Reference FlyE

FlyE

Generated by Doxygen 1.8.8

Mon Jan 12 2015 21:36:51

Contents

1 Main Page 1

2 Hierarchical Index 5

2.1 Class Hierarchy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

3 Class Index 7

3.1 Class List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

4 File Index 9

4.1 File List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

5 Class Documentation 11

5.1 AcceleratorConfig Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

5.1.1 Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

5.1.2 Constructor & Destructor Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

5.1.2.1 AcceleratorConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

5.1.3 Member Function Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5.1.3.1 populate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5.1.3.2 printOn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5.1.4 Member Data Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5.1.4.1 nElectrodes_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5.1.4.2 PAname_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5.2 AcceleratorGeometry Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13



5.2.2.1 AcceleratorGeometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14


5.2.3.1 applyElectrodeVoltages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

5.2.3.2 electrodeLocations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

5.2.3.3 getAcceleratorConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

5.2.3.4 makeSmartField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

5.2.3.5 makeVectorField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

5.3 AntiHydrogen Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

iv CONTENTS



5.3.2.1 AntiHydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17


5.3.3.1 ionisationLim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

5.3.3.2 ionise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

5.3.3.3 isDead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

5.3.3.4 isNeutralised . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

5.3.3.5 ITlim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

5.3.3.6 k . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

5.3.3.7 mu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

5.3.3.8 n . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

5.3.3.9 neutralisationTime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

5.3.3.10 neutralise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19


5.3.4.1 ITlim_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

5.4 ConfigLoader Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19



5.4.2.1 ConfigLoader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

5.5 Electrode Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20



5.5.2.1 Electrode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

5.5.2.2 Electrode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22


5.5.3.1 applyVoltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

5.5.3.2 getVoltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

5.5.3.3 import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

5.6 ElectrodeLocator Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23



5.6.2.1 ElectrodeLocator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

5.6.2.2 ElectrodeLocator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24


5.6.3.1 existsAt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

5.6.3.2 existsAt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

5.7 ExponentialScheme Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25



Generated on Mon Jan 12 2015 21:36:51 for FlyE by Doxygen

CONTENTS v

5.7.2.1 ExponentialScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27


5.7.3.1 getVoltages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

5.7.3.2 isActive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

5.8 ez::ezETAProgressBar Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

5.9 std::hash< tuple3Dint > Struct Template Reference . . . . . . . . . . . . . . . . . . . . . . . . . 29



5.9.2.1 operator() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

5.10 HDF5Container1D< T > Struct Template Reference . . . . . . . . . . . . . . . . . . . . . . . . . 30



5.10.2.1 vecs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

5.11 InstantaneousScheme Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31



5.11.2.1 InstantaneousScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32


5.11.3.1 getVoltages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

5.11.3.2 isActive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

5.12 IntegerDistribution Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33



5.12.2.1 operator() . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

5.13 MovingTrapScheme Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35



5.13.2.1 MovingTrapScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36


5.13.3.1 frequency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

5.13.3.2 getInitialVoltages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

5.13.3.3 getVoltages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

5.13.3.4 isActive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

5.14 Particle Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38



5.14.2.1 Particle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40


5.14.3.1 checkMaxField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

5.14.3.2 collide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40


vi CONTENTS

5.14.3.3 getIntLoc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

5.14.3.4 getLoc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

5.14.3.5 getLocDim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

5.14.3.6 getVel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

5.14.3.7 getVelDim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

5.14.3.8 isDead . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

5.14.3.9 maxField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

5.14.3.10 recallLoc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

5.14.3.11 recallLoc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

5.14.3.12 recallVel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

5.14.3.13 recallVel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

5.14.3.14 setLoc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

5.14.3.15 setLoc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

5.14.3.16 setVel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

5.14.3.17 setVel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

5.14.3.18 succeed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

5.14.3.19 succeeded . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

5.15 ParticleGenerator< PType > Class Template Reference . . . . . . . . . . . . . . . . . . . . . . . 43



5.15.2.1 ParticleGenerator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44


5.15.3.1 generateNormDist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

5.15.3.2 generateNormDist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.15.3.3 generateParticles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.15.3.4 generateParticles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.15.3.5 generateSynchronousParticle . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.15.3.6 generateSynchronousParticle . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.15.3.7 generateUniformDist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.15.3.8 generateUniformDist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

5.15.3.9 generateUniformVels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

5.15.3.10 getParticles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

5.16 ParticlesConfig Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48



5.16.2.1 ParticlesConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50


5.16.3.1 distRadius . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

5.16.3.2 populate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

5.16.3.3 printOn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51


CONTENTS vii


5.16.4.1 k_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

5.16.4.2 positionDist_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

5.17 SimulationConfig Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51



5.17.2.1 SimulationConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53


5.17.3.1 populate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

5.17.3.2 printOn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

5.17.3.3 setAccelerationScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

5.17.3.4 setDuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

5.17.3.5 setInglisTeller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

5.17.3.6 setMaxVoltage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

5.17.3.7 setTargetVel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

5.17.3.8 setTimeStep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54


5.17.4.1 inglisTeller_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

5.18 SimulationNumbers Struct Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55


5.18.2 Friends And Related Function Documentation . . . . . . . . . . . . . . . . . . . . . . . . 55

5.18.2.1 operator

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5.21.3.2 at . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

