diff --git a/src/Structure/DataSink.cpp b/src/Structure/DataSink.cpp
index 446203fc9b8fad247f6aaf7a6425c7d7a60ddffc..779c17993a769174f817c254bdd95b7fade0976b 100644
--- a/src/Structure/DataSink.cpp
+++ b/src/Structure/DataSink.cpp
@@ -41,9 +41,9 @@
#include "Utility/FieldDebugFunctions.h"
#ifdef __linux__
- #include "MemoryProfiler.h"
+ #include "Structure/MemoryProfiler.h"
#else
- #include "MemoryWriter.h"
+ #include "Structure/MemoryWriter.h"
#endif
#ifdef ENABLE_AMR
@@ -56,6 +56,7 @@
#include <sstream>
+
DataSink::DataSink()
: isMultiBunch_m(false)
{
@@ -63,7 +64,7 @@ DataSink::DataSink()
}
-DataSink::DataSink(H5PartWrapper *h5wrapper, bool restart, short numBunch)
+DataSink::DataSink(H5PartWrapper* h5wrapper, bool restart, short numBunch)
: isMultiBunch_m(numBunch > 1)
{
if (restart && !Options::enableHDF5) {
@@ -78,7 +79,7 @@ DataSink::DataSink(H5PartWrapper *h5wrapper, bool restart, short numBunch)
}
-DataSink::DataSink(H5PartWrapper *h5wrapper, short numBunch)
+DataSink::DataSink(H5PartWrapper* h5wrapper, short numBunch)
: DataSink(h5wrapper, false, numBunch)
{ }
@@ -90,7 +91,7 @@ void DataSink::dumpH5(PartBunchBase<double, 3> *beam, Vector_t FDext[]) const {
}
-int DataSink::dumpH5(PartBunchBase<double, 3> *beam, Vector_t FDext[], double meanEnergy,
+int DataSink::dumpH5(PartBunchBase<double, 3>* beam, Vector_t FDext[], double meanEnergy,
double refPr, double refPt, double refPz,
double refR, double refTheta, double refZ,
double azimuth, double elevation, bool local) const
@@ -102,15 +103,15 @@ int DataSink::dumpH5(PartBunchBase<double, 3> *beam, Vector_t FDext[], double me
}
-void DataSink::dumpSDDS(PartBunchBase<double, 3> *beam, Vector_t FDext[],
+void DataSink::dumpSDDS(PartBunchBase<double, 3>* beam, Vector_t FDext[],
const double& azimuth) const
{
this->dumpSDDS(beam, FDext, losses_t(), azimuth);
}
-void DataSink::dumpSDDS(PartBunchBase<double, 3> *beam, Vector_t FDext[],
- const losses_t &losses, const double& azimuth) const
+void DataSink::dumpSDDS(PartBunchBase<double, 3>* beam, Vector_t FDext[],
+ const losses_t& losses, const double& azimuth) const
{
beam->calcBeamParameters();
@@ -124,8 +125,9 @@ void DataSink::dumpSDDS(PartBunchBase<double, 3> *beam, Vector_t FDext[],
beam->gatherLoadBalanceStatistics();
- for (size_t i = 0; i < sddsWriter_m.size(); ++i)
+ for (size_t i = 0; i < sddsWriter_m.size(); ++i) {
sddsWriter_m[i]->write(beam);
+ }
IpplTimings::stopTimer(StatMarkerTimer_m);
}
@@ -138,34 +140,34 @@ void DataSink::storeCavityInformation() {
}
-void DataSink::changeH5Wrapper(H5PartWrapper *h5wrapper) {
+void DataSink::changeH5Wrapper(H5PartWrapper* h5wrapper) {
if (!Options::enableHDF5) return;
h5Writer_m->changeH5Wrapper(h5wrapper);
}
