diff --git a/ippl/src/AppTypes/Vektor.h b/ippl/src/AppTypes/Vektor.h
index 92f1fcd9a6f314db9f85d655d93c87c4f337fd6a..7f92412ccaaa370542d42311b4593044958bb655 100644
--- a/ippl/src/AppTypes/Vektor.h
+++ b/ippl/src/AppTypes/Vektor.h
@@ -40,10 +40,6 @@ public:
TSV_MetaAssignScalar<Vektor<T,D>,T,OpAssign>::apply(*this,T(0));
}
- // A noninitializing ctor.
- class DontInitialize {};
- Vektor(DontInitialize) {}
-
// Copy Constructor
Vektor(const Vektor<T,D> &rhs) {
TSV_MetaAssign< Vektor<T,D> , Vektor<T,D> ,OpAssign >::apply(*this,rhs);
diff --git a/ippl/src/Message/Message.h b/ippl/src/Message/Message.h
index 392540111fe8b07fde4c4554ae7bdcdcf543e41f..4505bf58a9bd479e5125392d3d85b03473fac835 100644
--- a/ippl/src/Message/Message.h
+++ b/ippl/src/Message/Message.h
@@ -211,7 +211,7 @@ public:
}
// copy constructor
- MsgItem(const MsgItem &m) : item(&defbuf), elements(m.elements), bytesize(m.bytesize),
+ MsgItem(const MsgItem &m) : item(&defbuf), elements(m.elements), bytesize(m.bytesize),
defbuf(m.defbuf), needDelete(m.needDelete)
{
// either we just copy the 'item' pointer, or we copy the default buf
diff --git a/optimizer/Optimizer/EA/Variator.h b/optimizer/Optimizer/EA/Variator.h
index 8cb72b35bbba93566c1724ce03d30d39a6bf287c..77183e0cb370c19365fc48594c6a1dd2a00e6640 100644
--- a/optimizer/Optimizer/EA/Variator.h
+++ b/optimizer/Optimizer/EA/Variator.h
@@ -213,7 +213,7 @@ public:
if (viableA == true && viableB == true) {
break;
}
- std::cout << "Individual not viable, I try again: iter= " << iter << std::endl;
+ std::cout << "Individuals not viable, I try again: iter= " << iter << std::endl;
iter++;
// if maximum number of tries then create new individual(s)
if (iter > 100) {
diff --git a/src/BasicActions/DumpFields.cpp b/src/BasicActions/DumpFields.cpp
index 2bbcf654de568897cdb622dfc477b0712874c50b..b9c029e1f84d22442ef1f2a2b769164d1bc3a453 100644
--- a/src/BasicActions/DumpFields.cpp
+++ b/src/BasicActions/DumpFields.cpp
@@ -34,8 +34,6 @@
#include "Attributes/Attributes.h"
#include "BasicActions/DumpFields.h"
-// extern Inform *gmsg;
-
std::unordered_set<DumpFields*> DumpFields::dumpsSet_m;
std::string DumpFields::dumpfields_docstring =
@@ -116,9 +114,7 @@ void DumpFields::buildGrid() {
checkInt(nx, "X_STEPS");
checkInt(ny, "Y_STEPS");
checkInt(nz, "Z_STEPS");
- if (grid_m != NULL) {
- delete grid_m;
- }
+ delete grid_m;
grid_m = new interpolation::ThreeDGrid(dx, dy, dz,
x0, y0, z0,
@@ -148,11 +144,11 @@ void DumpFields::checkInt(double real, std::string name, double tolerance) {
void DumpFields::writeFieldThis(Component* field) {
if (grid_m == NULL) {
- throw OpalException("DumpFields::writeField",
+ throw OpalException("DumpFields::writeFieldThis",
"The grid was NULL; there was a problem with the DumpFields initialisation.");
}
if (field == NULL) {
- throw OpalException("DumpFields::writeField",
+ throw OpalException("DumpFields::writeFieldThis",
"The field to be written was NULL.");
}
double time = 0.;
@@ -160,7 +156,7 @@ void DumpFields::writeFieldThis(Component* field) {
Vector_t centroid(0., 0., 0.);
std::ofstream fout(filename_m.c_str(), std::ofstream::out);
if (!fout.good()) {
- throw OpalException("DumpFields::writeField",
+ throw OpalException("DumpFields::writeFieldThis",
"Failed to open DumpFields file "+filename_m);
}
// set precision
@@ -183,7 +179,7 @@ void DumpFields::writeFieldThis(Component* field) {
fout << B[0] << " " << B[1] << " " << B[2] << "\n";
}
if (!fout.good()) {
- throw OpalException("DumpFields::writeField",
+ throw OpalException("DumpFields::writeFieldThis",
"Something went wrong during writing "+filename_m);
}
fout.close();
diff --git a/src/Classic/AbsBeamline/Bend2D.cpp b/src/Classic/AbsBeamline/Bend2D.cpp
index 14554e0712988f510edff40cace87220ed66eb0c..53b138bdc9a6b9b5352fe3d03347821295b872c3 100644
--- a/src/Classic/AbsBeamline/Bend2D.cpp
+++ b/src/Classic/AbsBeamline/Bend2D.cpp
@@ -46,20 +46,22 @@ Bend2D::Bend2D(const Bend2D &right):
messageHeader_m(" * "),
pusher_m(right.pusher_m),
fieldmap_m(right.fieldmap_m),
- fast_m(right.fast_m),
designRadius_m(right.designRadius_m),
exitAngle_m(right.exitAngle_m),
fieldIndex_m(right.fieldIndex_m),
startField_m(right.startField_m),
endField_m(right.endField_m),
+ widthEntranceFringe_m(right.widthEntranceFringe_m),
+ widthExitFringe_m(right.widthExitFringe_m),
reinitialize_m(right.reinitialize_m),
- recalcRefTraj_m(right.recalcRefTraj_m),
entranceParameter1_m(right.entranceParameter1_m),
entranceParameter2_m(right.entranceParameter2_m),
entranceParameter3_m(right.entranceParameter3_m),
exitParameter1_m(right.exitParameter1_m),
exitParameter2_m(right.exitParameter2_m),
exitParameter3_m(right.exitParameter3_m),
+ engeCoeffsEntry_m(right.engeCoeffsEntry_m),
+ engeCoeffsExit_m(right.engeCoeffsExit_m),
entryFieldValues_m(NULL),
exitFieldValues_m(NULL),
entryFieldAccel_m(NULL),
@@ -67,8 +69,6 @@ Bend2D::Bend2D(const Bend2D &right):
deltaBeginEntry_m(right.deltaBeginEntry_m),
deltaEndEntry_m(right.deltaEndEntry_m),
polyOrderEntry_m(right.polyOrderEntry_m),
- xExit_m(right.xExit_m),
- zExit_m(right.zExit_m),
deltaBeginExit_m(right.deltaBeginExit_m),
deltaEndExit_m(right.deltaEndExit_m),
polyOrderExit_m(right.polyOrderExit_m),
@@ -76,6 +76,12 @@ Bend2D::Bend2D(const Bend2D &right):
sinEntranceAngle_m(right.sinEntranceAngle_m),
tanEntranceAngle_m(right.tanEntranceAngle_m),
tanExitAngle_m(right.tanExitAngle_m),
+ beginToEnd_m(right.beginToEnd_m),
+ beginToEnd_lcs_m(right.beginToEnd_lcs_m),
+ toEntranceRegion_m(right.toEntranceRegion_m),
+ toExitRegion_m(right.toExitRegion_m),
+ computeAngleTrafo_m(right.computeAngleTrafo_m),
+ maxAngle_m(right.maxAngle_m),
nSlices_m(right.nSlices_m){
setElType(isDipole);
@@ -87,14 +93,14 @@ Bend2D::Bend2D(const std::string &name):
messageHeader_m(" * "),
pusher_m(),
fieldmap_m(NULL),
- fast_m(false),
designRadius_m(0.0),
exitAngle_m(0.0),
fieldIndex_m(0.0),
startField_m(0.0),
endField_m(0.0),
+ widthEntranceFringe_m(0.0),
+ widthExitFringe_m(0.0),
reinitialize_m(false),
- recalcRefTraj_m(false),
entranceParameter1_m(0.0),
entranceParameter2_m(0.0),
entranceParameter3_m(0.0),
@@ -108,8 +114,6 @@ Bend2D::Bend2D(const std::string &name):
deltaBeginEntry_m(0.0),
deltaEndEntry_m(0.0),
polyOrderEntry_m(0),
- xExit_m(0.0),
- zExit_m(0.0),
deltaBeginExit_m(0.0),
deltaEndExit_m(0.0),
polyOrderExit_m(0),
@@ -117,6 +121,7 @@ Bend2D::Bend2D(const std::string &name):
sinEntranceAngle_m(0.0),
tanEntranceAngle_m(0.0),
tanExitAngle_m(0.0),
+ maxAngle_m(0.0),
nSlices_m(1){
setElType(isDipole);
@@ -133,13 +138,9 @@ Bend2D::~Bend2D() {
}
delete[] entryFieldValues_m;
delete[] exitFieldValues_m;
- entryFieldValues_m = NULL;
- exitFieldValues_m = NULL;
gsl_interp_accel_free(entryFieldAccel_m);
gsl_interp_accel_free(exitFieldAccel_m);
- entryFieldAccel_m = NULL;
- exitFieldAccel_m = NULL;
}
}
/*
@@ -155,24 +156,8 @@ bool Bend2D::apply(const size_t &i,
const double &t,
Vector_t &E,
Vector_t &B) {
-
- if(designRadius_m > 0.0) {
-
- // Shift position to magnet frame.
