LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
karml/__init__.py
karml/_version.py
karml/karml.py
karml/paths.py
karml.egg-info/PKG-INFO
karml.egg-info/SOURCES.txt
karml.egg-info/dependency_links.txt
karml.egg-info/entry_points.txt
karml.egg-info/not-zip-safe
karml.egg-info/requires.txt
karml.egg-info/top_level.txt
karml/acquisition/__init__.py
karml/acquisition/ids.py
karml/acquisition/labels.py
karml/acquisition/linear_student.py
karml/acquisition/md_eval.py
karml/acquisition/metrics.py
karml/acquisition/pca.py
karml/acquisition/physnet_readout.py
karml/acquisition/pipeline.py
karml/acquisition/pooling.py
karml/acquisition/report.py
karml/acquisition/representations.py
karml/acquisition/selection.py
karml/acquisition/splits.py
karml/acquisition/synthetic.py
karml/acquisition/train.py
karml/analysis/__init__.py
karml/analysis/acetone_crystal.py
karml/analysis/crystal_contacts.py
karml/analysis/dcm_crystal.py
karml/analysis/dimer_cgenff.py
karml/analysis/dimer_molecules.py
karml/analysis/dimer_scans.py
karml/analysis/hybrid_force_breakdown.py
karml/analysis/interaction_pes.py
karml/analysis/interaction_pes_geom.py
karml/analysis/interaction_pes_plot.py
karml/analysis/lattice_energy.py
karml/analysis/liquid_md.py
karml/analysis/mm_nonbonded_tune_plots.py
karml/analysis/npz_comparison.py
karml/analysis/residue_geometry.py
karml/cli/__init__.py
karml/cli/__main__.py
karml/cli/argparse_suggest.py
karml/cli/base.py
karml/cli/commands_help.py
karml/cli/completion.py
karml/cli/configure.py
karml/cli/configure_presets.py
karml/cli/doctor.py
karml/cli/env.py
karml/cli/help_style.py
karml/cli/help_text.py
karml/cli/md_system_help.py
karml/cli/parser_utils.py
karml/cli/registry.py
karml/cli/make/__init__.py
karml/cli/make/make_box.py
karml/cli/make/make_mixed_box.py
karml/cli/make/make_res.py
karml/cli/make/make_training.py
karml/cli/misc/__init__.py
karml/cli/misc/active_learning.py
karml/cli/misc/analyze_liquid.py
karml/cli/misc/build_crystal.py
karml/cli/misc/build_crystal_cli.py
karml/cli/misc/calculator.py
karml/cli/misc/clean_data.py
karml/cli/misc/compare_charmm_ml.py
karml/cli/misc/compare_equivariant_models.py
karml/cli/misc/compare_npz.py
karml/cli/misc/compare_training_runs.py
karml/cli/misc/convert_npz_traj.py
karml/cli/misc/convert_res_traj.py
karml/cli/misc/cross_check.py
karml/cli/misc/diagnose_learning_curve_outliers.py
karml/cli/misc/dimer_scan.py
karml/cli/misc/dynamics.py
karml/cli/misc/ef_md.py
karml/cli/misc/efield_evaluate.py
karml/cli/misc/efield_md.py
karml/cli/misc/efield_train.py
karml/cli/misc/eval_hybrid_accuracy.py
karml/cli/misc/evaluate_model.py
karml/cli/misc/explore_data.py
karml/cli/misc/extract_checkpoint_metrics.py
karml/cli/misc/filter_close_contacts.py
karml/cli/misc/fix_and_split.py
karml/cli/misc/ic_scan.py
karml/cli/misc/inspect_checkpoint.py
karml/cli/misc/interpolate_xyz.py
karml/cli/misc/kernel_fit.py
karml/cli/misc/kernnn_evaluate.py
karml/cli/misc/kernnn_train.py
karml/cli/misc/label_acquire.py
karml/cli/misc/make_box_cli.py
karml/cli/misc/make_res_cli.py
karml/cli/misc/mode_check.py
karml/cli/misc/neb.py
karml/cli/misc/normal_mode_sample.py
karml/cli/misc/opt_karml.py
karml/cli/misc/orbax_to_json_cmd.py
karml/cli/misc/pes_design.py
karml/cli/misc/pet_box_dataset.py
karml/cli/misc/pet_interaction_pes.py
karml/cli/misc/pet_physnet_distill.py
karml/cli/misc/physnet_evaluate.py
karml/cli/misc/physnet_md.py
karml/cli/misc/physnet_train.example.yaml
karml/cli/misc/physnet_train.py
karml/cli/misc/physnet_train_transfer.example.yaml
karml/cli/misc/prepare_mm_dataset.py
karml/cli/misc/pyscf_dft.py
karml/cli/misc/pyscf_evaluate.py
karml/cli/misc/pyscf_evaluate_mp2.py