-void DataSink::writeGeomToVtk(BoundaryGeometry &bg, std::string fn) {
+void DataSink::writeGeomToVtk(BoundaryGeometry& bg, const std::string& fn) {
if (Ippl::myNode() == 0 && Options::enableVTK) {
- bg.writeGeomToVtk (fn);
+ bg.writeGeomToVtk(fn);
}
}
-void DataSink::writeImpactStatistics(const PartBunchBase<double, 3> *beam, long long &step, size_t &impact, double &sey_num,
+void DataSink::writeImpactStatistics(const PartBunchBase<double, 3>* beam, long long& step, size_t& impact, double& sey_num,
size_t numberOfFieldEmittedParticles, bool nEmissionMode, std::string fn) {
double charge = 0.0;
size_t Npart = 0;
double Npart_d = 0.0;
- if(!nEmissionMode) {
+ if (!nEmissionMode) {
charge = -1.0 * beam->getCharge();
//reduce(charge, charge, OpAddAssign());
Npart_d = -1.0 * charge / beam->getChargePerParticle();
} else {
Npart = beam->getTotalNum();
}
- if(Ippl::myNode() == 0) {
+ if (Ippl::myNode() == 0) {
std::string ffn = fn + std::string(".dat");
std::unique_ptr<Inform> ofp(new Inform(nullptr, ffn.c_str(), Inform::APPEND, 0));
@@ -173,9 +175,9 @@ void DataSink::writeImpactStatistics(const PartBunchBase<double, 3> *beam, long
fid.precision(6);
fid << std::setiosflags(std::ios::scientific);
double t = beam->getT() * Units::s2ns;
- if(!nEmissionMode) {
+ if (!nEmissionMode) {
- if(step == 0) {
+ if (step == 0) {
fid << "#Time/ns" << std::setw(18) << "#Geometry impacts" << std::setw(18) << "tot_sey" << std::setw(18)
<< "TotalCharge" << std::setw(18) << "PartNum" << " numberOfFieldEmittedParticles " << endl;
}
@@ -183,7 +185,7 @@ void DataSink::writeImpactStatistics(const PartBunchBase<double, 3> *beam, long
<< std::setw(18) << Npart_d << std::setw(18) << numberOfFieldEmittedParticles << endl;
} else {
- if(step == 0) {
+ if (step == 0) {
fid << "#Time/ns" << std::setw(18) << "#Geometry impacts" << std::setw(18) << "tot_sey" << std::setw(18)
<< "ParticleNumber" << " numberOfFieldEmittedParticles " << endl;
}
@@ -194,7 +196,7 @@ void DataSink::writeImpactStatistics(const PartBunchBase<double, 3> *beam, long
}
-void DataSink::writeMultiBunchStatistics(PartBunchBase<double, 3> *beam,
+void DataSink::writeMultiBunchStatistics(PartBunchBase<double, 3>* beam,
MultiBunchHandler* mbhandler_p) {
/// Start timer.
IpplTimings::startTimer(StatMarkerTimer_m);
diff --git a/src/Structure/DataSink.h b/src/Structure/DataSink.h
index 80a8c19a1b9e8542d8b6ee30504c903c9c72fc81..e8e036fa70a32cabffd4e65f76609a874bee59a7 100644
--- a/src/Structure/DataSink.h
+++ b/src/Structure/DataSink.h
@@ -52,7 +52,7 @@ private:
typedef std::unique_ptr<SDDSWriter> sddsWriter_t;
typedef std::unique_ptr<H5Writer> h5Writer_t;
typedef std::unique_ptr<MultiBunchDump> mbWriter_t;
-
+
public:
/** \brief Default constructor.
