.flake8
LICENSE.md
README.md
__init__.py
pyproject.toml
setup.py
version.py
./.flake8
./__init__.py
./setup.py
./version.py
./core/__init__.py
./core/basejob.py
./core/enums.py
./core/errors.py
./core/formatters.py
./core/functions.py
./core/jobmanager.py
./core/jobrunner.py
./core/logging.py
./core/private.py
./core/results.py
./core/settings.py
./core/threading_utils.py
./examples/BAND_NiO_HubbardU.py
./examples/ConvertToAMSRKFTrajectory.py
./examples/CustomASECalculator.py
./examples/MoleculesFromRKFTrajectory.py
./examples/MoleculesTable.py
./examples/QE_AMS_AFM_HubbardU.py
./examples/README.md
./examples/ReactionEnergyBenchmark.py
./examples/ReductionOxidationPotentials.py
./examples/SellaTransitionStateSearch.py
./examples/ams_crs.py
./examples/ams_pyCRS.py
./examples/balance_equations.py
./examples/generate_example.sh
./examples/get_hbonds.py
./examples/get_irspectrum.py
./examples/get_water_indices.py
./examples/molecules_ReactionEnergyBenchmark.zip
./examples/nbconvert_utils.py
./examples/numgrad.py
./examples/rkf_to_wrapped_dcd.py
./examples/ADFFrag/adffrag.ipynb
./examples/ADFFrag/adffrag.py
./examples/ADFFrag/butadiene.xyz
./examples/ADFFrag/ethene.xyz
./examples/ADFNBO/ADFNBO.ipynb
./examples/ADFNBO/ADFNBO.py
./examples/ADFVibronicDOS/ADFVibronicDOS.ipynb
./examples/ADFVibronicDOS/ADFVibronicDOS.py
./examples/AMSPlumedMD/ams_plumed.ipynb
./examples/AMSPlumedMD/ams_plumed.py
./examples/AMSSettingsInput/ams_settings_input.ipynb
./examples/AMSSettingsInput/ams_settings_input.py
./examples/AMSSettingsSystem/ams_settings_system.ipynb
./examples/AMSSettingsSystem/ams_settings_system.py
./examples/AMSTSWorkflow/diels_alder_addition.ipynb
./examples/AMSTSWorkflow/diels_alder_addition.py
./examples/ASECalculator/ASECalculator.ipynb
./examples/ASECalculator/ASECalculator.py
./examples/ASECalculator/ase_calculator.py
./examples/BandStructure/BandStructure.ipynb
./examples/BandStructure/BandStructure.py
./examples/BasicMDAnalysis/BasicMDPostanalysis.ipynb
./examples/BasicMDAnalysis/BasicMDPostanalysis.py
./examples/BasicMDAnalysis/ams.rkf
./examples/BasisSetBenchmark/BasisSetBenchmark.ipynb
./examples/BasisSetBenchmark/BasisSetBenchmark.py
./examples/COSMORSCompound/compounds_xyz.zip
./examples/COSMORSCompound/cosmors_compound.ipynb
./examples/COSMORSCompound/cosmors_compound.py
./examples/COSMORSConformers/cosmors_conformers.ipynb
./examples/COSMORSConformers/cosmors_conformers.py
./examples/ChargeTransferIntegralsADF/BenzeneDimer.xyz
./examples/ChargeTransferIntegralsADF/ChargeTransferIntegralsADF.ipynb
./examples/ChargeTransferIntegralsADF/ChargeTransferIntegralsADF.py
./examples/ChargedAMSCalculator/ChargedAMSCalculator.ipynb
./examples/ChargedAMSCalculator/ChargedAMSCalculator.py
./examples/ConformersGeneration/ConformersGeneration.py
./examples/ConformersGeneration/conformers.ipynb
./examples/ConformersGeneration/conformers.py
./examples/ConformersMultipleMolecules/conformers.ipynb
./examples/ConformersMultipleMolecules/conformers.py
./examples/ConstrainedGOAMSWorker/ConstrainedGOAMSWorker.ipynb
./examples/ConstrainedGOAMSWorker/ConstrainedGOAMSWorker.py
./examples/ExcitationsWorkflow/ExcitationsWorkflow.ipynb
