diff --git a/ippl/test/particle/p3m3dHeating.cpp b/ippl/test/particle/p3m3dHeating.cpp
index 217251023159cc1d3c540b08ca552429d8832e5c..ca6209f4c63dccb9a3a7779a11a74a313a2920ed 100644
--- a/ippl/test/particle/p3m3dHeating.cpp
+++ b/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);
}
diff --git a/ippl/test/particle/p3m3dMicrobunching.cpp b/ippl/test/particle/p3m3dMicrobunching.cpp
index 5251efda61f1c63739cdd381425409c35185bf5e..13cafb213c1fce9088474d4341fa1184ff2ef29e 100644
--- a/ippl/test/particle/p3m3dMicrobunching.cpp
+++ b/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);
}
diff --git a/src/Amr/AmrBoxLib.cpp b/src/Amr/AmrBoxLib.cpp
index f5a985c7395f0fd3484a47164edb49108fa545f5..06d1e292e956e33e2742a2a10bb64d8462a8d414 100644
--- a/src/Amr/AmrBoxLib.cpp
+++ b/src/Amr/AmrBoxLib.cpp
@@ -27,9 +27,10 @@
#include "Algorithms/AmrPartBunch.h"
#include "Structure/FieldSolver.h"
#include "Solvers/PoissonSolver.h"
+#include "Utility/PAssert.h"
#include "Amr/AmrYtWriter.h"
-
+
#include <AMReX_MultiFabUtil.H>
#include <AMReX_ParmParse.H> // used in initialize function
@@ -721,7 +722,7 @@ void AmrBoxLib::doRegrid_m(int lbase, double time) {
MakeNewGrids(lbase, time, new_finest, new_grids);
- BL_ASSERT(new_finest <= finest_level+1);
+ PAssert(new_finest <= finest_level+1);
for (int lev = lbase+1; lev <= new_finest; ++lev)
{
diff --git a/src/Amr/BoxLibLayout.hpp b/src/Amr/BoxLibLayout.hpp
index c898753d4f07a595418b9644f66103a487dcaeca..82e4f28fc0d09a9e010f02bed640eb3c9745b121 100644
--- a/src/Amr/BoxLibLayout.hpp
+++ b/src/Amr/BoxLibLayout.hpp
@@ -39,9 +39,9 @@
#include "BoxLibLayout.h"
#include "Message/Formatter.h"
+#include "Utility/PAssert.h"
#include "Utilities/OpalException.h"
-#include <cassert>
#include <cmath>
template <class T, unsigned Dim>
@@ -473,7 +473,7 @@ 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());
+ PAssert(lev < (int)masks_m.size());
masks_m[lev].reset(nullptr);
}
@@ -548,9 +548,9 @@ bool BoxLibLayout<T, Dim>::Where(AmrParticleBase< BoxLibLayout<T,Dim> >& p,
if (lev_max == -1)
lev_max = finestLevel();
- BL_ASSERT(lev_max <= finestLevel());
+ PAssert(lev_max <= finestLevel());
- BL_ASSERT(nGrow == 0 || (nGrow >= 0 && lev_min == lev_max));
+ PAssert(nGrow == 0 || (nGrow >= 0 && lev_min == lev_max));
std::vector< std::pair<int, AmrBox_t> > isects;
@@ -558,7 +558,7 @@ bool BoxLibLayout<T, Dim>::Where(AmrParticleBase< BoxLibLayout<T,Dim> >& p,
{
const AmrIntVect_t& iv = Index(p, ip, lev);
const AmrGrid_t& ba = ParticleBoxArray(lev);
- BL_ASSERT(ba.ixType().cellCentered());
+ PAssert(ba.ixType().cellCentered());
if (lev == (int)p.Level[ip]) {
// The fact that we are here means this particle does not belong to any finer grids.
@@ -605,7 +605,7 @@ bool BoxLibLayout<T, Dim>::EnforcePeriodicWhere (AmrParticleBase< BoxLibLayout<T
if (lev_max == -1)
lev_max = finestLevel();
- BL_ASSERT(lev_max <= finestLevel());
+ PAssert(lev_max <= finestLevel());
//
// Create a copy "dummy" particle to check for periodic outs.
