replace C assert with PAssert; typo and include fixes

ippl/test/particle/p3m3dHeating.cpp

@@ -36,10 +36,10 @@
 #include "Particle/PairBuilder/HashPairBuilderPeriodic.h"
 #include "Particle/PairBuilder/HashPairBuilderPeriodicParallel.h"
 #include "Particle/PairBuilder/PairConditions.h"
+#include "Utility/PAssert.h"
 #include "math.h"
 
 #include <random>
-#include <cassert>
 
 #include "VTKFieldWriterParallel.hpp"
 #include "ChargedParticleFactory.hpp"
@@ -477,9 +477,9 @@ public:
 #if defined (NDEBUG)
         (void)h5err;
 #endif
-        assert (h5err != H5_ERR);
+        PAssert (h5err != H5_ERR);
         H5f_m = H5OpenFile (fn.c_str(), H5_O_RDONLY, props);
-        assert (H5f_m != (h5_file_t)H5_ERR);
+        PAssert (H5f_m != (h5_file_t)H5_ERR);
         H5CloseProp (props);
     }
 

ippl/test/particle/p3m3dMicrobunching.cpp

@@ -22,7 +22,6 @@
 // along with OPAL. If not, see <https://www.gnu.org/licenses/>.
 //
 #include "Ippl.h"
-#include <cassert>
 #include <string>
 #include <vector>
 #include <iostream>
@@ -35,6 +34,7 @@
 #include "Particle/PairBuilder/HashPairBuilderPeriodic.h"
 #include "Particle/PairBuilder/HashPairBuilderPeriodicParallel.h"
 #include "Particle/PairBuilder/PairConditions.h"
+#include "Utility/PAssert.h"
 #include "math.h"
 //#include "FixedAlgebra/FMatrix.h"
 
@@ -61,8 +61,8 @@ typedef Field<std::complex<double>, Dim, Mesh_t, Center_t>            CxField_t;
 typedef FFT<CCTransform, Dim, double>                                 FFT_t;
 
 typedef IntCIC                                                        IntrplCIC_t;
-typedef IntNGP                                                        IntrplNGP_t;
-typedef IntTSC                                                        IntrplTSC_t;
+//typedef IntNGP                                                        IntrplNGP_t;
+//typedef IntTSC                                                        IntrplTSC_t;
 
 typedef UniformCartesian<2, double>                                   Mesh2d_t;
 typedef CenteredFieldLayout<2, Mesh2d_t, Center_t>                    FieldLayout2d_t;
@@ -464,7 +464,7 @@ class ChargedParticles : public IpplParticleBase<PL> {
                     h5_prop_t props = H5CreateFileProp ();
                     MPI_Comm comm = Ippl::getComm();
                     h5_err_t h5err = H5SetPropFileMPIOCollective (props, &comm);
-                    assert (h5err != H5_ERR);
+                    PAssert (h5err != H5_ERR);
                     H5f_m = H5OpenFile(fn.c_str(), H5_O_WRONLY, props);
                 }
 

src/Amr/BoxLibLayout.hpp

@@ -41,7 +41,6 @@
 #include "Message/Formatter.h"
 #include "Utilities/OpalException.h"
 
-#include <cassert>
 #include <cmath>
 
 template <class T, unsigned Dim>
@@ -473,7 +472,7 @@ void BoxLibLayout<T, Dim>::buildLevelMask(int lev, const int ncells) {
 
 template <class T, unsigned Dim>
 void BoxLibLayout<T, Dim>::clearLevelMask(int lev) {
-    assert(lev < (int)masks_m.size());
+    BL_ASSERT(lev < (int)masks_m.size());
     masks_m[lev].reset(nullptr);
 }
 
@@ -810,8 +809,8 @@ void BoxLibLayout<T, Dim>::initBaseBox_m(int nGridPoints,
     AmrDomain_t real_box;
     for (int d = 0; d < AMREX_SPACEDIM; ++d) {
 