karml/cli/misc/pyscf_mp2.py
karml/cli/misc/remove_padding.py
karml/cli/misc/split_dataset.py
karml/cli/misc/subtract_element_refs.py
karml/cli/misc/test_deps.py
karml/cli/misc/train_charge_spin.py
karml/cli/misc/train_joint.py
karml/cli/misc/train_memmap.py
karml/cli/misc/training_helpers.py
karml/cli/misc/tune_mm_nonbonded.py
karml/cli/misc/umbrella_mbar.py
karml/cli/misc/umbrella_sample.py
karml/cli/misc/unwrap_traj.py
karml/cli/misc/validate_cli.py
karml/cli/misc/validate_pot.py
karml/cli/misc/verify_esp_alignment.py
karml/cli/misc/xml2npz.py
karml/cli/plot/__init__.py
karml/cli/plot/plot_checkpoint_history.py
karml/cli/plot/plot_restart_velocities.py
karml/cli/plot/plot_training.py
karml/cli/run/__init__.py
karml/cli/run/dcm20_liquid_smoke.example.yaml
karml/cli/run/dcm27_liquid_box.example.yaml
karml/cli/run/dcm_liquid_workflow.resilient.example.yaml
karml/cli/run/dcm_long_range_solvers.example.yaml
karml/cli/run/health_check.py
karml/cli/run/jaxmd_runner.py
karml/cli/run/lambda_dynamics.py
karml/cli/run/lambda_jaxmd.py
karml/cli/run/lambda_mbar.py
karml/cli/run/liquid_box.py
karml/cli/run/md_campaign.py
karml/cli/run/md_config.py
karml/cli/run/md_dyna_probe.py
karml/cli/run/md_embedding.py
karml/cli/run/md_embedding_aaa_train.example.yaml
karml/cli/run/md_embedding_aaa_train_long.example.yaml
karml/cli/run/md_embedding_aaa_train_short.example.yaml
karml/cli/run/md_evaluate_npz.py
karml/cli/run/md_handoff.py
karml/cli/run/md_optimize_cutoffs.py
karml/cli/run/md_run_advice.py
karml/cli/run/md_stage_summary.py
karml/cli/run/md_system.aco178_certified_nvt_nve.example.yaml
karml/cli/run/md_system.dcm103_equil.example.yaml
karml/cli/run/md_system.dcm206_certified_nvt_nve.example.yaml
karml/cli/run/md_system.dcm52_equil.example.yaml
karml/cli/run/md_system.dense_liquid_prep.example.yaml
karml/cli/run/md_system.example.yaml
karml/cli/run/md_system.py
karml/cli/run/md_system.serial_mpi_probe.example.yaml
karml/cli/run/md_system.spatial_mpi.example.yaml
karml/cli/run/md_system.stability_smoke.example.yaml
karml/cli/run/md_system.thermalize.example.yaml
karml/cli/run/md_system_unified.py
karml/cli/run/mpi_check.py
karml/cli/run/mpi_launch.py
karml/cli/run/pycharmm_runner.py
karml/cli/run/pycharmm_sampling_args.py
karml/cli/run/pycharmm_two_residue_sample.py
karml/cli/run/shared.py
karml/cli/run/summaries.py
karml/cli/run/warmup_mlpot_jax.py
karml/cli/run/md_pbc_suite/__init__.py
karml/cli/run/md_pbc_suite/check_fd.py
karml/cli/run/md_pbc_suite/cluster.py
karml/cli/run/md_pbc_suite/composition.py
karml/cli/run/md_pbc_suite/jaxmd.py
karml/cli/run/md_pbc_suite/minimize_log.py
karml/cli/run/md_pbc_suite/pycharmm_mlpot.py
karml/cli/run/presets/base-dt0.25.yaml
karml/cli/run/presets/base-dt0.5.yaml
karml/cli/run/presets/certified-box-handoff.yaml
karml/cli/run/presets/dynamics-flyoff-guard.yaml
karml/cli/run/presets/dynamics-flyoff-strict.yaml
karml/cli/run/presets/dynamics-overlap-rescue.yaml
karml/cli/run/presets/heat-dt0.25-conservative.yaml
karml/cli/run/presets/heat-dt0.25-scale.yaml
karml/cli/run/presets/liquid-prep-dense.yaml
karml/cli/run/presets/pre-sd-calculator.yaml
karml/cli/run/presets/thermalize.yaml
karml/cli/templates/workflows/heat_scaling_smoke/Snakefile
karml/cli/templates/workflows/heat_scaling_smoke/config.yaml
karml/cli/templates/workflows/heat_scaling_smoke/profiles/slurm/config.yaml
karml/cli/templates/workflows/heat_scaling_smoke/scripts/job_shell.sh
karml/cli/templates/workflows/md_benchmark/Snakefile
karml/cli/templates/workflows/md_benchmark/config.yaml
karml/cli/templates/workflows/md_benchmark/profiles/slurm/config.yaml
karml/cli/templates/workflows/md_benchmark/scripts/collect_shell.sh