./examples/ExcitationsWorkflow/ExcitationsWorkflow.py
./examples/ExcitationsWorkflow/molecules.tar
./examples/He2DissociationCurve/He2DissociationCurve.ipynb
./examples/He2DissociationCurve/He2DissociationCurve.py
./examples/IRSpectrumFromMD/ir_spectrum_from_md.ipynb
./examples/IRSpectrumFromMD/ir_spectrum_from_md.py
./examples/IonicConductivity/NaClwater.py
./examples/IonicConductivity/get_ionic_conductivity.py
./examples/JobAnalysis/job_analysis.ipynb
./examples/JobAnalysis/job_analysis.py
./examples/Logging/logging_example.ipynb
./examples/Logging/logging_example.py
./examples/M3GNet/M3GNet.ipynb
./examples/M3GNet/M3GNet.py
./examples/ManyJobsInParallel/ManyJobsInParallel.ipynb
./examples/ManyJobsInParallel/ManyJobsInParallel.py
./examples/ManyJobsInParallel/molecules.tar
./examples/MoleculeFormats/MoleculeFormats.ipynb
./examples/MoleculeFormats/MoleculeFormats.py
./examples/MoleculeSubstitution/MoleculeSubstitution.ipynb
./examples/MoleculeSubstitution/MoleculeSubstitution.py
./examples/MoleculeTools/molecule_tools.ipynb
./examples/NumGrad/NumGrad.ipynb
./examples/NumGrad/NumGrad.py
./examples/NumHess/NumHess.ipynb
./examples/NumHess/NumHess.py
./examples/PackMolExample/PackMol.ipynb
./examples/PackMolExample/PackMol.py
./examples/PlotCorrelation/plot_correlation.ipynb
./examples/PlotCorrelation/plot_correlation.py
./examples/PlotReaction2D/PlotReaction2D.ipynb
./examples/PlotReaction2D/PlotReaction2D.py
./examples/PropertyPrediction/property_prediction.ipynb
./examples/PropertyPrediction/property_prediction.py
./examples/ReactionEnergyBenchmark/ReactionEnergyBenchmark.ipynb
./examples/ReactionEnergyBenchmark/ReactionEnergyBenchmark.py
./examples/ReactionsDiscovery/reactions_discovery.ipynb
./examples/ReactionsDiscovery/reactions_discovery.py
./examples/ReorganizationEnergy/ReorganizationEnergy.ipynb
./examples/ReorganizationEnergy/ReorganizationEnergy.py
./examples/ReuseForceFieldParams/reuse_forcefield_params.ipynb
./examples/ReuseForceFieldParams/reuse_forcefield_params.py
./examples/SerenityAMS_DataTransfer_examples/C2H4.xyz
./examples/SerenityAMS_DataTransfer_examples/C2H4_CCSD.py
./examples/SerenityAMS_DataTransfer_examples/HF.xyz
./examples/SerenityAMS_DataTransfer_examples/HF_CCSD_T.py
./examples/SerenityAMS_DataTransfer_examples/N2.xyz
./examples/SerenityAMS_DataTransfer_examples/N2_CCSD.py
./examples/SerenityCalculator/example.py
./examples/SerenityCalculator/my_calculator.py
./examples/SerenityInterface_examples/dft_res.py
./examples/SerenityInterface_examples/fde.py
./examples/SerenityInterface_examples/gly-gly-gly.xyz
./examples/SerenityInterface_examples/hf_res.py
./examples/SerenityInterface_examples/hf_unres.py
./examples/SerenityInterface_examples/localization.py
./examples/SerenityInterface_examples/methylRadical.xyz
./examples/SerenityInterface_examples/mp2.py
./examples/SerenityInterface_examples/oldhf_res.py
./examples/SerenityInterface_examples/riboflavin.xyz
./examples/TuningRangeSeparation/TuningRangeSeparation.ipynb
./examples/TuningRangeSeparation/TuningRangeSeparation.py
./examples/UseLowestEnergy/UseLowestEnergy.ipynb
./examples/UseLowestEnergy/UseLowestEnergy.py
./examples/ViscosityGreenKubo/ViscosityGreenKubo.ipynb