- Vector_t X = RefPartBunch_m->R[i];
-
- Vector_t bField(0.0);
- if (!calculateMapField(X, bField)) {
-
- B += fieldAmplitude_m * bField;
-
- return false;
- }
-
- return true;
- }
-
- return false;
+ Vector_t P;
+ return apply(RefPartBunch_m->R[i], P, t, E, B);
}
bool Bend2D::apply(const Vector_t &R,
@@ -203,21 +188,7 @@ bool Bend2D::applyToReferenceParticle(const Vector_t &R,
const double &t,
Vector_t &E,
Vector_t &B) {
- if(designRadius_m > 0.0) {
-
- // Get field from field map.
- Vector_t bField(0.0);
- Vector_t X = R;// + Vector_t(0, 0, startField_m/* - elementEdge_m*/);
- if (!calculateMapField(X, bField)) {
-
- B += fieldAmplitude_m * bField;
-
- return false;
- }
-
- return true;
- }
- return false;
+ return apply(R, P, t, E, B);
}
void Bend2D::goOnline(const double &) {
@@ -244,7 +215,6 @@ void Bend2D::initialise(PartBunchBase<double, 3> *bunch,
double bendAngleX = 0.0;
double bendAngleY = 0.0;
calculateRefTrajectory(bendAngleX, bendAngleY);
- recalcRefTraj_m = true;
print(msg, bendAngleX, bendAngleY);
// Pass start and end of field to calling function.
@@ -816,7 +786,7 @@ bool Bend2D::findIdealBendParameters(double chordLength) {
if(angle_m < 0.0) {
// Negative angle is a positive bend rotated 180 degrees.
entranceAngle_m = copysign(1, angle_m) * entranceAngle_m;
- exitAngle_m = copysign(1, angle_m) * exitAngle_m;
+ setExitAngle(copysign(1, angle_m) * exitAngle_m);
angle_m = std::abs(angle_m);
rotationZAxis_m += Physics::pi;
}
@@ -845,27 +815,6 @@ bool Bend2D::findIdealBendParameters(double chordLength) {
return reinitialize;
}
-void Bend2D::findReferenceExitOrigin(double &x, double &z) {
-
- /*
- * Find x,z coordinates of reference trajectory as it passes exit edge
- * of the bend magnet. This assumes an entrance position of (x,z) = (0,0).
- */
- if(angle_m <= Physics::pi / 2.0) {
- x = - designRadius_m * (1.0 - std::cos(angle_m));
- z = designRadius_m * std::sin(angle_m);
- } else if(angle_m <= Physics::pi) {
- x = -designRadius_m * (1.0 + std::sin(angle_m - Physics::pi / 2.0));
- z = designRadius_m * std::cos(angle_m - Physics::pi / 2.0);
- } else if(angle_m <= 3.0 * Physics::pi / 2.0) {
- x = -designRadius_m * (2.0 - std::cos(angle_m - Physics::pi));
- z = -designRadius_m * std::sin(angle_m - Physics::pi);
- } else {
- x = -designRadius_m * (1.0 - std::cos(angle_m - 3.0 * Physics::pi / 2.0));
- z = -designRadius_m * std::sin(angle_m - 3.0 * Physics::pi / 2.0);
- }
-}
-
bool Bend2D::initializeFieldMap(Inform &msg) {
fieldmap_m = Fieldmap::getFieldmap(fileName_m, fast_m);
@@ -1110,22 +1059,6 @@ void Bend2D::readFieldMap(Inform &msg) {
}
}
-bool Bend2D::reinitialize() {
-
- setBendStrength();
- double bendAngleX = 0.0;
- double bendAngleY = 0.0;
- calculateRefTrajectory(bendAngleX, bendAngleY);
-
- // INFOMSG(level2 << "Bend design energy changed to: "
- // << designEnergy_m * 1.0e-6
- // << " MeV"
- // << endl);
- print(*Ippl::Info, bendAngleX, bendAngleY);
-
- return false;
-}
-
void Bend2D::setBendEffectiveLength(double startField, double endField) {
// Find initial angle.
@@ -1183,15 +1116,13 @@ void Bend2D::setFieldCalcParam() {
tanEntranceAngle_m = tan(entranceAngle_m);
deltaBeginEntry_m = std::abs(entranceParameter1_m - entranceParameter2_m);
- deltaEndEntry_m = std::abs(entranceParameter2_m - entranceParameter3_m);
+ deltaEndEntry_m = std::abs(entranceParameter2_m - entranceParameter3_m);
deltaBeginExit_m = std::abs(exitParameter1_m - exitParameter2_m);
- deltaEndExit_m = std::abs(exitParameter2_m - exitParameter3_m);
+ deltaEndExit_m = std::abs(exitParameter2_m - exitParameter3_m);
double bendAngle = getBendAngle();
double entranceAngle = getEntranceAngle();
- double exitAngle = getExitAngle();
- tanExitAngle_m = tan(exitAngle);
double rotationAngleAboutZ = getRotationAboutZ();
Quaternion_t rotationAboutZ(cos(0.5 * rotationAngleAboutZ),
@@ -1200,8 +1131,8 @@ void Bend2D::setFieldCalcParam() {
Vector_t rotationAxis(0, -1, 0);
Quaternion_t halfRotationAboutAxis(cos(0.5 * (0.5 * bendAngle - entranceAngle)),
sin(0.5 * (0.5 * bendAngle - entranceAngle)) * rotationAxis);
- Quaternion_t exitFaceRotation(cos(0.5 * (bendAngle - entranceAngle - exitAngle)),
- sin(0.5 * (bendAngle - entranceAngle - exitAngle)) * rotationAxis);
+ Quaternion_t exitFaceRotation(cos(0.5 * (bendAngle - entranceAngle - exitAngle_m)),
+ sin(0.5 * (bendAngle - entranceAngle - exitAngle_m)) * rotationAxis);
Vector_t chord = getChordLength() * halfRotationAboutAxis.rotate(Vector_t(0, 0, 1));
beginToEnd_lcs_m = CoordinateSystemTrafo(chord, exitFaceRotation.conjugate());
beginToEnd_m = beginToEnd_lcs_m * CoordinateSystemTrafo(Vector_t(0.0), rotationAboutZ.conjugate());
@@ -1295,7 +1226,6 @@ bool Bend2D::setupBendGeometry(Inform &msg, double &startField, double &endField
if (getType() == RBEND) {
setEntranceAngle(getEntranceAngle());
}
- findReferenceExitOrigin(xExit_m, zExit_m);
/*
* Set field map geometry.
@@ -1797,7 +1727,5 @@ std::array<double,2> Bend2D::getExitFringeFieldLength() const {
extFFL[0] = ( exitParameter3_m-exitParameter2_m ); //after edge
extFFL[1] = ( exitParameter2_m-exitParameter1_m ); //before edge
-
-
return extFFL;
}
\ No newline at end of file
diff --git a/src/Classic/AbsBeamline/Bend2D.h b/src/Classic/AbsBeamline/Bend2D.h
index aa87c162806ad90b7e80a1f76e5e1bb4970b78db..822a361ed4203bd8dbd678b13dd25dad5408ad46 100644
--- a/src/Classic/AbsBeamline/Bend2D.h
+++ b/src/Classic/AbsBeamline/Bend2D.h
@@ -33,6 +33,7 @@
#endif
#include <array>
+#include <string>
#include <vector>
class Fieldmap;
@@ -110,9 +111,6 @@ public:
/// Set quadrupole field component.
void setK1(double k1);
- void resetReinitializeFlag();
- void resetRecalcRefTrajFlag();
-
void setExitAngle(double exitAngle);
virtual double getExitAngle() const;
@@ -185,7 +183,6 @@ private:
virtual bool findChordLength(Inform &msg,
double &chordLength) = 0;
bool findIdealBendParameters(double chordLength);
- void findReferenceExitOrigin(double &x, double &z);
bool initializeFieldMap(Inform &msg);
bool inMagnetCentralRegion(const Vector_t &R) const;
bool inMagnetEntranceRegion(const Vector_t &R) const;
@@ -194,7 +191,6 @@ private:
bool isPositionInExitField(const Vector_t &R) const;
void print(Inform &msg, double bendAngleX, double bendAngle);
void readFieldMap(Inform &msg);
- bool reinitialize();
void setBendEffectiveLength(double startField, double endField);
void setBendStrength();
void setEngeOriginDelta(double delta);
@@ -217,7 +213,7 @@ private:
/// through the bend.
Fieldmap *fieldmap_m; /// Magnet field map.
- bool fast_m; /// Flag to turn on fast field calculation.