-        assert(lowerBound[d] < 0);
-        assert(upperBound[d] > 0);
+        BL_ASSERT(lowerBound[d] < 0);
+        BL_ASSERT(upperBound[d] > 0);
 
         real_box.setLo(d, lowerBound[d] * (1.0 + dh));
         real_box.setHi(d, upperBound[d] * (1.0 + dh));

src/Classic/Fields/Fieldmap.cpp

 #include "Fields/Fieldmap.h"
+
+#include "Utility/PAssert.h"
+
 #include "Fields/FM3DDynamic.h"
 #include "Fields/FM3DH5BlockBase.h"
 #include "Fields/FM3DH5Block.h"
@@ -38,7 +41,6 @@
 #include <iostream>
 #include <fstream>
 #include <ios>
-#include <cassert>
 
 namespace fs = boost::filesystem;
 
@@ -366,22 +368,22 @@ MapType Fieldmap::readHeader(std::string Filename) {
         h5_prop_t props = H5CreateFileProp ();
         MPI_Comm comm = Ippl::getComm();
         h5err = H5SetPropFileMPIOCollective (props, &comm);
-        assert (h5err != H5_ERR);
+        PAssert (h5err != H5_ERR);
         h5_file_t file = H5OpenFile (Filename.c_str(), H5_O_RDONLY, props);
-        assert (file != (h5_file_t)H5_ERR);
+        PAssert (file != (h5_file_t)H5_ERR);
         H5CloseProp (props);
 
         h5err = H5SetStep(file, 0);
-        assert (h5err != H5_ERR);
+        PAssert (h5err != H5_ERR);
 
         h5_int64_t num_fields = H5BlockGetNumFields(file);
-        assert (num_fields != H5_ERR);
+        PAssert (num_fields != H5_ERR);
         MapType maptype = UNKNOWN;
 
         for (h5_ssize_t i = 0; i < num_fields; ++ i) {
             h5err = H5BlockGetFieldInfo(
                 file, (h5_size_t)i, name, len_name, NULL, NULL, NULL, NULL);
-            assert (h5err != H5_ERR);
+            PAssert (h5err != H5_ERR);
             // using field name "Bfield" and "Hfield" to distinguish the type
             if (std::strcmp(name, "Bfield") == 0) {
                 maptype = T3DMagnetoStaticH5Block;
@@ -392,7 +394,7 @@ MapType Fieldmap::readHeader(std::string Filename) {
             }
         }
         h5err = H5CloseFile(file);
-        assert (h5err != H5_ERR);
+        PAssert (h5err != H5_ERR);
         if (maptype != UNKNOWN)
             return maptype;
     }
@@ -747,7 +749,7 @@ void Fieldmap::write3DField(unsigned int nx,
     });
     std::ofstream of;
     of.open (fname);
-    assert (of.is_open ());
+    PAssert (of.is_open ());
     of.precision (6);
 
     const double hx = (xrange.second - xrange.first) / (nx - 1);

src/Classic/Solvers/GreenWakeFunction.cpp

@@ -136,9 +136,9 @@ void GreenWakeFunction::apply(PartBunchBase<double, 3> *bunch) {
             spacing = rmax(0) * rmax(0) + rmax(1) * rmax(1);
             break;
         default:
-            throw GeneralClassicException("GreenWakeFunction", "invalid direction specified");
+            throw GeneralClassicException("GreenWakeFunction::apply", "invalid direction specified");
     }
-    assert(NBin_m > 0);
+    PAssert(NBin_m > 0);
     spacing /= (NBin_m - 1); //FIXME: why -1? CKR: because grid spacings = grid points - 1
 
     // Calculate the Wakefield if needed
@@ -187,7 +187,7 @@ void GreenWakeFunction::apply(PartBunchBase<double, 3> *bunch) {
                 int idx = (int)(floor((bunch->R[i](2) - mindist) / spacing));
                 //IFF: should be ok
                 if(idx == NBin_m) idx--;
-                assert(idx >= 0 && idx < NBin_m);
+                PAssert(idx >= 0 && idx < NBin_m);
                 double dE = OutEnergy[idx];
                 bunch->Ef[i](2) += dE;
 
