Index

A

ablator() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] ablator_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] AbstractBaseCalculator (class in SimEx.Calculators.AbstractBaseCalculator), [1] AbstractPhotonAnalyzer (class in SimEx.Calculators.AbstractPhotonAnalyzer), [1] AbstractPhotonDetector (class in SimEx.Calculators.AbstractPhotonDetector), [1] AbstractPhotonDiffractor (class in SimEx.Calculators.AbstractPhotonDiffractor), [1] AbstractPhotonInteractor (class in SimEx.Calculators.AbstractPhotonInteractor), [1]

AbstractPhotonPropagator (class in SimEx.Calculators.AbstractPhotonPropagator), [1] AbstractPhotonSource (class in SimEx.Calculators.AbstractPhotonSource), [1] amplitude_reduction_factor() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property), [1] animate() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis method), [1] (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method), [1] animatePatterns() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method), [1] atoms() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property), [1] averaging_start() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property), [1]

B

backengine() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator method), [1] (SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator method), [1] (SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method), [1] (SimEx.Calculators.DMPhasing.DMPhasing method), [1] (SimEx.Calculators.EMCOrientation.EMCOrientation method), [1] (SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor method), [1] (SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor method), [1] (SimEx.Calculators.GenesisPhotonSource.GenesisPhotonSource method), [1] (SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector method), [1] (SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator method), [1] (SimEx.Calculators.S2EReconstruction.S2EReconstruction method), [1] (SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor method), [1] (SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method), [1] (SimEx.Calculators.XFELPhotonPropagator.XFELPhotonPropagator method), [1] (SimEx.Calculators.XFELPhotonSource.XFELPhotonSource method), [1] (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor method), [1] (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method), [1]

band_gap() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] beam_diameter_fwhm() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property), [1] beam_parameters() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] (SimEx.Parameters.PhotonMatterInteractorParameters.PhotonMatterInteractorParameters property), [1] (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1] beamline() (SimEx.Parameters.WavePropagatorParameters.WavePropagatorParameters property), [1] beamstop() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property), [1]

C

calculate_Compton() (SimEx.Parameters.PhotonMatterInteractorParameters.PhotonMatterInteractorParameters property), [1] (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1] calculate_displacement() (in module SimEx.Analysis.XMDYNPhotonMatterAnalysis), [1] calculate_ion_charge() (in module SimEx.Analysis.XMDYNPhotonMatterAnalysis), [1] calculateLaserIntensity() (in module SimEx.Utilities.IntensityCalc), [1] checkAndGetPDB() (in module SimEx.Utilities.IOUtilities), [1] checkAndSetAblator() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetAblatorThickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetBandGap() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetBaseCalculator() (in module SimEx.Calculators.AbstractBaseCalculator), [1] checkAndSetDebyeTemperature() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetDeltaTime() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetDensitiesAndCharge() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetElectronTemperature() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetElements() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetEnergyRange() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetIO() (in module SimEx.Calculators.AbstractBaseCalculator), [1] checkAndSetIonTemperature() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetLaserIntensity() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetLaserPulse() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetLaserPulseDuration() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetLaserWavelength() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetLayer1() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetLayer1Thickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetLayer2() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetLayer2Thickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetLFC() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetModelIPL() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetModelMix() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetModelSbf() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1]