+ const bool fast_m = false; /// Flag to turn on fast field calculation.
double designRadius_m; /// Bend design radius (m).
@@ -239,8 +235,6 @@ private:
*/
bool reinitialize_m;
- bool recalcRefTraj_m; /// Re-calculate reference trajectory.
-
/*
* Enge function field map members.
*/
@@ -278,12 +272,6 @@ private:
/// function origin that Enge function ends.
int polyOrderEntry_m; /// Enge function order for entry region.
- /*
- * The ideal reference trajectory passes through (xExit_m, zExit_m).
- */
- double xExit_m;
- double zExit_m;
-
double deltaBeginExit_m; /// Perpendicular distance from exit Enge
/// function origin that Enge function starts.
double deltaEndExit_m; /// Perpendicular distance from exit Enge
@@ -347,16 +335,6 @@ void Bend2D::setK1(double k1) {
fieldIndex_m = k1;
}
-inline
-void Bend2D::resetReinitializeFlag() {
- reinitialize_m = true;
-}
-
-inline
-void Bend2D::resetRecalcRefTrajFlag() {
- recalcRefTraj_m = true;
-}
-
inline
void Bend2D::setMessageHeader(const std::string & header)
{
@@ -385,6 +363,7 @@ inline
void Bend2D::setExitAngle(double angle)
{
exitAngle_m = angle;
+ tanExitAngle_m = tan(exitAngle_m);
}
inline
diff --git a/src/Classic/AbsBeamline/Cyclotron.cpp b/src/Classic/AbsBeamline/Cyclotron.cpp
index 7d018d14502bf95cda640830bc13fac1deb283dc..df86975637e58890c5e4182058c940408dea20a8 100644
--- a/src/Classic/AbsBeamline/Cyclotron.cpp
+++ b/src/Classic/AbsBeamline/Cyclotron.cpp
@@ -1037,10 +1037,10 @@ void Cyclotron::initialise(PartBunchBase<double, 3> *bunch, const int &fieldflag
void Cyclotron::getFieldFromFile_FFA(const double &scaleFactor) {
/*
- Field is read in from ascci file (COSY output) in the oder:
+ Field is read in from ascii file (COSY output) in the order:
R(m) theta(Deg) x(m) y(m) Bz(T).
- Theta is the fast varing variable
+ Theta is the fast varying variable
2.0000 0.0 2.0000 0.0000 0.0000000000000000
2.0000 1.0 1.9997 0.0349 0.0000000000000000
diff --git a/src/Classic/AbsBeamline/Ring.cpp b/src/Classic/AbsBeamline/Ring.cpp
index d2478854037af880ed1262a42d1334276713d7b0..eece8fb5fd7d8e633249179b356d775520e648a3 100644
--- a/src/Classic/AbsBeamline/Ring.cpp
+++ b/src/Classic/AbsBeamline/Ring.cpp
@@ -275,7 +275,7 @@ void Ring::appendElement(const Component &element) {
<< section->getStartNormal()(0) << ", "
<< section->getStartNormal()(1) << ", "
<< section->getStartNormal()(2) << "), phi " << dphi << endl;
- msg << "* End position ("
+ msg << "* End position ("
<< section->getEndPosition()(0) << ", "
<< section->getEndPosition()(1) << ", "
<< section->getEndPosition()(2) << ") normal ("
diff --git a/src/Classic/AbsBeamline/ScalingFFAMagnet.cpp b/src/Classic/AbsBeamline/ScalingFFAMagnet.cpp
index dbdaeb3e1f11aea50307f3617270254225576aa0..9bf76ef91ad077ad6fda6f62ba889dda49cdd858 100644
--- a/src/Classic/AbsBeamline/ScalingFFAMagnet.cpp
+++ b/src/Classic/AbsBeamline/ScalingFFAMagnet.cpp
@@ -46,9 +46,7 @@ ScalingFFAMagnet::ScalingFFAMagnet(const ScalingFFAMagnet &right)
phiEnd_m(right.phiEnd_m), azimuthalExtent_m(right.azimuthalExtent_m),
verticalExtent_m(right.verticalExtent_m), centre_m(right.centre_m),
dfCoefficients_m(right.dfCoefficients_m) {
- if (endField_m != NULL) {
- delete endField_m;
- }
+ delete endField_m;
endField_m = right.endField_m->clone();
RefPartBunch_m = right.RefPartBunch_m;
setElType(isDrift);
@@ -57,9 +55,7 @@ ScalingFFAMagnet::ScalingFFAMagnet(const ScalingFFAMagnet &right)
}
ScalingFFAMagnet::~ScalingFFAMagnet() {
- if (endField_m != NULL) {
- delete endField_m;
- }
+ delete endField_m;
}
ElementBase* ScalingFFAMagnet::clone() const {
diff --git a/src/Classic/Algorithms/PartBunch.cpp b/src/Classic/Algorithms/PartBunch.cpp
index aff6a5bf258b6306989998bddaf7cdda4272935d..9612695d365c1fc0e9325a961d46e859a42f0431 100644
--- a/src/Classic/Algorithms/PartBunch.cpp
+++ b/src/Classic/Algorithms/PartBunch.cpp
@@ -33,7 +33,6 @@
#include "Distribution/Distribution.h" // OPAL file
#include "Structure/FieldSolver.h" // OPAL file
#include "Utilities/GeneralClassicException.h"
-#include "Structure/LossDataSink.h"
#include "Algorithms/ListElem.h"
diff --git a/src/Classic/Algorithms/PartBunchBase.h b/src/Classic/Algorithms/PartBunchBase.h
index d60377d1d990d45b1df15b023ef4d4c9464c9f7c..fb1f57be2e40483a8e828f9eacabbec69c0c74d2 100644
--- a/src/Classic/Algorithms/PartBunchBase.h
+++ b/src/Classic/Algorithms/PartBunchBase.h
@@ -149,7 +149,7 @@ public:
/** delete particles which are too far away from the center of beam*/
void boundp_destroy();
- /** This is only temporary in order to get the collimator and pepperpot workinh */
+ /** This is only temporary in order to get the collimator and pepperpot working */
size_t boundp_destroyT();
size_t destroyT();
@@ -574,7 +574,7 @@ protected:
double t_m;
/// mean energy of the bunch (MeV)
double eKin_m;
- /// energy spread of the beam in keV
+ /// energy spread of the beam in MeV
double dE_m;
/// the position along design trajectory
double spos_m;
diff --git a/src/Classic/Algorithms/PartBunchBase.hpp b/src/Classic/Algorithms/PartBunchBase.hpp
index 1078afed21cb48affe09e90168282e1e8995bbfa..3df9b5d0bc5beecc0234897ff3928ada7a0cbece 100644
--- a/src/Classic/Algorithms/PartBunchBase.hpp
+++ b/src/Classic/Algorithms/PartBunchBase.hpp
@@ -1278,7 +1278,6 @@ void PartBunchBase<T, Dim>::get_PBounds(Vector_t &min, Vector_t &max) const {
template <class T, unsigned Dim>
void PartBunchBase<T, Dim>::calcBeamParameters() {
- using Physics::c;
Vector_t eps2, fac, rsqsum, psqsum, rpsum;
@@ -1330,10 +1329,10 @@ void PartBunchBase<T, Dim>::calcBeamParameters() {
rprms_m = rpsum * fac;
- Dx_m = moments_m(0, 5) / N;
+ Dx_m = moments_m(0, 5) / N;
DDx_m = moments_m(1, 5) / N;
- Dy_m = moments_m(2, 5) / N;
+ Dy_m = moments_m(2, 5) / N;
DDy_m = moments_m(3, 5) / N;
// Find unnormalized emittance.