*
@@ -63,45 +63,44 @@ public:
DataSink(H5PartWrapper *h5wrapper, bool restart, short numBunch);
DataSink(H5PartWrapper *h5wrapper, short numBunch);
- void dumpH5(PartBunchBase<double, 3> *beam, Vector_t FDext[]) const;
-
- int dumpH5(PartBunchBase<double, 3> *beam, Vector_t FDext[], double meanEnergy,
+ void dumpH5(PartBunchBase<double, 3>* beam, Vector_t FDext[]) const;
+
+ int dumpH5(PartBunchBase<double, 3>* beam, Vector_t FDext[], double meanEnergy,
double refPr, double refPt, double refPz,
double refR, double refTheta, double refZ,
double azimuth, double elevation, bool local) const;
-
- void dumpSDDS(PartBunchBase<double, 3> *beam, Vector_t FDext[],
+
+ void dumpSDDS(PartBunchBase<double, 3>* beam, Vector_t FDext[],
const double& azimuth = -1) const;
-
- void dumpSDDS(PartBunchBase<double, 3> *beam, Vector_t FDext[],
- const losses_t &losses = losses_t(), const double& azimuth = -1) const;
-
+
+ void dumpSDDS(PartBunchBase<double, 3>* beam, Vector_t FDext[],
+ const losses_t& losses = losses_t(), const double& azimuth = -1) const;
+
/** \brief Write cavity information from H5 file
*/
void storeCavityInformation();
-
- void changeH5Wrapper(H5PartWrapper *h5wrapper);
-
+
+ void changeH5Wrapper(H5PartWrapper* h5wrapper);
+
/**
* Write geometry points and surface triangles to vtk file
*
* @param fn specifies the name of vtk file contains the geometry
*
*/
- void writeGeomToVtk(BoundaryGeometry &bg, std::string fn);
- //void writeGeoContourToVtk(BoundaryGeometry &bg, std::string fn);
-
-
+ void writeGeomToVtk(BoundaryGeometry& bg, const std::string& fn);
+ //void writeGeoContourToVtk(BoundaryGeometry& bg, std::string fn);
+
/**
* Write impact number and outgoing secondaries in each time step
*
* @param fn specifies the name of vtk file contains the geometry
*
*/
- void writeImpactStatistics(const PartBunchBase<double, 3> *beam,
- long long int &step,
- size_t &impact,
- double &sey_num,
+ void writeImpactStatistics(const PartBunchBase<double, 3>* beam,
+ long long int& step,
+ size_t& impact,
+ double& sey_num,
size_t numberOfFieldEmittedParticles,
bool nEmissionMode,
std::string fn);
@@ -110,7 +109,7 @@ public:
* @param beam
* @param mbhandler is the multi-bunch handler
*/
- void writeMultiBunchStatistics(PartBunchBase<double, 3> *beam,
+ void writeMultiBunchStatistics(PartBunchBase<double, 3>* beam,
MultiBunchHandler* mbhandler);
/**
@@ -130,7 +129,6 @@ private:
H5PartWrapper* h5wrapper = nullptr,
short numBunch = 1);
-
h5Writer_t h5Writer_m;
statWriter_t statWriter_m;
std::vector<sddsWriter_t> sddsWriter_m;
@@ -157,5 +155,4 @@ std::string DataSink::convertToString(int number, int setw) {
return ss.str();
}
-
#endif // DataSink_H_
diff --git a/src/Structure/LBalWriter.cpp b/src/Structure/LBalWriter.cpp
index f71cdf280fe05f5e0f448d5318a699e739b30272..59580a3cd1cceff68f7a0b3bff97c899faaf684a 100644
--- a/src/Structure/LBalWriter.cpp
+++ b/src/Structure/LBalWriter.cpp
@@ -16,18 +16,18 @@
// You should have received a copy of the GNU General Public License
// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
//
-#include "LBalWriter.h"
+#include "Structure/LBalWriter.h"
-#include "OPALconfig.h"
#include "AbstractObjects/OpalData.h"
-#include "Utilities/Util.h"
-#include "Utilities/Timer.h"
-#include "Algorithms/PartBunchBase.h"