./examples/ViscosityGreenKubo/ViscosityGreenKubo.py
./examples/WaterOptimization/water_optimization.ipynb
./examples/WaterOptimization/water_optimization.py
./examples/XRD/batio3.cif
./examples/XRD/xrd.ipynb
./examples/XRD/xrd.py
./examples/i-PI-AMS/firstframe.xyz
./examples/i-PI-AMS/input.xml
./examples/i-PI-AMS/run-ase.py
./examples/i-PI-AMS/run-server.sh
./examples/with_new_input_system/BasisSetBenchmark.py
./examples/with_new_input_system/ConformersGeneration.py
./examples/with_new_input_system/ExcitationsWorkflow.py
./examples/with_new_input_system/He2DissociationCurve.py
./examples/with_new_input_system/TuningRangeSeparation.py
./examples/with_new_input_system/WaterOptimization.py
./interfaces/__init__.py
./interfaces/adfsuite/__init__.py
./interfaces/adfsuite/ams.py
./interfaces/adfsuite/amsanalysis.py
./interfaces/adfsuite/amsworker.py
./interfaces/adfsuite/ase_calculator.py
./interfaces/adfsuite/crs.py
./interfaces/adfsuite/densf.py
./interfaces/adfsuite/fcf.py
./interfaces/adfsuite/forcefieldparams.py
./interfaces/adfsuite/inputparser.py
./interfaces/adfsuite/quickjobs.py
./interfaces/adfsuite/scmjob.py
./interfaces/adfsuite/unifac.py
./interfaces/molecule/__init__.py
./interfaces/molecule/ase.py
./interfaces/molecule/packmol.py
./interfaces/molecule/rdkit.py
./interfaces/thirdparty/__init__.py
./interfaces/thirdparty/cp2k.py
./interfaces/thirdparty/crystal.py
./interfaces/thirdparty/dftbplus.py
./interfaces/thirdparty/dirac.py
./interfaces/thirdparty/gamess.py
./interfaces/thirdparty/orca.py
./interfaces/thirdparty/raspa.py
./interfaces/thirdparty/serenity.py
./interfaces/thirdparty/serenity_calculator.py
./interfaces/thirdparty/vasp.py
./mol/__init__.py
./mol/atom.py
./mol/bond.py
./mol/context.py
./mol/identify.py
./mol/molecule.py
./mol/pdbtools.py
./recipes/__init__.py
./recipes/adfcosmorscompound.py
./recipes/adfcosmorsconformers.py
./recipes/adffragment.py
./recipes/adfnbo.py
./recipes/ams_crs.py
./recipes/assign_charged_ions.py
./recipes/counterpoise.py
./recipes/fcf_dos.py
./recipes/global_minimum.py
./recipes/numgrad.py
./recipes/numhess.py
./recipes/ox_potential.py
./recipes/redox.py
./recipes/redox_defaults.py
./recipes/redox_potential.py
./recipes/reorganization_energy.py
./recipes/md/__init__.py
./recipes/md/amsmdjob.py
./recipes/md/equilibratedensity.py
./recipes/md/greenkuboviscosity.py
./recipes/md/movingrestraints.py
./recipes/md/nvespawner.py
./recipes/md/scandensity.py
./recipes/md/trajectoryanalysis.py
./recipes/pestools/__init__.py
./recipes/pestools/optimizer.py
./recipes/ts/__init__.py
./recipes/ts/reaction_boost_workflow.py
./tools/__init__.py
./tools/converters.py
./tools/geometry.py
./tools/hbc_utilities.py
./tools/job_analysis.py
./tools/kftools.py
./tools/periodic_table.py
./tools/plams_matrix.py
./tools/plot.py
./tools/postprocess_results.py
./tools/reaction.py
./tools/reaction_energies.py
./tools/table_formatter.py
./tools/units.py
./trajectories/__init__.py
./trajectories/analysis.py
./trajectories/dcdfile.py
./trajectories/rkffile.py
./trajectories/rkfhistoryfile.py
./trajectories/sdffile.py
./trajectories/sdfhistoryfile.py
./trajectories/trajectory.py
./trajectories/trajectoryfile.py