checkAndSetModelSee() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetModelSii() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetNumberOfLayers() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetParameters() (in module SimEx.Calculators.AbstractBaseCalculator), [1] (in module SimEx.Calculators.ComptonScatteringCalculator), [1] (in module SimEx.Calculators.PlasmaXRTSCalculator), [1] checkAndSetPhotonAnalyzer() (in module SimEx.Calculators.AbstractPhotonAnalyzer), [1], [2], [3] checkAndSetPhotonDetector() (in module SimEx.Calculators.AbstractPhotonDetector), [1], [2], [3] checkAndSetPhotonDiffractor() (in module SimEx.Calculators.AbstractPhotonDiffractor), [1], [2], [3] checkAndSetPhotonEnergy() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetPhotonInteractor() (in module SimEx.Calculators.AbstractPhotonInteractor), [1], [2], [3] checkAndSetPhotonPropagator() (in module SimEx.Calculators.AbstractPhotonPropagator), [1], [2], [3] checkAndSetPhotonSource() (in module SimEx.Calculators.AbstractPhotonSource), [1], [2], [3] checkAndSetRunTime() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetSample() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetSampleThickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetSbfNorm() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetScatteringAngle() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetSourceSpectrum() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetSourceSpectrumFWHM() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] checkAndSetWindow() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] checkAndSetWindowThickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] ComptonScatteringCalculator (class in SimEx.Calculators.ComptonScatteringCalculator), [1] computeNTasks() (SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method), [1] convertToOPMD() (in module SimEx.Utilities.wpg_to_opmd), [1] convertTxtToOPMD() (in module SimEx.Utilities.hydro_txt_to_opmd), [1] createTestScatteringGeometry() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] crystal_size_max() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] crystal_size_min() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] CrystFELPhotonDiffractor (class in SimEx.Calculators.CrystFELPhotonDiffractor), [1] CrystFELPhotonDiffractorParameters (class in SimEx.Parameters.CrystFELPhotonDiffractorParameters), [1]

D

data() (SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator property), [1] (SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor property), [1] (SimEx.Calculators.DMPhasing.DMPhasing property), [1] (SimEx.Calculators.EMCOrientation.EMCOrientation property), [1] (SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor property), [1] (SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor property), [1] (SimEx.Calculators.GenesisPhotonSource.GenesisPhotonSource property), [1] (SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector property), [1] (SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator property), [1] (SimEx.Calculators.S2EReconstruction.S2EReconstruction property), [1] (SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor property), [1] (SimEx.Calculators.XFELPhotonPropagator.XFELPhotonPropagator property), [1] (SimEx.Calculators.XFELPhotonSource.XFELPhotonSource property), [1] (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor property), [1] (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor property), [1]

debye_temperature() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] delta_time() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] detailed_output() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property), [1] detector_geometry() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1] detector_type() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property), [1] DiffractionAnalysis (class in SimEx.Analysis.DiffractionAnalysis), [1] diffractionParameters() (in module SimEx.Analysis.DiffractionAnalysis), [1] diffractTestCase() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] divergence() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property), [1] DMPhasing (class in SimEx.Calculators.DMPhasing), [1] DMPhasingParameters (class in SimEx.Parameters.DMPhasingParameters), [1] dumpLoader() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator class method), [1] dumpToFile() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator method), [1]

E

edge() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property), [1] effective_path_distance() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property), [1] electron_density() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] electron_temperature() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] elements() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis property), [1] (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] EMCCaseGenerator (class in SimEx.Calculators.EMCCaseGenerator), [1] EMCOrientation (class in SimEx.Calculators.EMCOrientation), [1] EMCOrientationParameters (class in SimEx.Parameters.EMCOrientationParameters), [1] energy_range() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] EstherExperiment (class in SimEx.PhotonExperimentSimulation.EstherExperiment), [1] EstherPhotonMatterInteractor (class in SimEx.Calculators.EstherPhotonMatterInteractor), [1] EstherPhotonMatterInteractorParameters (class in SimEx.Parameters.EstherPhotonMatterInteractorParameters), [1] expectedData() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator method), [1] (SimEx.Calculators.AbstractPhotonPropagator.AbstractPhotonPropagator method), [1] (SimEx.Calculators.AbstractPhotonSource.AbstractPhotonSource method), [1] (SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator method), [1] (SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method), [1] (SimEx.Calculators.DMPhasing.DMPhasing method), [1] (SimEx.Calculators.EMCOrientation.EMCOrientation method), [1] (SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor method), [1] (SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor method), [1] (SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector method), [1] (SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator method), [1] (SimEx.Calculators.S2EReconstruction.S2EReconstruction method), [1] (SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor method), [1] (SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method), [1] (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor method), [1] (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method), [1]

extractDate() (in module SimEx.Calculators.PlasmaXRTSCalculator), [1]

