LICENSE
MANIFEST.in
README.md
pyproject.toml
Tutorials/analysis_helpers.py
Tutorials/T1_5min_intro/tutorial_1_5min_intro.ipynb
Tutorials/T2_automated_random_gen/tutorial_2_automated_random_gen.ipynb
Tutorials/T3_random_gen/tutorial_3_random_generation.ipynb
Tutorials/T4_MQ_via_7_steps/tutorial_4_melt_quench.ipynb
Tutorials/T5_mix_random_MQ/tutorial_5_batch_quench.ipynb
Tutorials/T6_classical_potential/tutorial_6_classical_potential.ipynb
Tutorials/T7_application_dimer_dissociation/tutorial_7_dimer_dissociation.ipynb
amorphgen/__init__.py
amorphgen/cli.py
amorphgen/scattering_cli.py
amorphgen/slurm.py
amorphgen/slurm_runtime.sh
amorphgen.egg-info/PKG-INFO
amorphgen.egg-info/SOURCES.txt
amorphgen.egg-info/dependency_links.txt
amorphgen.egg-info/entry_points.txt
amorphgen.egg-info/requires.txt
amorphgen.egg-info/top_level.txt
amorphgen/analysis/__init__.py
amorphgen/analysis/_rdf_kernel.py
amorphgen/analysis/_serialization.py
amorphgen/analysis/analyser.py
amorphgen/analysis/bond_order.py
amorphgen/analysis/comparison_plots.py
amorphgen/analysis/convergence.py
amorphgen/analysis/convergence_output.py
amorphgen/analysis/cutoff.py
amorphgen/analysis/descriptors.py
amorphgen/analysis/elasticity.py
amorphgen/analysis/energy.py
amorphgen/analysis/experiment.py
amorphgen/analysis/melt_memory.py
amorphgen/analysis/oxygen.py
amorphgen/analysis/plotting.py
amorphgen/analysis/rdf.py
amorphgen/analysis/rings.py
amorphgen/analysis/robustness.py
amorphgen/analysis/scattering_output.py
amorphgen/analysis/screening.py
amorphgen/analysis/sequential.py
amorphgen/analysis/structure.py
amorphgen/analysis/uncertainty.py
amorphgen/analysis/validate.py
amorphgen/analysis/vibrations.py
amorphgen/analysis/voids.py
amorphgen/analysis/voronoi.py
amorphgen/analysis/xrd.py
amorphgen/configs/__init__.py
amorphgen/configs/_defaults.py
amorphgen/configs/default_config.py
amorphgen/configs/descriptor_names.py
amorphgen/configs/example_classical.yaml
amorphgen/configs/example_config.yaml
amorphgen/configs/example_lammps.yaml
amorphgen/configs/yaml_config.py
amorphgen/pipeline/__init__.py
amorphgen/pipeline/batch_quench.py
amorphgen/pipeline/equilibrate.py
amorphgen/pipeline/final_opt.py
amorphgen/pipeline/manifest.py
amorphgen/pipeline/md_ramp.py
amorphgen/pipeline/melt_cell.py
amorphgen/pipeline/opt_cell.py
amorphgen/pipeline/quench.py
amorphgen/pipeline/random_gen.py
amorphgen/pipeline/run_pipeline.py
amorphgen/pipeline/until_converged.py
amorphgen/utils/__init__.py
amorphgen/utils/ace_potential.py
amorphgen/utils/calculators.py
amorphgen/utils/classical.py
amorphgen/utils/common.py
amorphgen/utils/convert.py
amorphgen/utils/equilibration.py
amorphgen/utils/lammps_potential.py
amorphgen/utils/md_diagnostics.py
amorphgen/utils/persistence.py
amorphgen/utils/preemption.py
amorphgen/utils/radii.py
amorphgen/utils/relaxation.py
amorphgen/utils/repulsion.py
amorphgen/utils/run_lock.py
amorphgen/utils/run_provenance.py
amorphgen/utils/safety.py
amorphgen/utils/snapshot_sampling.py
amorphgen/utils/structure_io.py
amorphgen/utils/torchsim_engine.py
amorphgen/utils/torchsim_md.py
examples/run_ensemble_resume_bluebear.slurm
examples/run_gpu_tests_bluebear.slurm
examples/run_quench_array_bluebear.slurm
examples/run_sio2_gen_array_bluebear.slurm
examples/run_sio2_relax_bluebear.slurm
examples/slurm_workflow.yaml
examples/softwarex_analyse_oxide.slurm
