From 75e6276d5a0174c0e9bcdb9dec9c1b70d811ddb3 Mon Sep 17 00:00:00 2001
From: ext-calvo_p <pedro.calvo@ciemat.es>
Date: Wed, 20 Sep 2023 15:08:18 +0200
Subject: [PATCH] Resolve "h5 file initialization"
---
src/Track/TrackRun.cpp | 232 ++++++++++++++++++++---------------------
src/Track/TrackRun.h | 17 +--
2 files changed, 123 insertions(+), 126 deletions(-)
diff --git a/src/Track/TrackRun.cpp b/src/Track/TrackRun.cpp
index b916639d1..49e4da61a 100644
--- a/src/Track/TrackRun.cpp
+++ b/src/Track/TrackRun.cpp
@@ -2,7 +2,7 @@
// Class TrackRun
// The RUN command.
//
-// Copyright (c) 200x - 2022, Paul Scherrer Institut, Villigen PSI, Switzerland
+// Copyright (c) 200x - 2023, Paul Scherrer Institut, Villigen PSI, Switzerland
// All rights reserved
//
// This file is part of OPAL.
@@ -61,7 +61,7 @@
extern Inform *gmsg;
-std::shared_ptr<Tracker> TrackRun::itsTracker = nullptr;
+std::shared_ptr<Tracker> TrackRun::itsTracker_m = nullptr;
namespace {
// The attributes of class TrackRun.
@@ -94,9 +94,9 @@ TrackRun::TrackRun():
Action(SIZE, "RUN",
"The \"RUN\" sub-command tracks the defined particles through "
"the given lattice."),
- dist(nullptr),
- fs(nullptr),
- ds(nullptr),
+ dist_m(nullptr),
+ fieldSolver_m(nullptr),
+ dataSink_m(nullptr),
phaseSpaceSink_m(nullptr),
isFollowupTrack_m(false),
method_m(RunMethod::NONE),
@@ -139,21 +139,21 @@ TrackRun::TrackRun():
("TRACKBACK", "Track in reverse direction, default: false.", false);
registerOwnership(AttributeHandler::SUB_COMMAND);
- opal = OpalData::getInstance();
+ opalData_m = OpalData::getInstance();
}
TrackRun::TrackRun(const std::string& name, TrackRun* parent):
Action(name, parent),
- dist(nullptr),
- fs(nullptr),
- ds(nullptr),
+ dist_m(nullptr),
+ fieldSolver_m(nullptr),
+ dataSink_m(nullptr),
phaseSpaceSink_m(nullptr),
isFollowupTrack_m(false),
method_m(RunMethod::NONE),
macromass_m(0.0),
macrocharge_m(0.0) {
- opal = OpalData::getInstance();
+ opalData_m = OpalData::getInstance();
}
@@ -196,7 +196,7 @@ void TrackRun::execute() {
}
}
- isFollowupTrack_m = opal->hasBunchAllocated();
+ isFollowupTrack_m = opalData_m->hasBunchAllocated();
if (!itsAttr[DISTRIBUTION] && !isFollowupTrack_m) {
throw OpalException("TrackRun::execute",
"\"DISTRIBUTION\" must be set in \"RUN\" command.");
@@ -232,22 +232,22 @@ void TrackRun::execute() {
}
if (method_m == RunMethod::THICK) {
- int turns = int(std::round(Attributes::getReal(itsAttr[TURNS])));
+ int turns = int(std::round(Attributes::getReal(itsAttr[TURNS])));
// Track for the all but last turn.
for (int turn = 1; turn < turns; ++turn) {
- itsTracker->execute();
+ itsTracker_m->execute();
}
// Track the last turn.