//
@@ -678,7 +678,7 @@ bool BoxLibLayout<T, Dim>::PeriodicShift (SingleParticlePos_t R) const
//
R[i] += .125*geom.CellSize(i);
- BL_ASSERT(R[i] >= geom.ProbLo(i));
+ PAssert(R[i] >= geom.ProbLo(i));
shifted = true;
}
@@ -700,7 +700,7 @@ bool BoxLibLayout<T, Dim>::PeriodicShift (SingleParticlePos_t R) const
//
R[i] -= .125*geom.CellSize(i);
- BL_ASSERT(R[i] <= geom.ProbHi(i));
+ PAssert(R[i] <= geom.ProbHi(i));
shifted = true;
}
@@ -810,8 +810,8 @@ 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);
+ PAssert(lowerBound[d] < 0);
+ PAssert(upperBound[d] > 0);
real_box.setLo(d, lowerBound[d] * (1.0 + dh));
real_box.setHi(d, upperBound[d] * (1.0 + dh));
diff --git a/src/Classic/Algorithms/PartBins.cpp b/src/Classic/Algorithms/PartBins.cpp
index fd6652b615d389ecf1beec6a8941aa980079f469..1cc6efe7a0980f4f1fa0075854b1137789d19f5c 100644
--- a/src/Classic/Algorithms/PartBins.cpp
+++ b/src/Classic/Algorithms/PartBins.cpp
@@ -1,12 +1,30 @@
+//
+// Class PartBins
+// Defines a structure to hold energy bins and their associated data
+//
+// Copyright (c) 2007-2020, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (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/>.
+//
+
#include "Algorithms/PartBins.h"
#include "Algorithms/PBunchDefs.h"
#include "Physics/Physics.h"
+#include "Utility/Inform.h"
#include <cfloat>
#include <limits>
#include <vector>
#include <cmath>
-
PartBins::PartBins(int bins, int sbins) :
gamma_m(1.0),
bins_m(bins),
@@ -14,17 +32,16 @@ PartBins::PartBins(int bins, int sbins) :
xmin_m(0.0),
xmax_m(0.0),
hBin_m(0.0),
- nemittedBins_m(0),
- nemittedSBins_m(0) {
-
+ nemittedBins_m(0) {
+
// number of particles in the bins on the local node
nBin_m = std::unique_ptr<size_t[]>(new size_t[bins_m]);
xbinmin_m = std::unique_ptr<double[]>(new double[bins_m]);
xbinmax_m = std::unique_ptr<double[]>(new double[bins_m]);
-
+
// flag whether the bin contain particles or not
binsEmitted_m = std::unique_ptr<bool[]>(new bool[bins_m]);
-
+
nDelBin_m = std::unique_ptr<size_t[]>(new size_t[bins_m]);
for(int i = 0; i < bins_m; i++) {
@@ -57,46 +74,6 @@ size_t PartBins::getTotalNumPerBin(int b) {
return s;
}
-void PartBins::updateStatus(const int bunchCount, const size_t partInBin) {
- // array index of binsEmitted_m[] starts from 0
- // nemittedBins_m and bins_m index starts from 1
- binsEmitted_m[bunchCount - 1] = true;
- size_t NpartInBin = partInBin;
- reduce(NpartInBin, NpartInBin, OpAddAssign());
- nBin_m[bunchCount - 1] = NpartInBin;
- nemittedBins_m++;
-}
-
-void PartBins::updateDeletedPartsInBin(size_t countLost[]) {
- Inform msg("updateDeletedPartsInBin ");
-
- const int lastEmittedBin = getLastemittedBin();
- reduce(&(countLost[0]), &(countLost[0]) + lastEmittedBin, &(countLost[0]), OpAddAssign());
- for(int ii = 0; ii < lastEmittedBin; ii++) {
- if(countLost[ii] > 0) {
- nDelBin_m[ii] = countLost[ii];
- msg << "In Bin: " << ii << ", " << nDelBin_m[ii] << " particle(s) lost" << endl;
- }
- }
