Prismatique

prismatique is a Python library that functions essentially as a wrapper to the Python library pyprismatic, which itself is a thin wrapper to prismatic, a CUDA/C++ package for fast image simulations in scanning transmission electron microscopy and high-resolution transmission electron microscopy. You can find more information about pyprismatic and prismatic here.

The source code can be found in the prismatique GitHub repository.

Instructions for installing and uninstalling prismatique

For instructions on installing the prismatique library, see the Instructions for installing and uninstalling prismatique page.

Learning how to use prismatique

For those new to the prismatique library, it is recommended that they take a look at the Examples page, which contain code examples that show how one can use the prismatique library. While going through the examples, readers can consult the prismatique reference guide to understand what each line of code is doing.

Contents

• Home
• 1. Instructions for installing and uninstalling prismatique
  • 1.1. Installing prismatique
    • 1.1.1. Installing prismatique using pip and conda together
  • 1.2. Uninstalling prismatique
• 2. Reference
  • 2.1. prismatique.aperture
    • 2.1.1. prismatique.aperture.Params
      • Params
        • Params.core_attrs
        • Params.de_pre_serialization_funcs
        • Params.de_pre_serialize()
        • Params.dump()
        • Params.dumps()
        • Params.get_core_attrs()
        • Params.get_de_pre_serialization_funcs()
        • Params.get_pre_serialization_funcs()
        • Params.get_validation_and_conversion_funcs()
        • Params.load()
        • Params.loads()
        • Params.pre_serialization_funcs
        • Params.pre_serialize()
        • Params.update()
        • Params.validation_and_conversion_funcs
  • 2.2. prismatique.cbed
    • 2.2.1. prismatique.cbed.blank_unprocessed_pattern_signal
      • blank_unprocessed_pattern_signal()
    • 2.2.2. prismatique.cbed.Params
      • Params
        • Params.core_attrs
        • Params.de_pre_serialization_funcs
        • Params.de_pre_serialize()
        • Params.dump()
        • Params.dumps()
        • Params.get_core_attrs()
        • Params.get_de_pre_serialization_funcs()
        • Params.get_pre_serialization_funcs()
        • Params.get_validation_and_conversion_funcs()
        • Params.load()
        • Params.loads()
        • Params.pre_serialization_funcs
        • Params.pre_serialize()
        • Params.update()
        • Params.validation_and_conversion_funcs
  • 2.3. prismatique.discretization
    • 2.3.1. prismatique.discretization.Params
      • Params
        • Params.core_attrs
        • Params.de_pre_serialization_funcs
        • Params.de_pre_serialize()
        • Params.dump()
        • Params.dumps()
        • Params.get_core_attrs()
        • Params.get_de_pre_serialization_funcs()
        • Params.get_pre_serialization_funcs()
        • Params.get_validation_and_conversion_funcs()
        • Params.load()
        • Params.loads()
        • Params.pre_serialization_funcs
        • Params.pre_serialize()
        • Params.update()
        • Params.validation_and_conversion_funcs
  • 2.4. prismatique.hrtem
    • 2.4.1. prismatique.hrtem.image
      • 2.4.1.1. prismatique.hrtem.image.blank_unprocessed_image_signal
        • blank_unprocessed_image_signal()
      • 2.4.1.2. prismatique.hrtem.image.Params
        • Params
          • Params.core_attrs
          • Params.de_pre_serialization_funcs
          • Params.de_pre_serialize()
          • Params.dump()
          • Params.dumps()