- itsTracker->execute();
+ itsTracker_m->execute();
} else {
- itsTracker->execute();
+ itsTracker_m->execute();
- opal->setRestartRun(false);
+ opalData_m->setRestartRun(false);
}
- opal->bunchIsAllocated();
+ opalData_m->bunchIsAllocated();
}
void TrackRun::setRunMethod() {
@@ -277,30 +277,17 @@ void TrackRun::setupThickTracker() {
setupFieldsolver();
- if (opal->inRestartRun()) {
- phaseSpaceSink_m = new H5PartWrapperForPT(opal->getInputBasename() + std::string(".h5"),
- opal->getRestartStep(),
- OpalData::getInstance()->getRestartFileName(),
- H5_O_WRONLY);
- } else if (isFollowupTrack_m) {
- phaseSpaceSink_m = new H5PartWrapperForPT(opal->getInputBasename() + std::string(".h5"),
- -1,
- opal->getInputBasename() + std::string(".h5"),
- H5_O_WRONLY);
- } else {
- phaseSpaceSink_m = new H5PartWrapperForPT(opal->getInputBasename() + std::string(".h5"),
- H5_O_WRONLY);
- }
+ initPhaseSpaceSink();
macrocharge_m = setDistributionParallelT(beam);
- *gmsg << *this << endl;
+ *gmsg << *this << endl;
Track::block->bunch->setdT(Track::block->dT.front());
Track::block->bunch->dtScInit_m = Track::block->dtScInit;
Track::block->bunch->deltaTau_m = Track::block->deltaTau;
- if (!isFollowupTrack_m && !opal->inRestartRun()) {
+ if (!isFollowupTrack_m && !opalData_m->inRestartRun()) {
Track::block->bunch->setT(Track::block->t0_m);
}
@@ -320,7 +307,7 @@ void TrackRun::setupThickTracker() {
initDataSink();
if (!isFollowupTrack_m) {
- *gmsg << *dist << endl;
+ *gmsg << *dist_m << endl;
}
if (Track::block->bunch->getTotalNum() > 0) {
@@ -344,10 +331,10 @@ void TrackRun::setupThickTracker() {
}
*gmsg << *beam << endl;
- *gmsg << *fs << endl;
+ *gmsg << *fieldSolver_m << endl;
- itsTracker.reset(new ThickTracker(*Track::block->use->fetchLine(),
- Track::block->bunch, *beam, *ds, Track::block->reference,
+ itsTracker_m.reset(new ThickTracker(*Track::block->use->fetchLine(),
+ Track::block->bunch, *beam, *dataSink_m, Track::block->reference,
false, false, Track::block->localTimeSteps,
Track::block->zstart, Track::block->zstop, Track::block->dT,
Track::block->truncOrder));
@@ -355,7 +342,7 @@ void TrackRun::setupThickTracker() {
void TrackRun::setupTTracker(){
- OpalData::getInstance()->setInOPALTMode();
+ opalData_m->setInOPALTMode();
if (isFollowupTrack_m) {
Track::block->bunch->setLocalTrackStep(0);
@@ -369,31 +356,18 @@ void TrackRun::setupTTracker(){
setupFieldsolver();
- if (opal->inRestartRun()) {
- phaseSpaceSink_m = new H5PartWrapperForPT(opal->getInputBasename() + std::string(".h5"),
- opal->getRestartStep(),
- OpalData::getInstance()->getRestartFileName(),
- H5_O_WRONLY);
- } else if (isFollowupTrack_m) {
- phaseSpaceSink_m = new H5PartWrapperForPT(opal->getInputBasename() + std::string(".h5"),
- -1,
- opal->getInputBasename() + std::string(".h5"),
- H5_O_WRONLY);
- } else {
- phaseSpaceSink_m = new H5PartWrapperForPT(opal->getInputBasename() + std::string(".h5"),
- H5_O_WRONLY);
- }
+ initPhaseSpaceSink();
macrocharge_m = setDistributionParallelT(beam);