-}
-
-
-void PartBins::updatePartInBin(size_t countLost[]) {
-
- Inform msg0("updatePartInBin ");
-
- for(int ii = 0; ii < nemittedBins_m; ii++) {
- msg0 << "In Bin: " << ii << ", " << nBin_m[ii] << " particles " << endl;
- }
-
- reduce(&(countLost[0]), &(countLost[0]) + nemittedBins_m, &(countLost[0]), OpAddAssign());
- for(int ii = 0; ii < nemittedBins_m; ii++) {
- if(countLost[ii] > 0) {
- nBin_m[ii] -= countLost[ii];
- msg0 << "In Bin: " << ii << ", " << countLost[ii] << " particle(s) lost" << endl;
- }
- }
-}
void PartBins::updatePartInBin_cyc(size_t countLost[]) {
@@ -106,16 +83,6 @@ void PartBins::updatePartInBin_cyc(size_t countLost[]) {
}
}
-
-void PartBins::resetPartInBin(size_t newPartNum[]) {
- reduce(&(newPartNum[0]), &(newPartNum[0]) + nemittedBins_m, &(newPartNum[0]), OpAddAssign());
- for(int ii = 0; ii < nemittedBins_m; ii++) {
- nBin_m[ii] = newPartNum[ii];
- INFOMSG("After reset Bin: " << ii << ", particle(s): " << newPartNum[ii] << endl);
- }
-}
-
-
void PartBins::resetPartInBin_cyc(size_t newPartNum[], int maxbinIndex) {
reduce(maxbinIndex, maxbinIndex, OpMaxAssign());
nemittedBins_m = maxbinIndex + 1;
@@ -127,7 +94,6 @@ void PartBins::resetPartInBin_cyc(size_t newPartNum[], int maxbinIndex) {
}
-
PartBins::~PartBins() {
tmppart_m.clear();
isEmitted_m.clear();
@@ -171,10 +137,6 @@ void PartBins::sortArray() {
}
-void PartBins::sortArrayT() {
- setActualemittedBin(0);
-}
-
void PartBins::calcHBins() {
for(unsigned int n = 0; n < tmppart_m.size(); n++)
@@ -182,27 +144,6 @@ void PartBins::calcHBins() {
calcExtrema();
}
-size_t PartBins::getSum() {
- size_t s = 0;
- for(int n = 0; n < bins_m; n++)
- s += nBin_m[n];
- return s;
-}
-
-void PartBins::calcGlobalExtrema() {
- xmin_m = std::numeric_limits<double>::max();
- xmax_m = -xmin_m;
- for(unsigned int n = 0; n < tmppart_m.size(); n++) {
- if(tmppart_m[n][2] <= xmin_m)
- xmin_m = tmppart_m[n][2];
- if(tmppart_m[n][2] >= xmax_m)
- xmax_m = tmppart_m[n][2];
- }
- double xdiff = 0.01 * (xmax_m - xmin_m);
- xmin_m -= xdiff;
- xmax_m += xdiff;
-}
-
void PartBins::calcExtrema() {
for(unsigned int n = 0; n < tmppart_m.size(); n++) {
if(xbinmin_m[(int)tmppart_m[n][6]] >= tmppart_m[n][2])
diff --git a/src/Classic/Algorithms/PartBins.h b/src/Classic/Algorithms/PartBins.h
index 67637a9b516f3c6516594130065671b51506696e..7d77d894193ccb4027c74f25c362952db9e8e3ba 100644
--- a/src/Classic/Algorithms/PartBins.h
+++ b/src/Classic/Algorithms/PartBins.h
@@ -1,33 +1,33 @@
-/** \file
- * \brief Defines a structure to hold energy bins and their
- * associated data
- *
- *
- *
- * \author Andreas Adelmann
- * \date xx. November 2007
- *
- * \warning None.
- * \attention
- * \bug sure no bug in this code :=)
- * \todo
- */
+//
+// Class PartBins
+// Defines a structure to hold energy bins and their associated data
+//
+// Copyright (c) 2007-2020, Paul Scherrer Institut, Villigen PSI, Switzerland
+// All rights reserved
+//
+// This file is part of OPAL.