          • Params.get_core_attrs()
          • Params.get_de_pre_serialization_funcs()
          • Params.get_pre_serialization_funcs()
          • Params.get_validation_and_conversion_funcs()
          • Params.load()
          • Params.loads()
          • Params.pre_serialization_funcs
          • Params.pre_serialize()
          • Params.update()
          • Params.validation_and_conversion_funcs
    • 2.4.2. prismatique.hrtem.output
      • 2.4.2.1. prismatique.hrtem.output.data_size
        • data_size()
      • 2.4.2.2. prismatique.hrtem.output.Params
        • Params
          • Params.core_attrs
          • Params.de_pre_serialization_funcs
          • Params.de_pre_serialize()
          • Params.dump()
          • Params.dumps()
          • Params.get_core_attrs()
          • Params.get_de_pre_serialization_funcs()
          • Params.get_pre_serialization_funcs()
          • Params.get_validation_and_conversion_funcs()
          • Params.load()
          • Params.loads()
          • Params.pre_serialization_funcs
          • Params.pre_serialize()
          • Params.update()
          • Params.validation_and_conversion_funcs
    • 2.4.3. prismatique.hrtem.sim
      • 2.4.3.1. prismatique.hrtem.sim.run
        • run()
      • 2.4.3.2. prismatique.hrtem.sim.Params
        • Params
          • Params.core_attrs
          • Params.de_pre_serialization_funcs
          • Params.de_pre_serialize()
          • Params.dump()
          • Params.dumps()
          • Params.get_core_attrs()
          • Params.get_de_pre_serialization_funcs()
          • Params.get_pre_serialization_funcs()
          • Params.get_validation_and_conversion_funcs()
          • Params.load()
          • Params.loads()
          • Params.pre_serialization_funcs
          • Params.pre_serialize()
          • Params.update()
          • Params.validation_and_conversion_funcs
    • 2.4.4. prismatique.hrtem.system
      • 2.4.4.1. prismatique.hrtem.system.ModelParams
        • ModelParams
          • ModelParams.core_attrs
          • ModelParams.de_pre_serialization_funcs
          • ModelParams.de_pre_serialize()
          • ModelParams.dump()
          • ModelParams.dumps()
          • ModelParams.get_core_attrs()
          • ModelParams.get_de_pre_serialization_funcs()
          • ModelParams.get_pre_serialization_funcs()
          • ModelParams.get_validation_and_conversion_funcs()
          • ModelParams.load()
          • ModelParams.loads()
          • ModelParams.pre_serialization_funcs
          • ModelParams.pre_serialize()
          • ModelParams.update()
          • ModelParams.validation_and_conversion_funcs
  • 2.5. prismatique.load
    • 2.5.1. prismatique.load.S_matrix_k_xy_vectors
      • S_matrix_k_xy_vectors()
    • 2.5.2. prismatique.load.S_matrix_wavefunctions
      • S_matrix_wavefunctions()
    • 2.5.3. prismatique.load.azimuthally_integrated_cbed_intensity_patterns
      • azimuthally_integrated_cbed_intensity_patterns()
    • 2.5.4. prismatique.load.cbed_intensity_patterns
      • cbed_intensity_patterns()
    • 2.5.5. prismatique.load.cbed_k_x_coords
      • cbed_k_x_coords()
    • 2.5.6. prismatique.load.cbed_k_y_coords
      • cbed_k_y_coords()
    • 2.5.7. prismatique.load.cbed_wavefunctions
      • cbed_wavefunctions()
    • 2.5.8. prismatique.load.com_momenta
      • com_momenta()
    • 2.5.9. prismatique.load.defocii
      • defocii()
    • 2.5.10. prismatique.load.grid_dims_in_units_of_probe_shifts
      • grid_dims_in_units_of_probe_shifts()
    • 2.5.11. prismatique.load.hrtem_beam_tilts
      • hrtem_beam_tilts()