5.21.3.3 gradientXat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

5.21.3.4 magnitudeAt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

5.21.3.5 magnitudeAt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

5.22 StorageConfig Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62



5.22.2.1 StorageConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63


5.22.3.1 populate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

5.22.3.2 printOn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64


5.22.4.1 compression_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

5.23 SubConfig Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64



5.23.2.1 populate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

5.23.2.2 printOn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

5.23.3 Friends And Related Function Documentation . . . . . . . . . . . . . . . . . . . . . . . . 66

5.23.3.1 operator

CONTENTS ix

5.27 VectorField Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72



5.27.2.1 VectorField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

5.27.2.2 VectorField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

5.27.2.3 VectorField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75


5.27.3.1 at . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

5.27.3.2 magnitudeAt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

5.27.3.3 magnitudeAt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

5.27.3.4 sumVectorFields . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

5.27.3.5 vectorMagnitude . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

5.28 VoltageScheme Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76



5.28.2.1 VoltageScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78


5.28.3.1 getInitialVoltages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

5.28.3.2 getVoltages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

5.28.3.3 isActive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

5.29 Writer Class Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80



5.29.2.1 Writer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81


5.29.3.1 countParams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

5.29.3.2 startParams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81


5.29.4.1 typeNames_ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

6 File Documentation 83

6.1 AcceleratorGeometry.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83


6.2 AntiHydrogen.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84


6.3 ConfigLoader.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86


6.4 Electrode.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87


6.5 ElectrodeLocator.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88


x CONTENTS


6.6 FlyE.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90


6.7 IntegerDistribution.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90


6.8 Particle.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91


6.9 ParticleGenerator.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93


6.10 PhysicalConstants.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94


6.11 Simulator.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95


6.12 SmartField.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96


6.13 SubConfig.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97


6.14 tupleDefs.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99


6.14.2 Typedef Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

6.14.2.1 tuple3Dint . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

6.15 VectorField.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101


6.16 VoltageScheme.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102


6.17 Writer.h File Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103


Index 105


Chapter 1

Main Page

FlyE is a piece of software written in C++ for simulating the acceleration of particles in an electric field. This build isspecifically for simulation the acceleration of Hydrogen/Antihydrogen for the AEgIS experiment at CERN.

The software is fully object-oriented and is documented in these pages. An explanation of the basic usage of thesoftware as well as a manual for the config file follows.

Basic Usage

FlyE does not deal directly with the calculation of electric fields. It is designed to import electric field files that havebeen produced by EXSIMECK, which in turn takes SIMION files as input. The naming convention for the electricfield files is [PA name]_E[electrode number]_L[layer number]_[X/Y/Z].dat. A mostly un-documented helper script, makefields.py, to run EXSIMECK for an entire geometry as a batch job is includedin the Non-FlyE directory. This script also generates the [accelerator] section of the FlyE configuration file.

Including "FlyE.h" is necessary to access any of FlyEs classes. The HDF5 and Blitz++ libraries must be installedand compilation requires a version of G++ with support for C++11. Also, the config file parser inih should bepresent in the working directory, as should the ezETAProgressBar.hpp script. The following compiler/linkerflags are also required:

-DBZ_THREADSAFE

-D_GLIBCXX_PARALLEL

-fopenmp

-lblitz

-lpthread

-lconfig++

The following optimisations are recommended:

-O3

-march=native

-ffast-math

-pipe

-flto

Below is an example of a basic program to run one simulation from one config file, print out some basic statisticsfrom the simulation and write the results to an HDF5 file.

2 Main Page

#include #include "FlyE.h"

int main(int argc, char* argv[]) {ConfigLoader myConfig("/home/jamie/git/FlyE/FlyE/flyE.conf");

AcceleratorGeometry myAccelerator(myConfig.getAcceleratorConfig());myAccelerator.importElectrodes();

ParticleGenerator myGenerator(myConfig.getParticlesConfig(),myConfig.getAcceleratorConfig());

myGenerator.generateParticles();std::vector particles = myGenerator.getParticles();

Simulator mySimulator(myAccelerator, particles,myConfig.getSimulationConfig(),myConfig.getStorageConfig());

mySimulator->run();

SimulationNumbers stats = mySimulator->getBasicStats();std::cout

3 temperature - The temperature of the distribution of particles (kelvin, float).

n - The principal quantum number of the particles (integer).

k_dist - How to distribute the values of k, the Stark quantum number. Can be one of the following:(string)

* single - All particles take the given value of k.

* uniform - Values of k are uniformly distributed between 1 and (n-1).

* triangle - Values of k are distributed between 1 and (n-1) according to a triangle distribution whichis maximum at (n-1).

k - If k_dist is single, then all particles have this value of k.

storage

store_trajectories - Whether to store the complete trajectories of the particles, or just theirstart and end locations/velocities (boolean).

store_collisions - Whether to store any data at all for particles which collide with the acceleratorgeometry (boolean).

compression - The level of GZIP compression to apply in the HDF5 output files (1-9, where 9 is maxcompression. integer).

Output file specification

Output files are written in the HDF5 scienfic data format. The hierarchy inside this files is as follows.

Groups

Succeeded - for particles which reach the end of the accelerator.

Collided - for particles which collide with the accelerator geometry.

Ionised - for particles which are ionised in the course of the simulation.

Remaining - for particles which were still active at the end of the simulation.

Datasets

data - A 4D array of the particle trajectories. This is arranged like so:

1st dimension - Index of particle.

2nd dimension - Timestep index. If trajectories are not being stored, then 1 is initial and 2 is final.

3rd dimension - Phase axis: 1 for location, 2 for velocity.

4th dimension - Cartesian axis - 1 for x, 2 for y, 3 for z.

neutralTimes - The times at which particles dipole moments were neutralised. -1 if never neutralised.

ks - The k-values of the particles.

maxFields - The maximum |E| encountered by the particles.

So an example address in the file would be /Succeeded/data for the trajectories of successful particles.

Use on Amazon Web Services

The easiest way to get FlyE running on an EC2 instance with an Ubuntu AMI is to run these commands:

Update repositories with sudo apt-get update


4 Main Page

Install everything we need with sudo apt-get install git gcc g++ make libhdf5-devlibblitz-dev

Clone the git remote repository from GitHub: git clone [.git remote url] cd into the Release directory and run make


Chapter 2

Hierarchical Index

2.1 Class Hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:

AcceleratorGeometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13Array

ElectrodeLocator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23VectorField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Electrode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20ConfigLoader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19ez::ezETAProgressBar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29std::hash< tuple3Dint > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29HDF5Container1D< T > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30HDF5Container1D< float > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30HDF5Container1D< int > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30IntegerDistribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

SingleDistribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58TriangleDistribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69UniformDistribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Particle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

AntiHydrogen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

ParticleGenerator< PType > . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43SimulationNumbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55Simulator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56SmartField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59SubConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

AcceleratorConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11ParticlesConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48SimulationConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51StorageConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

VoltageScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

MovingTrapScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35SynchronousParticleScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

ExponentialScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25InstantaneousScheme . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Writer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

6 Hierarchical Index


Chapter 3

Class Index

3.1 Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

AcceleratorConfigFor storing configuration data pertaining to the accelerator geometry . . . . . . . . . . . . . . 11

AcceleratorGeometryA class for handling the complete geometry of the accelerator . . . . . . . . . . . . . . . . . . 13