./trajectories/xyzfile.py
./trajectories/xyzhistoryfile.py
./unit_tests/__init__.py
./unit_tests/conftest.py
./unit_tests/test_ASECalculator.py
./unit_tests/test_amsjob.py
./unit_tests/test_amsresults.py
./unit_tests/test_atom.py
./unit_tests/test_basejob.py
./unit_tests/test_bond.py
./unit_tests/test_enums.py
./unit_tests/test_functions.py
./unit_tests/test_geometry.py
./unit_tests/test_helpers.py
./unit_tests/test_identify.py
./unit_tests/test_inputparser.py
./unit_tests/test_interfaces.py
./unit_tests/test_job_analysis.py
./unit_tests/test_jobmanager.py
./unit_tests/test_jobrunner.py
./unit_tests/test_kftools.py
./unit_tests/test_logging.py
./unit_tests/test_molecule.py
./unit_tests/test_molecule_interfaces.py
./unit_tests/test_periodic_table.py
./unit_tests/test_results.py
./unit_tests/test_settings.py
./unit_tests/test_threading_utils.py
./unit_tests/test_tools_plot.py
./unit_tests/test_tools_table_formatter.py
./unit_tests/test_trajectories.py
./unit_tests/test_version.py
./unit_tests/baseline_images/test_tools_plot/plot_band_structure.png
./unit_tests/baseline_images/test_tools_plot/plot_correlation.png
./unit_tests/baseline_images/test_tools_plot/plot_grid_molecules.png
./unit_tests/baseline_images/test_tools_plot/plot_molecule.png
./unit_tests/baseline_images/test_tools_plot/plot_msd.png
./unit_tests/baseline_images/test_tools_plot/plot_phonons_band_structure.png
./unit_tests/baseline_images/test_tools_plot/plot_phonons_dos.png
./unit_tests/baseline_images/test_tools_plot/plot_work_function.png
./unit_tests/coskf/Benzene.coskf
./unit_tests/coskf/IL_anion_acetate.coskf
./unit_tests/coskf/IL_cation_ethylpyridinium.coskf
./unit_tests/coskf/Water.coskf
./unit_tests/pdb/1BXU.pdb
./unit_tests/pdb/1DYZ.pdb
./unit_tests/pdb/2kpq.pdb
./unit_tests/pdb/MET.pdb
./unit_tests/pdb/chymotrypsin.pdb
./unit_tests/pdb/pentapeptide.pdb
./unit_tests/rkf/conformers/conformers.rkf
./unit_tests/rkf/propanenitrile/ams.rkf
./unit_tests/rkf/propanenitrile/forcefield.rkf
./unit_tests/rkf/tools_plot/Al_surface/ams.rkf
./unit_tests/rkf/tools_plot/Al_surface/quantumespresso.rkf
./unit_tests/rkf/tools_plot/Diamond/ams.rkf
./unit_tests/rkf/tools_plot/Diamond/dftb.rkf
./unit_tests/rkf/tools_plot/NiO/ams.rkf
./unit_tests/rkf/tools_plot/NiO/band.rkf
./unit_tests/rkf/tools_plot/glycine-engine1/ams.rkf
./unit_tests/rkf/tools_plot/glycine-engine1/gfnff.rkf
./unit_tests/rkf/tools_plot/glycine-engine2/ams.rkf
./unit_tests/rkf/tools_plot/glycine-engine2/dftb.rkf
./unit_tests/rkf/tools_plot/md/MDStep200.rkf
./unit_tests/rkf/tools_plot/md/ams.rkf
./unit_tests/rkf/tools_plot/md/msd/msd.kf
./unit_tests/rkf/water_optimization/ams.rkf
./unit_tests/rkf/water_optimization/dftb.rkf
./unit_tests/xyz/C7H8N2_fragments.xyz
./unit_tests/xyz/CO_6_1.xyz
./unit_tests/xyz/CO_6_2.xyz
./unit_tests/xyz/CO_6_3.xyz
./unit_tests/xyz/CO_6_4.xyz
./unit_tests/xyz/CO_6_5.xyz
./unit_tests/xyz/CO_flat4_1.xyz
./unit_tests/xyz/CO_flat4_2.xyz
./unit_tests/xyz/CO_flat4_3.xyz
./unit_tests/xyz/CO_flat4_4.xyz
./unit_tests/xyz/EZ1.xyz
./unit_tests/xyz/EZ2.xyz
./unit_tests/xyz/NiO.xyz
./unit_tests/xyz/RS1.xyz
./unit_tests/xyz/RS2.xyz
./unit_tests/xyz/benzene.xyz
./unit_tests/xyz/benzene_dimer.xyz