@@ -1717,7 +1716,6 @@ double PartBunchBase<T, Dim>::calcMeanPhi() {
return meanPhi;
}
-
// this function reset the BinID for each particles according to its current beta*gamma
// it is for multi-turn extraction cyclotron with small energy gain
// the bin number can be different with the bunch number
@@ -1901,7 +1899,7 @@ template <class T, unsigned Dim>
void PartBunchBase<T, Dim>::calcEMean() {
const double totalNp = static_cast<double>(getTotalNum());
- const double locNp = static_cast<double>(getLocalNum());
+ const double locNp = static_cast<double>(getLocalNum());
eKin_m = 0.0;
diff --git a/src/Classic/Algorithms/Vektor.h b/src/Classic/Algorithms/Vektor.h
index 87fd5d29b8057a87c494b938fc7c29075f5a639f..fe755ff0f8987866a9916606361f9019c25106b0 100644
--- a/src/Classic/Algorithms/Vektor.h
+++ b/src/Classic/Algorithms/Vektor.h
@@ -1,8 +1,6 @@
#ifndef OPAL_VEKTOR_HH
#define OPAL_VEKTOR_HH
-#include <limits>
-
#include "AppTypes/Vektor.h"
typedef Vektor<double, 3> Vector_t;
diff --git a/src/Classic/Fields/Interpolation/Interpolator3dGridTo3d.cpp b/src/Classic/Fields/Interpolation/Interpolator3dGridTo3d.cpp
index 3e4ee2d863498c8dbea3ceb9bf2e0f49044d41c5..1553606ffeb672e1e49955b241429da46d195dca 100644
--- a/src/Classic/Fields/Interpolation/Interpolator3dGridTo3d.cpp
+++ b/src/Classic/Fields/Interpolation/Interpolator3dGridTo3d.cpp
@@ -73,7 +73,7 @@ void Interpolator3dGridTo3d::setAll(ThreeDGrid* grid,
break;
default:
throw(LogicalError(
- "Interpolator3dGridTo3d::Set",
+ "Interpolator3dGridTo3d::setAll",
"Did not recognise interpolation algorithm"
)
);
diff --git a/src/Classic/Fields/Interpolation/TriLinearInterpolator.cpp b/src/Classic/Fields/Interpolation/TriLinearInterpolator.cpp
index f89764e88fc7e5f46f8995021caef6152038b7d8..95d4febfa6096dc6342aa7be77cebd876336f741 100644
--- a/src/Classic/Fields/Interpolation/TriLinearInterpolator.cpp
+++ b/src/Classic/Fields/Interpolation/TriLinearInterpolator.cpp
@@ -64,9 +64,9 @@ void TriLinearInterpolator::function
double dx = (Point[0]-coordinates_m->x(i+1))/
(coordinates_m->x(i+2)-coordinates_m->x(i+1));
double f_x[2][2];
- f_x[0][0] = (f_m[i+1][j][k] - f_m[i][j][k]) * dx + f_m[i][j][k];
- f_x[1][0] = (f_m[i+1][j+1][k] - f_m[i][j+1][k]) * dx + f_m[i][j+1][k];
- f_x[0][1] = (f_m[i+1][j][k+1] - f_m[i][j][k+1]) * dx + f_m[i][j][k+1];
+ f_x[0][0] = (f_m[i+1][j] [k] - f_m[i][j] [k]) * dx + f_m[i][j] [k];
+ f_x[1][0] = (f_m[i+1][j+1][k] - f_m[i][j+1][k]) * dx + f_m[i][j+1][k];
+ f_x[0][1] = (f_m[i+1][j] [k+1] - f_m[i][j] [k+1]) * dx + f_m[i][j] [k+1];
f_x[1][1] = (f_m[i+1][j+1][k+1] - f_m[i][j+1][k+1]) * dx + f_m[i][j+1][k+1];
// interpolation in y
double f_xy[2];
diff --git a/src/Classic/Fields/SectorMagneticFieldMap.cpp b/src/Classic/Fields/SectorMagneticFieldMap.cpp
index c518a3a65720b67b1dfb77ba5447fc6bf6054dce..28c6fafb4d0f8d89db919685a1be403b139822a3 100644
--- a/src/Classic/Fields/SectorMagneticFieldMap.cpp
+++ b/src/Classic/Fields/SectorMagneticFieldMap.cpp
@@ -337,7 +337,7 @@ VectorMap* SectorMagneticFieldMap::IO::getInterpolatorPolyPatch(
// too lazy to write code to handle this case - not available to user anyway
if (sym != SectorMagneticFieldMap::dipole) {
throw(LogicalError(
- "SectorMagneticFieldMap::IO::ReadMap",
+ "SectorMagneticFieldMap::IO::getInterpolatorPolyPatch",
"Failed to recognise symmetry type"
));
}
diff --git a/src/Classic/Structure/MeshGenerator.cpp b/src/Classic/Structure/MeshGenerator.cpp
index bf70f5eea17414b794c371886137745e7dca0ce8..5bc1f4573a1f00a5e83730381aa4907493b02a91 100644
--- a/src/Classic/Structure/MeshGenerator.cpp
+++ b/src/Classic/Structure/MeshGenerator.cpp
@@ -15,7 +15,6 @@ MeshGenerator::MeshGenerator():
{ }
void MeshGenerator::add(const ElementBase &element) {
- auto apert = element.getAperture();
double start = 0.0;
MeshData mesh;
@@ -35,6 +34,7 @@ void MeshGenerator::add(const ElementBase &element) {
double end, length;
element.getElementDimensions(start, end);
length = end - start;
+ auto apert = element.getAperture();
switch (apert.first) {
case ElementBase::RECTANGULAR:
diff --git a/src/Classic/Structure/PeakFinder.cpp b/src/Classic/Structure/PeakFinder.cpp
index e7be6f2f70515d9a27d801c4dd5ece4a2ff05d01..5c6150269376d0a9103ad44440b32b5ea0f0d755 100644
--- a/src/Classic/Structure/PeakFinder.cpp
+++ b/src/Classic/Structure/PeakFinder.cpp
@@ -29,39 +29,39 @@ PeakFinder::PeakFinder(std::string elem, double min,
void PeakFinder::addParticle(const Vector_t& R) {
-
+
double radius = std::hypot(R(0),R(1));
radius_m.push_back(radius);
-
+
peakRadius_m += radius;
++registered_m;
}
void PeakFinder::evaluate(const int& turn) {
-
+
if ( first_m ) {
turn_m = turn;
first_m = false;
}
-
+
if ( turn_m != turn ) {
finished_m = true;
}
-
+
bool globFinished = false;
-
+
if ( !singlemode_m )
allreduce(finished_m, globFinished, 1, std::logical_and<bool>());
else
globFinished = finished_m;
-
+
if ( globFinished ) {
-
+
this->computeCentroid_m();
-
+
turn_m = turn;
-
+
// reset
peakRadius_m = 0.0;
registered_m = 0;
@@ -71,29 +71,29 @@ void PeakFinder::evaluate(const int& turn) {
void PeakFinder::save() {
-
+
createHistogram_m();
-
+
// last turn is not yet computed
this->computeCentroid_m();
-
+
if ( !peaks_m.empty() ) {
// only rank 0 will go in here
-
+
fn_m = element_m + std::string(".peaks");
hist_m = element_m + std::string(".hist");
-
+
INFOMSG("Save " << fn_m << " and " << hist_m << endl);
-
+
if(OpalData::getInstance()->inRestartRun())
this->append_m();
else
this->open_m();
-
+
this->saveASCII_m();
-
+
this->close_m();
-
+
}
radius_m.clear();
@@ -104,16 +104,16 @@ void PeakFinder::save() {
void PeakFinder::computeCentroid_m() {
double globPeakRadius = 0.0;
int globRegister = 0;
-
+
//FIXME inefficient
if ( !singlemode_m ) {
reduce(peakRadius_m, globPeakRadius, 1, std::plus<double>());
- reduce(registered_m, globRegister, 1, std::plus<int>());
+ reduce(registered_m, globRegister, 1, std::plus<int>());
} else {
globPeakRadius = peakRadius_m;
globRegister = registered_m;
}
-
+
if ( Ippl::myNode() == 0 ) {
if ( globRegister > 0 )
peaks_m.push_back(globPeakRadius / double(globRegister));
@@ -124,7 +124,7 @@ void PeakFinder::createHistogram_m() {
/*
* create local histograms
*/
-
+
globHist_m.resize(nBins_m);
container_t locHist(nBins_m,0.0);
@@ -134,7 +134,7 @@ void PeakFinder::createHistogram_m() {
if (bin < 0 || (unsigned int)bin >= nBins_m) continue; // Probe might save particles outside its boundary
++locHist[bin];
}
-
+
/*
* create global histograms
*/
@@ -144,7 +144,7 @@ void PeakFinder::createHistogram_m() {
} else {
globHist_m.swap(locHist);
}
-
+
// reduce(locHist.data(), globHist_m.data(), locHist.size(), std::plus<double>());
}
diff --git a/src/Classic/Structure/PeakFinder.h b/src/Classic/Structure/PeakFinder.h
index 2fbf8e5c342721f86ee224f56a0ef11ab3a57990..a6b0777e8c4318f3defb3ba1f00db714318ecec6 100644
--- a/src/Classic/Structure/PeakFinder.h
+++ b/src/Classic/Structure/PeakFinder.h
@@ -23,34 +23,34 @@
#include <list>
class PeakFinder {
-
+
public:
using container_t = std::vector<double>;
-
+
public:
-
+
PeakFinder() = delete;
PeakFinder(std::string elem, double min, double max, double binwidth, bool singlemode);
-
+
/*!
* Append the particle coordinates to the container
* @param R is a particle position (x, y, z)
*/
void addParticle(const Vector_t& R);
-
+
/*!
* Evaluate the centroid of a turn.
