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I
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Z
A
ablator() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
ablator_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
AbstractAnalysis (class in SimEx.Analysis.AbstractAnalysis)
AbstractBaseCalculator (class in SimEx.Calculators.AbstractBaseCalculator)
AbstractCalculatorParameters (class in SimEx.Parameters.AbstractCalculatorParameters)
AbstractPhotonAnalyzer (class in SimEx.Calculators.AbstractPhotonAnalyzer)
AbstractPhotonDetector (class in SimEx.Calculators.AbstractPhotonDetector)
AbstractPhotonDiffractor (class in SimEx.Calculators.AbstractPhotonDiffractor)
AbstractPhotonDiffractorParameters (class in SimEx.Parameters.AbstractPhotonDiffractorParameters)
AbstractPhotonInteractor (class in SimEx.Calculators.AbstractPhotonInteractor)
AbstractPhotonPropagator (class in SimEx.Calculators.AbstractPhotonPropagator)
AbstractPhotonSource (class in SimEx.Calculators.AbstractPhotonSource)
amplitude_reduction_factor() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property)
animate() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis method)
(SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method)
animatePatterns() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method)
atoms() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property)
averaging_start() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property)
azimuthalIntegration() (in module SimEx.Analysis.DiffractionAnalysis)
B
backengine() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator method)
(SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator method)
(SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method)
(SimEx.Calculators.DMPhasing.DMPhasing method)
(SimEx.Calculators.EMCOrientation.EMCOrientation method)
(SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor method)
(SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor method)
(SimEx.Calculators.GenesisPhotonSource.GenesisPhotonSource method)
(SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector method)
(SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator method)
(SimEx.Calculators.S2EReconstruction.S2EReconstruction method)
(SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor method)
(SimEx.Calculators.WavePropagator.WavePropagator method)
(SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method)
(SimEx.Calculators.XFELPhotonSource.XFELPhotonSource method)
(SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor method)
(SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method)
bad_bit_mask() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
badregion_flag() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
band_gap() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
beam_diameter_fwhm() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property)
beam_parameters() (SimEx.Parameters.AbstractPhotonDiffractorParameters.AbstractPhotonDiffractorParameters property)
(SimEx.Parameters.PhotonMatterInteractorParameters.PhotonMatterInteractorParameters property)
beamline() (SimEx.Parameters.WavePropagatorParameters.WavePropagatorParameters property)
beamstop() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property)
C
calculate_Compton() (SimEx.Parameters.PhotonMatterInteractorParameters.PhotonMatterInteractorParameters property)
(SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property)
calculate_displacement() (in module SimEx.Analysis.XMDYNPhotonMatterAnalysis)
calculate_fwhm() (in module SimEx.Analysis.XFELPhotonAnalysis)
calculate_ion_charge() (in module SimEx.Analysis.XMDYNPhotonMatterAnalysis)
checkAndSetAblator() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetAblatorThickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetBandGap() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetBaseCalculator() (in module SimEx.Analysis.AbstractAnalysis)
(in module SimEx.Calculators.AbstractBaseCalculator)
checkAndSetDebyeTemperature() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetDeltaTime() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetDensitiesAndCharge() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetElectronTemperature() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetElements() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetEnergyRange() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetIO() (in module SimEx.Calculators.AbstractBaseCalculator)
checkAndSetIonTemperature() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetLaserIntensity() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetLaserPulse() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetLaserPulseDuration() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetLaserWavelength() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetLayer1() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetLayer1Thickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetLayer2() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetLayer2Thickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetLFC() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetModelIPL() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetModelMix() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetModelSbf() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetModelSee() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetModelSii() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetNumberOfLayers() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetParameters() (in module SimEx.Calculators.AbstractBaseCalculator)
(in module SimEx.Calculators.ComptonScatteringCalculator)
(in module SimEx.Calculators.PlasmaXRTSCalculator)