F

FEFFPhotonMatterInteractor (class in SimEx.Calculators.FEFFPhotonMatterInteractor), [1] FEFFPhotonMatterInteractorParameters (class in SimEx.Parameters.FEFFPhotonMatterInteractorParameters), [1]

fermihalf() (in module SimEx.Calculators.ComptonScatteringCalculator), [1] finalize() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters method), [1] finalized() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property), [1]

G

genesis_dfl_to_wavefront() (in module SimEx.Utilities.IOUtilities), [1] GenesisPhotonSource (class in SimEx.Calculators.GenesisPhotonSource), [1] get_basePath() (in module SimEx.Utilities.OpenPMDTools), [1]

get_dict_from_lines() (in module SimEx.Utilities.IOUtilities), [1] getCUDAEnvironment() (in module SimEx.Utilities.ParallelUtilities), [1] getParallelResourceInfo() (in module SimEx.Utilities.ParallelUtilities), [1] getTmpFileName() (in module SimEx.Utilities.IOUtilities), [1]

I

IdealPhotonDetector (class in SimEx.Calculators.IdealPhotonDetector), [1] initial_number_of_quaternions() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property), [1] input_path() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis property), [1] (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator property), [1] (SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector property), [1]

intensities_file() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] intensity() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis property), [1] ion_charge() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] ion_temperature() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1]

L

laser_intensity() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] laser_pulse() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] laser_pulse_duration() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] laser_wavelength() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] layer1() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] layer1_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] layer2() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] layer2_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1]

leash() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property), [1] lfc() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] load_sample() (in module SimEx.Analysis.XMDYNPhotonMatterAnalysis), [1] load_snapshot() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method), [1] load_snp_from_dir() (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method), [1] load_trajectory() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method), [1] loadPDB() (in module SimEx.Utilities.IOUtilities), [1] loadXYZ() (in module SimEx.Utilities.IOUtilities), [1]

M

makeTestParticleAndSupport() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] mask() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property), [1] mask_nans() (in module SimEx.Analysis.XFELPhotonAnalysis), [1] mass_density() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] max_number_of_iterations() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property), [1] max_number_of_quaternions() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property), [1]

min_error() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property), [1] model_IPL() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] model_Mix() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] model_Sbf() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] model_See() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] model_Sii() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1]

N

number_of_background_photons() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] number_of_diffraction_patterns() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1] number_of_iterations() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property), [1] number_of_layers() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1]

number_of_shrink_cycles() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property), [1] number_of_slices() (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1] number_of_snapshots() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method), [1] number_of_trajectories() (SimEx.Parameters.PhotonMatterInteractorParameters.PhotonMatterInteractorParameters property), [1] number_of_trials() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property), [1]

O

output_path() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator property), [1] (SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector property), [1]

P

parameters() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator property), [1] (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor property), [1] path_to_executable() (SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor property), [1] pattern_indices() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property), [1] patternGenerator() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method), [1] patterns() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property), [1] photon_energy() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property), [1] (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] photon_energy_relative_bandwidth() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property), [1] photon_energy_spectrum_type() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property), [1] PhotonBeamParameters (class in SimEx.Parameters.PhotonBeamParameters), [1] PhotonMatterInteractorParameters (class in SimEx.Parameters.PhotonMatterInteractorParameters), [1] photonStatistics() (in module SimEx.Analysis.DiffractionAnalysis), [1] pic2dist() (in module SimEx.Utilities.IOUtilities), [1] placePixel() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] plasma_search_flag() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property), [1] plasma_simulation_flag() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property), [1] PlasmaXRTSCalculator (class in SimEx.Calculators.PlasmaXRTSCalculator), [1] PlasmaXRTSCalculatorParameters (class in SimEx.Parameters.PlasmaXRTSCalculatorParameters), [1] plot_charge() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method), [1] plot_displacement() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method), [1] plot_energies() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method), [1] plotImage() (in module SimEx.Analysis.DiffractionAnalysis), [1] plotIntensityMap() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis method), [1] plotOnAxisPowerDensity() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis method), [1] plotPattern() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method), [1] plotRadialProjection() (in module SimEx.Analysis.DiffractionAnalysis), [1] (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method), [1] plotResolutionRings() (in module SimEx.Analysis.DiffractionAnalysis), [1]