./unit_tests/xyz/chlorophyl1.xyz
./unit_tests/xyz/chlorophyl2.xyz
./unit_tests/xyz/hydroxide.xyz
./unit_tests/xyz/multiple_mols_in_xyz.xyz
./unit_tests/xyz/product1.xyz
./unit_tests/xyz/product2.xyz
./unit_tests/xyz/reactant1.xyz
./unit_tests/xyz/reactant2.xyz
./unit_tests/xyz/water.xyz
./unit_tests/xyz/water_box.xyz
core/__init__.py
core/basejob.py
core/enums.py
core/errors.py
core/formatters.py
core/functions.py
core/jobmanager.py
core/jobrunner.py
core/logging.py
core/private.py
core/results.py
core/settings.py
core/threading_utils.py
examples/BAND_NiO_HubbardU.py
examples/ConvertToAMSRKFTrajectory.py
examples/CustomASECalculator.py
examples/MoleculesFromRKFTrajectory.py
examples/MoleculesTable.py
examples/QE_AMS_AFM_HubbardU.py
examples/README.md
examples/ReactionEnergyBenchmark.py
examples/ReductionOxidationPotentials.py
examples/SellaTransitionStateSearch.py
examples/ams_crs.py
examples/ams_pyCRS.py
examples/balance_equations.py
examples/generate_example.sh
examples/get_hbonds.py
examples/get_irspectrum.py
examples/get_water_indices.py
examples/molecules_ReactionEnergyBenchmark.zip
examples/nbconvert_utils.py
examples/numgrad.py
examples/rkf_to_wrapped_dcd.py
examples/ADFFrag/adffrag.ipynb
examples/ADFFrag/adffrag.py
examples/ADFFrag/butadiene.xyz
examples/ADFFrag/ethene.xyz
examples/ADFNBO/ADFNBO.ipynb
examples/ADFNBO/ADFNBO.py
examples/ADFVibronicDOS/ADFVibronicDOS.ipynb
examples/ADFVibronicDOS/ADFVibronicDOS.py
examples/AMSPlumedMD/ams_plumed.ipynb
examples/AMSPlumedMD/ams_plumed.py
examples/AMSSettingsInput/ams_settings_input.ipynb
examples/AMSSettingsInput/ams_settings_input.py
examples/AMSSettingsSystem/ams_settings_system.ipynb
examples/AMSSettingsSystem/ams_settings_system.py
examples/AMSTSWorkflow/diels_alder_addition.ipynb
examples/AMSTSWorkflow/diels_alder_addition.py
examples/ASECalculator/ASECalculator.ipynb
examples/ASECalculator/ASECalculator.py
examples/ASECalculator/ase_calculator.py
examples/BandStructure/BandStructure.ipynb
examples/BandStructure/BandStructure.py
examples/BasicMDAnalysis/BasicMDPostanalysis.ipynb
examples/BasicMDAnalysis/BasicMDPostanalysis.py
examples/BasicMDAnalysis/ams.rkf
examples/BasisSetBenchmark/BasisSetBenchmark.ipynb
examples/BasisSetBenchmark/BasisSetBenchmark.py
examples/COSMORSCompound/compounds_xyz.zip
examples/COSMORSCompound/cosmors_compound.ipynb
examples/COSMORSCompound/cosmors_compound.py
examples/COSMORSConformers/cosmors_conformers.ipynb
examples/COSMORSConformers/cosmors_conformers.py
examples/ChargeTransferIntegralsADF/BenzeneDimer.xyz
examples/ChargeTransferIntegralsADF/ChargeTransferIntegralsADF.ipynb
examples/ChargeTransferIntegralsADF/ChargeTransferIntegralsADF.py
examples/ChargedAMSCalculator/ChargedAMSCalculator.ipynb
examples/ChargedAMSCalculator/ChargedAMSCalculator.py
examples/ConformersGeneration/ConformersGeneration.py
examples/ConformersGeneration/conformers.ipynb
examples/ConformersGeneration/conformers.py
examples/ConformersMultipleMolecules/conformers.ipynb
examples/ConformersMultipleMolecules/conformers.py
examples/ConstrainedGOAMSWorker/ConstrainedGOAMSWorker.ipynb
examples/ConstrainedGOAMSWorker/ConstrainedGOAMSWorker.py