-#include "Physics/Units.h"
-
#ifdef ENABLE_AMR
#include "Algorithms/AmrPartBunch.h"
#endif
+#include "Algorithms/PartBunchBase.h"
+#include "OPALconfig.h"
+#include "Physics/Units.h"
+#include "Utilities/Timer.h"
+#include "Utilities/Util.h"
+
LBalWriter::LBalWriter(const std::string& fname, bool restart)
: SDDSWriter(fname, restart)
@@ -35,7 +35,7 @@ LBalWriter::LBalWriter(const std::string& fname, bool restart)
#ifdef ENABLE_AMR
-void LBalWriter::fillHeader(PartBunchBase<double, 3> * beam) {
+void LBalWriter::fillHeader(PartBunchBase<double, 3>* beam) {
#else
void LBalWriter::fillHeader() {
#endif
@@ -71,11 +71,11 @@ void LBalWriter::fillHeader() {
}
#endif
- if ( mode_m == std::ios::app )
+ if ( mode_m == std::ios::app ) {
return;
+ }
OPALTimer::Timer simtimer;
-
std::string dateStr(simtimer.date());
std::string timeStr(simtimer.time());
@@ -88,24 +88,18 @@ void LBalWriter::fillHeader() {
this->addDefaultParameters();
-
this->addInfo("ascii", 1);
}
-
+void LBalWriter::write(PartBunchBase<double, 3>* beam) {
#ifdef ENABLE_AMR
-void LBalWriter::write(PartBunchBase<double, 3> *beam) {
-
if ( AmrPartBunch* amrbeam = dynamic_cast<AmrPartBunch*>(beam) ) {
amrbeam->gatherLevelStatistics();
}
-#else
-void LBalWriter::write(const PartBunchBase<double, 3> *beam) {
#endif
-
- if ( Ippl::myNode() != 0 )
+ if ( Ippl::myNode() != 0 ) {
return;
-
+ }
#ifdef ENABLE_AMR
this->fillHeader(beam);
#else
@@ -116,7 +110,7 @@ void LBalWriter::write(const PartBunchBase<double, 3> *beam) {
this->writeHeader();
- columns_m.addColumnValue("t", beam->getT() * Units::s2ns); // 1
+ columns_m.addColumnValue("t", beam->getT() * Units::s2ns);
size_t nProcs = Ippl::getNodes();
for (size_t p = 0; p < nProcs; ++ p) {
diff --git a/src/Structure/LBalWriter.h b/src/Structure/LBalWriter.h
index ef769c519299f9da126a1e69eba7d9c099428890..f629b380238344cd569c5e72900dfea99a5d9c7b 100644
--- a/src/Structure/LBalWriter.h
+++ b/src/Structure/LBalWriter.h
@@ -19,26 +19,21 @@
#ifndef OPAL_LBAL_WRITER_H
#define OPAL_LBAL_WRITER_H
-#include "SDDSWriter.h"
+#include "Structure/SDDSWriter.h"
-class LBalWriter : public SDDSWriter {
+class LBalWriter: public SDDSWriter {
public:
LBalWriter(const std::string& fname, bool restart);
-#ifdef ENABLE_AMR
- void write(PartBunchBase<double, 3> *beam);
-#else
- void write(const PartBunchBase<double, 3> *beam) override;
-#endif
+ void write(PartBunchBase<double, 3>* beam) override;
private:
#ifdef ENABLE_AMR
- void fillHeader(PartBunchBase<double, 3> *beam);
+ void fillHeader(PartBunchBase<double, 3>* beam);
#else
void fillHeader();
#endif
};
-
-#endif
\ No newline at end of file
+#endif
diff --git a/src/Structure/MemoryProfiler.cpp b/src/Structure/MemoryProfiler.cpp
index 34f9568849674416cb11c073330c0f014a9b5625..53dbc1ef3204b444c742ffdf30e7e1b3d43ffbc3 100644
--- a/src/Structure/MemoryProfiler.cpp
+++ b/src/Structure/MemoryProfiler.cpp
@@ -18,23 +18,22 @@
// You should have received a copy of the GNU General Public License
// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
//
-#include "MemoryProfiler.h"
+#include "Structure/MemoryProfiler.h"
-#ifdef __linux__
-#include <sys/types.h>
-#include <unistd.h>
-#endif
-
-#include "Utilities/Timer.h"
-#include "Utilities/OpalException.h"
#include "AbstractObjects/OpalData.h"
#include "Algorithms/PartBunchBase.h"