    • 2.5.12. prismatique.load.hrtem_image_wavefunctions
      • hrtem_image_wavefunctions()
    • 2.5.13. prismatique.load.hrtem_image_x_coords
      • hrtem_image_x_coords()
    • 2.5.14. prismatique.load.hrtem_image_y_coords
      • hrtem_image_y_coords()
    • 2.5.15. prismatique.load.hrtem_intensity_image
      • hrtem_intensity_image()
    • 2.5.16. prismatique.load.integration_limits_of_2d_stem_output
      • integration_limits_of_2d_stem_output()
    • 2.5.17. prismatique.load.k_xy_coords_of_3d_stem_output
      • k_xy_coords_of_3d_stem_output()
    • 2.5.18. prismatique.load.num_frozen_phonon_configs_in_subset
      • num_frozen_phonon_configs_in_subset()
    • 2.5.19. prismatique.load.num_slices
      • num_slices()
    • 2.5.20. prismatique.load.output_layer_depths
      • output_layer_depths()
    • 2.5.21. prismatique.load.potential_slices
      • potential_slices()
    • 2.5.22. prismatique.load.probe_positions
      • probe_positions()
    • 2.5.23. prismatique.load.scan_pattern_type
      • scan_pattern_type()
    • 2.5.24. prismatique.load.stem_intensity_images
      • stem_intensity_images()
  • 2.6. prismatique.sample
    • 2.6.1. prismatique.sample.S_matrix_k_xy_vectors
      • S_matrix_k_xy_vectors()
    • 2.6.2. prismatique.sample.S_matrix_set_data_size
      • S_matrix_set_data_size()
    • 2.6.3. prismatique.sample.S_matrix_subset_data_size
      • S_matrix_subset_data_size()
    • 2.6.4. prismatique.sample.check_atomic_coords_file_format
      • check_atomic_coords_file_format()
    • 2.6.5. prismatique.sample.generate_S_matrices
      • generate_S_matrices()
    • 2.6.6. prismatique.sample.generate_potential_slices
      • generate_potential_slices()
    • 2.6.7. prismatique.sample.num_frozen_phonon_config_subsets
      • num_frozen_phonon_config_subsets()
    • 2.6.8. prismatique.sample.num_frozen_phonon_configs_in_subset
      • num_frozen_phonon_configs_in_subset()
    • 2.6.9. prismatique.sample.num_slices
      • num_slices()
    • 2.6.10. prismatique.sample.potential_slice_set_data_size
      • potential_slice_set_data_size()
    • 2.6.11. prismatique.sample.potential_slice_subset_data_size
      • potential_slice_subset_data_size()
    • 2.6.12. prismatique.sample.supercell_dims
      • supercell_dims()
    • 2.6.13. prismatique.sample.supercell_lateral_pixel_size
      • supercell_lateral_pixel_size()
    • 2.6.14. prismatique.sample.supercell_slice_thickness
      • supercell_slice_thickness()
    • 2.6.15. prismatique.sample.supercell_xy_dims_in_pixels
      • supercell_xy_dims_in_pixels()
    • 2.6.16. prismatique.sample.total_num_frozen_phonon_configs
      • total_num_frozen_phonon_configs()
    • 2.6.17. prismatique.sample.unit_cell_dims
      • unit_cell_dims()
    • 2.6.18. prismatique.sample.ModelParams
      • ModelParams
        • ModelParams.core_attrs
        • ModelParams.de_pre_serialization_funcs
        • ModelParams.de_pre_serialize()
        • ModelParams.dump()
        • ModelParams.dumps()
        • ModelParams.get_core_attrs()
        • ModelParams.get_de_pre_serialization_funcs()
        • ModelParams.get_pre_serialization_funcs()
        • ModelParams.get_validation_and_conversion_funcs()
        • ModelParams.load()
        • ModelParams.loads()
        • ModelParams.pre_serialization_funcs
        • ModelParams.pre_serialize()
        • ModelParams.update()
        • ModelParams.validation_and_conversion_funcs
    • 2.6.19. prismatique.sample.PotentialSliceAndSMatrixSubsetIDs
      • PotentialSliceAndSMatrixSubsetIDs
        • PotentialSliceAndSMatrixSubsetIDs.core_attrs