examples/ExcitationsWorkflow/ExcitationsWorkflow.ipynb
examples/ExcitationsWorkflow/ExcitationsWorkflow.py
examples/ExcitationsWorkflow/molecules.tar
examples/He2DissociationCurve/He2DissociationCurve.ipynb
examples/He2DissociationCurve/He2DissociationCurve.py
examples/IRSpectrumFromMD/ir_spectrum_from_md.ipynb
examples/IRSpectrumFromMD/ir_spectrum_from_md.py
examples/IonicConductivity/NaClwater.py
examples/IonicConductivity/get_ionic_conductivity.py
examples/JobAnalysis/job_analysis.ipynb
examples/JobAnalysis/job_analysis.py
examples/Logging/logging_example.ipynb
examples/Logging/logging_example.py
examples/M3GNet/M3GNet.ipynb
examples/M3GNet/M3GNet.py
examples/ManyJobsInParallel/ManyJobsInParallel.ipynb
examples/ManyJobsInParallel/ManyJobsInParallel.py
examples/ManyJobsInParallel/molecules.tar
examples/MoleculeFormats/MoleculeFormats.ipynb
examples/MoleculeFormats/MoleculeFormats.py
examples/MoleculeSubstitution/MoleculeSubstitution.ipynb
examples/MoleculeSubstitution/MoleculeSubstitution.py
examples/MoleculeTools/molecule_tools.ipynb
examples/NumGrad/NumGrad.ipynb
examples/NumGrad/NumGrad.py
examples/NumHess/NumHess.ipynb
examples/NumHess/NumHess.py
examples/PackMolExample/PackMol.ipynb
examples/PackMolExample/PackMol.py
examples/PlotCorrelation/plot_correlation.ipynb
examples/PlotCorrelation/plot_correlation.py
examples/PlotReaction2D/PlotReaction2D.ipynb
examples/PlotReaction2D/PlotReaction2D.py
examples/PropertyPrediction/property_prediction.ipynb
examples/PropertyPrediction/property_prediction.py
examples/ReactionEnergyBenchmark/ReactionEnergyBenchmark.ipynb
examples/ReactionEnergyBenchmark/ReactionEnergyBenchmark.py
examples/ReactionsDiscovery/reactions_discovery.ipynb
examples/ReactionsDiscovery/reactions_discovery.py
examples/ReorganizationEnergy/ReorganizationEnergy.ipynb
examples/ReorganizationEnergy/ReorganizationEnergy.py
examples/ReuseForceFieldParams/reuse_forcefield_params.ipynb
examples/ReuseForceFieldParams/reuse_forcefield_params.py
examples/SerenityAMS_DataTransfer_examples/C2H4.xyz
examples/SerenityAMS_DataTransfer_examples/C2H4_CCSD.py
examples/SerenityAMS_DataTransfer_examples/HF.xyz
examples/SerenityAMS_DataTransfer_examples/HF_CCSD_T.py
examples/SerenityAMS_DataTransfer_examples/N2.xyz
examples/SerenityAMS_DataTransfer_examples/N2_CCSD.py
examples/SerenityCalculator/example.py
examples/SerenityCalculator/my_calculator.py
examples/SerenityInterface_examples/dft_res.py
examples/SerenityInterface_examples/fde.py
examples/SerenityInterface_examples/gly-gly-gly.xyz
examples/SerenityInterface_examples/hf_res.py
examples/SerenityInterface_examples/hf_unres.py
examples/SerenityInterface_examples/localization.py
examples/SerenityInterface_examples/methylRadical.xyz
examples/SerenityInterface_examples/mp2.py
examples/SerenityInterface_examples/oldhf_res.py
examples/SerenityInterface_examples/riboflavin.xyz
examples/TuningRangeSeparation/TuningRangeSeparation.ipynb
examples/TuningRangeSeparation/TuningRangeSeparation.py
examples/UseLowestEnergy/UseLowestEnergy.ipynb
examples/UseLowestEnergy/UseLowestEnergy.py
examples/ViscosityGreenKubo/ViscosityGreenKubo.ipynb
examples/ViscosityGreenKubo/ViscosityGreenKubo.py