*/
void evaluate(const int& turn);
-
+
void save();
-
+
private:
-
+
// compute global histogram, involves some inter-node communication
void createHistogram_m();
-
+
/***************
* Output file *
***************/
@@ -62,29 +62,29 @@ private:
void close_m();
/// Write to output file
void saveASCII_m();
-
+
void computeCentroid_m();
private:
container_t radius_m;
/// global histogram values
container_t globHist_m;
-
+
/// filename with extension (.peaks)
std::string fn_m;
-
+
/// histogram filename with extension (.hist)
std::string hist_m;
/// used to write out the data
std::ofstream os_m;
-
+
/// used to write out the histrogram
std::ofstream hos_m;
-
+
/// Element/probe name, for name output file
std::string element_m;
-
+
// Histogram details
/// Number of bins
unsigned int nBins_m;
@@ -92,7 +92,7 @@ private:
double binWidth_m;
///@{ histogram size
double min_m, max_m;
-
+
int turn_m;
double peakRadius_m;
int registered_m;
diff --git a/src/Distribution/Distribution.cpp b/src/Distribution/Distribution.cpp
index 4393c8246ba264ca76cc15bfa472a45f827533bb..efee18c1018fff4889f734db0e61ea2e3d5f2ac2 100644
--- a/src/Distribution/Distribution.cpp
+++ b/src/Distribution/Distribution.cpp
@@ -1377,7 +1377,7 @@ void Distribution::createMatchedGaussDistribution(size_t numberOfParticles, doub
std::array<double,3> Emit = siggen->getEmittances();
if (rguess > 0)
- *gmsg << "* RGUESS " << rguess/1000.0 << " (m) " << endl;
+ *gmsg << "* RGUESS " << rguess << " (m) " << endl;
*gmsg << "* Converged (Ex, Ey, Ez) = (" << Emit[0] << ", " << Emit[1] << ", "
<< Emit[2] << ") pi mm mrad for E= " << E_m*1E-6 << " (MeV)" << endl;
@@ -1552,7 +1552,7 @@ void Distribution::createOpalCycl(PartBunchBase<double, 3> *beam,
// Set distribution type.
setDistType();
- // Emitting particles in not supported in OpalCyclT.
+ // Emitting particles is not supported in OPAL-cycl.
emitting_m = false;
// Create distribution.
@@ -1911,12 +1911,12 @@ size_t Distribution::emitParticles(PartBunchBase<double, 3> *beam, double eZ) {
* is much slower than doing a swap and popping off the end
* of the vector.
*/
- std::swap(xDist_m.at(*ptbErasedIt), xDist_m.back());
- std::swap(pxDist_m.at(*ptbErasedIt), pxDist_m.back());
- std::swap(yDist_m.at(*ptbErasedIt), yDist_m.back());
- std::swap(pyDist_m.at(*ptbErasedIt), pyDist_m.back());
+ std::swap( xDist_m.at(*ptbErasedIt), xDist_m.back());
+ std::swap(pxDist_m.at(*ptbErasedIt), pxDist_m.back());
+ std::swap( yDist_m.at(*ptbErasedIt), yDist_m.back());
+ std::swap(pyDist_m.at(*ptbErasedIt), pyDist_m.back());
std::swap(tOrZDist_m.at(*ptbErasedIt), tOrZDist_m.back());
- std::swap(pzDist_m.at(*ptbErasedIt), pzDist_m.back());
+ std::swap(pzDist_m.at(*ptbErasedIt), pzDist_m.back());
if (additionalRNs_m.size() == xDist_m.size()) {
std::swap(additionalRNs_m.at(*ptbErasedIt), additionalRNs_m.back());
@@ -2488,7 +2488,7 @@ void Distribution::generateGaussZ(size_t numberOfParticles) {
}
#endif
/*
- //Sets the GSL error handler off, exception will be handled internaly with a renormalization method
+ //Sets the GSL error handler off, exception will be handled internally with a renormalization method
gsl_set_error_handler_off();
*/
int errcode = gsl_linalg_cholesky_decomp(corMat);
@@ -4497,34 +4497,27 @@ void Distribution::writeOutFileHeader() {
} else {
outputFile.setf(std::ios::left);
outputFile << "# ";
+ outputFile.width(17);
+ outputFile << "x [m]";
+ outputFile.width(17);
+ outputFile << "px [betax gamma]";
+ outputFile.width(17);
+ outputFile << "y [m]";
+ outputFile.width(17);
+ outputFile << "py [betay gamma]";
if (emitting_m) {
- outputFile.width(17);
- outputFile << "x [m]";
- outputFile.width(17);
- outputFile << "px [betax gamma]";
- outputFile.width(17);
- outputFile << "y [m]";
- outputFile.width(17);
- outputFile << "py [betay gamma]";
outputFile.width(17);
outputFile << "t [s]";
- outputFile.width(17);
- outputFile << "pz [betaz gamma]" ;
- outputFile.width(17);
- outputFile << "Bin Number" << std::endl;
} else {
- outputFile.width(17);
- outputFile << "x [m]";
- outputFile.width(17);
- outputFile << "px [betax gamma]";
- outputFile.width(17);
- outputFile << "y [m]";
- outputFile.width(17);
- outputFile << "py [betay gamma]";
outputFile.width(17);
outputFile << "z [m]";
+ }
+ outputFile.width(17);
+ outputFile << "pz [betaz gamma]" ;
+ if (emitting_m) {
outputFile.width(17);
- outputFile << "pz [betaz gamma]";
+ outputFile << "Bin Number" << std::endl;
+ } else {
if (numberOfEnergyBins_m > 0) {
outputFile.width(17);
outputFile << "Bin Number";
@@ -4737,10 +4730,10 @@ void Distribution::adjustPhaseSpace(double massIneV) {
}
double avrg[6];
- avrg[0] = std::accumulate(xDist_m.begin(), xDist_m.end(), 0.0) / totalNumberParticles_m;
- avrg[1] = std::accumulate(pxDist_m.begin(), pxDist_m.end(), 0.0) / totalNumberParticles_m;
- avrg[2] = std::accumulate(yDist_m.begin(), yDist_m.end(), 0.0) / totalNumberParticles_m;
- avrg[3] = std::accumulate(pyDist_m.begin(), pyDist_m.end(), 0.0) / totalNumberParticles_m;
+ avrg[0] = std::accumulate( xDist_m.begin(), xDist_m.end(), 0.0) / totalNumberParticles_m;
+ avrg[1] = std::accumulate(pxDist_m.begin(), pxDist_m.end(), 0.0) / totalNumberParticles_m;
+ avrg[2] = std::accumulate( yDist_m.begin(), yDist_m.end(), 0.0) / totalNumberParticles_m;
+ avrg[3] = std::accumulate(pyDist_m.begin(), pyDist_m.end(), 0.0) / totalNumberParticles_m;
avrg[4] = std::accumulate(tOrZDist_m.begin(), tOrZDist_m.end(), 0.0) / totalNumberParticles_m;
avrg[5] = 0.0;
for (unsigned int i = 0; i < pzDist_m.size(); ++ i) {
@@ -4756,10 +4749,10 @@ void Distribution::adjustPhaseSpace(double massIneV) {
// \sum_{i = 0}^{N-1} \sqrt{(pz_i + \eps)^2 + px_i^2 + py_i^2} = N p
double eps = avrgpz_m - avrg[5];
for (unsigned int i = 0; i < pzDist_m.size(); ++ i) {
- xDist_m[i] -= avrg[0];
- pxDist_m[i] -= avrg[1];
- yDist_m[i] -= avrg[2];
- pyDist_m[i] -= avrg[3];
+ xDist_m[i] -= avrg[0];
+ pxDist_m[i] -= avrg[1];
+ yDist_m[i] -= avrg[2];
+ pyDist_m[i] -= avrg[3];
tOrZDist_m[i] -= avrg[4];
pzDist_m[i] += eps;
}
diff --git a/src/Elements/OpalBeamline.cpp b/src/Elements/OpalBeamline.cpp
index 785db4170a0308bae99c69839f5c7ea832d2884d..24f3c4c4206d033850740c87aefddb7a33207e29 100644
--- a/src/Elements/OpalBeamline.cpp
+++ b/src/Elements/OpalBeamline.cpp
@@ -1,5 +1,5 @@
#include "Elements/OpalBeamline.h"
-#include "Utilities/OpalException.h"
+
#include "Utilities/Options.h"
#include "Utilities/Util.h"
#include "AbstractObjects/OpalData.h"
@@ -9,7 +9,6 @@
#include <boost/filesystem.hpp>
#include <boost/regex.hpp>
#include <fstream>
-using namespace std;
OpalBeamline::OpalBeamline():
elements_m(),
@@ -47,10 +46,6 @@ std::set<std::shared_ptr<Component>> OpalBeamline::getElements(const Vector_t &x
return elementSet;
}
-void OpalBeamline::getKFactors(const unsigned int &index, const Vector_t &pos, const long &sindex, const double &t, Vector_t &KR, Vector_t &KT) {
-
-}
-
unsigned long OpalBeamline::getFieldAt(const unsigned int &index, const Vector_t &pos, const long &sindex, const double &t, Vector_t &E, Vector_t &B) {
unsigned long rtv = 0x00;
@@ -131,16 +126,6 @@ void OpalBeamline::switchElements(const double &min, const double &max, const do
}
}
-
-void OpalBeamline::switchAllElements() {
- for(FieldList::iterator flit = elements_m.begin(); flit != elements_m.end(); ++ flit) {
- if(!(*flit).isOn()) {
- (*flit).setOn(-1.0);
- }
- }
-
-}
-
void OpalBeamline::switchElementsOff(const double &min, ElementBase::ElementType eltype) {
if(eltype == ElementBase::ANY) {
for(FieldList::iterator flit = elements_m.begin(); flit != elements_m.end(); ++ flit) {
@@ -174,11 +159,6 @@ void OpalBeamline::prepareSections() {