checkAndSetPhotonAnalyzer() (in module SimEx.Calculators.AbstractPhotonAnalyzer)
checkAndSetPhotonDetector() (in module SimEx.Calculators.AbstractPhotonDetector)
checkAndSetPhotonDiffractor() (in module SimEx.Calculators.AbstractPhotonDiffractor)
checkAndSetPhotonEnergy() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetPhotonInteractor() (in module SimEx.Calculators.AbstractPhotonInteractor)
checkAndSetPhotonPropagator() (in module SimEx.Calculators.AbstractPhotonPropagator)
checkAndSetPhotonSource() (in module SimEx.Calculators.AbstractPhotonSource)
checkAndSetRunTime() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetSample() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetSampleThickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetSbfNorm() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetScatteringAngle() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetSourceSpectrum() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetSourceSpectrumFWHM() (in module SimEx.Parameters.PlasmaXRTSCalculatorParameters)
checkAndSetWindow() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkAndSetWindowThickness() (in module SimEx.Parameters.EstherPhotonMatterInteractorParameters)
checkConsistency() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters method)
cluster_two_means() (in module SimEx.Calculators.EMCCaseGenerator)
ComptonScatteringCalculator (class in SimEx.Calculators.ComptonScatteringCalculator)
computeNTasks() (SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method)
(SimEx.Calculators.EMCOrientation.EMCOrientation method)
(SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor method)
(SimEx.Calculators.WavePropagator.WavePropagator method)
corners() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
cpus_per_task() (SimEx.Parameters.AbstractCalculatorParameters.AbstractCalculatorParameters property)
createTestScatteringGeometry() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
crystal_size_max() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property)
crystal_size_min() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property)
CrystFELPhotonDiffractor (class in SimEx.Calculators.CrystFELPhotonDiffractor)
CrystFELPhotonDiffractorParameters (class in SimEx.Parameters.CrystFELPhotonDiffractorParameters)
D
data() (SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator property)
(SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor property)
(SimEx.Calculators.DMPhasing.DMPhasing property)
(SimEx.Calculators.EMCOrientation.EMCOrientation property)
(SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor property)
(SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor property)
(SimEx.Calculators.GenesisPhotonSource.GenesisPhotonSource property)
(SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector property)
(SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator property)
(SimEx.Calculators.S2EReconstruction.S2EReconstruction property)
(SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor property)
(SimEx.Calculators.WavePropagator.WavePropagator property)
(SimEx.Calculators.XFELPhotonSource.XFELPhotonSource property)
(SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor property)
(SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor property)
debye_temperature() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
delta_time() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
detailed_output() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property)
detector_geometry() (SimEx.Parameters.AbstractPhotonDiffractorParameters.AbstractPhotonDiffractorParameters property)
detector_type() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property)
DetectorGeometry (class in SimEx.Parameters.DetectorGeometry)
detectorGeometryFromFile() (in module SimEx.Parameters.DetectorGeometry)
DetectorPanel (class in SimEx.Parameters.DetectorGeometry)
DiffractionAnalysis (class in SimEx.Analysis.DiffractionAnalysis)
diffractionParameters() (in module SimEx.Analysis.DiffractionAnalysis)
diffractTestCase() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
distance_from_interaction_plane() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
distance_offset() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
divergence() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property)
DMPhasing (class in SimEx.Calculators.DMPhasing)
DMPhasingParameters (class in SimEx.Parameters.DMPhasingParameters)
dumpLoader() (SimEx.Analysis.AbstractAnalysis.AbstractAnalysis class method)
(SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator class method)
dumpToFile() (SimEx.Analysis.AbstractAnalysis.AbstractAnalysis method)
(SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator method)
E
edge() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property)
effective_path_distance() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property)
electron_density() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
electron_temperature() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
elements() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis property)
(SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
EMCCaseGenerator (class in SimEx.Calculators.EMCCaseGenerator)
EMCOrientation (class in SimEx.Calculators.EMCOrientation)
EMCOrientationParameters (class in SimEx.Parameters.EMCOrientationParameters)
energy_range() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
energy_response() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
EstherPhotonMatterInteractor (class in SimEx.Calculators.EstherPhotonMatterInteractor)
EstherPhotonMatterInteractorParameters (class in SimEx.Parameters.EstherPhotonMatterInteractorParameters)