macromass_m = beam->getMassPerParticle();
- *gmsg << *this << endl;
+ *gmsg << *this << endl;
Track::block->bunch->setdT(Track::block->dT.front());
Track::block->bunch->dtScInit_m = Track::block->dtScInit;
Track::block->bunch->deltaTau_m = Track::block->deltaTau;
- if (!isFollowupTrack_m && !opal->inRestartRun()) {
+ if (!isFollowupTrack_m && !opalData_m->inRestartRun()) {
Track::block->bunch->setT(Track::block->t0_m);
}
@@ -415,7 +389,7 @@ void TrackRun::setupTTracker(){
if (!isFollowupTrack_m) {
*gmsg << std::scientific;
- *gmsg << *dist << endl;
+ *gmsg << *dist_m << endl;
}
if (Track::block->bunch->getTotalNum() > 0) {
@@ -435,13 +409,13 @@ void TrackRun::setupTTracker(){
}
*gmsg << *beam << endl;
- *gmsg << *fs << endl;
+ *gmsg << *fieldSolver_m << endl;
// findPhasesForMaxEnergy();
-
- itsTracker.reset(new ParallelTTracker(*Track::block->use->fetchLine(),
+
+ itsTracker_m.reset(new ParallelTTracker(*Track::block->use->fetchLine(),
Track::block->bunch,
- *ds,
+ *dataSink_m,
Track::block->reference,
false,
Attributes::getBool(itsAttr[TRACKBACK]),
@@ -452,8 +426,8 @@ void TrackRun::setupTTracker(){
}
void TrackRun::setupCyclotronTracker(){
+ opalData_m->setInOPALCyclMode();
- OpalData::getInstance()->setInOPALCyclMode();
Beam* beam = Beam::find(Attributes::getString(itsAttr[BEAM]));
setBoundaryGeometry();
@@ -465,9 +439,9 @@ void TrackRun::setupCyclotronTracker(){
std::vector<std::string> distr_str = Attributes::getStringArray(itsAttr[DISTRIBUTION]);
if (distr_str.size() == 0) {
- dist = Distribution::find(defaultDistribution);
+ dist_m = Distribution::find(defaultDistribution);
} else {
- dist = Distribution::find(distr_str.at(0));
+ dist_m = Distribution::find(distr_str.at(0));
}
// multi-bunch parameters
@@ -477,25 +451,12 @@ void TrackRun::setupCyclotronTracker(){
const double mbEta = Attributes::getReal(itsAttr[MB_ETA]);
const std::string mbBinning = Attributes::getString(itsAttr[MB_BINNING]);
- if (opal->inRestartRun()) {
- phaseSpaceSink_m = new H5PartWrapperForPC(opal->getInputBasename() + std::string(".h5"),
- opal->getRestartStep(),
- OpalData::getInstance()->getRestartFileName(),
- H5_O_WRONLY);
- } else if (isFollowupTrack_m) {
- phaseSpaceSink_m = new H5PartWrapperForPC(opal->getInputBasename() + std::string(".h5"),
- -1,
- opal->getInputBasename() + std::string(".h5"),
- H5_O_WRONLY);
- } else {
- phaseSpaceSink_m = new H5PartWrapperForPC(opal->getInputBasename() + std::string(".h5"),
- H5_O_WRONLY);
- }
+ initPhaseSpaceSink();
if (beam->getNumberOfParticles() < 3 || beam->getCurrent() == 0.0) {
macrocharge_m = beam->getCharge() * Physics::q_e;
macromass_m = beam->getMass();
- Track::block->bunch->setDistribution(dist,
+ Track::block->bunch->setDistribution(dist_m,
beam->getNumberOfParticles(),
beam->getCurrent(),
*Track::block->use->fetchLine());
@@ -509,16 +470,16 @@ void TrackRun::setupCyclotronTracker(){
macromass_m = beam->getMassPerParticle();
if (!isFollowupTrack_m) {
- if (!opal->inRestartRun()) {
- Track::block->bunch->setDistribution(dist,