        • PotentialSliceAndSMatrixSubsetIDs.de_pre_serialization_funcs
        • PotentialSliceAndSMatrixSubsetIDs.de_pre_serialize()
        • PotentialSliceAndSMatrixSubsetIDs.dump()
        • PotentialSliceAndSMatrixSubsetIDs.dumps()
        • PotentialSliceAndSMatrixSubsetIDs.get_core_attrs()
        • PotentialSliceAndSMatrixSubsetIDs.get_de_pre_serialization_funcs()
        • PotentialSliceAndSMatrixSubsetIDs.get_pre_serialization_funcs()
        • PotentialSliceAndSMatrixSubsetIDs.get_validation_and_conversion_funcs()
        • PotentialSliceAndSMatrixSubsetIDs.load()
        • PotentialSliceAndSMatrixSubsetIDs.loads()
        • PotentialSliceAndSMatrixSubsetIDs.pre_serialization_funcs
        • PotentialSliceAndSMatrixSubsetIDs.pre_serialize()
        • PotentialSliceAndSMatrixSubsetIDs.update()
        • PotentialSliceAndSMatrixSubsetIDs.validation_and_conversion_funcs
    • 2.6.20. prismatique.sample.PotentialSliceSubsetIDs
      • PotentialSliceSubsetIDs
        • PotentialSliceSubsetIDs.core_attrs
        • PotentialSliceSubsetIDs.de_pre_serialization_funcs
        • PotentialSliceSubsetIDs.de_pre_serialize()
        • PotentialSliceSubsetIDs.dump()
        • PotentialSliceSubsetIDs.dumps()
        • PotentialSliceSubsetIDs.get_core_attrs()
        • PotentialSliceSubsetIDs.get_de_pre_serialization_funcs()
        • PotentialSliceSubsetIDs.get_pre_serialization_funcs()
        • PotentialSliceSubsetIDs.get_validation_and_conversion_funcs()
        • PotentialSliceSubsetIDs.load()
        • PotentialSliceSubsetIDs.loads()
        • PotentialSliceSubsetIDs.pre_serialization_funcs
        • PotentialSliceSubsetIDs.pre_serialize()
        • PotentialSliceSubsetIDs.update()
        • PotentialSliceSubsetIDs.validation_and_conversion_funcs
    • 2.6.21. prismatique.sample.SMatrixSubsetIDs
      • SMatrixSubsetIDs
        • SMatrixSubsetIDs.core_attrs
        • SMatrixSubsetIDs.de_pre_serialization_funcs
        • SMatrixSubsetIDs.de_pre_serialize()
        • SMatrixSubsetIDs.dump()
        • SMatrixSubsetIDs.dumps()
        • SMatrixSubsetIDs.get_core_attrs()
        • SMatrixSubsetIDs.get_de_pre_serialization_funcs()
        • SMatrixSubsetIDs.get_pre_serialization_funcs()
        • SMatrixSubsetIDs.get_validation_and_conversion_funcs()
        • SMatrixSubsetIDs.load()
        • SMatrixSubsetIDs.loads()
        • SMatrixSubsetIDs.pre_serialization_funcs
        • SMatrixSubsetIDs.pre_serialize()
        • SMatrixSubsetIDs.update()
        • SMatrixSubsetIDs.validation_and_conversion_funcs
  • 2.7. prismatique.scan
    • 2.7.1. prismatique.scan.generate_probe_positions
      • generate_probe_positions()
    • 2.7.2. prismatique.scan.grid_dims_in_units_of_probe_shifts
      • grid_dims_in_units_of_probe_shifts()
    • 2.7.3. prismatique.scan.pattern_type
      • pattern_type()
    • 2.7.4. prismatique.scan.rectangular
      • 2.7.4.1. prismatique.scan.rectangular.Params
        • Params
          • Params.core_attrs
          • Params.de_pre_serialization_funcs
          • Params.de_pre_serialize()
          • Params.dump()
          • Params.dumps()
          • Params.get_core_attrs()
          • Params.get_de_pre_serialization_funcs()
          • Params.get_pre_serialization_funcs()
          • Params.get_validation_and_conversion_funcs()
          • Params.load()
          • Params.loads()
          • Params.pre_serialization_funcs
          • Params.pre_serialize()
          • Params.update()
          • Params.validation_and_conversion_funcs
  • 2.8. prismatique.stem
    • 2.8.1. prismatique.stem.output