expectedData() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator method)
(SimEx.Calculators.AbstractPhotonPropagator.AbstractPhotonPropagator method)
(SimEx.Calculators.AbstractPhotonSource.AbstractPhotonSource method)
(SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator method)
(SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method)
(SimEx.Calculators.DMPhasing.DMPhasing method)
(SimEx.Calculators.EMCOrientation.EMCOrientation method)
(SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor method)
(SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor method)
(SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector method)
(SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator method)
(SimEx.Calculators.S2EReconstruction.S2EReconstruction method)
(SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor method)
(SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method)
(SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor method)
(SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method)
extractDate() (in module SimEx.Calculators.PlasmaXRTSCalculator)
F
f_dbase_setup() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_dbase_Zq2id() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_eval_disp() (in module SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
f_eval_numE() (in module SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
f_h5_out2in() (in module SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
f_hdf5_simple_read() (in module SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
f_init_random() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_load_pulse() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_load_sample() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_load_snp_content() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_load_snp_from_dir() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_load_snp_xxx() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_md_step() (in module SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
f_num_snp_xxx() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_pmi_diagnostics_help() (in module SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
f_rotate_sample() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_s2e_setup() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_save_data() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_save_info() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_save_snp() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_system_setup() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
f_time_evolution() (SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.PMIDemo method)
fast_scan_xyz() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
FEFFPhotonMatterInteractor (class in SimEx.Calculators.FEFFPhotonMatterInteractor)
FEFFPhotonMatterInteractorParameters (class in SimEx.Parameters.FEFFPhotonMatterInteractorParameters)
fermihalf() (in module SimEx.Calculators.ComptonScatteringCalculator)
finalize() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters method)
finalized() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property)
find_two_means() (in module SimEx.Calculators.EMCCaseGenerator)
forced_mpi_command() (SimEx.Parameters.AbstractCalculatorParameters.AbstractCalculatorParameters property)
G
GenesisPhotonSource (class in SimEx.Calculators.GenesisPhotonSource)
getChargeData() (SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method)
getInteractionData() (SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method)
getPhotonData() (SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method)
good_bit_mask() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
gpus_per_task() (SimEx.Parameters.AbstractCalculatorParameters.AbstractCalculatorParameters property)
H
h5_out2in() (in module SimEx.Calculators.XMDYNPhotonMatterInteractor)
I
IdealPhotonDetector (class in SimEx.Calculators.IdealPhotonDetector)
initial_number_of_quaternions() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property)
input_path() (SimEx.Analysis.AbstractAnalysis.AbstractAnalysis property)
(SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis property)
(SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator property)
(SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector property)
intensities_file() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property)
intensity() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis property)
ion_charge() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
ion_temperature() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
L
laser_intensity() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
laser_pulse() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
laser_pulse_duration() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
laser_wavelength() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
layer1() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
layer1_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
layer2() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
layer2_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
leash() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property)
lfc() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
load_ff_database() (in module SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
load_intensities() (in module SimEx.Calculators.EMCCaseGenerator)
load_sample() (in module SimEx.Analysis.XMDYNPhotonMatterAnalysis)
load_snapshot() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method)
load_snp_from_dir() (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method)
