├── .gitattributes ├── .gitignore ├── LICENSE ├── PSF.py ├── PSF_api.py ├── README.md ├── bak ├── LICENSE ├── NOTE ├── PSF.py ├── PSF_api.py ├── PSF_bak.py ├── README.md ├── input_params.py ├── psf │ ├── __init__.py │ ├── _template.py │ ├── defaults.py │ ├── m_PSF.py │ ├── m_Qpoints.py │ ├── m_command_line.py │ ├── m_communicator.py │ ├── m_config.py │ ├── m_empty.py │ ├── m_error.py │ ├── m_import.py │ ├── m_io.py │ ├── m_lattice.py │ ├── m_parallel.py │ ├── m_printing.py │ ├── m_scattering_lengths.py │ ├── m_structure_factors.py │ ├── m_structure_factors_dev.py │ ├── m_symmetry.py │ ├── m_threads.py │ ├── m_timing.py │ ├── m_trajectory.py │ └── scattering_data │ │ ├── __init__.py │ │ ├── neutron_scattering_lengths.py │ │ └── xray_scattering_params.py └── tools │ └── convert_lammps_to_hdf5.py ├── doc ├── Qpts_grid.pdf ├── Qpts_grid.svg ├── compile.py ├── example_figs │ ├── MD_vs_LD.png │ ├── Q_dot_e.png │ ├── bz_path.png │ ├── example_figs.svg │ ├── mapi_diffuse.png │ ├── mapi_elastic.png │ ├── mapi_phonons.png │ ├── mapi_pm_1.png │ ├── mapi_total.png │ ├── rutile_diffuse.png │ ├── rutile_phonons.png │ ├── silicon_diffuse.png │ └── silicon_phonons.png ├── intro_to_neutron_scattering_ref.pdf ├── manual.pdf ├── trajectory_blocks.pdf ├── trajectory_blocks.svg └── validation │ └── harmonic_lattice_dynamics │ ├── FORCE_SETS │ ├── POSCAR │ ├── README │ ├── euphonic_phonons.pdf │ ├── euphonic_sqw.pdf │ ├── euphonic_sqw.py │ ├── phonopy.conf │ └── phonopy.yaml ├── examples ├── mapi │ ├── diffuse │ │ ├── input.py │ │ ├── plots │ │ │ ├── make_plots.py │ │ │ ├── make_plots_pm_1.py │ │ │ ├── make_plots_pm_1_xrays.py │ │ │ ├── make_plots_total.py │ │ │ ├── make_plots_total_xrays.py │ │ │ ├── make_plots_xrays.py │ │ │ ├── mapi_elastic_neutrons.pdf │ │ │ ├── mapi_elastic_xrays_vs_neutrons.pdf │ │ │ ├── mapi_pm_1_neutrons.pdf │ │ │ ├── mapi_pm_1_neutrons_vs_xrays.pdf │ │ │ ├── mapi_total_neutrons.pdf │ │ │ ├── mapi_total_neutrons_vs_xrays.pdf │ │ │ ├── mapi_vs_xrays.pdf │ │ │ ├── plot_vs_exp.py │ │ │ └── xds_cut_L2.5.tar.gz │ │ └── run_api.py │ ├── lammps │ │ ├── MAPI_cubic.prim │ │ └── lammps.in │ └── phonons │ │ ├── input.py │ │ ├── plots │ │ ├── make_plots.py │ │ ├── make_plots_xrays.py │ │ ├── mapi_phonons_neutrons.pdf │ │ └── mapi_phonons_neutrons_vs_xrays.pdf │ │ └── run_api.py ├── rutile │ ├── diffuse │ │ ├── input_pristine.py │ │ ├── plots │ │ │ ├── make_plots.py │ │ │ ├── make_plots_total.py │ │ │ ├── make_plots_total_xrays.py │ │ │ ├── make_plots_xrays.py │ │ │ ├── rutile_elastic_neutrons.pdf │ │ │ ├── rutile_elastic_xrays.pdf │ │ │ ├── rutile_total_neutrons.pdf │ │ │ └── rutile_total_xrays.pdf │ │ └── run_api.py │ ├── lammps │ │ ├── pristine │ │ │ ├── lammps.in │ │ │ └── rutile_12x12x16.supercell │ │ └── vacancies │ │ │ ├── lammps.in │ │ │ ├── make_vacancies.py │ │ │ └── rutile_Ov_500_Tiv_250_12x12x16.supercell │ └── phonons │ │ ├── PSF.py │ │ ├── input_pristine.py │ │ ├── plots │ │ ├── make_plots.py │ │ ├── make_plots_xrays.py │ │ ├── rutile_phonons_neutrons.pdf │ │ ├── rutile_phonons_xrays.pdf │ │ └── simple_plot.py │ │ └── run_api.py └── silicon │ ├── lammps │ ├── pristine │ │ ├── SiCGe.tersoff │ │ ├── lammps.in │ │ └── si_12x12x12.supercell │ └── substitutions │ │ ├── SiCGe.tersoff │ │ ├── lammps.in │ │ ├── make_substitutions.py │ │ └── si_ge_0.10_12x12x12.supercell │ └── phonons │ ├── answers │ ├── input_pristine.py │ └── run_api.py │ └── plots │ ├── make_plots.py │ ├── make_plots_xrays.py │ ├── si_neutrons_phonons.pdf │ └── si_xrays_phonons.pdf ├── input_params.py ├── psf ├── __init__.py ├── _template.py ├── defaults.py ├── m_PSF.py ├── m_Qpoints.py ├── m_command_line.py ├── m_communicator.py ├── m_config.py ├── m_empty.py ├── m_error.py ├── m_import.py ├── m_io.py ├── m_lattice.py ├── m_parallel.py ├── m_printing.py ├── m_scattering_lengths.py ├── m_structure_factors.py ├── m_symmetry.py ├── m_threads.py ├── m_timing.py ├── m_trajectory.py └── scattering_data │ ├── .~lock.scattering_lenghts.csv# │ ├── __init__.py │ ├── bak │ └── neutron_scattering_lengths.py │ ├── neutron_scattering_lengths.py │ └── xray_scattering_params.py ├── test ├── incoherent │ ├── rutile │ │ ├── convert_lammps_to_hdf5.py │ │ ├── get_latvecs.py │ │ ├── input_params.py │ │ ├── lammps.in │ │ ├── log │ │ ├── log.lammps │ │ ├── plot.py │ │ ├── rutile.post_sqw.pos │ │ ├── rutile.prim.pos │ │ └── test.png │ └── si │ │ ├── SiCGe.tersoff │ │ ├── convert_lammps_to_hdf5.py │ │ ├── input_params.py │ │ ├── lammps.in │ │ ├── log.lammps │ │ ├── plot.py │ │ ├── si_12x12x12.supercell │ │ └── test.png └── symmetry │ ├── SiCGe.tersoff │ ├── convert_lammps_to_hdf5.py │ ├── input_params.py │ ├── lammps.in │ ├── plot_diffuse.py │ └── si_12x12x12.supercell └── tools └── convert_lammps_to_hdf5.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/tyst3273/pynamic-structure-factor/HEAD/.gitattributes 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