_ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z _ __call__() (matlantis_features.features.base.FeatureBaseCaller method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature method) (matlantis_features.features.common.hessian.HessianFeature method) (matlantis_features.features.common.neb.NEBFeature method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) (matlantis_features.features.common.opt.OptFeatureBase method) (matlantis_features.features.common.vibration.VibrationFeature method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) (matlantis_features.features.md.ase_simulation.ASECheckpoint method) (matlantis_features.features.md.ase_simulation.ASETrajWriter method) (matlantis_features.features.md.md.MDFeature method) (matlantis_features.features.md.md_extensions.DeformScheduler method) (matlantis_features.features.md.md_extensions.MDExtensionBase method) (matlantis_features.features.md.md_extensions.TemperatureScheduler method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature method) (matlantis_features.features.md.post_features.rnemd_extension.RNEMDExtension method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature method) (matlantis_features.features.phonon.band.PostPhononBandFeature method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature method) (matlantis_features.features.phonon.mode.PostPhononModeFeature method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature method) (matlantis_features.features.reaction.rest_scan.RestScanFeature method) (matlantis_features.filters.MatlantisASEFilter method) (matlantis_features.filters.MatlantisFilter method) (matlantis_features.functions.eos.BirchMurnaghanEOS method) __init__() (matlantis_features.ase_ext.optimize.FIRELBFGS method) (matlantis_features.atoms.MatlantisAtoms method) (matlantis_features.features.base.FeatureBase method) (matlantis_features.features.base.FeatureBaseCaller method) (matlantis_features.features.base.FeatureBaseOutput method) (matlantis_features.features.base.FeatureBaseResult method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeatureResult method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeatureResult method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeatureResult method) (matlantis_features.features.common.hessian.HessianFeature method) (matlantis_features.features.common.hessian.HessianFeatureResult method) (matlantis_features.features.common.neb.NEBFeature method) (matlantis_features.features.common.neb.NEBFeatureOutput method) (matlantis_features.features.common.neb.NEBFeatureResult method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) (matlantis_features.features.common.opt.OptFeatureBase method) (matlantis_features.features.common.opt.OptFeatureOutput method) (matlantis_features.features.common.opt.OptFeatureResult method) (matlantis_features.features.common.vibration.FastVibrations method) (matlantis_features.features.common.vibration.FastVibrationsResult method) (matlantis_features.features.common.vibration.VibrationFeature method) (matlantis_features.features.common.vibration.VibrationFeatureResult method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeatureResult method) (matlantis_features.features.elasticity.elastic_properties.ElasticProperties method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensor method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) (matlantis_features.features.elasticity.tensors.DeformTensor method) (matlantis_features.features.elasticity.tensors.DeformTensorList method) (matlantis_features.features.elasticity.tensors.StrainTensor method) (matlantis_features.features.elasticity.tensors.StrainTensorList method) (matlantis_features.features.elasticity.tensors.StressTensor method) (matlantis_features.features.elasticity.tensors.StressTensorList method) (matlantis_features.features.md.ase_integrators.AndersenIntegrator method) (matlantis_features.features.md.ase_integrators.ASEIntegrator method) (matlantis_features.features.md.ase_integrators.LangevinIntegrator method) (matlantis_features.features.md.ase_integrators.NPTBerendsenIntegrator method) (matlantis_features.features.md.ase_integrators.NPTIntegrator method) (matlantis_features.features.md.ase_integrators.NVTBerendsenIntegrator method) (matlantis_features.features.md.ase_integrators.VelocityVerletIntegrator method) (matlantis_features.features.md.ase_md_system.ASEMDState method) (matlantis_features.features.md.ase_md_system.ASEMDSystem method) (matlantis_features.features.md.ase_simulation.ASECheckpoint method) (matlantis_features.features.md.ase_simulation.ASESimulation method) (matlantis_features.features.md.ase_simulation.ASETrajWriter method) (matlantis_features.features.md.md.MDFeature method) (matlantis_features.features.md.md.MDFeatureResult method) (matlantis_features.features.md.md_extensions.DeformScheduler method) (matlantis_features.features.md.md_extensions.MDExtensionBase method) (matlantis_features.features.md.md_extensions.TemperatureScheduler method) (matlantis_features.features.md.md_integrator_base.MDIntegratorBase method) (matlantis_features.features.md.md_simulation_base.MDSimulationBase