load_trajectory() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method)
M
makeTestParticleAndSupport() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
mask() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property)
(SimEx.Parameters.DetectorGeometry.DetectorPanel property)
mask_nans() (in module SimEx.Analysis.XFELPhotonAnalysis)
mass_density() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
max_number_of_iterations() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property)
max_number_of_quaternions() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property)
min_error() (SimEx.Parameters.EMCOrientationParameters.EMCOrientationParameters property)
model_IPL() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
model_Mix() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
model_Sbf() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
model_See() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
model_Sii() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
module
SimEx.Analysis.AbstractAnalysis
SimEx.Analysis.DiffractionAnalysis
SimEx.Analysis.XFELPhotonAnalysis
SimEx.Analysis.XMDYNPhotonMatterAnalysis
SimEx.Calculators.AbstractBaseCalculator
SimEx.Calculators.AbstractPhotonAnalyzer
SimEx.Calculators.AbstractPhotonDetector
SimEx.Calculators.AbstractPhotonDiffractor
SimEx.Calculators.AbstractPhotonInteractor
SimEx.Calculators.AbstractPhotonPropagator
SimEx.Calculators.AbstractPhotonSource
SimEx.Calculators.ComptonScatteringCalculator
SimEx.Calculators.CrystFELPhotonDiffractor
SimEx.Calculators.DMPhasing
SimEx.Calculators.EMCCaseGenerator
SimEx.Calculators.EMCOrientation
SimEx.Calculators.EstherPhotonMatterInteractor
SimEx.Calculators.FEFFPhotonMatterInteractor
SimEx.Calculators.GenesisPhotonSource
SimEx.Calculators.IdealPhotonDetector
SimEx.Calculators.PlasmaXRTSCalculator
SimEx.Calculators.S2EReconstruction
SimEx.Calculators.SingFELPhotonDiffractor
SimEx.Calculators.WavePropagator
SimEx.Calculators.XCSITPhotonDetector
SimEx.Calculators.XFELPhotonSource
SimEx.Calculators.XMDYNDemoPhotonMatterInteractor
SimEx.Calculators.XMDYNPhotonMatterInteractor
SimEx.Parameters.AbstractCalculatorParameters
SimEx.Parameters.AbstractPhotonDiffractorParameters
SimEx.Parameters.CrystFELPhotonDiffractorParameters
SimEx.Parameters.DetectorGeometry
SimEx.Parameters.DMPhasingParameters
SimEx.Parameters.EMCOrientationParameters
SimEx.Parameters.EstherPhotonMatterInteractorParameters
SimEx.Parameters.FEFFPhotonMatterInteractorParameters
SimEx.Parameters.PhotonBeamParameters
SimEx.Parameters.PhotonMatterInteractorParameters
SimEx.Parameters.PlasmaXRTSCalculatorParameters
SimEx.Parameters.SingFELPhotonDiffractorParameters
SimEx.Parameters.WavePropagatorParameters
SimEx.Parameters.XCSITPhotonDetectorParameters
N
nodes_per_task() (SimEx.Parameters.AbstractCalculatorParameters.AbstractCalculatorParameters property)
npattern() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property)
number_of_background_photons() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property)
number_of_diffraction_patterns() (SimEx.Parameters.AbstractPhotonDiffractorParameters.AbstractPhotonDiffractorParameters property)
number_of_iterations() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property)
number_of_layers() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
number_of_shrink_cycles() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property)
number_of_slices() (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property)
number_of_snapshots() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method)
number_of_trajectories() (SimEx.Parameters.PhotonMatterInteractorParameters.PhotonMatterInteractorParameters property)
number_of_trials() (SimEx.Parameters.DMPhasingParameters.DMPhasingParameters property)
numpyPattern() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method)
numpyTotalPower() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis method)
O
output_path() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator property)
(SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector property)
P
panels() (SimEx.Parameters.DetectorGeometry.DetectorGeometry property)
parameters() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property)
(SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator property)
(SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor property)
path_to_executable() (SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor property)
pattern_indices() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property)
patternGenerator() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method)
patterns() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property)
patterns_iterator() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property)
photon_energy() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property)
(SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
photon_energy_relative_bandwidth() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property)
photon_energy_spectrum_type() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property)
photon_response() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
PhotonBeamParameters (class in SimEx.Parameters.PhotonBeamParameters)
PhotonMatterInteractorParameters (class in SimEx.Parameters.PhotonMatterInteractorParameters)
photonStatistics() (in module SimEx.Analysis.DiffractionAnalysis)
pixel_size() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
placePixel() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
plasma_search_flag() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property)
plasma_simulation_flag() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property)