plotTargetAndTransmission() (in module SimEx.Utilities.RadHydroInputPlots), [1] plotTotalPower() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis method), [1] plotTransmission() (in module SimEx.Utilities.RadHydroInputPlots), [1] pmi_start_ID() (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1] pmi_stop_ID() (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1] point_simulation_method() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property), [1] poissonize() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property), [1] (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] potentials() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property), [1] powder() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] prepareMPICommandArguments() (in module SimEx.Utilities.ParallelUtilities), [1] propToBeamParameters() (in module SimEx.Parameters.PhotonBeamParameters), [1] providedData() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator method), [1] (SimEx.Calculators.AbstractPhotonPropagator.AbstractPhotonPropagator method), [1] (SimEx.Calculators.AbstractPhotonSource.AbstractPhotonSource method), [1] (SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator method), [1] (SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method), [1] (SimEx.Calculators.DMPhasing.DMPhasing method), [1] (SimEx.Calculators.EMCOrientation.EMCOrientation method), [1] (SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor method), [1] (SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor method), [1] (SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector method), [1] (SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator method), [1] (SimEx.Calculators.S2EReconstruction.S2EReconstruction method), [1] (SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor method), [1] (SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method), [1] (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor method), [1] (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method), [1] pulse_energy() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property), [1]

R

radHydroAnalysis() (in module SimEx.Utilities.RadHydroAnalysis), [1] read_h5_dataset() (in module SimEx.Analysis.XMDYNPhotonMatterAnalysis), [1] readGeomFromDetectorFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] readGeomFromPhotonData() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1]

root_path() (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor property), [1] rotation() (SimEx.Parameters.PhotonMatterInteractorParameters.PhotonMatterInteractorParameters property), [1] run_time() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] runFromCLI() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator class method), [1]

S

S2EReconstruction (class in SimEx.Calculators.S2EReconstruction), [1] sample() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1] sample_path() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis property), [1] (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor property), [1] sample_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] saveH5() (SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator method), [1] (SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method), [1] (SimEx.Calculators.DMPhasing.DMPhasing method), [1] (SimEx.Calculators.EMCOrientation.EMCOrientation method), [1] (SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor method), [1] (SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor method), [1] (SimEx.Calculators.GenesisPhotonSource.GenesisPhotonSource method), [1] (SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector method), [1] (SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator method), [1] (SimEx.Calculators.S2EReconstruction.S2EReconstruction method), [1] (SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor method), [1] (SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method), [1] (SimEx.Calculators.XFELPhotonPropagator.XFELPhotonPropagator method), [1] (SimEx.Calculators.XFELPhotonSource.XFELPhotonSource method), [1] (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor method), [1] (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method), [1] Sbf_norm() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] scattering_angle() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] serialize() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters method), [1] setup_base_path() (in module SimEx.Utilities.OpenPMDTools), [1] setup_hierarchy() (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method), [1] setup_root_attr() (in module SimEx.Utilities.OpenPMDTools), [1] showDensity() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] showDetector() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] showLogIntensity() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] showLogIntensitySlices() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] SimEx.Analysis.DiffractionAnalysis (module), [1] SimEx.Analysis.XFELPhotonAnalysis (module), [1] SimEx.Analysis.XMDYNPhotonMatterAnalysis (module), [1] SimEx.Calculators.AbstractBaseCalculator (module), [1] SimEx.Calculators.AbstractPhotonAnalyzer (module), [1] SimEx.Calculators.AbstractPhotonDetector (module), [1] SimEx.Calculators.AbstractPhotonDiffractor (module), [1] SimEx.Calculators.AbstractPhotonInteractor (module), [1] SimEx.Calculators.AbstractPhotonPropagator (module), [1] SimEx.Calculators.AbstractPhotonSource (module), [1]