karml/cli/templates/workflows/md_benchmark/scripts/job_shell.sh
karml/cli/templates/workflows/nve_cutoff_smoke/Snakefile
karml/cli/templates/workflows/nve_cutoff_smoke/config.yaml
karml/cli/templates/workflows/nve_cutoff_smoke/scripts/job_shell.sh
karml/data/__init__.py
karml/data/atomic_references.py
karml/data/cgenff_dataset.py
karml/data/loaders.py
karml/data/npz_schema.py
karml/data/orbax_shards.py
karml/data/packed_memmap_loader.py
karml/data/preprocessing.py
karml/data/reference_state_points.py
karml/data/rmd17.py
karml/data/spice_alpha.py
karml/data/spice_alpha_ragged.py
karml/data/units.py
karml/data/xml_to_npz.py
karml/data/adapters/__init__.py
karml/data/adapters/dcmnet.py
karml/data/adapters/physnetjax.py
karml/data/charmm/alad_reference.pdb
karml/data/charmm/crystal_image.str
karml/data/charmm/heme_mbco_coords.txt
karml/data/charmm/par_all36_cgenff.prm
karml/data/charmm/par_trialanine_backbone_cmap.prm
karml/data/charmm/tip3.pdb
karml/data/charmm/top_all36_cgenff.rtf
karml/data/charmm/top_trialanine_cgenff.rtf
karml/data/charmm/trialanine-water-smoke.extxyz
karml/data/charmm/trialanine-water-smoke.pdb
karml/data/external/__init__.py
karml/data/external/aaa_ama.py
karml/data/external/aaa_ama_dataset_summary.json
karml/data/molecules/benz_monomer.pdb
karml/data/molecules/dcm.xyz
karml/data/molecules/dcm_monomer.pdb
karml/data/qcml/atomic_reference_energies.json
karml/data/structures/acetone_cmcm_15kbar_cod7110462.cif
karml/data/structures/acetone_cmcm_160k_cod7110463.cif
karml/data/structures/acetone_pbca_110k_cod7110466.cif
karml/data/structures/acetone_pbca_150k_cod7110464.cif
karml/data/structures/acetone_pbca_5k_cod7110465.cif
karml/data/structures/benzene_p21c_cod4501704.cif
karml/data/structures/dcm_pbcn_133gpa_cod2100014.cif
karml/data/structures/dcm_pbcn_cod2100015.cif
karml/data/structures/make-box-aco-8x22A.pdb
karml/dimer_scan/__init__.py
karml/dimer_scan/calculators.py
karml/dimer_scan/config.py
karml/dimer_scan/evaluate.py
karml/dimer_scan/plotting.py
karml/dimer_scan/result.py
karml/distill/__init__.py
karml/distill/acetone_pool.py
karml/distill/batched_teacher.py
karml/distill/box_clusters.py
karml/distill/box_cohesion.py
karml/distill/box_dataset.py
karml/distill/gas_monomer_md.py
karml/distill/npz_export.py
karml/distill/teacher_label.py
karml/generate/__init__.py
karml/generate/descriptors.py
karml/generate/dimers.py
karml/generate/dmc/__init__.py
karml/generate/dmc/dmc.py
karml/generate/sample/__init__.py
karml/generate/sample/benchmark_sampling.py
karml/generate/sample/compare_ensemble_entropy.py
karml/generate/sample/features.py
karml/generate/sample/npz_ensemble_entropy.py
karml/generate/sample/pycharmm_dimers.py
karml/generate/sample/sample_cc.py
karml/generate/sample/sample_diverse_xyz.py
karml/generate/sample/sample_mesh.py
karml/generate/sample/select_points.py
karml/generate/sample/pdb/aco_monomer.pdb
karml/generate/sample/pdb/initial.pdb
karml/generate/sample/pdb/meoh.pdb
karml/generate/sample/psf/initial.psf
karml/generate/sample/psf/meoh-1.psf
karml/ic_scan/__init__.py
karml/ic_scan/calculators.py
karml/ic_scan/config.py
karml/ic_scan/evaluate.py
karml/ic_scan/geometry.py
karml/ic_scan/grid.py
karml/ic_scan/plotting.py
karml/ic_scan/relax.py
karml/ic_scan/result.py
karml/ic_scan/topology.py
karml/interfaces/__init__.py
karml/interfaces/crystal_charmm.py
karml/interfaces/crystal_reference.py
karml/interfaces/pyxtal_optimize.py
karml/interfaces/pyxtal_placement.py
karml/interfaces/calculators/__init__.py
karml/interfaces/calculators/ase_fragment_hybrid.py
karml/interfaces/calculators/checkpoint_loading.py
karml/interfaces/calculators/hybrid.py