AntiHydrogenAn implementation of Particle with some specific properties . . . . . . . . . . . . . . . . . . . 15

ConfigLoaderA class for loading a config file and storing its contents appropriately . . . . . . . . . . . . . . 19

ElectrodeRepresents a single electrode in the accelerator geometry . . . . . . . . . . . . . . . . . . . 20

ElectrodeLocatorA class for finding the physical location of electrodes in an E-Field . . . . . . . . . . . . . . . 23

ExponentialSchemeA SynchronousParticleScheme which exponentially increases the voltage on sections as thesynchronous particle enters them . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

ez::ezETAProgressBar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29std::hash< tuple3Dint >

Template specialisation for std::hash . . . . . . . . . . . . . . . . . . . . . . . . . . 29HDF5Container1D< T >

A basic container for the HDF5 components for the scalar data that will be stored . . . . . . . 30InstantaneousScheme

A SynchronousParticleScheme that switches on sections instantaneously as the synchronousparticle enters them . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

IntegerDistributionA wrapper class for some C++11 RNGs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

MovingTrapSchemeA VoltageScheme which appplies a periodic oscillating voltage to create a moving trap . . . . 35

ParticleBasic/generic particle class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

ParticleGenerator< PType >A class to generate a vector of particles for the simulation . . . . . . . . . . . . . . . . . . . . 43

ParticlesConfigFor storing configuration data pertaining to the particles in the simulation . . . . . . . . . . . . 48

SimulationConfigFor storing configuration data pertaining to the nature of the simulation . . . . . . . . . . . . . 51

SimulationNumbersA struct which stores the numbers of each particle type . . . . . . . . . . . . . . . . . . . . . 55

8 Class Index

SimulatorA class to actually run the simulation we want . . . . . . . . . . . . . . . . . . . . . . . . . . 56

SingleDistributionA single integer. Dirac delta distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

SmartFieldA clever way to access the superposed fields of electrodes . . . . . . . . . . . . . . . . . . . 59

StorageConfigFor storing configuration data pertaining to the storage of simulation results . . . . . . . . . . 62

SubConfigAbstract class which the config data containers inherit from . . . . . . . . . . . . . . . . . . . 64

SynchronousParticleSchemeAn abstract class for VoltageSchemes that rely on a synchronous particle . . . . . . . . . . . 66

TriangleDistributionA triangular integer distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

UniformDistributionUniform distribution of integers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

VectorFieldA general 3D vector field class, with basic operators . . . . . . . . . . . . . . . . . . . . . . . 72

VoltageSchemeAn abstract class for voltage schemes for the accelerator . . . . . . . . . . . . . . . . . . . . 76

WriterA class for writing the simulation data out to a file . . . . . . . . . . . . . . . . . . . . . . . . 80


Chapter 4

File Index

4.1 File List

Here is a list of all documented files with brief descriptions:

AcceleratorGeometry.hThis file contains the AcceleratorGeometry class . . . . . . . . . . . . . . . . . . . . . . . . 83

AntiHydrogen.hThis file contains the AntiHydrogen class . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

ConfigLoader.hThis file contains the ConfigLoader class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

Electrode.hThis file contains the Electrode class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

ElectrodeLocator.hThis file contains the ElectrodeLocator class . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

ezETAProgressBar.hpp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ??FlyE.h

This file includes all the necessary classes for a FlyE program . . . . . . . . . . . . . . . . . 90IntegerDistribution.h

This file contains the (abstract) IntegerDistribution class and all its subclasses . . . . . . . . . 90Particle.h

This file contains the Particle class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91ParticleGenerator.h

This file contains the ParticleGenerator class . . . . . . . . . . . . . . . . . . . . . . . . . . 93PhysicalConstants.h

All the constants needed in the program are stored here in the namespace "Physics" . . . . . 94Simulator.h

This file contains the Simulator class, and the SimuationNumbers struct . . . . . . . . . . . . 95SmartField.h

This file contains the SmartField class and the std::hash specialization . . . . . . . 96SubConfig.h

This file contains the SubConfig class, and its subclasses . . . . . . . . . . . . . . . . . . . . 97tupleDefs.h

Just contains the typedefs for 3D integer and float tuples . . . . . . . . . . . . . . . . . . . . 99VectorField.h

This file contains the VectorField class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101VoltageScheme.h

This file contains the VoltageScheme abstract class, and its subclasses . . . . . . . . . . . . 102Writer.h

This file contains the Writer class and the HDF5Container1D struct . . . . . . . . . . . . . . . 103

10 File Index


Chapter 5

Class Documentation

5.1 AcceleratorConfig Class Reference

For storing configuration data pertaining to the accelerator geometry.

#include

Inheritance diagram for AcceleratorConfig:

AcceleratorConfig

SubConfig

Collaboration diagram for AcceleratorConfig:

AcceleratorConfig

SubConfig

12 Class Documentation

Public Member Functions

AcceleratorConfig (INIReader &reader)

Generates the object using the INIReader.

void populate (INIReader &reader)

Populates the member variables of the object using the data in the INIReader object.

const std::string & datDirectory () const

Directory in which the E-Field .dat files are stored.

int nElectrodes () const

Number of electrodes in the accelerator.

const std::string & PAname () const

Prefix for EXSIMECK-named files.

int x () const

Dimension in x of accelerator geometry.

int y () const

Dimension in y of accelerator geometry.

int z () const

Dimension in z of accelerator geometry.

Protected Member Functions

void printOn (std::ostream &out)

Acts on an ostream to give formatted contents of member variables.

Protected Attributes

int nElectrodes_ std::string datDirectory_

Directory in which the E-Field .dat files are stored.

std::string PAname_

prefix for EXSIMECK-named files

int x_

x, y, z dimensions of the accelerator

int y_ int z_

5.1.1 Detailed Description

For storing configuration data pertaining to the accelerator geometry.

5.1.2 Constructor & Destructor Documentation

5.1.2.1 AcceleratorConfig::AcceleratorConfig ( INIReader & reader )

Generates the object using the INIReader.


5.2 AcceleratorGeometry Class Reference 13

Parameters

reader An INIReader object, usually supplied by ConfigLoader

Returns

AcceleratorConfig objectPopulates the member variables of the object using the data in the INIReader object.