#include "Physics/Units.h"
-
-#include <boost/filesystem.hpp>
+#include "Utilities/Timer.h"
+#include "Utilities/OpalException.h"
#include "Ippl.h"
+#include <boost/filesystem.hpp>
+
+#ifdef __linux__
+#include <sys/types.h>
+#include <unistd.h>
+#endif
#include <sstream>
MemoryProfiler::MemoryProfiler(const std::string& fname, bool restart)
@@ -197,7 +196,7 @@ void MemoryProfiler::compute(vm_t& vmMin,
}
-void MemoryProfiler::write(const PartBunchBase<double, 3> *beam) {
+void MemoryProfiler::write(PartBunchBase<double, 3>* beam) {
this->update();
diff --git a/src/Structure/MemoryProfiler.h b/src/Structure/MemoryProfiler.h
index e35a46d9b367b84091e41697dcc3c4ba80cd1071..acb32dc90daddb3cac5c8fdf19196a63f9bb86be 100644
--- a/src/Structure/MemoryProfiler.h
+++ b/src/Structure/MemoryProfiler.h
@@ -21,23 +21,24 @@
#ifndef OPAL_MEMORY_PROFILER_H
#define OPAL_MEMORY_PROFILER_H
+#include "Structure/SDDSWriter.h"
+
#include <fstream>
-#include <string>
#include <map>
+#include <string>
#include <vector>
-#include "SDDSWriter.h"
-class MemoryProfiler : public SDDSWriter {
+class MemoryProfiler: public SDDSWriter {
/* Pay attention with units. /proc/[pid]/status returns values in
* KiB (Kibibyte) although the units say kB.
* KiB has base 2 not base 10
*/
-
+
public:
typedef std::vector<long double> vm_t;
typedef std::vector<std::string> units_t;
-
+
MemoryProfiler(const std::string& fname, bool restart);
enum VirtualMemory {
@@ -57,14 +58,14 @@ public:
VMSWAP // VmSwap: Swapped-out virtual memory size by anonymous private pages; shmem swap usage is not
// included (since Linux 2.6.34).
};
-
- void write(const PartBunchBase<double, 3> *beam) override;
-
+
+ void write(PartBunchBase<double, 3>* beam) override;
+
private:
void header();
void update();
void compute(vm_t& vmMin, vm_t& vmMax, vm_t& vmAvg);
-
+
private:
std::map<std::string, int> procinfo_m;
vm_t vmem_m;
diff --git a/src/Structure/MemoryWriter.cpp b/src/Structure/MemoryWriter.cpp
index bb26410d0e9a629e30e6733788350266d06624fa..ca775e733a2e128642a88be85018bfd0ffbcf5d5 100644
--- a/src/Structure/MemoryWriter.cpp
+++ b/src/Structure/MemoryWriter.cpp
@@ -18,12 +18,13 @@
// You should have received a copy of the GNU General Public License
// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
//
-#include "MemoryWriter.h"
+#include "Structure/MemoryWriter.h"
#include "AbstractObjects/OpalData.h"
#include "Algorithms/PartBunchBase.h"
-#include "Utilities/Timer.h"
#include "Physics/Units.h"
+#include "Utilities/Timer.h"
+
#include "Ippl.h"
MemoryWriter::MemoryWriter(const std::string& fname, bool restart)
@@ -61,7 +62,6 @@ void MemoryWriter::fillHeader() {
std::string dateStr(simtimer.date());
std::string timeStr(simtimer.time());
-
std::stringstream ss;
ss << "Memory statistics '"
@@ -72,13 +72,12 @@ void MemoryWriter::fillHeader() {
this->addDefaultParameters();
-
this->addInfo("ascii", 1);
}
-void MemoryWriter::write(const PartBunchBase<double, 3> *beam)
-{
+void MemoryWriter::write(PartBunchBase<double, 3>* beam) {
+
IpplMemoryUsage::IpplMemory_p memory = IpplMemoryUsage::getInstance();
memory->sample();
@@ -114,4 +113,4 @@ void MemoryWriter::write(const PartBunchBase<double, 3> *beam)
this->writeRow();
this->close();
-}
\ No newline at end of file
+}
diff --git a/src/Structure/MemoryWriter.h b/src/Structure/MemoryWriter.h