      • 2.8.1.1. prismatique.stem.output.data_size
        • data_size()
      • 2.8.1.2. prismatique.stem.output.layer_depths
        • layer_depths()
      • 2.8.1.3. prismatique.stem.output.Params
        • Params
          • Params.core_attrs
          • Params.de_pre_serialization_funcs
          • Params.de_pre_serialize()
          • Params.dump()
          • Params.dumps()
          • Params.get_core_attrs()
          • Params.get_de_pre_serialization_funcs()
          • Params.get_pre_serialization_funcs()
          • Params.get_validation_and_conversion_funcs()
          • Params.load()
          • Params.loads()
          • Params.pre_serialization_funcs
          • Params.pre_serialize()
          • Params.update()
          • Params.validation_and_conversion_funcs
      • 2.8.1.4. prismatique.stem.output.base
        • 2.8.1.4.1. prismatique.stem.output.base.Params
          • Params
      • 2.8.1.5. prismatique.stem.output.multislice
        • 2.8.1.5.1. prismatique.stem.output.multislice.Params
          • Params
      • 2.8.1.6. prismatique.stem.output.prism
        • 2.8.1.6.1. prismatique.stem.output.prism.Params
          • Params
    • 2.8.2. prismatique.stem.sim
      • 2.8.2.1. prismatique.stem.sim.run
        • run()
      • 2.8.2.2. prismatique.stem.sim.Params
        • Params
          • Params.core_attrs
          • Params.de_pre_serialization_funcs
          • Params.de_pre_serialize()
          • Params.dump()
          • Params.dumps()
          • Params.get_core_attrs()
          • Params.get_de_pre_serialization_funcs()
          • Params.get_pre_serialization_funcs()
          • Params.get_validation_and_conversion_funcs()
          • Params.load()
          • Params.loads()
          • Params.pre_serialization_funcs
          • Params.pre_serialize()
          • Params.update()
          • Params.validation_and_conversion_funcs
    • 2.8.3. prismatique.stem.system
      • 2.8.3.1. prismatique.stem.system.ModelParams
        • ModelParams
          • ModelParams.core_attrs
          • ModelParams.de_pre_serialization_funcs
          • ModelParams.de_pre_serialize()
          • ModelParams.dump()
          • ModelParams.dumps()
          • ModelParams.get_core_attrs()
          • ModelParams.get_de_pre_serialization_funcs()
          • ModelParams.get_pre_serialization_funcs()
          • ModelParams.get_validation_and_conversion_funcs()
          • ModelParams.load()
          • ModelParams.loads()
          • ModelParams.pre_serialization_funcs
          • ModelParams.pre_serialize()
          • ModelParams.update()
          • ModelParams.validation_and_conversion_funcs
  • 2.9. prismatique.thermal
    • 2.9.1. prismatique.thermal.Params
      • Params
        • Params.core_attrs
        • Params.de_pre_serialization_funcs
        • Params.de_pre_serialize()
        • Params.dump()
        • Params.dumps()
        • Params.get_core_attrs()
        • Params.get_de_pre_serialization_funcs()
        • Params.get_pre_serialization_funcs()
        • Params.get_validation_and_conversion_funcs()
        • Params.load()
        • Params.loads()
        • Params.pre_serialization_funcs
        • Params.pre_serialize()
        • Params.update()
        • Params.validation_and_conversion_funcs
  • 2.10. prismatique.tilt
    • 2.10.1. prismatique.tilt.series
      • series()
    • 2.10.2. prismatique.tilt.step_size
      • step_size()
    • 2.10.3. prismatique.tilt.Params
      • Params
        • Params.core_attrs
        • Params.de_pre_serialization_funcs
        • Params.de_pre_serialize()
        • Params.dump()