PlasmaXRTSCalculator (class in SimEx.Calculators.PlasmaXRTSCalculator)
PlasmaXRTSCalculatorParameters (class in SimEx.Parameters.PlasmaXRTSCalculatorParameters)
plot_charge() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method)
plot_displacement() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method)
plot_energies() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis method)
plotImage() (in module SimEx.Analysis.DiffractionAnalysis)
plotIntensityMap() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis method)
plotOnAxisPowerDensity() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis method)
plotPattern() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method)
plotRadialProjection() (in module SimEx.Analysis.DiffractionAnalysis)
(SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method)
plotResolutionRings() (in module SimEx.Analysis.DiffractionAnalysis)
plotTotalPower() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis method)
pmi_start_ID() (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property)
pmi_stop_ID() (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property)
PMIDemo (class in SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
point_simulation_method() (SimEx.Parameters.XCSITPhotonDetectorParameters.XCSITPhotonDetectorParameters property)
poissonize() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property)
(SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property)
potentials() (SimEx.Parameters.FEFFPhotonMatterInteractorParameters.FEFFPhotonMatterInteractorParameters property)
powder() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property)
propToBeamParameters() (in module SimEx.Parameters.PhotonBeamParameters)
providedData() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator method)
(SimEx.Calculators.AbstractPhotonPropagator.AbstractPhotonPropagator method)
(SimEx.Calculators.AbstractPhotonSource.AbstractPhotonSource method)
(SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator method)
(SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method)
(SimEx.Calculators.DMPhasing.DMPhasing method)
(SimEx.Calculators.EMCOrientation.EMCOrientation method)
(SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor method)
(SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor method)
(SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector method)
(SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator method)
(SimEx.Calculators.S2EReconstruction.S2EReconstruction method)
(SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor method)
(SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method)
(SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor method)
(SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method)
pulse_energy() (SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters property)
Q
qMap() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property)
R
ranges() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
read_h5_dataset() (in module SimEx.Analysis.XMDYNPhotonMatterAnalysis)
readGeomFromDetectorFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
readGeomFromPhotonData() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
root_path() (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor property)
rotation() (SimEx.Parameters.PhotonMatterInteractorParameters.PhotonMatterInteractorParameters property)
run_files_path() (SimEx.Calculators.EMCOrientation.EMCOrientation property)
run_time() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
runFromCLI() (SimEx.Analysis.AbstractAnalysis.AbstractAnalysis class method)
(SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator class method)
S
s2e_gen_randrot_quat() (in module SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
s2e_rand_orient() (in module SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
S2EReconstruction (class in SimEx.Calculators.S2EReconstruction)
sample() (SimEx.Parameters.AbstractPhotonDiffractorParameters.AbstractPhotonDiffractorParameters property)
(SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
sample_path() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis property)
(SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor property)
sample_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
saturation_adu() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
saturation_map() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
saveH5() (SimEx.Calculators.AbstractBaseCalculator.AbstractBaseCalculator method)
(SimEx.Calculators.ComptonScatteringCalculator.ComptonScatteringCalculator method)
(SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method)
(SimEx.Calculators.DMPhasing.DMPhasing method)
(SimEx.Calculators.EMCOrientation.EMCOrientation method)
(SimEx.Calculators.EstherPhotonMatterInteractor.EstherPhotonMatterInteractor method)
(SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor method)
(SimEx.Calculators.GenesisPhotonSource.GenesisPhotonSource method)
(SimEx.Calculators.IdealPhotonDetector.IdealPhotonDetector method)
(SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator method)
(SimEx.Calculators.S2EReconstruction.S2EReconstruction method)
(SimEx.Calculators.SingFELPhotonDiffractor.SingFELPhotonDiffractor method)
(SimEx.Calculators.WavePropagator.WavePropagator method)
(SimEx.Calculators.XCSITPhotonDetector.XCSITPhotonDetector method)
(SimEx.Calculators.XFELPhotonSource.XFELPhotonSource method)
(SimEx.Calculators.XMDYNDemoPhotonMatterInteractor.XMDYNDemoPhotonMatterInteractor method)
(SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method)
saveH5_geom() (SimEx.Calculators.CrystFELPhotonDiffractor.CrystFELPhotonDiffractor method)
Sbf_norm() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