index 2f282683cfb5fc8b501bfb567c156fa30b326061..b55c9b12f322485f78512b7e7e4ef7e2efeaf703 100644
--- a/src/Structure/MemoryWriter.h
+++ b/src/Structure/MemoryWriter.h
@@ -21,17 +21,17 @@
#ifndef OPAL_MEMORY_WRITER_H
#define OPAL_MEMORY_WRITER_H
-#include "SDDSWriter.h"
+#include "Structure/SDDSWriter.h"
-class MemoryWriter : public SDDSWriter {
+class MemoryWriter: public SDDSWriter {
public:
MemoryWriter(const std::string& fname, bool restart);
- void write(const PartBunchBase<double, 3> *beam) override;
+ void write(PartBunchBase<double, 3>* beam) override;
private:
void fillHeader();
};
-#endif
\ No newline at end of file
+#endif
diff --git a/src/Structure/SDDSWriter.cpp b/src/Structure/SDDSWriter.cpp
index 579b7ff0e90946ae1dc14c271f98f1dcec8e81b7..73433b05a8ce83a5c4e50f181ba9c49a7c46701d 100644
--- a/src/Structure/SDDSWriter.cpp
+++ b/src/Structure/SDDSWriter.cpp
@@ -63,7 +63,6 @@ void SDDSWriter::rewindLines(size_t numberOfLines) {
}
fs.close();
-
fs.open (fname_m.c_str(), std::fstream::out);
if (!fs.is_open()) return;
@@ -99,7 +98,6 @@ void SDDSWriter::replaceVersionString() {
}
fs.close();
-
fs.open (fname_m.c_str(), std::fstream::out);
if (!fs.is_open()) return;
@@ -228,4 +226,4 @@ void SDDSWriter::addDefaultParameters() {
addParameter("revision", "string", "git revision of opal", revision.str());
addParameter("flavor", "string", "OPAL flavor that wrote file", flavor);
-}
\ No newline at end of file
+}
diff --git a/src/Structure/SDDSWriter.h b/src/Structure/SDDSWriter.h
index 39e1d1a4f85c3f1784334c6197335007bacdfbd5..5858415d66f91eeab7d27b8bb447d8941d5a667b 100644
--- a/src/Structure/SDDSWriter.h
+++ b/src/Structure/SDDSWriter.h
@@ -20,15 +20,15 @@
#define OPAL_SDDS_WRITER_H
#include <fstream>
-#include <string>
-#include <queue>
+#include <iomanip>
#include <map>
-#include <vector>
-#include <tuple>
-#include <utility>
#include <ostream>
-#include <iomanip>
+#include <queue>
#include <sstream>
+#include <string>
+#include <tuple>
+#include <utility>
+#include <vector>
#include <boost/filesystem.hpp>
@@ -58,12 +58,11 @@ public:
std::string,
std::string> cols_t;
-
SDDSWriter(const std::string& fname, bool restart);
virtual ~SDDSWriter() { };
- virtual void write(const PartBunchBase<double, 3>* /*beam*/) { };
+ virtual void write(PartBunchBase<double, 3>* /*beam*/) { };
/** \brief
* delete the last 'numberOfLines' lines of the file 'fileName'
@@ -77,7 +76,6 @@ public:
bool exists() const;
protected:
-
void addDescription(const std::string& text,
const std::string& content);
@@ -131,7 +129,6 @@ protected:
bool hasColumns() const;
private:
-
void writeDescription();
void writeParameters();
@@ -162,8 +159,7 @@ bool SDDSWriter::exists() const {
inline
void SDDSWriter::addDescription(const std::string& text,
- const std::string& content)
-{
+ const std::string& content) {
desc_m = std::make_pair(text, content);
}
@@ -172,8 +168,7 @@ template<typename T>
void SDDSWriter::addParameter(const std::string& name,
const std::string& type,
const std::string& desc,
- const T& value)
-{
+ const T& value) {
params_m.push(std::make_tuple(name, type, desc));
std::stringstream ss;
ss << value;
@@ -208,4 +203,4 @@ bool SDDSWriter::hasColumns() const {
return columns_m.hasColumns();
}
-#endif
\ No newline at end of file
+#endif