method) (matlantis_features.features.md.md_system_base.MDSystemBase method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeatureResult method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeatureResult method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeatureResult method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeatureResult method) (matlantis_features.features.md.post_features.rnemd_extension.RNEMDExtension method) (matlantis_features.features.md.post_features.specific_heat.EnthalpyResult method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeatureResult method) (matlantis_features.features.md.post_features.specific_heat.SpecificHeatResult method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeatureResult method) (matlantis_features.features.md.post_features.thermal_expansion.ThermalExpansionResult method) (matlantis_features.features.md.post_features.thermal_expansion.VolumeResult method) (matlantis_features.features.phonon.band.PostPhononBandFeature method) (matlantis_features.features.phonon.band.PostPhononBandFeatureResult method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature method) (matlantis_features.features.phonon.dos.PostPhononDOSFeatureResult method) (matlantis_features.features.phonon.force_constant.FastPhonons method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature method) (matlantis_features.features.phonon.force_constant.ForceConstantFeatureResult method) (matlantis_features.features.phonon.mode.PostPhononModeFeature method) (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult method) (matlantis_features.features.phonon.symmetry.SymmetryOperations method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult method) (matlantis_features.features.phonon.utils.KptPath method) (matlantis_features.features.phonon.utils.PhononFrequency method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureOutput method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult method) (matlantis_features.features.reaction.rest_scan.RestScanFeature method) (matlantis_features.features.reaction.rest_scan.RestScanFeatureResult method) (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) (matlantis_features.features.reaction.rest_scan.ScanRestraint method) (matlantis_features.filters.ExpCellASEFilter method) (matlantis_features.filters.IsotropicASEFilter method) (matlantis_features.filters.IsotropicFilter method) (matlantis_features.filters.MatlantisASEFilter method) (matlantis_features.filters.StrainASEFilter method) (matlantis_features.filters.UnitCellASEFilter method) (matlantis_features.functions.eos.BirchMurnaghanEOS method) (matlantis_features.utils.atoms_util.MoleculeLinearity method) A acf_avg (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult attribute) acf_segment (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult attribute) adjust_forces() (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) (matlantis_features.features.reaction.rest_scan.ScanRestraint method) adjust_momenta() (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) (matlantis_features.features.reaction.rest_scan.ScanRestraint method) adjust_positions() (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) (matlantis_features.features.reaction.rest_scan.ScanRestraint method) all_forces (matlantis_features.features.common.vibration.FastVibrationsResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) amplitude (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult attribute) AndersenIntegrator (class in matlantis_features.features.md.ase_integrators) append_extension() (matlantis_features.features.md.ase_simulation.ASESimulation method) ase_atoms (matlantis_features.atoms.MatlantisAtoms property) ASECheckpoint (class in matlantis_features.features.md.ase_simulation) ASEIntegrator (class in matlantis_features.features.md.ase_integrators) ASEMDState (class in matlantis_features.features.md.ase_md_system) ASEMDSystem (class in matlantis_features.features.md.ase_md_system) ASEOptFeature (class in matlantis_features.features.common.opt) ASESimulation (class in matlantis_features.features.md.ase_simulation) ASETrajWriter (class in matlantis_features.features.md.ase_simulation) atom_indices (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) atoms (matlantis_features.features.common.hessian.HessianFeatureResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) attach() (matlantis_features.ase_ext.optimize.FIRELBFGS method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) attach_ctx() (matlantis_features.features.base.FeatureBase method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature method) (matlantis_features.features.common.hessian.HessianFeature method) (matlantis_features.features.common.neb.NEBFeature method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) (matlantis_features.features.common.opt.OptFeatureBase method) (matlantis_features.features.common.vibration.VibrationFeature method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) (matlantis_features.features.md.md.MDFeature method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature method) (matlantis_features.features.phonon.band.PostPhononBandFeature