scattering_angle() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
serialize() (SimEx.Parameters.DetectorGeometry.DetectorGeometry method)
(SimEx.Parameters.PhotonBeamParameters.PhotonBeamParameters method)
setup_hierarchy() (SimEx.Calculators.XMDYNPhotonMatterInteractor.XMDYNPhotonMatterInteractor method)
shannonPixelPhoton() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method)
show_support() (in module SimEx.Calculators.DMPhasing)
showDensity() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
showDetector() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
showLogIntensity() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
showLogIntensitySlices() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
SimEx.Analysis.AbstractAnalysis
module
SimEx.Analysis.DiffractionAnalysis
module
SimEx.Analysis.XFELPhotonAnalysis
module
SimEx.Analysis.XMDYNPhotonMatterAnalysis
module
SimEx.Calculators.AbstractBaseCalculator
module
SimEx.Calculators.AbstractPhotonAnalyzer
module
SimEx.Calculators.AbstractPhotonDetector
module
SimEx.Calculators.AbstractPhotonDiffractor
module
SimEx.Calculators.AbstractPhotonInteractor
module
SimEx.Calculators.AbstractPhotonPropagator
module
SimEx.Calculators.AbstractPhotonSource
module
SimEx.Calculators.ComptonScatteringCalculator
module
SimEx.Calculators.CrystFELPhotonDiffractor
module
SimEx.Calculators.DMPhasing
module
SimEx.Calculators.EMCCaseGenerator
module
SimEx.Calculators.EMCOrientation
module
SimEx.Calculators.EstherPhotonMatterInteractor
module
SimEx.Calculators.FEFFPhotonMatterInteractor
module
SimEx.Calculators.GenesisPhotonSource
module
SimEx.Calculators.IdealPhotonDetector
module
SimEx.Calculators.PlasmaXRTSCalculator
module
SimEx.Calculators.S2EReconstruction
module
SimEx.Calculators.SingFELPhotonDiffractor
module
SimEx.Calculators.WavePropagator
module
SimEx.Calculators.XCSITPhotonDetector
module
SimEx.Calculators.XFELPhotonSource
module
SimEx.Calculators.XMDYNDemoPhotonMatterInteractor
module
SimEx.Calculators.XMDYNPhotonMatterInteractor
module
SimEx.Parameters.AbstractCalculatorParameters
module
SimEx.Parameters.AbstractPhotonDiffractorParameters
module
SimEx.Parameters.CrystFELPhotonDiffractorParameters
module
SimEx.Parameters.DetectorGeometry
module
SimEx.Parameters.DMPhasingParameters
module
SimEx.Parameters.EMCOrientationParameters
module
SimEx.Parameters.EstherPhotonMatterInteractorParameters
module
SimEx.Parameters.FEFFPhotonMatterInteractorParameters
module
SimEx.Parameters.PhotonBeamParameters
module
SimEx.Parameters.PhotonMatterInteractorParameters
module
SimEx.Parameters.PlasmaXRTSCalculatorParameters
module
SimEx.Parameters.SingFELPhotonDiffractorParameters
module
SimEx.Parameters.WavePropagatorParameters
module
SimEx.Parameters.XCSITPhotonDetectorParameters
module
SingFELPhotonDiffractor (class in SimEx.Calculators.SingFELPhotonDiffractor)
SingFELPhotonDiffractorParameters (class in SimEx.Parameters.SingFELPhotonDiffractorParameters)
slice_interval() (SimEx.Parameters.SingFELPhotonDiffractorParameters.SingFELPhotonDiffractorParameters property)
slow_scan_xyz() (SimEx.Parameters.DetectorGeometry.DetectorPanel property)
snapshot_indices() (SimEx.Analysis.XMDYNPhotonMatterAnalysis.XMDYNPhotonMatterAnalysis property)
solidAngles() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis property)
source_spectrum() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
source_spectrum_fwhm() (SimEx.Parameters.PlasmaXRTSCalculatorParameters.PlasmaXRTSCalculatorParameters property)
static_data() (SimEx.Calculators.PlasmaXRTSCalculator.PlasmaXRTSCalculator property)
statistics() (SimEx.Analysis.DiffractionAnalysis.DiffractionAnalysis method)
support_from_autocorr() (in module SimEx.Calculators.EMCCaseGenerator)
suppress_fringes() (SimEx.Parameters.CrystFELPhotonDiffractorParameters.CrystFELPhotonDiffractorParameters property)
T
tmp_files_path() (SimEx.Calculators.EMCOrientation.EMCOrientation property)
totalNPattern() (in module SimEx.Analysis.DiffractionAnalysis)
U
uniform_rotation() (SimEx.Parameters.AbstractPhotonDiffractorParameters.AbstractPhotonDiffractorParameters property)
use_opmd() (SimEx.Parameters.WavePropagatorParameters.WavePropagatorParameters property)
W
wavefront() (SimEx.Analysis.XFELPhotonAnalysis.XFELPhotonAnalysis property)
WavePropagator (class in SimEx.Calculators.WavePropagator)
WavePropagatorParameters (class in SimEx.Parameters.WavePropagatorParameters)
window() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
window_thickness() (SimEx.Parameters.EstherPhotonMatterInteractorParameters.EstherPhotonMatterInteractorParameters property)
working_directory() (SimEx.Calculators.FEFFPhotonMatterInteractor.FEFFPhotonMatterInteractor property)
writeAllOuputToFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
writeDensityToFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
writeDetectorToFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
writeSparsePhotonFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
writeSupportToFile() (SimEx.Calculators.EMCCaseGenerator.EMCCaseGenerator method)
X
XCSITPhotonDetector (class in SimEx.Calculators.XCSITPhotonDetector)
XCSITPhotonDetectorParameters (class in SimEx.Parameters.XCSITPhotonDetectorParameters)
XFELPhotonAnalysis (class in SimEx.Analysis.XFELPhotonAnalysis)
XFELPhotonSource (class in SimEx.Calculators.XFELPhotonSource)
XMDYNDemoPhotonMatterInteractor (class in SimEx.Calculators.XMDYNDemoPhotonMatterInteractor)
XMDYNPhotonMatterAnalysis (class in SimEx.Analysis.XMDYNPhotonMatterAnalysis)
XMDYNPhotonMatterInteractor (class in SimEx.Calculators.XMDYNPhotonMatterInteractor)
Z
zero_neg() (in module SimEx.Calculators.EMCCaseGenerator)
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