+//
+// OPAL is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (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/>.
+//
#ifndef OPAL_Bins_HH
#define OPAL_Bins_HH
-#ifndef PartBinTest
-#include "Algorithms/PBunchDefs.h"
-#else
-#include "ranlib.h"
-#define Inform ostream
-#endif
-
-#include <gsl/gsl_rng.h>
#include <gsl/gsl_histogram.h>
-#include <gsl/gsl_cdf.h>
-#include <gsl/gsl_randist.h>
+#include <functional>
+#include <memory>
+#include <vector>
+
+#include "Algorithms/PBunchDefs.h"
+
+class Inform;
class PartBins {
@@ -48,14 +48,6 @@ public:
virtual ~PartBins();
- /** \brief How many deleted particles are on one bin */
- inline int getDelBinCont(int bin) {
- int a = nDelBin_m[bin];
- reduce(a, a, OpAddAssign());
- return a;
- }
-
-
/** \brief Add a particle to the temporary container */
void fill(std::vector<double> &p) {
tmppart_m.push_back(p);
@@ -73,11 +65,6 @@ public:
/** set particles number in given bin */
void setPartNum(int bin, long long num) {nBin_m[bin] = num;}
- /** assume we emmit in monotinic increasing order */
- void setBinEmitted(int bin) {binsEmitted_m[bin] = true;}
-
- bool getBinEmitted(int bin) {return binsEmitted_m[bin];}
-
/** \brief Is true if we still have particles to emit */
bool doEmission() {return getNp() > 0;}
@@ -85,19 +72,6 @@ public:
return isEmitted_m[n]; //(isEmitted_m[n][0]==1) && (isEmitted_m[n][1] == bin);
}
- void setEmitted(int n, int /*bin*/) {
- isEmitted_m[n] = true;
- }
-
- void updatePartPos(int n, int /*bin*/, double z) {
- tmppart_m[n][2] = z;
- }
-
- void updateExtramePos(int bin, double dz) {
- xbinmax_m[bin] += dz;
- xbinmin_m[bin] += dz;
- }
-
/** assigns the proper position of particle n if it belongs to bin 'bin' */
bool getPart(size_t n, int bin, std::vector<double> &p);
@@ -106,29 +80,19 @@ public:
*/
void sortArray();
+ private:
/** assigns the particles to the bins */
void calcHBins();
- size_t getSum();
- void calcGlobalExtrema();
void calcExtrema();
- void getExtrema(double &min, double &max) {
- min = xmin_m;
- max = xmax_m;
- }
+ /** assume we emit in monotonic increasing order */
+ void setBinEmitted(int bin) {binsEmitted_m[bin] = true;}
- /** update global bin parameters after inject a new bunch */
- void updateStatus(int bunchCount, size_t nPartInBin);
- /** update particles number in bin after reset Bin ID of PartBunch */
- void resetPartInBin(size_t newPartNum[]);
+ public:
/** update local particles number in bin after reset Bin ID of PartBunch */
void resetPartInBin_cyc(size_t newPartNum[], int binID);
- /** update particles number in bin after particle deletion */
- void updatePartInBin(size_t countLost[]);
/** update local particles number in bin after particle deletion */
void updatePartInBin_cyc(size_t countLost[]);
- void updateDeletedPartsInBin(size_t countLost[]) ;
-
void setGamma(double gamma) { gamma_m = gamma;}
double getGamma() {return gamma_m;}
@@ -159,13 +123,8 @@ protected:
std::vector< std::vector<double> > tmppart_m;
std::vector< bool > isEmitted_m;
/** holds information whether all particles of a bin are emitted */
- // std::vector< bool > binsEmitted_m;
std::unique_ptr<bool[]> binsEmitted_m;
- /**