+ if (!opalData_m->inRestartRun()) {
+ Track::block->bunch->setDistribution(dist_m,
beam->getNumberOfParticles(),
beam->getCurrent(),
*Track::block->use->fetchLine());
} else {
- dist->doRestartOpalCycl(Track::block->bunch,
+ dist_m->doRestartOpalCycl(Track::block->bunch,
beam->getNumberOfParticles(),
- opal->getRestartStep(),
+ opalData_m->getRestartStep(),
specifiedNumBunch,
phaseSpaceSink_m);
}
@@ -539,15 +500,15 @@ void TrackRun::setupCyclotronTracker(){
initDataSink(specifiedNumBunch);
- itsTracker.reset(new ParallelCyclotronTracker(*Track::block->use->fetchLine(),
- Track::block->bunch, *ds, Track::block->reference,
+ itsTracker_m.reset(new ParallelCyclotronTracker(*Track::block->use->fetchLine(),
+ Track::block->bunch, *dataSink_m, Track::block->reference,
false, false, Track::block->localTimeSteps.front(),
Track::block->timeIntegrator,
specifiedNumBunch, mbEta, mbPara, mbMode, mbBinning));
- ParallelCyclotronTracker* cyclTracker = dynamic_cast<ParallelCyclotronTracker*>(itsTracker.get());
+ ParallelCyclotronTracker* cyclTracker = dynamic_cast<ParallelCyclotronTracker*>(itsTracker_m.get());
- if (opal->inRestartRun()) {
+ if (opalData_m->inRestartRun()) {
H5PartWrapperForPC *h5pw = static_cast<H5PartWrapperForPC*>(phaseSpaceSink_m);
cyclTracker->setBeGa(h5pw->getMeanMomentum());
@@ -565,30 +526,30 @@ void TrackRun::setupCyclotronTracker(){
cyclTracker->setPreviousH5Local(h5pw->getPreviousH5Local());
if ( specifiedNumBunch > 1 ) {
- cyclTracker->setLastDumpedStep(opal->getRestartStep());
+ cyclTracker->setLastDumpedStep(opalData_m->getRestartStep());
}
}
// statistical data are calculated (rms, eps etc.)
Track::block->bunch->calcBeamParameters();
- *gmsg << *this << endl;
- *gmsg << *dist << endl;
+ *gmsg << *this << endl;
+ *gmsg << *dist_m << endl;
*gmsg << *beam << endl;
- *gmsg << *fs << endl;
+ *gmsg << *fieldSolver_m << endl;
}
void TrackRun::setupFieldsolver() {
- fs = FieldSolver::find(Attributes::getString(itsAttr[FIELDSOLVER]));
+ fieldSolver_m = FieldSolver::find(Attributes::getString(itsAttr[FIELDSOLVER]));
- if (fs->getFieldSolverType() != FieldSolverType::NONE) {
- size_t numGridPoints = fs->getMX()*fs->getMY()*fs->getMT(); // total number of gridpoints
+ if (fieldSolver_m->getFieldSolverType() != FieldSolverType::NONE) {
+ size_t numGridPoints = fieldSolver_m->getMX()*fieldSolver_m->getMY()*fieldSolver_m->getMT(); // total number of gridpoints
Beam* beam = Beam::find(Attributes::getString(itsAttr[BEAM]));
size_t numParticles = beam->getNumberOfParticles();
- if (!opal->inRestartRun() && numParticles < numGridPoints
- && fs->getFieldSolverType() != FieldSolverType::SAAMG // in SPIRAL/SAAMG we're meshing the whole domain -DW
- && fs->getFieldSolverType() != FieldSolverType::P3M //In P3M with one-one mapping grid points can be less than particles
+ if (!opalData_m->inRestartRun() && numParticles < numGridPoints
+ && fieldSolver_m->getFieldSolverType() != FieldSolverType::SAAMG // in SPIRAL/SAAMG we're meshing the whole domain -DW