@@ -201,12 +201,12 @@ void GreenWakeFunction::apply(PartBunchBase<double, 3> *bunch) {
                 int idx = (int)(floor((bunch->R[i](2) - mindist) / spacing));
                 //IFF: should be ok
                 if(idx == NBin_m) idx--;
-                assert(idx >= 0 && idx < NBin_m);
+                PAssert(idx >= 0 && idx < NBin_m);
                 double dE = OutEnergy[idx];
 
                 // ACHTUNG spacing auch in transversal richtung
                 double dist = sqrt(bunch->R[i](0) * bunch->R[i](0) + bunch->R[i](1) * bunch->R[i](1));
-                assert(dist > 0);
+                PAssert(dist > 0);
                 bunch->Ef[i](0) += dE * bunch->R[i](0) / dist;
                 bunch->Ef[i](1) += dE * bunch->R[i](1) / dist;
 
@@ -214,7 +214,7 @@ void GreenWakeFunction::apply(PartBunchBase<double, 3> *bunch) {
             break;
 
         default:
-            throw GeneralClassicException("GreenWakeFunction", "invalid direction specified");
+            throw GeneralClassicException("GreenWakeFunction::apply", "invalid direction specified");
     }
 
 #ifdef ENABLE_WAKE_DUMP

src/Classic/Solvers/GreenWakeFunction.hh

@@ -21,9 +21,9 @@
 #include "Solvers/WakeFunction.hh"
 #include "Physics/Physics.h"
 #include "Utility/IpplInfo.h"
+#include "Utility/PAssert.h"
 
 #include <vector>
-#include <cassert>
 #include <map>
 #include <string>
 #include <complex>
@@ -138,8 +138,8 @@ private:
      *
      */
     template<class F> double simpson(F &f, double a, double b, unsigned int N) {
-        assert(b > a);
-        assert(N > 0);
+        PAssert(b > a);
+        PAssert(N > 0);
 
         double result = 0;
         double h = (b - a) / N;

src/Classic/Structure/LossDataSink.cpp

@@ -9,7 +9,9 @@
 #include <boost/filesystem.hpp>
 #include "OPALconfig.h"
 
-#include <cassert>
+#include "Message/GlobalComm.h"
+#include "Utility/IpplInfo.h"
+
 #include <cmath>
 
 #define ADD_ATTACHMENT( fname ) {             \
@@ -479,7 +481,7 @@ void LossDataSink::saveASCII() {
         }
         bool res = Ippl::Comm->send(smsg, 0, tag);
         if(! res)
-            ERRORMSG("LossDataSink Ippl::Comm->send(smsg, 0, tag) failed " << endl;);
+            ERRORMSG("LossDataSink Ippl::Comm->send(smsg, 0, tag) failed " << endl);
     }
 }
 

src/Expressions/Expressions.cpp

@@ -53,7 +53,6 @@
 #include "Utilities/ParseError.h"
 #include "ValueDefinitions/BoolConstant.h"
 #include <algorithm>
-#include <cassert>
 #include <cerrno>
 #include <cmath>
 #include <list>

src/OpalParser/OpalParser.cpp

@@ -34,7 +34,6 @@
 #include "Utilities/OpalException.h"
 #include "Utilities/ParseError.h"
 #include "Utilities/Options.h"
-#include <cassert>
 #include <cmath>
 #include <ctime>
 #include <exception>
@@ -178,7 +177,7 @@ void OpalParser::parseAction(Statement &stat) const {
     } else {
         std::string hint = getHint(cmdName, "command");
         if (hint != "") {
-            throw ParseError("OpalParser::parse()",
+            throw ParseError("OpalParser::parseAction()",
                              "Syntax error, " + hint);
         }
 

src/Solvers/ArbitraryDomain.cpp

@@ -34,7 +34,6 @@
 #include <cmath>
 #include <iostream>
 #include <tuple>
-#include <cassert>
 #include "Utilities/OpalException.h"
 
 ArbitraryDomain::ArbitraryDomain( BoundaryGeometry * bgeom,

src/Solvers/BoxCornerDomain.cpp

@@ -30,7 +30,6 @@
 #include <string>
 #include <cmath>
 #include <iostream>
-#include <cassert>
 
