProbeVariable {
 
         bool is_valid = true;
 
-        boost::scoped_ptr<ProbeReader> sim_probe(new ProbeReader(probe_filename_));
+        const std::unique_ptr<ProbeReader> sim_probe(new ProbeReader(probe_filename_));
 
         try {
             sim_probe->parseFile();

optimizer/Expression/RadialPeak.h

@@ -6,7 +6,6 @@
 #include "boost/type_traits/remove_cv.hpp"
 #include "boost/variant/get.hpp"
 #include "boost/variant/variant.hpp"
-#include "boost/smart_ptr.hpp"
 
 #include "Util/Types.h"
 #include "Util/PeakReader.h"
@@ -31,7 +30,7 @@ struct RadialPeak {
 
         bool is_valid = true;
 
-        boost::scoped_ptr<PeakReader> sim_peaks(new PeakReader(peak_filename_));
+        const std::unique_ptr<PeakReader> sim_peaks(new PeakReader(peak_filename_));
         try {
             sim_peaks->parseFile();
         } catch (OptPilotException &ex) {

optimizer/Expression/SDDSVariable.h

@@ -31,7 +31,6 @@
 
 #include "boost/variant/get.hpp"
 #include "boost/variant/variant.hpp"
-#include "boost/smart_ptr.hpp"
 
 #include "Util/Types.h"
 #include "Util/SDDSReader.h"
@@ -68,7 +67,7 @@ struct SDDSVariable {
 
         bool is_valid = true;
 
-        boost::scoped_ptr<SDDSReader> sim_stats(new SDDSReader(stat_filename_));
+        const std::unique_ptr<SDDSReader> sim_stats(new SDDSReader(stat_filename_));
         try {
             sim_stats->parseFile();
         } catch (SDDSParserException &ex) {

optimizer/Expression/SeptumExpr.h

@@ -51,10 +51,10 @@ struct SeptumExpr {
         double result = 0.0;
 
         try {
-            boost::scoped_ptr<PeakReader> sim_peaks(new PeakReader(probe + std::string(".peaks")));
+            const std::unique_ptr<PeakReader> sim_peaks(new PeakReader(probe + std::string(".peaks")));
             sim_peaks->parseFile();
 
-            boost::scoped_ptr<ProbeHistReader> sim_hist(new ProbeHistReader(probe + std::string(".hist")));
+            const std::unique_ptr<ProbeHistReader> sim_hist(new ProbeHistReader(probe + std::string(".hist")));
             sim_hist->parseFile();
 
             double upperBound = 0.0;

optimizer/Expression/SumErrSq.h

@@ -69,7 +69,7 @@ struct SumErrSq {
         parseMeasurements(measurement_filename);
         bool is_valid = true;
 
-        boost::scoped_ptr<SDDSReader> sim_stats(new SDDSReader(stat_filename_));
+        const std::unique_ptr<SDDSReader> sim_stats(new SDDSReader(stat_filename_));
         try {
             sim_stats->parseFile();
         } catch (OptPilotException &ex) {

optimizer/Expression/SumErrSqRadialPeak.h

@@ -35,7 +35,6 @@
 #include "boost/type_traits/remove_cv.hpp"
 #include "boost/variant/get.hpp"
 #include "boost/variant/variant.hpp"
-#include "boost/smart_ptr.hpp"
 
 #include "Util/Types.h"
 #include "Util/PeakReader.h"
@@ -58,8 +57,8 @@ struct SumErrSqRadialPeak {
 
         bool is_valid = true;
 
-        boost::scoped_ptr<PeakReader> meas_peaks(new PeakReader(meas_filename_));
-        boost::scoped_ptr<PeakReader> sim_peaks(new PeakReader(sim_filename_));
+        const std::unique_ptr<PeakReader> meas_peaks(new PeakReader(meas_filename_));
+        const std::unique_ptr<PeakReader> sim_peaks(new PeakReader(sim_filename_));
         try {
             sim_peaks->parseFile();
             meas_peaks->parseFile();