Parameters

reader An INIReader object, usually supplied by constructor

5.1.3 Member Function Documentation

5.1.3.1 void AcceleratorConfig::populate ( INIReader & reader ) [virtual]

Populates the member variables of the object using the data in the INIReader object.

Parameters

reader An INIReader object, usually supplied by constructor

Implements SubConfig.

5.1.3.2 void AcceleratorConfig::printOn ( std::ostream & out ) [protected], [virtual]

Acts on an ostream to give formatted contents of member variables.

Java-inspired method to print out the data in the object.

Implements SubConfig.

5.1.4 Member Data Documentation

5.1.4.1 int AcceleratorConfig::nElectrodes_ [protected]

Number of electrodes in the accelerator

5.1.4.2 std::string AcceleratorConfig::PAname_ [protected]

prefix for EXSIMECK-named files

Acts on an ostream to give formatted contents of member variables. Java-inspired method to print out the data inthe object.

The documentation for this class was generated from the following files:

SubConfig.h

SubConfig.cpp

5.2 AcceleratorGeometry Class Reference

A class for handling the complete geometry of the accelerator.

#include




AcceleratorGeometry (std::shared_ptr< AcceleratorConfig > config)

Constructs from a shared_ptr to an AcceleratorConfig instance.

void importElectrodes ()

Tells all electrodes to import their E-Field files.

void applyElectrodeVoltages (std::vector< float > voltages)

Applies electrode voltages in order from the vector.

SmartField makeSmartField ()

Returns a SmartField for the current state of the geometry.

VectorField makeVectorField ()

Sums all the Electrodes and returns the superposed field.

ElectrodeLocator electrodeLocations ()

Returns an ElectrodeLocator for everything in the accelerator.

std::shared_ptr< AcceleratorConfig > getAcceleratorConfig ()

Returns a shared_ptr to the AcceleratorConfig instance associated with this geometry.


std::vector< std::shared_ptr< Electrode > > electrodes_

For storing (pointers) to all the Electrodes in the accelerator.

std::shared_ptr< AcceleratorConfig > config_

The configuration data for the geometry.


A class for handling the complete geometry of the accelerator.

Predominantly a container for Electrodes.

Author

Jamie Parkinson [email protected]


5.2.2.1 AcceleratorGeometry::AcceleratorGeometry ( std::shared_ptr< AcceleratorConfig > config )

Constructs from a shared_ptr to an AcceleratorConfig instance.

Parameters

config Contains all of the configuration/geometry data


5.2.3.1 void AcceleratorGeometry::applyElectrodeVoltages ( std::vector< float > voltages )

Applies electrode voltages in order from the vector.


5.3 AntiHydrogen Class Reference 15

Parameters

voltages A vector of voltages to apply, respectively, to the electrodes

5.2.3.2 ElectrodeLocator AcceleratorGeometry::electrodeLocations ( )

Returns an ElectrodeLocator for everything in the accelerator.

Returns

ElectrodeLocator for all electrodes

5.2.3.3 std::shared_ptr< AcceleratorConfig > AcceleratorGeometry::getAcceleratorConfig ( )

Returns a shared_ptr to the AcceleratorConfig instance associated with this geometry.

Returns

A shared_ptr to the AcceleratorConfig instance associated with this geometry

5.2.3.4 SmartField AcceleratorGeometry::makeSmartField ( )

Returns a SmartField for the current state of the geometry.

Returns

Effectively the current field (given voltages) in the accelerator

5.2.3.5 VectorField AcceleratorGeometry::makeVectorField ( )

Sums all the Electrodes and returns the superposed field.

Returns

The total field in the accelerator


AcceleratorGeometry.h

AcceleratorGeometry.cpp

5.3 AntiHydrogen Class Reference

An implementation of Particle with some specific properties.

#include



Inheritance diagram for AntiHydrogen:

AntiHydrogen

Particle

Collaboration diagram for AntiHydrogen:

AntiHydrogen

Particle


AntiHydrogen (float x, float y, float z, float vx, float vy, float vz, int n, int k)

Constructor for starting initial position/velocity and quantum numbers.

float mu () void neutralise (int t)

Neutralises the particle.

bool isNeutralised ()

Whether the particle has been neutralised.

int neutralisationTime ()

Get time at which neutralisation occurred.

void ionise ()

Ionises the particle.

int isDead ()

Has the particle ionised or collided?

float ITlim ()

Gets the Inglis-Teller limit.

float ionisationLim ()

Gets the ionisation field limit.

int k ()


5.3 AntiHydrogen Class Reference 17

Gets the value of k.

int n ()

Gets the value of n.


int n_

Principal quantum number.

int k_

Stark quantum number.

float mu_

Dipole moment.

float ITlim_

Inglis-Teller limit Solution of:

float ionisationLim_

Ionisation limit.

bool ionised_

Whether the particle has ionised.

int neutralised_

Neutralisation time. -1 if not neutralised.


An implementation of Particle with some specific properties.

Adds n, k, mu (which is a function of n and k), Inglis-Teller limit and ionisation and neutralisation related methodsand member variables

Author



5.3.2.1 AntiHydrogen::AntiHydrogen ( float x, float y, float z, float vx, float vy, float vz, int n, int k )

Constructor for starting initial position/velocity and quantum numbers.

Parameters

x x-coordinatey y-coordinatez z-coordinate

vx velocity component in x-directionvy velocity component in y-directionvz velocity component in z-directionn Principal quantum numberk Stark quantum number


5.3.3.1 float AntiHydrogen::ionisationLim ( )

Gets the ionisation field limit.



Returns

The ionisation limit of this particle

5.3.3.2 void AntiHydrogen::ionise ( )

Ionises the particle.

Sets ionised_ to true

5.3.3.3 int AntiHydrogen::isDead ( )

Has the particle ionised or collided?

Shadows method in Particle

Returns

1 if collided, 2 if ionised, 0 otherwise

5.3.3.4 bool AntiHydrogen::isNeutralised ( )

Whether the particle has been neutralised.

Returns

true if neutralised, false if not

5.3.3.5 float AntiHydrogen::ITlim ( )

Gets the Inglis-Teller limit.

Returns

The Inglis-Teller limit of this particle

5.3.3.6 int AntiHydrogen::k ( )

Gets the value of k.

Returns

value of k

5.3.3.7 float AntiHydrogen::mu ( )

Getter for mu_ (dipole moment)

Returns

Dipole moment


5.4 ConfigLoader Class Reference 19

5.3.3.8 int AntiHydrogen::n ( )

Gets the value of n.