 //FIXME: ORDER HOW TO TRAVERSE NODES IS FIXED, THIS SHOULD BE MORE GENERIC! (PLACES MARKED)
 

src/Solvers/BoxLibSolvers/FMGPoissonSolver.cpp

@@ -22,13 +22,13 @@
 //
 #include "FMGPoissonSolver.h"
 
+#include "Utility/PAssert.h"
+
 #include "Utilities/OpalException.h"
 
 #include <AMReX_ParmParse.H>
 #include <AMReX_Interpolater.H>
 
-#include <cassert>
-
 FMGPoissonSolver::FMGPoissonSolver(AmrBoxLib* itsAmrObject_p)
     : AmrPoissonSolver<AmrBoxLib>(itsAmrObject_p),
       reltol_m(1.0e-15),
@@ -70,14 +70,14 @@ void FMGPoissonSolver::solve(AmrScalarFieldContainer_t& rho,
 
     amrex::Vector< AmrField_t > tmp(rho.size());
 
-    assert(baseLevel <= finestLevel);
-    assert(finestLevel < (int)rho.size());
+    PAssert(baseLevel <= finestLevel);
+    PAssert(finestLevel < (int)rho.size());
 
     for (int lev = baseLevel; lev <= finestLevel ; ++lev) {
         const AmrProcMap_t& dmap = rho[lev]->DistributionMap();
         grad_phi_edge[lev].resize(AMREX_SPACEDIM);
         tmp[lev].define(rho[lev]->boxArray(), dmap, AMREX_SPACEDIM, 1);
-        
+
         for (int n = 0; n < AMREX_SPACEDIM; ++n) {
             AmrGrid_t ba = rho[lev]->boxArray();
             grad_phi_edge[lev][n].reset(new AmrField_t(ba.surroundingNodes(n), dmap, 1, 1));

src/Solvers/EllipticDomain.cpp

@@ -30,7 +30,6 @@
 #include <map>
 #include <cmath>
 #include <iostream>
-#include <cassert>
 
 //FIXME: ORDER HOW TO TRAVERSE NODES IS FIXED, THIS SHOULD BE MORE GENERIC! (PLACES MARKED)
 

src/Solvers/IrregularDomain.cpp

@@ -25,9 +25,9 @@
 //
 
 #include "Solvers/IrregularDomain.h"
-#include "Utilities/OpalException.h"
 
-#include <cassert>
+#include "Utility/PAssert.h"
+#include "Utilities/OpalException.h"
 
 IrregularDomain::IrregularDomain(const IntVector_t& nr, const Vector_t& hr,
                                  const std::string& interpl)
@@ -114,7 +114,7 @@ void IrregularDomain::getBoundaryStencil(int x, int y, int z, StencilValue_t& va
     }
 
     // stencil center value has to be positive!
-    assert(value.center > 0);
+    PAssert(value.center > 0);
 }
 
 

src/Structure/BoundaryGeometry.cpp

@@ -13,15 +13,16 @@
 // (at your option) any later version.
 //
 // You should have received a copy of the GNU General Public License
-// along with OPAL.  If not, see <https://www.gnu.org/licenses/>.
+// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
 //
 
 //#define   ENABLE_DEBUG
 
 #include "Structure/BoundaryGeometry.h"
 
-#include <fstream>
 #include <cmath>
+#include <fstream>
+#include <string>
 
 #include "H5hut.h"
 
@@ -685,7 +686,7 @@ static inline Vector_t normalVector (
     ) {
     const Vector_t N = cross (B - A, C - A);
     const double magnitude = std::sqrt (SQR (N (0)) + SQR (N (1)) + SQR (N (2)));
-    assert (gsl_fcmp (magnitude, 0.0, EPS) > 0); // in case we have degenerted triangles
+    PAssert (gsl_fcmp (magnitude, 0.0, EPS) > 0); // in case we have degenerated triangles
     return N / magnitude;
 }
 