SimEx.Calculators.ComptonScatteringCalculator (module), [1] SimEx.Calculators.CrystFELPhotonDiffractor (module), [1] SimEx.Calculators.DMPhasing (module), [1] SimEx.Calculators.EMCCaseGenerator (module), [1] SimEx.Calculators.EMCOrientation (module), [1] SimEx.Calculators.EstherPhotonMatterInteractor (module), [1] SimEx.Calculators.FEFFPhotonMatterInteractor (module), [1] SimEx.Calculators.GenesisPhotonSource (module), [1] SimEx.Calculators.IdealPhotonDetector (module), [1] SimEx.Calculators.PlasmaXRTSCalculator (module), [1] SimEx.Calculators.S2EReconstruction (module), [1] SimEx.Calculators.SingFELPhotonDiffractor (module), [1] SimEx.Calculators.XCSITPhotonDetector (module), [1] SimEx.Calculators.XFELPhotonPropagator (module), [1] SimEx.Calculators.XFELPhotonSource (module), [1] SimEx.Calculators.XMDYNDemoPhotonMatterInteractor (module), [1] SimEx.Calculators.XMDYNPhotonMatterInteractor (module), [1] SimEx.Parameters.CrystFELPhotonDiffractorParameters (module), [1] SimEx.Parameters.DMPhasingParameters (module), [1] SimEx.Parameters.EMCOrientationParameters (module), [1] SimEx.Parameters.EstherPhotonMatterInteractorParameters (module), [1] SimEx.Parameters.FEFFPhotonMatterInteractorParameters (module), [1] SimEx.Parameters.PhotonBeamParameters (module), [1] SimEx.Parameters.PhotonMatterInteractorParameters (module), [1] SimEx.Parameters.PlasmaXRTSCalculatorParameters (module), [1] SimEx.Parameters.SingFELPhotonDiffractorParameters (module), [1] SimEx.Parameters.WavePropagatorParameters (module), [1] SimEx.Parameters.XCSITPhotonDetectorParameters (module), [1] SimEx.PhotonExperimentSimulation.EstherExperiment (module), [1] SimEx.Utilities.IOUtilities (module), [1] SimEx.Utilities.OpenPMDTools (module), [1] SimEx.Utilities.ParallelUtilities (module), [1] SimEx.Utilities.RadHydroAnalysis (module), [1] SimEx.Utilities.RadHydroInputPlots (module), [1] SimEx.Utilities.Utilities (module), [1] SingFELPhotonDiffractor (class in SimEx.Calculators.SingFELPhotonDiffractor), [1] SingFELPhotonDiffractorParameters (class in SimEx.Parameters.SingFELPhotonDiffractorParameters), [1] slice_interval() (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1] snapshot_indices() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis property), [1] source_spectrum() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] source_spectrum_fwhm() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property), [1] static_data() (SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator property), [1] statistics() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method), [1] suppress_fringes() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1]

U

uniform_rotation() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property), [1] (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property), [1]

use_opmd() (SimEx.Parameters.WavePropagatorParameters.WavePropagatorParameters property), [1]

W

wavefront() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis property), [1] WavePropagatorParameters (class in SimEx.Parameters.WavePropagatorParameters), [1] wgetData() (in module SimEx.Utilities.IOUtilities), [1] window() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1] window_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property), [1]

working_directory() (SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor property), [1] writeAllOuputToFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] writeDensityToFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] writeDetectorToFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] writeSparsePhotonFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1] writeSupportToFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method), [1]

X

XCSITPhotonDetector (class in SimEx.Calculators.XCSITPhotonDetector), [1] XCSITPhotonDetectorParameters (class in SimEx.Parameters.XCSITPhotonDetectorParameters), [1] XFELPhotonAnalysis (class in SimEx.Analysis.XFELPhotonAnalysis), [1] XFELPhotonPropagator (class in SimEx.Calculators.XFELPhotonPropagator), [1]

XFELPhotonSource (class in SimEx.Calculators.XFELPhotonSource), [1] XMDYNDemoPhotonMatterInteractor (class in SimEx.Calculators.XMDYNDemoPhotonMatterInteractor), [1] XMDYNPhotonMatterAnalysis (class in SimEx.Analysis.XMDYNPhotonMatterAnalysis), [1] XMDYNPhotonMatterInteractor (class in SimEx.Calculators.XMDYNPhotonMatterInteractor), [1]