karml/interfaces/calculators/link_atoms.py
karml/interfaces/calculators/metatomic.py
karml/interfaces/calculators/simple_inference.py
karml/interfaces/chemcoordInterface/__init__.py
karml/interfaces/chemcoordInterface/interface.py
karml/interfaces/cpptrajInterface/__init__.py
karml/interfaces/cpptrajInterface/cpptrajIO.py
karml/interfaces/dcmInterface/DCM.py
karml/interfaces/dcmInterface/__init__.py
karml/interfaces/dcmInterface/convert.py
karml/interfaces/dcmInterface/dcm_xyz.py
karml/interfaces/dcmInterface/dcmnet_to_mdcm.py
karml/interfaces/dcmInterface/evaluate_h5.py
karml/interfaces/dcmInterface/frame.py
karml/interfaces/dcmInterface/kernel_fit.py
karml/interfaces/dcmInterface/kernel_pipeline.py
karml/interfaces/dcmInterface/mdcm_writer.py
karml/interfaces/dcmInterface/optimize.py
karml/interfaces/dcmInterface/topology.py
karml/interfaces/energy_forces/__init__.py
karml/interfaces/energy_forces/adapters.py
karml/interfaces/energy_forces/ml.py
karml/interfaces/energy_forces/protocol.py
karml/interfaces/energy_forces/registry.py
karml/interfaces/energy_forces/spec.py
karml/interfaces/jaxmdInterface/__init__.py
karml/interfaces/jaxmdInterface/hybrid_energy.py
karml/interfaces/jaxmdInterface/jaxmdInterface.py
karml/interfaces/multiwfnInterface/__init__.py
karml/interfaces/multiwfnInterface/criticalPoints.py
karml/interfaces/multiwfnInterface/molden.py
karml/interfaces/orca_external/__init__.py
karml/interfaces/orca_external/__main__.py
karml/interfaces/orca_external/batch_inference.py
karml/interfaces/orca_external/client.py
karml/interfaces/orca_external/protocol.py
karml/interfaces/orca_external/runner.py
karml/interfaces/orca_external/server.py
karml/interfaces/orca_external/settings.py
karml/interfaces/parse_molpro/__init__.py
karml/interfaces/parse_molpro/example_usage.py
karml/interfaces/parse_molpro/read.py
karml/interfaces/parse_molpro/read_molden.py
karml/interfaces/pycharmmInterface/__init__.py
karml/interfaces/pycharmmInterface/calculator_utils.py
karml/interfaces/pycharmmInterface/canonical_paths.py
karml/interfaces/pycharmmInterface/cell_list.py
karml/interfaces/pycharmmInterface/cgenff_bonded.py
karml/interfaces/pycharmmInterface/cgenff_bonded_reference.py
karml/interfaces/pycharmmInterface/cgenff_cmap.py
karml/interfaces/pycharmmInterface/cgenff_residues.py
karml/interfaces/pycharmmInterface/cgenff_topology.py
karml/interfaces/pycharmmInterface/charmm_forces.py
karml/interfaces/pycharmmInterface/charmm_image_geometry.py
karml/interfaces/pycharmmInterface/charmm_jax_energy_benchmark.py
karml/interfaces/pycharmmInterface/charmm_jax_trajectory_energy.py
karml/interfaces/pycharmmInterface/charmm_levels.py
karml/interfaces/pycharmmInterface/charmm_mpi.py
karml/interfaces/pycharmmInterface/charmm_paths.py
karml/interfaces/pycharmmInterface/charmm_prm_zero.py
karml/interfaces/pycharmmInterface/charmm_restart_io.py
karml/interfaces/pycharmmInterface/cluster_geometry.py
karml/interfaces/pycharmmInterface/crystal_cell.py
karml/interfaces/pycharmmInterface/cutoffs.py
karml/interfaces/pycharmmInterface/dcm_liquid_box.py
karml/interfaces/pycharmmInterface/dcm_mp2_mm_compare.py
karml/interfaces/pycharmmInterface/ewald_native.py
karml/interfaces/pycharmmInterface/grid_placement.py
karml/interfaces/pycharmmInterface/heme_electronic.py
karml/interfaces/pycharmmInterface/heme_library.py
karml/interfaces/pycharmmInterface/hybrid_reference.py
karml/interfaces/pycharmmInterface/import_pycharmm.py
karml/interfaces/pycharmmInterface/jax_compile_threads.py
karml/interfaces/pycharmmInterface/jax_device_policy.py
karml/interfaces/pycharmmInterface/jax_md_neighbor_list.py