examples/WaterOptimization/water_optimization.ipynb
examples/WaterOptimization/water_optimization.py
examples/XRD/batio3.cif
examples/XRD/xrd.ipynb
examples/XRD/xrd.py
examples/i-PI-AMS/firstframe.xyz
examples/i-PI-AMS/input.xml
examples/i-PI-AMS/run-ase.py
examples/i-PI-AMS/run-server.sh
examples/with_new_input_system/BasisSetBenchmark.py
examples/with_new_input_system/ConformersGeneration.py
examples/with_new_input_system/ExcitationsWorkflow.py
examples/with_new_input_system/He2DissociationCurve.py
examples/with_new_input_system/TuningRangeSeparation.py
examples/with_new_input_system/WaterOptimization.py
interfaces/__init__.py
interfaces/adfsuite/__init__.py
interfaces/adfsuite/ams.py
interfaces/adfsuite/amsanalysis.py
interfaces/adfsuite/amsworker.py
interfaces/adfsuite/ase_calculator.py
interfaces/adfsuite/crs.py
interfaces/adfsuite/densf.py
interfaces/adfsuite/fcf.py
interfaces/adfsuite/forcefieldparams.py
interfaces/adfsuite/inputparser.py
interfaces/adfsuite/quickjobs.py
interfaces/adfsuite/scmjob.py
interfaces/adfsuite/unifac.py
interfaces/molecule/__init__.py
interfaces/molecule/ase.py
interfaces/molecule/packmol.py
interfaces/molecule/rdkit.py
interfaces/thirdparty/__init__.py
interfaces/thirdparty/cp2k.py
interfaces/thirdparty/crystal.py
interfaces/thirdparty/dftbplus.py
interfaces/thirdparty/dirac.py
interfaces/thirdparty/gamess.py
interfaces/thirdparty/orca.py
interfaces/thirdparty/raspa.py
interfaces/thirdparty/serenity.py
interfaces/thirdparty/serenity_calculator.py
interfaces/thirdparty/vasp.py
mol/__init__.py
mol/atom.py
mol/bond.py
mol/context.py
mol/identify.py
mol/molecule.py
mol/pdbtools.py
plams.egg-info/PKG-INFO
plams.egg-info/SOURCES.txt
plams.egg-info/dependency_links.txt
plams.egg-info/requires.txt
plams.egg-info/top_level.txt
recipes/__init__.py
recipes/adfcosmorscompound.py
recipes/adfcosmorsconformers.py
recipes/adffragment.py
recipes/adfnbo.py
recipes/ams_crs.py
recipes/assign_charged_ions.py
recipes/counterpoise.py
recipes/fcf_dos.py
recipes/global_minimum.py
recipes/numgrad.py
recipes/numhess.py
recipes/ox_potential.py
recipes/redox.py
recipes/redox_defaults.py
recipes/redox_potential.py
recipes/reorganization_energy.py
recipes/md/__init__.py
recipes/md/amsmdjob.py
recipes/md/equilibratedensity.py
recipes/md/greenkuboviscosity.py
recipes/md/movingrestraints.py
recipes/md/nvespawner.py
recipes/md/scandensity.py
recipes/md/trajectoryanalysis.py
recipes/pestools/__init__.py
recipes/pestools/optimizer.py
recipes/ts/__init__.py
recipes/ts/reaction_boost_workflow.py
scripts/plams
tools/__init__.py
tools/converters.py
tools/geometry.py
tools/hbc_utilities.py
tools/job_analysis.py
tools/kftools.py
tools/periodic_table.py
tools/plams_matrix.py
tools/plot.py
tools/postprocess_results.py
tools/reaction.py
tools/reaction_energies.py
tools/table_formatter.py
tools/units.py
trajectories/__init__.py
trajectories/analysis.py
trajectories/dcdfile.py
trajectories/rkffile.py
trajectories/rkfhistoryfile.py
trajectories/sdffile.py
trajectories/sdfhistoryfile.py
trajectories/trajectory.py
trajectories/trajectoryfile.py
trajectories/xyzfile.py
trajectories/xyzhistoryfile.py
unit_tests/__init__.py
unit_tests/conftest.py
unit_tests/test_ASECalculator.py