        • Params.dumps()
        • Params.get_core_attrs()
        • Params.get_de_pre_serialization_funcs()
        • Params.get_pre_serialization_funcs()
        • Params.get_validation_and_conversion_funcs()
        • Params.load()
        • Params.loads()
        • Params.pre_serialization_funcs
        • Params.pre_serialize()
        • Params.update()
        • Params.validation_and_conversion_funcs
  • 2.11. prismatique.version
  • 2.12. prismatique.worker
    • 2.12.1. prismatique.worker.Params
      • Params
        • Params.core_attrs
        • Params.de_pre_serialization_funcs
        • Params.de_pre_serialize()
        • Params.dump()
        • Params.dumps()
        • Params.get_core_attrs()
        • Params.get_de_pre_serialization_funcs()
        • Params.get_pre_serialization_funcs()
        • Params.get_validation_and_conversion_funcs()
        • Params.load()
        • Params.loads()
        • Params.pre_serialization_funcs
        • Params.pre_serialize()
        • Params.update()
        • Params.validation_and_conversion_funcs
    • 2.12.2. prismatique.worker.cpu
      • 2.12.2.1. prismatique.worker.cpu.Params
        • Params
          • Params.core_attrs
          • Params.de_pre_serialization_funcs
          • Params.de_pre_serialize()
          • Params.dump()
          • Params.dumps()
          • Params.get_core_attrs()
          • Params.get_de_pre_serialization_funcs()
          • Params.get_pre_serialization_funcs()
          • Params.get_validation_and_conversion_funcs()
          • Params.load()
          • Params.loads()
          • Params.pre_serialization_funcs
          • Params.pre_serialize()
          • Params.update()
          • Params.validation_and_conversion_funcs
    • 2.12.3. prismatique.worker.gpu
      • 2.12.3.1. prismatique.worker.gpu.Params
        • Params
          • Params.core_attrs
          • Params.de_pre_serialization_funcs
          • Params.de_pre_serialize()
          • Params.dump()
          • Params.dumps()
          • Params.get_core_attrs()
          • Params.get_de_pre_serialization_funcs()
          • Params.get_pre_serialization_funcs()
          • Params.get_validation_and_conversion_funcs()
          • Params.load()
          • Params.loads()
          • Params.pre_serialization_funcs
          • Params.pre_serialize()
          • Params.update()
          • Params.validation_and_conversion_funcs
• 3. Examples
  • 3.1. Example of atomic coordinate generation
    • 3.1.1. Prerequisites for running this example
    • 3.1.2. Example description
    • 3.1.3. Code
  • 3.2. Example of simulation parameter generation
    • 3.2.1. Prerequisites for running this example
    • 3.2.2. Example description
    • 3.2.3. Code
  • 3.3. Example of potential slice generation
    • 3.3.1. Prerequisites for running this example
    • 3.3.2. Example description
    • 3.3.3. Code
  • 3.4. Example of \(S\)-matrix generation
    • 3.4.1. Prerequisites for running this example
    • 3.4.2. Example description
    • 3.4.3. Code
  • 3.5. Example of running a STEM simulation using the multislice algorithm
    • 3.5.1. Prerequisites for running this example
    • 3.5.2. Example description
    • 3.5.3. Code
  • 3.6. Example of running a STEM simulation using the PRISM algorithm
    • 3.6.1. Prerequisites for running this example
    • 3.6.2. Example description
    • 3.6.3. Code
  • 3.7. Example of running a HRTEM simulation
    • 3.7.1. Prerequisites for running this example
    • 3.7.2. Example description
    • 3.7.3. Code
• 4. License

Indices and tables

• Index

• Module Index

• Search Page