karml/interfaces/pycharmmInterface/jax_pme_cross_monomer.py
karml/interfaces/pycharmmInterface/jax_pme_hybrid_coulomb.py
karml/interfaces/pycharmmInterface/jax_x64_config.py
karml/interfaces/pycharmmInterface/karml_calculator.py
karml/interfaces/pycharmmInterface/liquid_nb_parity.py
karml/interfaces/pycharmmInterface/long_range_backend.py
karml/interfaces/pycharmmInterface/lr_solver_grms_compare.py
karml/interfaces/pycharmmInterface/mbd_term.py
karml/interfaces/pycharmmInterface/mixed_ml_mm.py
karml/interfaces/pycharmmInterface/ml_batching.py
karml/interfaces/pycharmmInterface/ml_cut.py
karml/interfaces/pycharmmInterface/ml_dtypes.py
karml/interfaces/pycharmmInterface/mlpot_gpu.py
karml/interfaces/pycharmmInterface/mm_charge_correction.py
karml/interfaces/pycharmmInterface/mm_energy_forces.py
karml/interfaces/pycharmmInterface/mm_system_energy.py
karml/interfaces/pycharmmInterface/mm_system_plot.py
karml/interfaces/pycharmmInterface/mpi_rank_io.py
karml/interfaces/pycharmmInterface/multipolar_fmm_prototype.py
karml/interfaces/pycharmmInterface/myoglobin.py
karml/interfaces/pycharmmInterface/nbonds_config.py
karml/interfaces/pycharmmInterface/nl_backend.py
karml/interfaces/pycharmmInterface/nl_gpu.py
karml/interfaces/pycharmmInterface/nl_reference.py
karml/interfaces/pycharmmInterface/packmol_cache.py
karml/interfaces/pycharmmInterface/packmol_placement.py
karml/interfaces/pycharmmInterface/packmol_repack.py
karml/interfaces/pycharmmInterface/pbc_prep_factory.py
karml/interfaces/pycharmmInterface/pbc_utils_jax.py
karml/interfaces/pycharmmInterface/peptide_builder.py
karml/interfaces/pycharmmInterface/protein_charmm_build.py
karml/interfaces/pycharmmInterface/pycharmmCommands.py
karml/interfaces/pycharmmInterface/setupBox.py
karml/interfaces/pycharmmInterface/setupRes.py
karml/interfaces/pycharmmInterface/tip3_liquid_box.py
karml/interfaces/pycharmmInterface/trialanine_nb_parity.py
karml/interfaces/pycharmmInterface/trialanine_water_box.py
karml/interfaces/pycharmmInterface/utils.py
karml/interfaces/pycharmmInterface/mlpot/__init__.py
karml/interfaces/pycharmmInterface/mlpot/artifact_paths.py
karml/interfaces/pycharmmInterface/mlpot/block_terms.py
karml/interfaces/pycharmmInterface/mlpot/bonded_jax_recovery.py
karml/interfaces/pycharmmInterface/mlpot/bonded_mm_recovery.py
karml/interfaces/pycharmmInterface/mlpot/box_equil.py
karml/interfaces/pycharmmInterface/mlpot/box_lattice_abnr.py
karml/interfaces/pycharmmInterface/mlpot/box_pressure_opt.py
karml/interfaces/pycharmmInterface/mlpot/box_sizing.py
karml/interfaces/pycharmmInterface/mlpot/bussi_continuation_gate_diagnostics.py
karml/interfaces/pycharmmInterface/mlpot/calculator_minimize.py
karml/interfaces/pycharmmInterface/mlpot/callback_buffers.py
karml/interfaces/pycharmmInterface/mlpot/callback_failstop.py
karml/interfaces/pycharmmInterface/mlpot/cgenff_prm_swap.py
karml/interfaces/pycharmmInterface/mlpot/charmm_ase_velocities.py
karml/interfaces/pycharmmInterface/mlpot/charmm_energy_policy.py
karml/interfaces/pycharmmInterface/mlpot/charmm_eterm_routing.py
karml/interfaces/pycharmmInterface/mlpot/charmm_nbond_diagnostics.py
karml/interfaces/pycharmmInterface/mlpot/charmm_recovery_sidecar.py
karml/interfaces/pycharmmInterface/mlpot/charmm_restart_compat.py
karml/interfaces/pycharmmInterface/mlpot/cleanup_mode.py
karml/interfaces/pycharmmInterface/mlpot/cli_common.py
karml/interfaces/pycharmmInterface/mlpot/comp_velocities.py
karml/interfaces/pycharmmInterface/mlpot/composition_spec.py
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karml/interfaces/pycharmmInterface/mlpot/metatomic_mlpot.py
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karml/interfaces/pycharmmInterface/mlpot/monomer_physnet_mini.py