Returns

value of n

5.3.3.9 int AntiHydrogen::neutralisationTime ( )

Get time at which neutralisation occurred.

Returns

Time at which neutralisation occurred

5.3.3.10 void AntiHydrogen::neutralise ( int t )

Neutralises the particle.

Sets neutralised_ to t

Parameters

t The time at which neutralisation occurred


5.3.4.1 float AntiHydrogen::ITlim_ [protected]

Inglis-Teller limit Solution of:

32a0eFn(n+1) Rhc

(n+1)2=

32a0eFkn Rhcn2

limIT =2ch(2n+1)R

3a0en3(n+1)2(k+n+1)


AntiHydrogen.h AntiHydrogen.cpp

5.4 ConfigLoader Class Reference

A class for loading a config file and storing its contents appropriately.

#include


ConfigLoader (std::string configFilePath)

Constructs ConfigLoader from the file at the given path.

std::shared_ptr< AcceleratorConfig > getAcceleratorConfig ()



Getter for AcceleratorConfig object.

std::shared_ptr< ParticlesConfig > getParticlesConfig ()

Getter for ParticlesConfig object.

std::shared_ptr< SimulationConfig > getSimulationConfig ()

Getter for SimulationConfig object.

std::shared_ptr< StorageConfig > getStorageConfig ()

Getter for StorageConfig object.


A class for loading a config file and storing its contents appropriately.

The class uses the inih library - https://code.google.com/p/inih/ - to load and parse config files.Configuration data is stored in appropriate structs for each domain of usagem, and getters for (pointers to) this dataare provided.

Author



5.4.2.1 ConfigLoader::ConfigLoader ( std::string configFilePath )

Constructs ConfigLoader from the file at the given path.

Parameters

configFilePath Path to the config file

Returns

The ConfigLoader object


ConfigLoader.h

ConfigLoader.cpp

5.5 Electrode Class Reference

Represents a single electrode in the accelerator geometry.

#include


5.5 Electrode Class Reference 21

Inheritance diagram for Electrode:

Electrode

VectorField

blitz::Array< blitz::TinyVector< float,

3 >, 3 >

Collaboration diagram for Electrode:

Electrode

VectorField

blitz::Array< blitz::TinyVector< float,

3 >, 3 >


Electrode ()

Blank constructor.

Electrode (int electrodeNumber)

Constructs an "empty" Electrode with given index.

Electrode (const Electrode &elec)

Copy constructor.

void import (std::shared_ptr< AcceleratorConfig > config)



Imports the E-Field files associated with this electrode. void applyVoltage (float voltage)

Applies a voltage to the Electrode. float getVoltage ()

Gets the voltage that is currently applied to this Electrode.


int electrodeNumber_

The number/index of the electrode within the accelerator geometry. float currentVoltage_ = 1.0

The voltage that is currently being applied to the electrode.

Additional Inherited Members


Represents a single electrode in the accelerator geometry.

Derived from VectorField. Adds methods to import E-Field files, change its voltage and get its location. ElectrodeLocator is a friend class. Also remembers its number within the geometry.

See also

ElectrodeLocator

Author



5.5.2.1 Electrode::Electrode ( int electrodeNumber )

Constructs an "empty" Electrode with given index.

Parameters

electrodeNumber

The number/index of the electrode within the accelerator geometry.

5.5.2.2 Electrode::Electrode ( const Electrode & elec )

Copy constructor.

Parameters

elec Electrode to copy


5.5.3.1 void Electrode::applyVoltage ( float voltage )

Applies a voltage to the Electrode.

Trying a new approach for this: the scalar multiplication will only be done when we get values from the Electrode.


5.6 ElectrodeLocator Class Reference 23

Parameters

voltage The voltage to apply

5.5.3.2 float Electrode::getVoltage ( )

Gets the voltage that is currently applied to this Electrode.

Returns

The voltage that is currently applied to this Electrode

5.5.3.3 void Electrode::import ( std::shared_ptr< AcceleratorConfig > config )

Imports the E-Field files associated with this electrode.

Stores them as the base field of the Electrode. By convention, this is the field when the Electrode has a PD of 1Vapplied to it. As such, any other voltage can be obtained by multiplying the field by a scalar.

Parameters

config Relevant AcceleratorConfig, usually provided by ConfigLoader

See also

ConfigLoaderAcceleratorConfig


Electrode.h

Electrode.cpp

5.6 ElectrodeLocator Class Reference

A class for finding the physical location of electrodes in an E-Field.

#include

Inheritance diagram for ElectrodeLocator:

ElectrodeLocator

blitz::Array< bool, 3 >



Collaboration diagram for ElectrodeLocator:

ElectrodeLocator

blitz::Array< bool, 3 >


ElectrodeLocator (Electrode &electrode)

Constructs an ElectrodeLocator from an Electrode.

ElectrodeLocator (std::shared_ptr< Electrode > electrode)

For construction from a shared_ptr to an Electrode.

bool existsAt (int x, int y, int z)

Checks to see if the electrode exists at a given point.

bool existsAt (const tuple3Dint &r)



A class for finding the physical location of electrodes in an E-Field.

Author



5.6.2.1 ElectrodeLocator::ElectrodeLocator ( Electrode & electrode )

Constructs an ElectrodeLocator from an Electrode.

Parameters

electrode An Electrode, the location of which will be determined

5.6.2.2 ElectrodeLocator::ElectrodeLocator ( std::shared_ptr< Electrode > electrode )

For construction from a shared_ptr to an Electrode.

Useful because shared_ptrs are quite common


5.7 ExponentialScheme Class Reference 25

Parameters

electrode A shared_ptr to an Electrode to be located


5.6.3.1 bool ElectrodeLocator::existsAt ( int x, int y, int z )


Parameters

x x-coordinate to checky y-coordinate to checkz z-coordinate to check

Returns

true if it does exist at the point, false otherwise

5.6.3.2 bool ElectrodeLocator::existsAt ( const tuple3Dint & r )


Parameters

r A tuple of 3 integers (x, y, z)

Returns

true if it does exist at the point, false otherwise


ElectrodeLocator.h

ElectrodeLocator.cpp

5.7 ExponentialScheme Class Reference

A SynchronousParticleScheme which exponentially increases the voltage on sections as the synchronous particleenters them.