method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature method) (matlantis_features.features.phonon.mode.PostPhononModeFeature method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature method) (matlantis_features.features.reaction.rest_scan.RestScanFeature method) B BFGSASEOptFeature (class in matlantis_features.features.common.opt) BFGSLineSearchASEOptFeature (class in matlantis_features.features.common.opt) BirchMurnaghanEOS (class in matlantis_features.functions.eos) C calculate_dihedral() (in module matlantis_features.features.reaction.rest_scan) calculator_info (matlantis_features.features.base.FeatureBaseResult attribute) (matlantis_features.features.common.neb.NEBFeatureResult attribute) (matlantis_features.features.common.opt.OptFeatureResult attribute) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult attribute) call_decorate() (matlantis_features.features.base.FeatureBaseCaller class method) call_observers() (matlantis_features.ase_ext.optimize.FIRELBFGS method) call_params (matlantis_features.features.base.FeatureBaseResult attribute) (matlantis_features.features.common.neb.NEBFeatureResult attribute) (matlantis_features.features.common.opt.OptFeatureResult attribute) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult attribute) check_elastic_tensor_symmetry() (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) check_estimator_fn() (matlantis_features.features.base.FeatureBase method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature method) (matlantis_features.features.common.hessian.HessianFeature method) (matlantis_features.features.common.neb.NEBFeature method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) (matlantis_features.features.common.opt.OptFeatureBase method) (matlantis_features.features.common.vibration.VibrationFeature method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) (matlantis_features.features.md.md.MDFeature method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature method) (matlantis_features.features.phonon.band.PostPhononBandFeature method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature method) (matlantis_features.features.phonon.mode.PostPhononModeFeature method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature method) (matlantis_features.features.reaction.rest_scan.RestScanFeature method) check_linearity() (in module matlantis_features.utils.atoms_util) check_nonlinear() (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) check_symmetry_number() (in module matlantis_features.utils.atoms_util) check_zero_elems() (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) checkpoint_path (matlantis_features.features.md.md.MDFeatureResult attribute) close() (matlantis_features.ase_ext.optimize.FIRELBFGS method) (matlantis_features.features.md.ase_simulation.ASETrajWriter method) closelater() (matlantis_features.ase_ext.optimize.FIRELBFGS method) ComplexElasticFeature (class in matlantis_features.features.elasticity.complex_elastic_feature) ComplexElasticFeatureResult (class in matlantis_features.features.elasticity.complex_elastic_feature) ComplexGasFormationEnthalpyFeature (class in matlantis_features.features.common.gas_formation_enthalpy) ComplexGasFormationEnthalpyFeatureResult (class in matlantis_features.features.common.gas_formation_enthalpy) ComplexNEMDThermalConductivityFeature (class in matlantis_features.features.md.post_features.nemd_thermal_conductivity) ComplexNEMDThermalConductivityFeatureResult (class in matlantis_features.features.md.post_features.nemd_thermal_conductivity) ComplexNEMDViscosityFeature (class in matlantis_features.features.md.post_features.nemd_viscosity) ComplexNEMDViscosityFeatureResult (class in matlantis_features.features.md.post_features.nemd_viscosity) converged (matlantis_features.features.reaction.rest_scan.RestScanFeatureResult attribute) converged() (matlantis_features.ase_ext.optimize.FIRELBFGS method) convert_atoms_to_upper() (in module matlantis_features.utils.atoms_util) coords (matlantis_features.features.phonon.band.PostPhononBandFeatureResult attribute) copy() (matlantis_features.atoms.MatlantisAtoms method) copy_to_child_conversion() (in module matlantis_features.features.base) cost_estimate() (matlantis_features.features.base.FeatureBase method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature method) (matlantis_features.features.common.hessian.HessianFeature method) (matlantis_features.features.common.neb.NEBFeature method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) (matlantis_features.features.common.opt.OptFeatureBase method) (matlantis_features.features.common.vibration.VibrationFeature method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) (matlantis_features.features.md.md.MDFeature method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature method) (matlantis_features.features.phonon.band.PostPhononBandFeature method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature method) (matlantis_features.features.phonon.mode.PostPhononModeFeature method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature method) (matlantis_features.features.reaction.rest_scan.RestScanFeature