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karml/interfaces/pycharmmInterface/mlpot/overlap_guard.py
karml/interfaces/pycharmmInterface/mlpot/partial_mm.py
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karml/interfaces/pycharmmInterface/mlpot/scaled_cgenff_prm.py
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karml/interfaces/pycharmmInterface/mlpot/strain_virial.py
karml/interfaces/pycharmmInterface/mlpot/tier3_domdec_validate.py
karml/interfaces/pycharmmInterface/mlpot/topology_recovery.py
karml/interfaces/pycharmmInterface/mlpot/trimer_scan.py
karml/interfaces/pycharmmInterface/mlpot/virial_compare.py
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karml/interfaces/pycharmmInterface/mlpot/mpi_spatial/force_exchange.py
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karml/interfaces/pyscf4gpuInterface/aseInterface.py
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karml/interfaces/pyscf4gpuInterface/calcs_mp2.py
karml/interfaces/pyscf4gpuInterface/cli_parser.py
karml/interfaces/pyscf4gpuInterface/cpu.py
karml/interfaces/pyscf4gpuInterface/cpu_opt.py
karml/interfaces/pyscf4gpuInterface/efield.py
karml/interfaces/pyscf4gpuInterface/enums.py
karml/interfaces/pyscf4gpuInterface/esp_helpers.py
karml/interfaces/pyscf4gpuInterface/example-opt.py
karml/interfaces/pyscf4gpuInterface/finite_difference.py
karml/interfaces/pyscf4gpuInterface/helperfunctions.py
karml/interfaces/pyscf4gpuInterface/ref_atomic_energies.py
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karml/interfaces/qc_backends/factory.py
karml/interfaces/qc_backends/ml_backend.py
karml/interfaces/qc_backends/molpro.py
karml/interfaces/qc_backends/npz_output.py
karml/interfaces/qc_backends/orca_qm.py
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karml/interfaces/qc_backends/pyscf_backend.py
karml/interfaces/qc_backends/runner.py
karml/interfaces/qc_backends/structures.py
karml/interfaces/qc_backends/xtb.py
karml/interfaces/scafacosInterface/__init__.py
karml/interfaces/scafacosInterface/scafacos_session.py
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karml/md/config.py
karml/md/interactions.py
karml/md/lowering.py
karml/md/metatomic_pbc.py
karml/md/ml_region.py
karml/md/neighbor_cache.py
karml/md/neighbors.py
karml/md/nl_cadence.py
karml/md/restart.py
karml/md/results.py
karml/md/static_pairs.py
karml/md/step_batching.py
karml/md/system.py
karml/md/temperature.py
karml/md/builders/__init__.py
karml/md/builders/_topology.py
karml/md/builders/placement.py
karml/md/builders/psf.py
karml/md/constraints/__init__.py
karml/md/constraints/rattle.py
karml/md/drivers/__init__.py
karml/md/drivers/jaxmd.py
karml/md/energy/__init__.py
karml/md/energy/capacity.py
karml/md/energy/registry.py
karml/md/energy/terms/__init__.py
karml/md/energy/terms/_common.py
karml/md/energy/terms/dihedral.py
karml/md/energy/terms/mbd.py
karml/md/energy/terms/ml_intra.py
karml/md/energy/terms/ml_mm_elec.py
karml/md/energy/terms/ml_mm_pol.py
karml/md/energy/terms/ml_pep_water.py
karml/md/energy/terms/mm_bonded.py
karml/md/energy/terms/mm_nonbonded.py
karml/md/energy/terms/multipole.py
karml/md/energy/terms/rxncoor.py
karml/md/energy/terms/smd.py
karml/md/energy/terms/vdw_core.py
karml/md/energy/terms/zbl.py
karml/md/restraints/__init__.py
karml/md/restraints/dihedral.py
karml/md/restraints/dihedral_cv.py
karml/md/restraints/distance.py
karml/md/restraints/linear_distance.py
karml/md/restraints/psf_angles.py
karml/md/samplers/__init__.py
karml/md/samplers/rigid.py
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karml/mode_check/bonds.py
karml/mode_check/config.py