#include



Inheritance diagram for ExponentialScheme:

ExponentialScheme

SynchronousParticleScheme

VoltageScheme

Collaboration diagram for ExponentialScheme:

ExponentialScheme


VoltageScheme Particle

synchronousParticle_


ExponentialScheme (Particle &synchronousParticle, float maxVoltage, int nElectrodes, int sectionWidth, floattimeStep)

Constructs the SynchronousParticleScheme with all the necessary member variables.

std::vector< float > getVoltages (int t)

Returns a vector of the electrode voltages at time t.

bool isActive (int t)

Returns true if the voltages will be different from the previous access.


5.7 ExponentialScheme Class Reference 27


float deltaT_ = std::numeric_limits::max()

The estimated time until the particle will enter the next section.

float startRampTime_ = 0.0

The time at which the current section was activated.

Static Protected Attributes

static constexpr int timeConstant_ = 1000.0

The time constant of the exponential increase.


A SynchronousParticleScheme which exponentially increases the voltage on sections as the synchronous particleenters them.

Author



5.7.2.1 ExponentialScheme::ExponentialScheme ( Particle & synchronousParticle, float maxVoltage, int nElectrodes, intsectionWidth, float timeStep )


See also

VoltageScheme

Parameters

synchronousParticle

The synchronous particle (usually the first Particle in the vector of Particles)

maxVoltage The maximum voltage that can be appliednElectrodes The number of electrodes to generate voltages for

sectionWidth The width of a "section" of electrodes in the cylindrical acceleratortimeStep The time step being used in the simulation


5.7.3.1 std::vector< float > ExponentialScheme::getVoltages ( int t ) [virtual]


Parameters

t Time to get the voltage for

Returns

A vector of electrode voltages

Implements SynchronousParticleScheme.



5.7.3.2 bool ExponentialScheme::isActive ( int t ) [virtual]



5.8 ez::ezETAProgressBar Class Reference 29

Parameters

t The time to check activity

Returns

True if the voltages will be different from the previous access



VoltageScheme.h VoltageScheme.cpp

5.8 ez::ezETAProgressBar Class Reference


ezETAProgressBar (unsigned int _n=0) void reset (uint64_t _n) void start () void operator++ () void operator+= (const unsigned int d) void done () std::string durationString (duration t) void setPct (double Pct)

The documentation for this class was generated from the following file:

ezETAProgressBar.hpp

5.9 std::hash< tuple3Dint > Struct Template Reference

Template specialisation for std::hash

#include


size_t operator() (const tuple3Dint &t) const

For accessing the hashing algorithm.


templatestruct std::hash< tuple3Dint >

Template specialisation for std::hash


5.9.2.1 size_t std::hash< tuple3Dint >::operator() ( const tuple3Dint & t ) const [inline]

For accessing the hashing algorithm.



Parameters

t A tuple3D (aka std::tuple) of integer coords

Returns

A size_t (aka unsigned int) hash code

The documentation for this struct was generated from the following file:

SmartField.h

5.10 HDF5Container1D< T > Struct Template Reference

A basic container for the HDF5 components for the scalar data that will be stored.

#include

Public Attributes

std::vector< std::shared_ptr< H5::DataSet > > dSets

A vector of shared_ptrs to HDF5 DataSets.

std::vector< H5::DataSpace > dSpaces

A vector of HDF5 DataSpaces.

std::vector< std::vector< T > > vecs

A vector of vectors of values (of type T)


templatestruct HDF5Container1D< T >

A basic container for the HDF5 components for the scalar data that will be stored.

Hard to describe.

Author



5.10.2.1 template std::vector< std::vector> HDF5Container1D< T >::vecs

A vector of vectors of values (of type T)

Construct the container with 4 vectors in vecs

The documentation for this struct was generated from the following file:

Writer.h


5.11 InstantaneousScheme Class Reference 31

5.11 InstantaneousScheme Class Reference

A SynchronousParticleScheme that switches on sections instantaneously as the synchronous particle enters them.

#include

Inheritance diagram for InstantaneousScheme:

InstantaneousScheme


VoltageScheme

Collaboration diagram for InstantaneousScheme:

InstantaneousScheme


VoltageScheme Particle

synchronousParticle_


InstantaneousScheme (Particle &synchronousParticle, float maxVoltage, int nElectrodes, int sectionWidth,float timeStep)








Additional Inherited Members


A SynchronousParticleScheme that switches on sections instantaneously as the synchronous particle enters them.

Author



5.11.2.1 InstantaneousScheme::InstantaneousScheme ( Particle & synchronousParticle, float maxVoltage, int nElectrodes,int sectionWidth, float timeStep )


See also

VoltageScheme

Parameters

synchronousParticle

The synchronous particle (usually the first Particle in the vector of Particles)




5.11.3.1 std::vector< float > InstantaneousScheme::getVoltages ( int t ) [virtual]


Parameters


Returns



5.11.3.2 bool InstantaneousScheme::isActive ( int t ) [virtual]



5.12 IntegerDistribution Class Reference 33

Parameters


Returns




VoltageScheme.h

VoltageScheme.cpp

5.12 IntegerDistribution Class Reference

A wrapper class for some C++11 RNGs.

#include

Inheritance diagram for IntegerDistribution:

IntegerDistribution

SingleDistribution TriangleDistribution UniformDistribution


virtual int operator() (mersenne_twister &generator)=0

Virtual operator to get a number from a generator.

virtual IntegerDistribution ()Blank virtual destructor.


A wrapper class for some C++11 RNGs.

The integer RNGs in C++11 are curiously not all derived from some bass class. This means they can be a pain touse - this class offers a very limited level of abstraction. Note that the distributions can only use a Mersenne Twistergenerator.

Author





5.12.2.1 virtual int IntegerDistribution::operator() ( mersenne_twister & generator ) [pure virtual]

Virtual operator to get a number from a generator.


5.13 MovingTrapScheme Class Reference 35

Parameters

generator An instance of a mersenne_twister

Returns

A random integer

Implemented in TriangleDistribution, SingleDistribution, and UniformDistribution.


IntegerDistribution.h IntegerDistribution.cpp

5.13 MovingTrapScheme Class Reference

A VoltageScheme which appplies a periodic oscillating voltage to create a moving trap.