@@ -746,17 +747,17 @@ BoundaryGeometry::BoundaryGeometry() :
 
     itsAttr[L1] = Attributes::makeReal
         ("L1",
-         "In case of BOXCORNER Specifies first part with hight == B [m]",
+         "In case of BOXCORNER Specifies first part with height == B [m]",
          0.5);
 
     itsAttr[L2] = Attributes::makeReal
         ("L2",
-         "In case of BOXCORNER Specifies first second with hight == B-C [m]",
+         "In case of BOXCORNER Specifies first second with height == B-C [m]",
          0.2);
 
     itsAttr[C] = Attributes::makeReal
         ("C",
-         "In case of BOXCORNER Specifies hight of corner C [m]",
+         "In case of BOXCORNER Specifies height of corner C [m]",
          0.01);
 
     itsAttr[XYZSCALE] = Attributes::makeReal
@@ -1589,7 +1590,7 @@ Change orientation if diff is:
             for (unsigned int triangle_id = 0; triangle_id < bg->Triangles_m.size(); triangle_id++) {
                 for (unsigned int j = 1; j <= 3; j++) {
                     auto pt_id = bg->PointID (triangle_id, j);
-                    assert (pt_id < bg->Points_m.size ());
+                    PAssert (pt_id < bg->Points_m.size ());
                     adjacencies_to_pt [pt_id].insert (triangle_id);
                 }
             }
@@ -1708,7 +1709,7 @@ Change orientation if diff is:
                     }
                 }
             }
-            assert (n == 2);
+            PAssert (n == 2);
         edge_found:
             int diff = id[1] - id[0];
             if ((((ic[1] - ic[0]) == 1) && ((diff == 1) || (diff == -2))) ||
@@ -1798,7 +1799,7 @@ Change orientation if diff is:
     (void)rc;
 #endif
     rc = H5SetErrorHandler (H5AbortErrorhandler);
-    assert (rc != H5_ERR);
+    PAssert (rc != H5_ERR);
     H5SetVerbosityLevel (1);
 
     h5_prop_t props = H5CreateFileProp ();
@@ -2052,7 +2053,7 @@ BoundaryGeometry::intersectTinyLineSegmentBoundary (
             }
             break;
         case -1:                    // triangle is degenerated
-            assert (tmp_intersect_result != -1);
+            PAssert (tmp_intersect_result != -1);
             exit (42);              // terminate even if NDEBUG is set
         }
     }                   // end for all triangles
@@ -2192,7 +2193,7 @@ void
 BoundaryGeometry::writeGeomToVtk (std::string fn) {
     std::ofstream of;
     of.open (fn.c_str ());
-    assert (of.is_open ());
+    PAssert (of.is_open ());
     of.precision (6);
     of << "# vtk DataFile Version 2.0" << std::endl;
     of << "generated using DataSink::writeGeoToVtk" << std::endl;

src/Structure/BoundaryGeometry.h

@@ -36,20 +36,19 @@
 class OpalBeamline;
 class ElementBase;
 
-#include <cassert>
 #include <unordered_map>
 #include <unordered_set>
 #include <array>
+#include <vector>
 
 #include "AbstractObjects/Definition.h"
 #include "Attributes/Attributes.h"
 #include "Utilities/Util.h"
 #include "Utility/IpplTimings.h"
+#include "Utility/PAssert.h"
 
 #include <gsl/gsl_rng.h>
 
-extern Inform* gmsg;
-
 class BoundaryGeometry : public Definition {
 
 public:
@@ -286,7 +285,7 @@ private:
     }
 
     inline const Vector_t& getPoint (const int triangle_id, const int vertex_id) {
-        assert (1 <= vertex_id && vertex_id <=3);
+        PAssert (1 <= vertex_id && vertex_id <=3);
         return Points_m[Triangles_m[triangle_id][vertex_id]];
     }
 