karml/mode_check/constraints.py
karml/mode_check/cutoff_ladder.py
karml/mode_check/cutoff_sweep.py
karml/mode_check/forces.py
karml/mode_check/geometry.py
karml/mode_check/hybrid.py
karml/mode_check/kick.py
karml/mode_check/pbc_fd.py
karml/mode_check/result.py
karml/mode_check/run.py
karml/mode_check/vibrations.py
karml/models/__init__.py
karml/models/cgenff_mm.py
karml/models/dynamic_latent_charges.py
karml/models/ewald_hybrid_coulomb.py
karml/models/hybrid_energy.py
karml/models/latent_charge_template.py
karml/models/mm_charge_mode.py
karml/models/mm_lj_scales.py
karml/models/mm_nonbonded_tune.py
karml/models/nvalchemiops_hybrid_coulomb.py
karml/models/short_range_wall.py
karml/models/spookynet_calc.py
karml/models/EF/__init__.py
karml/models/EF/evaluate.py
karml/models/EF/training.py
karml/models/dcmnet/__init__.py
karml/models/dcmnet/dcmnet-ase.py
karml/models/dcmnet/dcmnet_ase.py
karml/models/dcmnet/dcmnet_charge_positions_demo.py
karml/models/dcmnet/dcmnet_charge_selection_demo.py
karml/models/dcmnet/dcmnet_ensemble_example.py
karml/models/dcmnet/dcmnet_mcts.py
karml/models/dcmnet/mcts.py
karml/models/dcmnet/project2D.py
karml/models/dcmnet/run_dcmnet_mcts.py
karml/models/dcmnet/setup.py
karml/models/dcmnet/dcmnet/__init__.py
karml/models/dcmnet/dcmnet/analysis.py
karml/models/dcmnet/dcmnet/analysis_multibatch.py
karml/models/dcmnet/dcmnet/cubes.py
karml/models/dcmnet/dcmnet/data.py
karml/models/dcmnet/dcmnet/electrostatics.py
karml/models/dcmnet/dcmnet/esp_atom.py
karml/models/dcmnet/dcmnet/esp_pyscf.py
karml/models/dcmnet/dcmnet/loss.py
karml/models/dcmnet/dcmnet/main.py
karml/models/dcmnet/dcmnet/models.py
karml/models/dcmnet/dcmnet/modules.py
karml/models/dcmnet/dcmnet/multimodel.py
karml/models/dcmnet/dcmnet/multipoles.py
karml/models/dcmnet/dcmnet/plotting.py
karml/models/dcmnet/dcmnet/plotting_3d.py
karml/models/dcmnet/dcmnet/pointcloudToMesh.py
karml/models/dcmnet/dcmnet/rdkit_utils.py
karml/models/dcmnet/dcmnet/train_runner.py
karml/models/dcmnet/dcmnet/training.py
karml/models/dcmnet/dcmnet/training_config.py
karml/models/dcmnet/dcmnet/training_multibatch.py
karml/models/dcmnet/dcmnet/utils.py
karml/models/efield/__init__.py
karml/models/efield/args.py
karml/models/efield/ase_calc_EF.py
karml/models/efield/ase_md.py
karml/models/efield/audit.py
karml/models/efield/calc_spectra.py
karml/models/efield/checkpointing.py
karml/models/efield/eval_paths.py
karml/models/efield/evaluate.py
karml/models/efield/jax_md.py
karml/models/efield/model.py
karml/models/efield/model_functions.py
karml/models/efield/notebook_md_spectra.py
karml/models/efield/packed.py
karml/models/efield/spectra_md.py
karml/models/efield/training.py
karml/models/kernnn/__init__.py
karml/models/kernnn/adapter.py
karml/models/kernnn/args.py
karml/models/kernnn/batch_apply.py
karml/models/kernnn/calculator.py
karml/models/kernnn/checkpoint.py
karml/models/kernnn/dihedrals.py
karml/models/kernnn/distances.py
karml/models/kernnn/evaluate.py
karml/models/kernnn/kernels.py
karml/models/kernnn/model.py
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karml/models/mbd/__init__.py
karml/models/mbd/calculator.py
karml/models/mbd/model.py
karml/models/mbd/qdo.py
karml/models/multipoles/__init__.py
karml/models/multipoles/config.py
karml/models/multipoles/electrostatics.py
karml/models/multipoles/model.py
karml/models/multipoles/representations.py
karml/models/physnetjax/__init__.py
karml/models/physnetjax/checkpoint_utils.py
karml/models/physnetjax/defaults/__init__.py
karml/models/physnetjax/defaults/meoh_dimer_portable.json
karml/models/physnetjax/defaults/model_config.json
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karml/models/physnetjax/physnetjax/__init__.py