#include

Inheritance diagram for MovingTrapScheme:

MovingTrapScheme

VoltageScheme

Collaboration diagram for MovingTrapScheme:

MovingTrapScheme

VoltageScheme


MovingTrapScheme (float maxVoltage, int nElectrodes, int sectionWidth, float timeStep, float targetVel, int k)



Constructs the MovingTrapScheme with the appropriate parameters.

std::vector< float > getInitialVoltages ()

Returns a vector of the initial voltages to apply before the simulation starts.






float frequency (int k)

Gets the frequency of transverse oscillation of particles with Stark quantum number k.


float targetVel_

The target velocity for the particles (oscillation frequency depends on this)

float offTime_

The time at which the E-Field should be switched off for the particles to fly freely.

Static Protected Attributes

static constexpr int trapWidth_ = 6

The number of sections that a trap should span.

static constexpr int nOscillations_ = 4

The number of transverse oscillations of the particles before the field is switched off.


A VoltageScheme which appplies a periodic oscillating voltage to create a moving trap.

Author



5.13.2.1 MovingTrapScheme::MovingTrapScheme ( float maxVoltage, int nElectrodes, int sectionWidth, float timeStep, floattargetVel, int k )

Constructs the MovingTrapScheme with the appropriate parameters.

Parameters




5.13 MovingTrapScheme Class Reference 37

targetVel The target velocity for the particles to reachk The k-value to estimate frequency from. Ideally this will be the average k-value.


5.13.3.1 float MovingTrapScheme::frequency ( int k ) [protected]

Gets the frequency of transverse oscillation of particles with Stark quantum number k.

This assumes that the particles are transversely oscillating in a nearly harmonic potential. The equation used in thesource was found in MATLAB by computing a regression from data at various k-values. Because k and V both havea linear effect on the dipole moment, we can generalise that regression to work for different k and V values. Thisfunction accesses the member variable maxVoltage_ to do this.

Parameters

k Any stark quantum number of the particles

Returns

An estimate of the frequency of transverse particle oscillation (Hz)

5.13.3.2 std::vector< float > MovingTrapScheme::getInitialVoltages ( ) [virtual]

Returns a vector of the initial voltages to apply before the simulation starts.

Returns

A vector of the initial voltages to apply before the simulation starts

Implements VoltageScheme.

5.13.3.3 std::vector< float > MovingTrapScheme::getVoltages ( int t ) [virtual]


Parameters


Returns



5.13.3.4 bool MovingTrapScheme::isActive ( int t ) [virtual]


Parameters




Returns




VoltageScheme.h VoltageScheme.cpp

5.14 Particle Class Reference

Basic/generic particle class.

#include

Inheritance diagram for Particle:

Particle

AntiHydrogen


Particle (float x, float y, float z, float vx, float vy, float vz)

Constructor to set initial position and velocity.

void memorise ()

Commit current location and velocity to memory.

void forget ()

Delete memory vectors.

void cutDownMemory ()

Delete all but first part of memory vectors.

std::vector< float > recallLoc (int d)

Return vector of locations in d (x1,x2,x3,...)

float recallLoc (int i, int d)

Return the d-location at the i-th position.

std::vector< float > recallVel (int d)

Return vector of velocities in d (vx1,vx2,vx3,...)

float recallVel (int i, int d)


void setLoc (float x, float y, float z)

Set the location.

void setLoc (tuple3Dfloat loc)


5.14 Particle Class Reference 39

Set the location with a location tuple.

void setVel (float vx, float vy, float vz)

Set the velocity.

void setVel (tuple3Dfloat vel)

Set the velocity with a velocity tuple.

tuple3Dfloat getLoc ()

Return the tuple {x,y,z}.

templatefloat getLocDim ()

Returns the location in the templated dimension d Template parameter d = 0 for x, d = 1 for y, d = 2 for z.

tuple3Dint getIntLoc ()

Returns the tuple {x,y,z} rounded to an integer grid.

tuple3Dfloat getVel ()

Return the tuple {vx,vy,vz}.

templatefloat getVelDim ()

Returns the velocity in the templated dimension d Template parameter d = 0 for x, d = 1 for y, d = 2 for z.

int isDead ()

Whether the particle has collided.

bool succeeded ()

Whether the particle has reached the end of the accelerator.

void collide ()

Call a collision event.

void succeed ()

Call a success event.

float maxField ()

Gets the maximum |E| that the particle encountered. void checkMaxField (float magnitude)

Checks to see if the field given is greater than the previous max.


tuple3Dfloat r_

Position.

tuple3Dfloat v_

Velocity.

bool collided_


bool succeeded_


float maxField_

The maximum E-Field magnitude that the particle encountered.

std::vector< float > xTraj_

Contain the trajectory coordinates.

std::vector< float > yTraj_ std::vector< float > zTraj_ std::vector< float > xvTraj_ std::vector< float > yvTraj_ std::vector< float > zvTraj_




Basic/generic particle class.

This will work but will need to be extended to add any specific properties or methods

Author



5.14.2.1 Particle::Particle ( float x, float y, float z, float vx, float vy, float vz )

Constructor to set initial position and velocity.

Parameters


vx velocity component in x-directionvy velocity component in y-directionvz velocity component in z-direction


5.14.3.1 void Particle::checkMaxField ( float magnitude )

Checks to see if the field given is greater than the previous max.

Parameters

magnitude An E-field magnitude

5.14.3.2 void Particle::collide ( )

Call a collision event.

Sets the collided_ int to 1

5.14.3.3 tuple3Dint Particle::getIntLoc ( )

Returns the tuple {x,y,z} rounded to an integer grid.

Returns

The tuple {x,y,z} rounded to an integer grid

5.14.3.4 tuple3Dfloat Particle::getLoc ( )

Return the tuple {x,y,z}.

Returns

The tuple (x, y, z)


5.14 Particle Class Reference 41

5.14.3.5 template float Particle::getLocDim ( ) [inline]

Returns the location in the templated dimension d Template parameter d = 0 for x, d = 1 for y, d = 2 for z.

Returns

The current d-location of the Particle

5.14.3.6 tuple3Dfloat Particle::getVel ( )

Return the tuple {vx,vy,vz}.

Returns

The tuple (vx, vy, vz)

5.14.3.7 template float Particle::getVelDim ( ) [inline]

Returns the velocity in the templated dimension d Template parameter d = 0 for x, d = 1 for y, d = 2 for z.