examples/softwarex_bks_sio2.yaml
examples/softwarex_run_oxide.slurm
examples/softwarex_run_sio2_bks.slurm
examples/softwarex_run_sio2_bks_cubic.slurm
examples/softwarex_run_sio2_bks_torchsim.slurm
examples/softwarex_run_sio2_slow.slurm
test/amorphgen_test_helpers.py
test/conftest.py
test/test_analyser_branches.py
test/test_analyser_convergence.py
test/test_analysis.py
test/test_analysis_advanced.py
test/test_analysis_input_edges.py
test/test_batch_opt.py
test/test_bond_order.py
test/test_calculator_dispatch.py
test/test_calculators.py
test/test_citation.py
test/test_classical.py
test/test_classical_torch_kernels.py
test/test_classification.py
test/test_cli.py
test/test_cli_argument_paths.py
test/test_cli_convergence.py
test/test_cli_cutoff_robustness.py
test/test_cli_modes.py
test/test_cli_until_converged.py
test/test_comparison_plots.py
test/test_config_contracts.py
test/test_convergence.py
test/test_convergence_output.py
test/test_convert_pipeline_slurm_edges.py
test/test_convert_safety.py
test/test_curve_uncertainty.py
test/test_cutoff_robustness.py
test/test_descriptor_uncertainty.py
test/test_descriptors_cli.py
test/test_divergence_guard.py
test/test_elasticity.py
test/test_ensemble_collection.py
test/test_equilibration.py
test/test_equilibration_statistics.py
test/test_experiment.py
test/test_experimental_elasticity.py
test/test_experimental_scattering.py
test/test_experimental_validation.py
test/test_external_potentials.py
test/test_hydrogenated.py
test/test_hydrogenated_analysis.py
test/test_imports.py
test/test_mace_integration.py
test/test_md_diagnostics.py
test/test_md_diagnostics_edges.py
test/test_md_stages.py
test/test_melt_memory.py
test/test_minsep_audit_families.py
test/test_minsep_cation_rich.py
test/test_npt_methods.py
test/test_oxoanions.py
test/test_oxygen_speciation.py
test/test_persistence.py
test/test_pipeline_config_regressions.py
test/test_pipeline_resume_safety.py
test/test_pipeline_stages.py
test/test_preemption.py
test/test_random_gen.py
test/test_random_gen_advanced.py
test/test_random_gen_branches.py
test/test_random_gen_resume.py
test/test_rdf_kernel.py
test/test_rdf_structure_edges.py
test/test_relaxation_helpers.py
test/test_repulsion.py
test/test_rings.py
test/test_run_lock.py
test/test_run_manifest.py
test/test_run_provenance.py
test/test_safety.py
test/test_safety_paths.py
test/test_scattering_cli.py
test/test_scattering_config.py
test/test_scattering_output.py
test/test_screening.py
test/test_screening_cli.py
test/test_screening_relaxation.py
test/test_sequential.py
test/test_shared_md.py
test/test_slurm.py
test/test_slurm_examples.py
test/test_snapshot_sampling.py
test/test_snapshot_sampling_cli.py
test/test_structure_io.py
test/test_topology_cli.py
test/test_topology_exports.py
test/test_torchsim_classical.py
test/test_torchsim_engine.py
test/test_torchsim_engine_paths.py
test/test_torchsim_gpu.py
test/test_torchsim_model_selection.py
test/test_torchsim_safety.py
test/test_tutorial_analysis.py
test/test_uncertainty.py
test/test_uncertainty_outputs.py
test/test_until_converged.py
test/test_until_converged_settings.py
test/test_utils.py
test/test_utils_edges.py
test/test_validate.py
test/test_vibrations.py
test/test_voids.py
test/test_xrd.py
test/test_yaml_config.py
test/data/experimental/README.md
test/data/experimental/si.xyz
test/data/experimental/sio2.xyz