@@ -312,12 +311,12 @@ private:
         FGEOM,    // file holding the geometry
         LENGTH,   // length of elliptic tube or boxcorner
         S,        // start of the geometry
-        L1,       // in case of BOXCORNER first part of geometry with hight B
-        L2,       // in case of BOXCORNER second part of geometry with hight B-C
+        L1,       // in case of BOXCORNER first part of geometry with height B
+        L2,       // in case of BOXCORNER second part of geometry with height B-C
         A,        // major semi-axis of elliptic tube
         B,        // minor semi-axis of ellitpic tube
-        C,        // in case of BOXCORNER hight of corner
-        TOPO,     // RECTANGULAR, BOXCORNER, ELLIPTIC if FGEOM is selected topo is over-written
+        C,        // in case of BOXCORNER height of corner
+        TOPO,     // RECTANGULAR, BOXCORNER, ELLIPTIC if FGEOM is selected TOPO is over-written
         ZSHIFT,   // Shift in z direction
         XYZSCALE, // Multiplicative scaling factor for coordinates
         XSCALE,   // Multiplicative scaling factor for x-coordinates
@@ -339,4 +338,4 @@ inline Inform &operator<< (Inform& os, const BoundaryGeometry& b) {
 // c-basic-offset: 4
 // indent-tabs-mode: nil
 // require-final-newline: nil
-// End:
+// End:
\ No newline at end of file

src/Structure/H5PartWrapper.cpp

@@ -6,8 +6,13 @@
 
 #include "OPALconfig.h"
 #include "AbstractObjects/OpalData.h"
-#include "Utilities/Options.h"
 #include "Physics/Physics.h"
+#include "Utilities/Options.h"
+#include "Utilities/OpalException.h"
+
+#include "Message/Communicate.h"
+#include "Message/Message.h"
+#include "Utility/PAssert.h"
 
 #include <boost/filesystem.hpp>
 
@@ -40,8 +45,6 @@ H5PartWrapper::H5PartWrapper(const std::string &fileName, int restartStep, std::
     numSteps_m(0),
     startedFromExistingFile_m(true)
 {
-    namespace fs = boost::filesystem;
-
     if (sourceFile == "") sourceFile = fileName_m;
 
     copyFile(sourceFile, restartStep, flags);
@@ -72,9 +75,9 @@ void H5PartWrapper::open(h5_int32_t flags) {
 #if defined (NDEBUG)
     (void)h5err;
 #endif
-    assert (h5err != H5_ERR);
+    PAssert (h5err != H5_ERR);
     file_m = H5OpenFile (fileName_m.c_str(), flags, props);
-    assert (file_m != (h5_file_t)H5_ERR);
+    PAssert (file_m != (h5_file_t)H5_ERR);
     H5CloseProp (props);
 }
 
@@ -135,9 +138,9 @@ void H5PartWrapper::copyFile(const std::string &sourceFile, int lastStep, h5_int
 #if defined (NDEBUG)
         (void)h5err;
 #endif
-        assert (h5err != H5_ERR);
+        PAssert (h5err != H5_ERR);
         h5_file_t source = H5OpenFile (sourceFile.c_str(), H5_O_RDONLY, props);
-        assert (source != (h5_file_t)H5_ERR);
+        PAssert (source != (h5_file_t)H5_ERR);
         H5CloseProp (props);
         h5_ssize_t numStepsInSource = H5GetNumSteps(source);
 
@@ -169,9 +172,9 @@ void H5PartWrapper::copyFile(const std::string &sourceFile, int lastStep, h5_int
         props = H5CreateFileProp ();
         comm = Ippl::getComm();
         h5err = H5SetPropFileMPIOCollective (props, &comm);
-        assert (h5err != H5_ERR);
+        PAssert (h5err != H5_ERR);
         source = H5OpenFile (sourceFileName.c_str(), H5_O_RDONLY, props);
-        assert (source != (h5_file_t)H5_ERR);
+        PAssert (source != (h5_file_t)H5_ERR);
         H5CloseProp (props);
         copyHeader(source);
 
@@ -204,9 +207,9 @@ void H5PartWrapper::copyFile(const std::string &sourceFile, int lastStep, h5_int
 #if defined (NDEBUG)
         (void)h5err;
 #endif
-        assert (h5err != H5_ERR);
+        PAssert (h5err != H5_ERR);
         h5_file_t source = H5OpenFile (sourceFile.c_str(), H5_O_RDONLY, props);
-        assert (source != (h5_file_t)H5_ERR);
+        PAssert (source != (h5_file_t)H5_ERR);
         H5CloseProp (props);
         h5_ssize_t numStepsInSource = H5GetNumSteps(source);