Returns

The current d-velocity of the Particle

5.14.3.8 int Particle::isDead ( )


Expected to be overloaded in derived classes for ionisation etc

Returns

0 if not collided, 1 if collided

5.14.3.9 float Particle::maxField ( )

Gets the maximum |E| that the particle encountered.Returns

The maximum |E| that the particle encountered

5.14.3.10 std::vector< float > Particle::recallLoc ( int d )

Return vector of locations in d (x1,x2,x3,...)

Parameters

d The dimension of locations to get

Returns

A vector of all d-locations

5.14.3.11 float Particle::recallLoc ( int i, int d )




Parameters

i The time/index in trajectory to getd The dimension to get

Returns

The corresponding position

5.14.3.12 std::vector< float > Particle::recallVel ( int d )

Return vector of velocities in d (vx1,vx2,vx3,...)

Parameters

d The dimension of velocities to get

Returns

A vector of all d-velocities

5.14.3.13 float Particle::recallVel ( int i, int d )


Parameters

i The time/index in trajectory to getd The dimension to get

Returns

The corresponding velocity

5.14.3.14 void Particle::setLoc ( float x, float y, float z )

Set the location.

Parameters


5.14.3.15 void Particle::setLoc ( tuple3Dfloat loc )

Set the location with a location tuple.

Parameters

loc (x,y,z) tuple

5.14.3.16 void Particle::setVel ( float vx, float vy, float vz )

Set the velocity.


5.15 ParticleGenerator< PType > Class Template Reference 43

Parameters

vx x-componentvy y-componentvz z-component

5.14.3.17 void Particle::setVel ( tuple3Dfloat vel )

Set the velocity with a velocity tuple.

Parameters

vel (vx, vy, vz) tuple

5.14.3.18 void Particle::succeed ( )

Call a success event.

Sets the succeeded_ bool to true

5.14.3.19 bool Particle::succeeded ( )


Returns

true if successful, false if not


Particle.h Particle.cpp

5.15 ParticleGenerator< PType > Class Template Reference

A class to generate a vector of particles for the simulation.

#include


ParticleGenerator (std::shared_ptr< ParticlesConfig > particlesConfig, std::shared_ptr< AcceleratorConfig> acceleratorConfig)

Constructs a ParticleGenerator from the given configuration objects.

void generateSynchronousParticle (int x, int y, int z, int vx, int vy, int vz)

Generates a single particle.

void generateParticles ()

Generates particles according to the particles configuration object.

std::vector< PType > & getParticles ()

Returns the generated particles.

templatevoid generateSynchronousParticle (int x, int y, int z, int vx, int vy, int vz)

templatevoid generateParticles ()




tuple3Dfloat generateUniformVels (float sigmaV, mersenne_twister generator)

Generates a radially uniform distribution of velocities with radius v_r.

void generateNormDist (mersenne_twister generator, float sigmaV, bool normVels, int sectionWidth, IntegerDistribution kDist)

Generates normally distributed particles.

void generateUniformDist (mersenne_twister generator, float sigmaV, bool normVels, int sectionWidth,IntegerDistribution kDist, bool full=false)

Generates uniformly distributed particles.

templatevoid generateNormDist (mersenne_twister generator, float sigmaV, bool normVels, int sectionWidth, IntegerDistribution kDist)

templatevoid generateUniformDist (mersenne_twister generator, float sigmaV, bool normVels, int sectionWidth,IntegerDistribution kDist, bool full)


std::shared_ptr< ParticlesConfig > particlesConfig_

Holds configuration data for particles.

std::shared_ptr< AcceleratorConfig > acceleratorConfig_

Holds configuration data for the geometry; necessary for putting particles in the right places.

std::vector< PType > particles_

The vector of particles which will be created.


templateclass ParticleGenerator< PType >

A class to generate a vector of particles for the simulation.

Particle parameters are held in the shared_ptr object. Type of particles is the template parameter.(Currently only AntiHydrogen)

Author



5.15.2.1 template ParticleGenerator< PType >::ParticleGenerator ( std::shared_ptr particlesConfig, std::shared_ptr< AcceleratorConfig > acceleratorConfig ) [inline]

Constructs a ParticleGenerator from the given configuration objects.

Parameters

particlesConfig Config data for particlesaccelerator

ConfigConfig data for the accelerator


5.15 ParticleGenerator< PType > Class Template Reference 45


5.15.3.1 template void ParticleGenerator< PType >::generateNormDist ( mersenne_twister generator,float sigmaV, bool normVels, int sectionWidth, IntegerDistribution kDist ) [protected]

Generates normally distributed particles.



Parameters

generator An instance of std::mt19937sigmaV Standard deviation of particle velocity (from temperature)

normVels Whether the velocities are normally distributedsectionWidth The width of one section of the accelerator

kDist A pointer to an IntegerDistribution

5.15.3.2 template void ParticleGenerator< AntiHydrogen >::generateNormDist ( mersenne_twister generator,float sigmaV, bool normVels, int sectionWidth, IntegerDistribution kDist ) [protected]

5.15.3.3 template void ParticleGenerator< PType >::generateParticles ( )

Generates particles according to the particles configuration object.

Calls either generateNormDist() or generateUniformDist()

5.15.3.4 template void ParticleGenerator< AntiHydrogen >::generateParticles ( )

5.15.3.5 template void ParticleGenerator< PType >::generateSynchronousParticle ( int x, int y, int z, intvx, int vy, int vz )

Generates a single particle.

To be used as the synchronous particle

Parameters

x x-coordinate of particley y-coordinate of particlez z-coordinate of particle

vx x-component of particle velocityvy y-component of particle velocityvz z-component of particle velocity

5.15.3.6 template void ParticleGenerator< AntiHydrogen >::generateSynchronousParticle ( int x, int y, int z, intvx, int vy, int vz )

5.15.3.7 template void ParticleGenerator< PType >::generateUniformDist ( mersenne_twistergenerator, float sigmaV, bool normVels, int sectionWidth, IntegerDistribution kDist, bool full = false )[protected]

Generates uniformly distributed particles.

Parameters

generator An instance of std::mt19937sigmaV Standard deviation of particle velocity (from temperature)

normVels Whether the velocities are normally distributedsectionWidth Th

Reference FlyE

Documents

class documentation

detailed description

class index

member data documentation

configloader class reference

antihydrogen class reference

class list

class hierarchy