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karml/models/physnetjax/physnetjax/analysis/ir.py
karml/models/physnetjax/physnetjax/analysis/plot_run.py
karml/models/physnetjax/physnetjax/analysis/povray_tool.py
karml/models/physnetjax/physnetjax/calc/__init__.py
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karml/models/physnetjax/physnetjax/calc/helper_mlp.py
karml/models/physnetjax/physnetjax/calc/pycharmm_calculator.py
karml/models/physnetjax/physnetjax/data/__init__.py
karml/models/physnetjax/physnetjax/data/batches.py
karml/models/physnetjax/physnetjax/data/cut_grid.py
karml/models/physnetjax/physnetjax/data/data.py
karml/models/physnetjax/physnetjax/data/datasets.py
karml/models/physnetjax/physnetjax/data/do_test_batches.py
karml/models/physnetjax/physnetjax/data/full_padding.py
karml/models/physnetjax/physnetjax/data/plot_data_summary.py
karml/models/physnetjax/physnetjax/data/read_ase.py
karml/models/physnetjax/physnetjax/data/read_h5.py
karml/models/physnetjax/physnetjax/data/read_npz.py
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karml/models/physnetjax/physnetjax/models/mpnn_kernels.py
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karml/models/physnetjax/physnetjax/models/spooky_model.py
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karml/neb/__init__.py
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karml/residual/__init__.py
karml/residual/build_residual.py
karml/residual/elec_fortran.py
karml/residual/electrostatics_jax.py
karml/spectra/__init__.py
karml/spectra/spectra_md.py
karml/umbrella/__init__.py
karml/umbrella/checkpoint.py
karml/umbrella/config.py
karml/umbrella/energy.py
karml/umbrella/hybrid.py
karml/umbrella/hybrid_windows.py
karml/umbrella/io.py
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karml/umbrella/rex.py
karml/umbrella/sample.py
karml/umbrella/structure.py
karml/utils/__init__.py
karml/utils/ase_structure_plot.py
karml/utils/charmm_ase.py
karml/utils/checkpoint_example.py
karml/utils/cli_args.py
karml/utils/dcd_reader.py
karml/utils/dcd_writer.py
karml/utils/domdec_ndir.py
karml/utils/domdec_psf_order.py
karml/utils/electrostatics.py
karml/utils/geometry_checks.py
karml/utils/hdf5_reporter.py
karml/utils/hybrid_optimization.py
karml/utils/intermonomer_geometry.py
karml/utils/jax_async_fix.py
karml/utils/jax_gpu_warmup.py
karml/utils/model_checkpoint.py
karml/utils/monomer_force_diag.py
karml/utils/monomer_internal_geometry.py
karml/utils/neighbor_list_snapshot.py
karml/utils/pbc_super_system_plot.py
karml/utils/potential_scan.py
karml/utils/prep_ladder_report.py
karml/utils/psf_reader.py
karml/utils/psf_subset.py
karml/utils/rich_report.py
karml/utils/rotations.py
karml/utils/simulation_utils.py
karml/utils/structure_align.py
karml/utils/training_run_check.py
karml/utils/io/__init__.py
karml/utils/io/aseTrajToData.py
karml/utils/io/parseCharmmOutput.py
karml/utils/io/parseOpenMMOutput.py
karml/utils/plotting/__init__.py
karml/utils/plotting/distributions.py
karml/utils/plotting/esp.py
karml/utils/plotting/fes.py
karml/utils/plotting/maxw.py
karml/utils/plotting/multipoles.py
karml/utils/plotting/regression.py
karml/utils/plotting/styles.py
karml/utils/plotting/trajectory_structure.py
karml/utils/transformations/__init__.py
karml/utils/transformations/dscribe_helpers.py
karml/utils/transformations/pca.py
karml/utils/transformations/tsne.py
karml/utils/visualize/__init__.py
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karml/utils/visualize/braille_molecule.py
karml/utils/visualize/povray_utils.py
karml/validation/__init__.py
karml/validation/smoke_matrix.py