void OpalBeamline::print(Inform &msg) const {
}
-
-double OpalBeamline::calcBeamlineLength() {
- return 0.0;
-}
-
void OpalBeamline::swap(OpalBeamline & rhs) {
std::swap(elements_m, rhs.elements_m);
std::swap(prepared_m, rhs.prepared_m);
@@ -210,7 +190,6 @@ FieldList OpalBeamline::getElementByType(ElementBase::ElementType type) {
void OpalBeamline::compute3DLattice() {
static unsigned int order = 0;
- FieldList::iterator it = elements_m.begin();
const FieldList::iterator end = elements_m.end();
unsigned int minOrder = order;
@@ -228,7 +207,7 @@ void OpalBeamline::compute3DLattice() {
return edgeA < edgeB;
});
- it = elements_m.begin();
+ FieldList::iterator it = elements_m.begin();
for (; it != end; ++ it) {
if ((*it).isPositioned()) {
continue;
@@ -293,7 +272,7 @@ void OpalBeamline::compute3DLattice() {
double endPriorPathLength = 0.0;
CoordinateSystemTrafo currentCoordTrafo = coordTransformationTo_m;
- it = elements_m.begin();
+ FieldList::iterator it = elements_m.begin();
for (; it != end; ++ it) {
if ((*it).isPositioned()) continue;
@@ -366,102 +345,6 @@ void OpalBeamline::compute3DLattice() {
elements_m.sort(ClassicField::SortAsc);
}
-void OpalBeamline::plot3DLattice() {
- auto opal = OpalData::getInstance();
- if (opal->isOptimizerRun() || Ippl::myNode() != 0) return;
-
- elements_m.sort([](const ClassicField& a, const ClassicField& b) {
- double edgeA = 0.0, edgeB = 0.0;
- if (a.getElement()->isElementPositionSet())
- edgeA = a.getElement()->getElementPosition();
-
- if (b.getElement()->isElementPositionSet())
- edgeB = b.getElement()->getElementPosition();
-
- return edgeA < edgeB;
- });
-
- FieldList::iterator it = elements_m.begin();
- FieldList::iterator end = elements_m.end();
-
- Quaternion rotDiagonal(0.5, 0.5 * Vector_t(-1, 1, -1));
-
- Vector_t origin = rotDiagonal.rotate(coordTransformationTo_m.getOrigin());
- Vector_t direction = rotDiagonal.rotate(coordTransformationTo_m.rotateFrom(Vector_t(0, 0, 1)));
- Vector_t minX = Vector_t(999999.9), maxX(-999999.9);
- std::map<std::string, std::vector<Vector_t > > elementCorners;
-
- for (; it != end; ++ it) {
- std::shared_ptr<Component> element = (*it).getElement();
- CoordinateSystemTrafo toBegin = (*it).getCoordTransformationTo();
- std::vector<Vector_t> corners;
-
- if (element->getType() == ElementBase::RBEND || element->getType() == ElementBase::SBEND) {
- std::vector<Vector_t> outline = static_cast<const Bend2D*>(element.get())->getOutline();
-
- for (auto point: outline) {
- corners.push_back(rotDiagonal.rotate(toBegin.transformFrom(point)));
- }
- } else {
- CoordinateSystemTrafo toEnd = element->getEdgeToEnd() * toBegin;
- auto aperture = element->getAperture();
- double elementHeightFront = aperture.second[0];
- double elementHeightBack = aperture.second[0] * aperture.second[2];
-
- corners.push_back(rotDiagonal.rotate(toEnd.transformFrom(Vector_t(0.0))));
- corners.push_back(rotDiagonal.rotate(toBegin.transformFrom(Vector_t(0))));
- corners.push_back(rotDiagonal.rotate(toBegin.transformFrom(-elementHeightFront * Vector_t(1, 0, 0))));
- corners.push_back(rotDiagonal.rotate(toEnd.transformFrom(-elementHeightBack * Vector_t(1, 0, 0))));
- corners.push_back(rotDiagonal.rotate(toEnd.transformFrom(Vector_t(0.0))));
- corners.push_back(rotDiagonal.rotate(toEnd.transformFrom(elementHeightBack * Vector_t(1, 0, 0))));
- corners.push_back(rotDiagonal.rotate(toBegin.transformFrom(elementHeightFront * Vector_t(1, 0, 0))));
- corners.push_back(rotDiagonal.rotate(toBegin.transformFrom(Vector_t(0))));
- }
-
- elementCorners.insert(std::make_pair(element->getName(), corners));
- const unsigned int numCorners = corners.size();
- for (unsigned int i = 0 ; i < numCorners; ++ i) {
- const Vector_t & X = corners[i];
-
- if (X(0) < minX(0)) minX(0) = X(0);
- else if (X(0) > maxX(0)) maxX(0) = X(0);
-
- if (X(1) < minX(1)) minX(1) = X(1);
- else if (X(1) > maxX(1)) maxX(1) = X(1);
- }
- }
-
- std::ofstream gpl;
- std::string fileName = "data/" + OpalData::getInstance()->getInputBasename() + "_ElementPositions.gpl";
- if (OpalData::getInstance()->getOpenMode() == OpalData::OPENMODE::APPEND &&
- boost::filesystem::exists(fileName)) {
- gpl.open(fileName, std::ios_base::app);
- } else {
- gpl.open(fileName);
- }
- gpl.precision(8);
-
- it = elements_m.begin();
- for (; it != end; ++ it) {
- std::shared_ptr<Component> element = (*it).getElement();
-
- if (element->getType() != ElementBase::DRIFT) {
- const std::vector<Vector_t> &corners = elementCorners[element->getName()];
- const unsigned int numCorners = corners.size();
-
- gpl << "# " << element->getName() << "\n";
- for (unsigned int i = 0; i < numCorners; ++ i) {
- gpl << std::setw(18) << corners[i](0)
- << std::setw(18) << -corners[i](1) << "\n";
- }
- gpl << std::setw(18) << corners.front()(0)
- << std::setw(18) << -corners.front()(1) << "\n\n";
- }
- }
-
- elements_m.sort(ClassicField::SortAsc);
-}
-
void OpalBeamline::save3DLattice() {
if (Ippl::myNode() != 0 || OpalData::getInstance()->isOptimizerRun()) return;
@@ -496,8 +379,8 @@ void OpalBeamline::save3DLattice() {
Bend2D * bendElement = static_cast<Bend2D*>(element.get());
std::vector<Vector_t> designPath = bendElement->getDesignPath();
- CoordinateSystemTrafo toEnd = bendElement->getBeginToEnd_local() * (*it).getCoordTransformationTo();
- Vector_t exit3D = toEnd.getOrigin();
+ toEnd = bendElement->getBeginToEnd_local() * (*it).getCoordTransformationTo();
+ exit3D = toEnd.getOrigin();
unsigned int size = designPath.size();
unsigned int minNumSteps = std::max(20.0,
@@ -519,12 +402,12 @@ void OpalBeamline::save3DLattice() {
for (unsigned int i = frequency; i + 1 < size; i += frequency) {
- Vector_t position = (*it).getCoordTransformationTo().transformFrom(designPath[i]);
+ position = (*it).getCoordTransformationTo().transformFrom(designPath[i]);
pos << std::setw(30) << std::left << std::string("\"MID: ") + element->getName() + std::string("\"")
<< std::setw(18) << std::setprecision(10) << position(2)
<< std::setw(18) << std::setprecision(10) << position(0)
<< std::setw(18) << std::setprecision(10) << position(1)
- << endl;
+ << std::endl;
}
position = (*it).getCoordTransformationTo().transformFrom(designPath.back());
@@ -599,7 +482,7 @@ namespace {
unsigned int getMinimalSignificantDigits(double num, const unsigned int maxDigits) {
char buf[32];
snprintf(buf, 32, "%.*f", maxDigits + 1, num);
- string numStr(buf);
+ std::string numStr(buf);
unsigned int length = numStr.length();
unsigned int numDigits = maxDigits;
diff --git a/src/Elements/OpalBeamline.h b/src/Elements/OpalBeamline.h
index ba24ab19678798e14069ac36d3d0412727203eab..6ef4455d236edb5b56c76f5480af820b39cd47e9 100644
--- a/src/Elements/OpalBeamline.h
+++ b/src/Elements/OpalBeamline.h
@@ -1,8 +1,6 @@
#ifndef OPAL_BEAMLINE_H
#define OPAL_BEAMLINE_H
-#include <list>
-#include <limits>
#include <set>
#include <string>
@@ -19,21 +17,17 @@
#include "AbsBeamline/Septum.h"
#include "AbsBeamline/Source.h"
-#include "BasicActions/Option.h"
-#include "Utilities/Options.h"
#include "Utilities/ClassicField.h"
#include "Algorithms/CoordinateSystemTrafo.h"
-class Tracker;
template <class T, unsigned Dim>
class PartBunchBase;
class ParticleMatterInteractionHandler;
class BoundaryGeometry;
-class WakeFunction;
-#define BEAMLINE_EOL 0x80000000 // end of line
-#define BEAMLINE_PARTICLEMATTERINTERACTION 0x08000000 // has particle matter interaction
+//#define BEAMLINE_EOL 0x80000000 // end of line
+//#define BEAMLINE_PARTICLEMATTERINTERACTION 0x08000000 // has particle matter interaction
class OpalBeamline {
@@ -66,19 +60,14 @@ public:
double getEnd(const Vector_t &) const;
void switchElements(const double &, const double &, const double &kineticEnergy, const bool &nomonitors = false);
- void switchAllElements();
void switchElementsOff(const double &, ElementBase::ElementType eltype = ElementBase::ANY);
void switchElementsOff();
- WakeFunction *getWakeFunction(const unsigned int &);
- std::shared_ptr<const ElementBase> getWakeFunctionOwner(const unsigned int &);
-
ParticleMatterInteractionHandler *getParticleMatterInteractionHandler(const unsigned int &);
BoundaryGeometry *getBoundaryGeometry(const unsigned int &);
- void getKFactors(const unsigned int &index, const Vector_t &pos, const long &sindex, const double &t, Vector_t &KR, Vector_t &KT);
unsigned long getFieldAt(const unsigned int &, const Vector_t &, const long &, const double &, Vector_t &, Vector_t &);
unsigned long getFieldAt(const Vector_t &, const Vector_t &, const double &, Vector_t &, Vector_t &);
@@ -87,18 +76,12 @@ public:
void prepareSections();
void compute3DLattice();
- void plot3DLattice();
void save3DLattice();
void save3DInput();
void print(Inform &) const;
FieldList getElementByType(ElementBase::ElementType);
- // need this for autophasing in case we have multiple tracks
- double calcBeamlineLength();
-
- void removeElement(const std::string &ElName);
-
void swap(OpalBeamline & rhs);
void merge(OpalBeamline &rhs);
@@ -169,16 +152,6 @@ void OpalBeamline::visit<Septum>(const Septum &element, BeamlineVisitor &, PartB
WARNMSG(element.getTypeString() << " not implemented yet!" << endl);
}
-inline
-void OpalBeamline::removeElement(const std::string &ElName) {
- for(FieldList::iterator flit = elements_m.begin(); flit != elements_m.end(); ++ flit) {
- if(flit->getElement()->getName() == ElName) {
- flit->setStart(-flit->getEnd());
- flit->setEnd(-flit->getEnd());
- }
- }
-}
-
inline
Vector_t OpalBeamline::transformTo(const Vector_t &r) const {
return coordTransformationTo_m.transformTo(r);
diff --git a/src/Lines/Sequence.cpp b/src/Lines/Sequence.cpp
index eb807065d5bd788dcfdc7932791f184ef89b0ca5..591a351a7d84d2106df6ad0e9b87cd2403e752bf 100644
--- a/src/Lines/Sequence.cpp
+++ b/src/Lines/Sequence.cpp
@@ -23,7 +23,6 @@
#include "BeamlineCore/DriftRep.h"
#include "Beamlines/Beamline.h"
#include "Elements/OpalDrift.h"
-#include "Lines/FlatWriter.h"
#include "Lines/Replacer.h"
#include "Lines/SequenceParser.h"
diff --git a/src/Optimize/OpalSimulation.cpp b/src/Optimize/OpalSimulation.cpp
index c8d9f9ada774bd5e5edeaa8914cbb4f8f0af9d44..a614394170890811da0c72af5c67bf50afe78677 100644
--- a/src/Optimize/OpalSimulation.cpp
+++ b/src/Optimize/OpalSimulation.cpp
@@ -350,17 +350,8 @@ void OpalSimulation::run() {
// setup OPAL command line options
std::ostringstream inputFileName;
inputFileName << simulationName_ << ".in";
-
- char exe_name[] = "opal";
char *inputfile = new char[inputFileName.str().size()+1] ;
strcpy(inputfile, inputFileName.str().c_str());
- char nocomm[] = "--nocomminit";
- char info[] = "--info";
- char info0[] = "0";
- char warn[] = "--warn";
- char warn0[] = "0";
- char *arg[] = { exe_name, inputfile, nocomm, info, info0, warn, warn0 };
-
int seed = Options::seed;
CmdArguments_t args = getArgs();
@@ -374,6 +365,14 @@ void OpalSimulation::run() {
"Restart specified but no restart H5 file available.");
}
+ char exe_name[] = "opal";
+ char nocomm[] = "--nocomminit";
+ char info[] = "--info";
+ char info0[] = "0";
+ char warn[] = "--warn";
+ char warn0[] = "0";
+ char *arg[] = { exe_name, inputfile, nocomm, info, info0, warn, warn0 };
+
//FIXME: this seems to crash OPAL in some cases
//redirectOutToFile();
#ifdef SUPRESS_OUTPUT
diff --git a/src/Sample/SampleCmd.cpp b/src/Sample/SampleCmd.cpp
index 4fa32f07a710885dc1a9d7b628f198f08bf668c6..01970fed664d9dce5ffe89f68b1109e5b43a971e 100644
--- a/src/Sample/SampleCmd.cpp
+++ b/src/Sample/SampleCmd.cpp
@@ -446,7 +446,7 @@ void SampleCmd::execute() {
boost::shared_ptr<Comm_t> comm(new Comm_t(args, MPI_COMM_WORLD));
if (comm->isWorker())
stashEnvironment();
-
+
if ( comm->isOptimizer() ) {
for (sampleMethods_t::iterator it = sampleMethods.begin();
it != sampleMethods.end(); ++it)
diff --git a/src/Structure/Beam.cpp b/src/Structure/Beam.cpp
index 8f9f54040a9dd0cafc6533cd8477f9df963c1549..856da90f664f80fc2a812956a0ca287145d0a9b7 100644
--- a/src/Structure/Beam.cpp
+++ b/src/Structure/Beam.cpp
@@ -268,7 +268,7 @@ void Beam::update() {
if(gamma > 1.0) {
reference.setGamma(gamma);
} else {
- throw OpalException("Beam::execute()",
+ throw OpalException("Beam::update()",
"\"GAMMA\" should be greater than 1.");
}
} else if(itsAttr[ENERGY]) {
@@ -276,7 +276,7 @@ void Beam::update() {
if(energy > reference.getM()) {
reference.setE(energy);
} else {
- throw OpalException("Beam::execute()",
+ throw OpalException("Beam::update()",
"\"ENERGY\" should be greater than \"MASS\".");
}
} else if(itsAttr[PC]) {
@@ -284,7 +284,7 @@ void Beam::update() {
if(pc > 0.0) {
reference.setP(pc);
} else {
- throw OpalException("Beam::execute()",
+ throw OpalException("Beam::update()",
"\"PC\" should be greater than 0.");
}
};
diff --git a/src/Structure/ElementPositionWriter.cpp b/src/Structure/ElementPositionWriter.cpp
index 62d83c9bbc8b90618fca2664f5b2ef98d48b6c99..4cd4b9bfae44c786651a57c94e4a9bf68e4a4367 100644
--- a/src/Structure/ElementPositionWriter.cpp
+++ b/src/Structure/ElementPositionWriter.cpp
@@ -1,5 +1,6 @@
#include "ElementPositionWriter.h"
-#include "Structure/LossDataSink.h"
+
+#include "Ippl.h"
#include "AbstractObjects/OpalData.h"
ElementPositionWriter::ElementPositionWriter(const std::string& fname)
diff --git a/src/Structure/H5PartWrapper.cpp b/src/Structure/H5PartWrapper.cpp
index a4bc79becc499f299deb17b78f1bc8cade8222d7..af3005f07187bbb35a6b183b5c24e8b0e5e489e5 100644
--- a/src/Structure/H5PartWrapper.cpp
+++ b/src/Structure/H5PartWrapper.cpp
@@ -13,8 +13,6 @@
#include <fstream>
-extern Inform *gmsg;
-
namespace {
const h5_int64_t H5TypesCHAR = H5_STRING_T;
const h5_int64_t H5TypesFLOAT = H5_FLOAT32_T;
diff --git a/src/Structure/H5PartWrapperForPC.cpp b/src/Structure/H5PartWrapperForPC.cpp
index 14e5237250f09e5785d4c180abc38c1dc82bf975..abff19b4770ca52e41250d768d2bb83c7e2d0c1d 100644
--- a/src/Structure/H5PartWrapperForPC.cpp
+++ b/src/Structure/H5PartWrapperForPC.cpp
@@ -205,7 +205,7 @@ void H5PartWrapperForPC::readStepData(PartBunchBase<double, 3>* bunch,
for(long int n = 0; n < numParticles; ++ n) {
bunch->M[n] = f64buffer[n];
}
-
+
if ( bunch->getNumBunch() > 1 ) {
std::vector<char> ibuffer(numParticles * sizeof(h5_int64_t));
h5_int64_t *i64buffer = reinterpret_cast<h5_int64_t*>(&ibuffer[0]);
@@ -459,7 +459,7 @@ void H5PartWrapperForPC::writeStepHeader(PartBunchBase<double, 3>* bunch,
} catch (std::out_of_range & m) {
ERRORMSG(m.what() << endl);
- throw OpalException("H5PartWrapperForPC::wirteStepHeader",
+ throw OpalException("H5PartWrapperForPC::writeStepHeader",
"some additional step attribute not found");
}
}
@@ -560,10 +560,10 @@ void H5PartWrapperForPC::writeStepData(PartBunchBase<double, 3>* bunch) {
i64buffer[i] = bunch->Bin[i];
for (size_t i = skipID; i < numLocalParticles; ++ i)
i64buffer[i] = bunch->Bin[i + 1];
-
+
WRITEDATA(Int64, file_m, "bin", i64buffer);
}
-
+
for (size_t i = 0; i < skipID; ++ i)
i64buffer[i] = bunch->bunchNum[i];
for (size_t i = skipID; i < numLocalParticles; ++ i)
diff --git a/src/Structure/H5PartWrapperForPC.h b/src/Structure/H5PartWrapperForPC.h
index e9eb295824a85297689af390a25669f71c192c1d..0b40133ddd12dfad93b8174ec97cde282b0eaf71 100644
--- a/src/Structure/H5PartWrapperForPC.h
+++ b/src/Structure/H5PartWrapperForPC.h
@@ -2,7 +2,7 @@
#define OPAL_H5PARTWRAPPERFORPC_H
/*!