unit_tests/test_amsjob.py
unit_tests/test_amsresults.py
unit_tests/test_atom.py
unit_tests/test_basejob.py
unit_tests/test_bond.py
unit_tests/test_enums.py
unit_tests/test_functions.py
unit_tests/test_geometry.py
unit_tests/test_helpers.py
unit_tests/test_identify.py
unit_tests/test_inputparser.py
unit_tests/test_interfaces.py
unit_tests/test_job_analysis.py
unit_tests/test_jobmanager.py
unit_tests/test_jobrunner.py
unit_tests/test_kftools.py
unit_tests/test_logging.py
unit_tests/test_molecule.py
unit_tests/test_molecule_interfaces.py
unit_tests/test_periodic_table.py
unit_tests/test_results.py
unit_tests/test_settings.py
unit_tests/test_threading_utils.py
unit_tests/test_tools_plot.py
unit_tests/test_tools_table_formatter.py
unit_tests/test_trajectories.py
unit_tests/test_version.py
unit_tests/baseline_images/test_tools_plot/plot_band_structure.png
unit_tests/baseline_images/test_tools_plot/plot_correlation.png
unit_tests/baseline_images/test_tools_plot/plot_grid_molecules.png
unit_tests/baseline_images/test_tools_plot/plot_molecule.png
unit_tests/baseline_images/test_tools_plot/plot_msd.png
unit_tests/baseline_images/test_tools_plot/plot_phonons_band_structure.png
unit_tests/baseline_images/test_tools_plot/plot_phonons_dos.png
unit_tests/baseline_images/test_tools_plot/plot_work_function.png
unit_tests/coskf/Benzene.coskf
unit_tests/coskf/IL_anion_acetate.coskf
unit_tests/coskf/IL_cation_ethylpyridinium.coskf
unit_tests/coskf/Water.coskf
unit_tests/pdb/1BXU.pdb
unit_tests/pdb/1DYZ.pdb
unit_tests/pdb/2kpq.pdb
unit_tests/pdb/MET.pdb
unit_tests/pdb/chymotrypsin.pdb
unit_tests/pdb/pentapeptide.pdb
unit_tests/rkf/conformers/conformers.rkf
unit_tests/rkf/propanenitrile/ams.rkf
unit_tests/rkf/propanenitrile/forcefield.rkf
unit_tests/rkf/tools_plot/Al_surface/ams.rkf
unit_tests/rkf/tools_plot/Al_surface/quantumespresso.rkf
unit_tests/rkf/tools_plot/Diamond/ams.rkf
unit_tests/rkf/tools_plot/Diamond/dftb.rkf
unit_tests/rkf/tools_plot/NiO/ams.rkf
unit_tests/rkf/tools_plot/NiO/band.rkf
unit_tests/rkf/tools_plot/glycine-engine1/ams.rkf
unit_tests/rkf/tools_plot/glycine-engine1/gfnff.rkf
unit_tests/rkf/tools_plot/glycine-engine2/ams.rkf
unit_tests/rkf/tools_plot/glycine-engine2/dftb.rkf
unit_tests/rkf/tools_plot/md/MDStep200.rkf
unit_tests/rkf/tools_plot/md/ams.rkf
unit_tests/rkf/tools_plot/md/msd/msd.kf
unit_tests/rkf/water_optimization/ams.rkf
unit_tests/rkf/water_optimization/dftb.rkf
unit_tests/xyz/C7H8N2_fragments.xyz
unit_tests/xyz/CO_6_1.xyz
unit_tests/xyz/CO_6_2.xyz
unit_tests/xyz/CO_6_3.xyz
unit_tests/xyz/CO_6_4.xyz
unit_tests/xyz/CO_6_5.xyz
unit_tests/xyz/CO_flat4_1.xyz
unit_tests/xyz/CO_flat4_2.xyz
unit_tests/xyz/CO_flat4_3.xyz
unit_tests/xyz/CO_flat4_4.xyz
unit_tests/xyz/EZ1.xyz
unit_tests/xyz/EZ2.xyz
unit_tests/xyz/NiO.xyz
unit_tests/xyz/RS1.xyz
unit_tests/xyz/RS2.xyz
unit_tests/xyz/benzene.xyz
unit_tests/xyz/benzene_dimer.xyz
unit_tests/xyz/chlorophyl1.xyz
unit_tests/xyz/chlorophyl2.xyz
unit_tests/xyz/hydroxide.xyz
unit_tests/xyz/multiple_mols_in_xyz.xyz
unit_tests/xyz/product1.xyz
unit_tests/xyz/product2.xyz
unit_tests/xyz/reactant1.xyz
unit_tests/xyz/reactant2.xyz
unit_tests/xyz/water.xyz
unit_tests/xyz/water_box.xyz