- Here comes the new stuff, t-binning
- */
-
public:
Inform &print(Inform &os);
@@ -175,35 +134,9 @@ public:
/** get the number of used bin */
virtual int getNBins() {return gsl_histogram_bins(h_m.get()) / sBins_m; }
- /** Get the total number of sampled bins */
- virtual int getNSBins() {return gsl_histogram_bins(h_m.get()); }
-
- int getBinToEmit() {
- int save;
- if(nemittedBins_m < getNBins()) {
- save = nemittedBins_m;
- nemittedBins_m++;
- return save;
- } else
- return -1;
- }
-
- int getSBinToEmit() {
- int save;
- if(nemittedSBins_m < getNSBins()) {
- save = nemittedSBins_m;
- nemittedSBins_m++;
- return save;
- } else
- return -1;
- }
-
/** the last emitted bin is always smaller or equal getNbins */
int getLastemittedBin() {return nemittedBins_m; }
- /** set the actual emitted bib */
- void setActualemittedBin(int bin) {nemittedBins_m = bin; }
-
/** \brief If the bunch object rebins we need to call resetBins() */
void resetBins() {
h_m.reset(nullptr);
@@ -213,31 +146,6 @@ public:
return h_m != nullptr;
}
- /** sort the vector of particles according to the bin number */
- void sortArrayT();
-
- inline void setHistogram(gsl_histogram *h) { h_m.reset(h);}
-
- /** \brief How many particles are on one bin */
- virtual inline size_t getGlobalBinCount(int bin) {
- size_t a = gsl_histogram_get(h_m.get(), bin);
- reduce(a, a, OpAddAssign());
- return a;
- }
-
- /** \brief How many particles are on one energy bin */
- virtual inline size_t getLocalBinCount(int bin) {
- size_t ret = 0;
- for(int i = sBins_m * bin; i < sBins_m * (bin + 1); i++) {
- ret += gsl_histogram_get(h_m.get(), i);
- }
- return ret;
- }
-
- /** \brief How many particles are in one sampling bin */
- inline size_t getLocalSBinCount(int bin) { return gsl_histogram_get(h_m.get(), bin);}
-
-
/** \brief How many particles are in all the bins */
size_t getTotalNum();
@@ -250,9 +158,6 @@ protected:
/** number of emitted bins */
int nemittedBins_m;
- /** Number of total sampled bins emitted */
- int nemittedSBins_m;
-
/** number of particles in the bins, the sum of all the nodes */
std::unique_ptr<size_t[]> nBin_m;
diff --git a/src/Classic/Algorithms/PartBinsCyc.cpp b/src/Classic/Algorithms/PartBinsCyc.cpp
index 9b047c2c4c68d45f3d881006f728b24d33f5b5ad..dfc15aab271e1fda7e0d061283fa72c5ddbc057c 100644
--- a/src/Classic/Algorithms/PartBinsCyc.cpp
+++ b/src/Classic/Algorithms/PartBinsCyc.cpp
@@ -26,6 +26,7 @@
//
#include "Algorithms/PartBinsCyc.h"
#include "Physics/Physics.h"
+#include "Utility/Inform.h"
#include <cfloat>
#include <vector>
extern Inform *gmsg;
@@ -36,7 +37,7 @@ PartBinsCyc::PartBinsCyc(int specifiedNumBins, int bins, size_t partInBin[])
bins_m = specifiedNumBins; // max bin number
nemittedBins_m = bins; // the bin number with particles
-
+
for(int i = 0; i < nemittedBins_m; i++) {
nBin_m[i] = partInBin[i];
@@ -51,8 +52,8 @@ PartBinsCyc::PartBinsCyc(int specifiedNumBins, int bins)
bins_m = specifiedNumBins; // max bin number
nemittedBins_m = bins; // the bin number with particles
-
+
for(int i = 0; i < nemittedBins_m; i++) {
binsEmitted_m[i] = true;
}
-}
+}
\ No newline at end of file
diff --git a/src/Classic/Algorithms/PartBinsCyc.h b/src/Classic/Algorithms/PartBinsCyc.h