+ && fieldSolver_m->getFieldSolverType() != FieldSolverType::P3M //In P3M with one-one mapping grid points can be less than particles
&& !Options::amr)
{
throw OpalException("TrackRun::setupFieldsolver()",
@@ -597,43 +558,78 @@ void TrackRun::setupFieldsolver() {
"Please increase the number of particles or reduce the size of the mesh.\n");
}
- OpalData::getInstance()->addProblemCharacteristicValue("MX", fs->getMX());
- OpalData::getInstance()->addProblemCharacteristicValue("MY", fs->getMY());
- OpalData::getInstance()->addProblemCharacteristicValue("MT", fs->getMT());
+ opalData_m->addProblemCharacteristicValue("MX", fieldSolver_m->getMX());
+ opalData_m->addProblemCharacteristicValue("MY", fieldSolver_m->getMY());
+ opalData_m->addProblemCharacteristicValue("MT", fieldSolver_m->getMT());
}
- fs->initCartesianFields();
- Track::block->bunch->setSolver(fs);
- if (fs->hasPeriodicZ()) {
+ fieldSolver_m->initCartesianFields();
+ Track::block->bunch->setSolver(fieldSolver_m);
+ if (fieldSolver_m->hasPeriodicZ()) {
Track::block->bunch->setBCForDCBeam();
} else {
Track::block->bunch->setBCAllOpen();
}
}
+void TrackRun::initPhaseSpaceSink() {
+ const std::string h5FileName = opalData_m->getInputBasename() + std::string(".h5");
+ if (opalData_m->isInOPALCyclMode()) {
+ if (opalData_m->inRestartRun()) {
+ phaseSpaceSink_m = new H5PartWrapperForPC(h5FileName,
+ opalData_m->getRestartStep(),
+ opalData_m->getRestartFileName(),
+ H5_O_WRONLY);
+ } else if (isFollowupTrack_m) {
+ phaseSpaceSink_m = new H5PartWrapperForPC(h5FileName,
+ -1,
+ h5FileName,
+ H5_O_WRONLY);
+ } else if (Options::enableHDF5) {
+ phaseSpaceSink_m = new H5PartWrapperForPC(h5FileName,
+ H5_O_WRONLY);
+ }
+ } else {
+ if (opalData_m->inRestartRun()) {
+ phaseSpaceSink_m = new H5PartWrapperForPT(h5FileName,
+ opalData_m->getRestartStep(),
+ opalData_m->getRestartFileName(),
+ H5_O_WRONLY);
+ } else if (isFollowupTrack_m) {
+ phaseSpaceSink_m = new H5PartWrapperForPT(h5FileName,
+ -1,
+ h5FileName,
+ H5_O_WRONLY);
+ } else if (Options::enableHDF5) {
+ phaseSpaceSink_m = new H5PartWrapperForPT(h5FileName,
+ H5_O_WRONLY);
+ }
+ }
+}
+
void TrackRun::initDataSink(const int& numBunch) {
- if (!opal->inRestartRun()) {
- if (!opal->hasDataSinkAllocated()) {
- opal->setDataSink(new DataSink(phaseSpaceSink_m, false, numBunch));
+ if (!opalData_m->inRestartRun()) {
+ if (!opalData_m->hasDataSinkAllocated()) {
+ opalData_m->setDataSink(new DataSink(phaseSpaceSink_m, false, numBunch));
} else {
- ds = opal->getDataSink();
- ds->changeH5Wrapper(phaseSpaceSink_m);
+ dataSink_m = opalData_m->getDataSink();
+ dataSink_m->changeH5Wrapper(phaseSpaceSink_m);
}
} else {
- opal->setDataSink(new DataSink(phaseSpaceSink_m, true, numBunch));
+ opalData_m->setDataSink(new DataSink(phaseSpaceSink_m, true, numBunch));
}
- ds = opal->getDataSink();
+ dataSink_m = opalData_m->getDataSink();
}
void TrackRun::setBoundaryGeometry() {
if (Attributes::getString(itsAttr[BOUNDARYGEOMETRY]) != "NONE") {
// Ask the dictionary if BoundaryGeometry is allocated.