- H5PartWrapperForPT: a class that manages calls to H5Part for the cyclotron tracker
+ H5PartWrapperForPC: a class that manages calls to H5Part for the cyclotron tracker
*/
#include "Structure/H5PartWrapper.h"
diff --git a/src/Structure/H5PartWrapperForPS.cpp b/src/Structure/H5PartWrapperForPS.cpp
index 7823bf3c5376069a9757fc0389c0ee91a52ed37b..0b2e8f7db324738dab4c321e94b63f283fa6da72 100644
--- a/src/Structure/H5PartWrapperForPS.cpp
+++ b/src/Structure/H5PartWrapperForPS.cpp
@@ -16,8 +16,6 @@
#include <sstream>
#include <set>
-extern Inform *gmsg;
-
H5PartWrapperForPS::H5PartWrapperForPS(const std::string &fileName, h5_int32_t flags):
H5PartWrapper(fileName, flags)
{ }
@@ -334,7 +332,7 @@ void H5PartWrapperForPS::writeStepHeader(PartBunchBase<double, 3>* bunch,
} catch (std::out_of_range & m) {
ERRORMSG(m.what() << endl);
- throw OpalException("H5PartWrapperForPC::wirteStepHeader",
+ throw OpalException("H5PartWrapperForPC::writeStepHeader",
"some additional step attribute not found");
}
++ numSteps_m;
diff --git a/src/Structure/H5PartWrapperForPT.cpp b/src/Structure/H5PartWrapperForPT.cpp
index 47e6cd468ed843e925feeeef8a904f9617d50111..8fe3529b4308a97f2fd90ae006f1aac7c8dc3dfe 100644
--- a/src/Structure/H5PartWrapperForPT.cpp
+++ b/src/Structure/H5PartWrapperForPT.cpp
@@ -16,8 +16,6 @@
#include <sstream>
#include <set>
-extern Inform *gmsg;
-
H5PartWrapperForPT::H5PartWrapperForPT(const std::string &fileName, h5_int32_t flags):
H5PartWrapper(fileName, flags)
{ }
@@ -194,34 +192,34 @@ void H5PartWrapperForPT::writeHeader() {
std::stringstream OPAL_version;
OPAL_version << OPAL_PROJECT_NAME << " " << OPAL_PROJECT_VERSION << " # git rev. " << Util::getGitRevision();
WRITESTRINGFILEATTRIB(file_m, "OPAL_version", OPAL_version.str().c_str());
-
-
+
+
WRITESTRINGFILEATTRIB(file_m, "idUnit", "1");
WRITESTRINGFILEATTRIB(file_m, "xUnit", "m");
WRITESTRINGFILEATTRIB(file_m, "yUnit", "m");
WRITESTRINGFILEATTRIB(file_m, "zUnit", "m");
-
+
WRITESTRINGFILEATTRIB(file_m, "pxUnit", "#beta#gamma");
WRITESTRINGFILEATTRIB(file_m, "pyUnit", "#beta#gamma");
WRITESTRINGFILEATTRIB(file_m, "pzUnit", "#beta#gamma");
-
+
WRITESTRINGFILEATTRIB(file_m, "ptypeUnit", "1");
WRITESTRINGFILEATTRIB(file_m, "qUnit", "C");
-
+
if (Options::ebDump) {
WRITESTRINGFILEATTRIB(file_m, "ExUnit", "MV/m");
WRITESTRINGFILEATTRIB(file_m, "EyUnit", "MV/m");
WRITESTRINGFILEATTRIB(file_m, "EzUnit", "MV/m");
-
+
WRITESTRINGFILEATTRIB(file_m, "BxUnit", "T");
WRITESTRINGFILEATTRIB(file_m, "ByUnit", "T");
WRITESTRINGFILEATTRIB(file_m, "BzUnit", "T");
}
-
+
if (Options::rhoDump) {
WRITESTRINGFILEATTRIB(file_m, "rhoUnit", "C/m^3");
}
-
+
WRITESTRINGFILEATTRIB(file_m, "TaitBryantAnglesUnit", "rad");
WRITESTRINGFILEATTRIB(file_m, "SPOSUnit", "m");
@@ -236,12 +234,12 @@ void H5PartWrapperForPT::writeHeader() {
WRITESTRINGFILEATTRIB(file_m, "centroidUnit", "m");
WRITESTRINGFILEATTRIB(file_m, "RMSPUnit", "#beta#gamma");
WRITESTRINGFILEATTRIB(file_m, "MEANPUnit", "#beta#gamma");
-
+
WRITESTRINGFILEATTRIB(file_m, "minXUnit", "m");
WRITESTRINGFILEATTRIB(file_m, "maxXUnit", "m");
WRITESTRINGFILEATTRIB(file_m, "minPUnit", "#beta#gamma");
WRITESTRINGFILEATTRIB(file_m, "maxPUnit", "#beta#gamma");
-
+
WRITESTRINGFILEATTRIB(file_m, "dEUnit", "MeV");
WRITESTRINGFILEATTRIB(file_m, "MASSUnit", "GeV");
@@ -259,7 +257,7 @@ void H5PartWrapperForPT::writeHeader() {
WRITESTRINGFILEATTRIB(file_m, "RefPartRUnit", "m");
WRITESTRINGFILEATTRIB(file_m, "RefPartPUnit", "#beta#gamma");
WRITESTRINGFILEATTRIB(file_m, "SteptoLastInjUnit", "1");
-
+
WRITESTRINGFILEATTRIB(file_m, "dump frequencyUnit", "1")
WRITESTRINGFILEATTRIB(file_m, "dPhiGlobalUnit", "rad")
@@ -378,7 +376,7 @@ void H5PartWrapperForPT::writeStepHeader(PartBunchBase<double, 3>* bunch, const
} catch (std::out_of_range & m) {
ERRORMSG(m.what() << endl);
- throw OpalException("H5PartWrapperForPC::wirteStepHeader",
+ throw OpalException("H5PartWrapperForPC::writeStepHeader",
"some additional step attribute not found");
}
diff --git a/src/Structure/MonitorStatisticsWriter.cpp b/src/Structure/MonitorStatisticsWriter.cpp
index ee67a48a5516715b03931599b58b2be66e19fdea..3aaf4c5514b95a41e1c6941cba43ab074f526ab1 100644
--- a/src/Structure/MonitorStatisticsWriter.cpp
+++ b/src/Structure/MonitorStatisticsWriter.cpp
@@ -1,6 +1,7 @@
#include "MonitorStatisticsWriter.h"
-#include "Structure/LossDataSink.h"
+#include "Structure/LossDataSink.h"
+#include "Ippl.h"
MonitorStatisticsWriter::MonitorStatisticsWriter(const std::string& fname, bool restart)
: SDDSWriter(fname, restart)
diff --git a/src/ValueDefinitions/RealVariable.cpp b/src/ValueDefinitions/RealVariable.cpp
index e2dda88adfac675ed51c707419cc66e977771af8..402c50b33500884b4ca55f18624314646587abe7 100644
--- a/src/ValueDefinitions/RealVariable.cpp
+++ b/src/ValueDefinitions/RealVariable.cpp
@@ -19,7 +19,6 @@
#include "ValueDefinitions/RealVariable.h"
#include "AbstractObjects/OpalData.h"
#include "Attributes/Attributes.h"
-#include "Utilities/Options.h"
#include <iostream>
diff --git a/src/ValueDefinitions/StringConstant.cpp b/src/ValueDefinitions/StringConstant.cpp
index 200fc2ff757aadb13b2352424bbd38d6d75ff2a7..0b14913967943db0bacaa83dd43a6acbf79a11bf 100644
--- a/src/ValueDefinitions/StringConstant.cpp
+++ b/src/ValueDefinitions/StringConstant.cpp
@@ -19,7 +19,6 @@
#include "ValueDefinitions/StringConstant.h"
#include "AbstractObjects/OpalData.h"
#include "Attributes/Attributes.h"
-#include "Utilities/Options.h"
#include "Utilities/Util.h"
#include <iostream>