index 2dd9233139998633658579028efeb77c0b39bdb1..021dcef123a0c6967d1e92675009b19f2a7489ec 100644
--- a/src/Classic/Algorithms/PartBinsCyc.h
+++ b/src/Classic/Algorithms/PartBinsCyc.h
@@ -4,7 +4,7 @@
// associated data for multi-bunch tracking in cyclotrons
//
// Copyright (c) 2010, Jianjun Yang, Paul Scherrer Institut, Villigen PSI, Switzerland
-// Copyright (c) 2017-2019, Paul Scherrer Institut, Villigen PSI, Switzerland
+// Copyright (c) 2017-2020, Paul Scherrer Institut, Villigen PSI, Switzerland
// All rights reserved
//
// Implemented as part of the PhD thesis
@@ -27,47 +27,22 @@
#ifndef OPAL_BinsCyc_HH
#define OPAL_BinsCyc_HH
-#ifndef PartBinTest
-#else
-#include "ranlib.h"
-#define Inform ostream
-#endif
-
#include "Algorithms/PartBins.h"
-#include <gsl/gsl_rng.h>
-#include <gsl/gsl_histogram.h>
-#include <gsl/gsl_cdf.h>
-#include <gsl/gsl_randist.h>
-
-#include <cassert>
class PartBinsCyc: public PartBins {
public:
- /** constructer function for cyclotron*/
+ /** constructor function for cyclotron*/
PartBinsCyc(int bunches, int bins, size_t partInBin[]);
PartBinsCyc(int specifiedNumBins, int bins);
/** get the number of used bin */
- int getNBins() {return bins_m; }
-
- /** \brief How many particles are on one bin */
- inline size_t getGlobalBinCount(int bin) {
- size_t a = nBin_m[bin];
- reduce(a, a, OpAddAssign());
- return a;
- }
-
- /** \brief How many particles are on one energy bin */
- inline size_t getLocalBinCount(int bin) {
- assert(bin < bins_m);
- return nBin_m[bin];
- }
+ virtual int getNBins() {return bins_m; }
- bool weHaveBins() {
- return ( nemittedBins_m > 0 );
+ virtual bool weHaveBins() {
+ return ( nemittedBins_m > 0 );
}
};
diff --git a/src/Classic/Fields/Fieldmap.cpp b/src/Classic/Fields/Fieldmap.cpp
index abaac55f96c8350746584159b130b7c5e8ed8af2..b01f97905c9abe24eadff81d4bcd35bd9de9d93b 100644
--- a/src/Classic/Fields/Fieldmap.cpp
+++ b/src/Classic/Fields/Fieldmap.cpp
@@ -1,4 +1,7 @@
#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);
diff --git a/src/Classic/Solvers/CollimatorPhysics.cpp b/src/Classic/Solvers/CollimatorPhysics.cpp
index b2ea0faa5aeb4fba8f6d1906134e6984849177ca..11e529447c39268fb911327c03d783e0a73576d2 100644
--- a/src/Classic/Solvers/CollimatorPhysics.cpp
+++ b/src/Classic/Solvers/CollimatorPhysics.cpp
@@ -37,6 +37,8 @@
#include "Ippl.h"
+#include <gsl/gsl_randist.h>
+
#include <cmath>
#include <iostream>
#include <fstream>
diff --git a/src/Classic/Solvers/GreenWakeFunction.cpp b/src/Classic/Solvers/GreenWakeFunction.cpp
index e429f4a5e402481e5f4ec028eb91b2d53aa91b66..2f08a8d096eacc769c28610ca01d0a700e91ad5d 100644
--- a/src/Classic/Solvers/GreenWakeFunction.cpp
+++ b/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
diff --git a/src/Classic/Solvers/GreenWakeFunction.hh b/src/Classic/Solvers/GreenWakeFunction.hh
index 52f6e0748bfdcff22e16c72e4fa673b892a9ce9c..a5da6e742ff89829e059eeeec1a3e0ce1a3d2337 100644
--- a/src/Classic/Solvers/GreenWakeFunction.hh
+++ b/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;
diff --git a/src/Classic/Structure/LossDataSink.cpp b/src/Classic/Structure/LossDataSink.cpp