// If it is allocated use the allocated BoundaryGeometry
- if (!OpalData::getInstance()->hasGlobalGeometry()) {
+ if (!opalData_m->hasGlobalGeometry()) {
const std::string geomDescriptor = Attributes::getString(itsAttr[BOUNDARYGEOMETRY]);
BoundaryGeometry* bg = BoundaryGeometry::find(geomDescriptor)->clone(geomDescriptor);
- OpalData::getInstance()->setGlobalGeometry(bg);
+ opalData_m->setGlobalGeometry(bg);
}
}
}
@@ -651,10 +647,10 @@ double TrackRun::setDistributionParallelT(Beam* beam) {
const size_t numberOfDistributions = distributionArray.size();
if (numberOfDistributions == 0) {
- dist = Distribution::find(defaultDistribution);
+ dist_m = Distribution::find(defaultDistribution);
} else {
- dist = Distribution::find(distributionArray.at(0));
- dist->setNumberOfDistributions(numberOfDistributions);
+ dist_m = Distribution::find(distributionArray.at(0));
+ dist_m->setNumberOfDistributions(numberOfDistributions);
if (numberOfDistributions > 1) {
*gmsg << endl
@@ -683,12 +679,12 @@ double TrackRun::setDistributionParallelT(Beam* beam) {
*/
size_t numberOfParticles = beam->getNumberOfParticles();
if (!isFollowupTrack_m) {
- if (!opal->inRestartRun()) {
+ if (!opalData_m->inRestartRun()) {
/*
* Here we are not doing a restart run
* and we do not have a bunch already allocated.
*/
- Track::block->bunch->setDistribution(dist,
+ Track::block->bunch->setDistribution(dist_m,
distrs_m,
numberOfParticles);
@@ -697,12 +693,12 @@ double TrackRun::setDistributionParallelT(Beam* beam) {
* make sure it doesn't have any particles at z < 0.
*/
- opal->setGlobalPhaseShift(0.5 * dist->getTEmission() + dist->getEmissionTimeShift());
+ opalData_m->setGlobalPhaseShift(0.5 * dist_m->getTEmission() + dist_m->getEmissionTimeShift());
} else {
/*
* Read in beam from restart file.
*/
- dist->doRestartOpalT(Track::block->bunch, numberOfParticles, opal->getRestartStep(), phaseSpaceSink_m);
+ dist_m->doRestartOpalT(Track::block->bunch, numberOfParticles, opalData_m->getRestartStep(), phaseSpaceSink_m);
}
}
@@ -735,5 +731,5 @@ Inform& TrackRun::print(Inform& os) const {
}
std::shared_ptr<Tracker> TrackRun::getTracker() {
- return itsTracker;
+ return itsTracker_m;
}
diff --git a/src/Track/TrackRun.h b/src/Track/TrackRun.h
index 2c938b716..c6cb82193 100644
--- a/src/Track/TrackRun.h
+++ b/src/Track/TrackRun.h
@@ -2,7 +2,7 @@
// Class TrackRun
// The RUN command.
//
-// Copyright (c) 200x - 2022, Paul Scherrer Institut, Villigen PSI, Switzerland
+// Copyright (c) 200x - 2023, Paul Scherrer Institut, Villigen PSI, Switzerland
// All rights reserved
//
// This file is part of OPAL.
@@ -77,29 +77,30 @@ private:
void setupThickTracker();
void setupFieldsolver();
+ void initPhaseSpaceSink();
+
void initDataSink(const int& numBunch = 1);
void setBoundaryGeometry();
double setDistributionParallelT(Beam* beam);
- /* itsTracker is a static object; this enables access to the last executed
+ /* itsTracker_m is a static object; this enables access to the last executed
* tracker object without excessive gymnastics, e.g. for access to the
* field maps in PyField
*/
- static std::shared_ptr<Tracker> itsTracker;
-
- Distribution* dist;
+ static std::shared_ptr<Tracker> itsTracker_m;
+ Distribution* dist_m;
std::vector<Distribution*> distrs_m;
- FieldSolver* fs;
+ FieldSolver* fieldSolver_m;
- DataSink* ds;
+ DataSink* dataSink_m;
H5PartWrapper* phaseSpaceSink_m;
- OpalData* opal;
+ OpalData* opalData_m;
bool isFollowupTrack_m;
--
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