index 866a39b3f62bb7a7a416c1bf6c8a21f3ada5f123..fe465ead4b393cd8849f9bf2c0aa41c4afcfb874 100644
--- a/src/Classic/Structure/LossDataSink.cpp
+++ b/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);
}
}
diff --git a/src/Expressions/Expressions.cpp b/src/Expressions/Expressions.cpp
index 47a8044129bb79312dbfa510a4bd618bdac26de9..8f0170bb4fd8b6ef7e4c44ea20b1d0e5bb51ce8d 100644
--- a/src/Expressions/Expressions.cpp
+++ b/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>
diff --git a/src/OpalParser/OpalParser.cpp b/src/OpalParser/OpalParser.cpp
index 4e5e24f9ff31e7a6ec3ab409ba62400143b96925..8cd8ecbc022814922c8a689a9b78d639cafda26e 100644
--- a/src/OpalParser/OpalParser.cpp
+++ b/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);
}
diff --git a/src/Solvers/ArbitraryDomain.cpp b/src/Solvers/ArbitraryDomain.cpp
index d878d959405d8652f9b928a6452767065e9d0725..26fc09696474c51b84a4fe2bc8049afa51c62a78 100644
--- a/src/Solvers/ArbitraryDomain.cpp
+++ b/src/Solvers/ArbitraryDomain.cpp
@@ -34,7 +34,6 @@
#include <cmath>
#include <iostream>
#include <tuple>
-#include <cassert>
#include "Utilities/OpalException.h"
ArbitraryDomain::ArbitraryDomain( BoundaryGeometry * bgeom,
diff --git a/src/Solvers/BoxCornerDomain.cpp b/src/Solvers/BoxCornerDomain.cpp
index 0980a52a91eb32dbf0c73056baa9ce04f3cc969c..8f0bd5d32453f85d0398c52e28f2e05b742f0be8 100644
--- a/src/Solvers/BoxCornerDomain.cpp
+++ b/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)
diff --git a/src/Solvers/BoxLibSolvers/FMGPoissonSolver.cpp b/src/Solvers/BoxLibSolvers/FMGPoissonSolver.cpp
index 8e7cda8ac756990ab09e0e34a1a577fdd6eb7d0d..8db36e7236309b65aa0bbe32da3a39c23e0ba498 100644
--- a/src/Solvers/BoxLibSolvers/FMGPoissonSolver.cpp
+++ b/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));
diff --git a/src/Solvers/EllipticDomain.cpp b/src/Solvers/EllipticDomain.cpp
index 0b7be840f88885c8b7000bbfd15eeda3858c5c7d..ac9d2a03798c4461ec3b0401e96a5f9ee9c7ecf6 100644
--- a/src/Solvers/EllipticDomain.cpp
+++ b/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)
diff --git a/src/Solvers/IrregularDomain.cpp b/src/Solvers/IrregularDomain.cpp
index 0597bcc8406e38c509b23f5861168afa54b55fcc..f9e1cc6a2e26704b3ba718099b22c8ee99cf177e 100644
--- a/src/Solvers/IrregularDomain.cpp
+++ b/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);
}
diff --git a/src/Structure/BoundaryGeometry.cpp b/src/Structure/BoundaryGeometry.cpp
index 8c59c6e2f421c9324cd40fade1e929e72de321ef..4fd93edb990830bfcc52128d661bdb17dbe35e15 100644
--- a/src/Structure/BoundaryGeometry.cpp
+++ b/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;
diff --git a/src/Structure/BoundaryGeometry.h b/src/Structure/BoundaryGeometry.h
index 549b2e45ea0754c3632409bcff13b73dbc0878bb..2ec308c6307b3e1ffb257f9a9116c6035fb54e0e 100644
--- a/src/Structure/BoundaryGeometry.h
+++ b/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
diff --git a/src/Structure/H5PartWrapper.cpp b/src/Structure/H5PartWrapper.cpp
index 109ef19225d6963ed66a089614a8b338f0c06435..a8184b2f0053b8531869a60d579cdac752e5d21a 100644
--- a/src/Structure/H5PartWrapper.cpp
+++ b/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);