method) create_ase_dynamics() (matlantis_features.features.md.ase_integrators.AndersenIntegrator method) (matlantis_features.features.md.ase_integrators.ASEIntegrator method) (matlantis_features.features.md.ase_integrators.LangevinIntegrator method) (matlantis_features.features.md.ase_integrators.NPTBerendsenIntegrator method) (matlantis_features.features.md.ase_integrators.NPTIntegrator method) (matlantis_features.features.md.ase_integrators.NVTBerendsenIntegrator method) (matlantis_features.features.md.ase_integrators.VelocityVerletIntegrator method) D DeformScheduler (class in matlantis_features.features.md.md_extensions) DeformTensor (class in matlantis_features.features.elasticity.tensors) DeformTensorList (class in matlantis_features.features.elasticity.tensors) delta (matlantis_features.features.common.hessian.HessianFeatureResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) (matlantis_features.features.phonon.force_constant.ForceConstantFeatureResult attribute) dict (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeatureResult attribute) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeatureResult attribute) (matlantis_features.features.common.hessian.HessianFeatureResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) (matlantis_features.features.phonon.band.PostPhononBandFeatureResult attribute) (matlantis_features.features.phonon.dos.PostPhononDOSFeatureResult attribute) (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult attribute) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) diffusion_coefficient (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) diffusion_coefficient_converter() (in module matlantis_features.utils.units_util) diffusion_coefficient_converter_old() (in module matlantis_features.utils.units_util) diffusion_coefficient_molecule (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) diffusion_coefficient_molecule_std (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) diffusion_coefficient_std (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) direction (matlantis_features.features.common.hessian.HessianFeatureResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) dos (matlantis_features.features.phonon.dos.PostPhononDOSFeatureResult attribute) draw_phase_diagram() (in module matlantis_features.features.phonon.qha_gibbs_free_energy) dump() (matlantis_features.ase_ext.optimize.FIRELBFGS method) E effective_msd_range (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) elastic_properties (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeatureResult attribute) elastic_tensor (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeatureResult attribute) ElasticProperties (class in matlantis_features.features.elasticity.elastic_properties) ElasticTensor (class in matlantis_features.features.elasticity.elastic_tensor) ElasticTensorFeature (class in matlantis_features.features.elasticity.elastic_tensor) energy (matlantis_features.features.phonon.dos.PostPhononDOSFeatureResult attribute) enthalpy (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeatureResult attribute) (matlantis_features.features.md.post_features.specific_heat.EnthalpyResult attribute) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeatureResult attribute) EnthalpyResult (class in matlantis_features.features.md.post_features.specific_heat) entropy (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeatureResult attribute) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) equilibrium_volume (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult attribute) expand_units() (in module matlantis_features.features.elasticity.elastic_properties) ExpCellASEFilter (class in matlantis_features.filters) F FastPhonons (class in matlantis_features.features.phonon.force_constant) FastVibrations (class in matlantis_features.features.common.vibration) FastVibrationsResult (class in matlantis_features.features.common.vibration) feature (matlantis_features.features.base.FeatureBaseResult attribute) (matlantis_features.features.common.neb.NEBFeatureResult attribute) (matlantis_features.features.common.opt.OptFeatureResult attribute) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult attribute) FeatureBase (class in matlantis_features.features.base) FeatureBaseCaller (class in matlantis_features.features.base) FeatureBaseOutput (class in matlantis_features.features.base) FeatureBaseResult (class in matlantis_features.features.base) FireASEOptFeature (class in matlantis_features.features.common.opt) FIRELBFGS (class in matlantis_features.ase_ext.optimize) FireLBFGSASEOptFeature (class in matlantis_features.features.common.opt) fit_diffusion_coefficients() (in module matlantis_features.features.md.post_features.diffusion) fit_slope() (in module matlantis_features.features.md.post_features.rnemd_extension) fitting_result_linear() (matlantis_features.features.elasticity.elastic_tensor.ElasticTensor method) force_constant (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) (matlantis_features.features.phonon.force_constant.ForceConstantFeatureResult attribute) force_constant_list (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult attribute) ForceConstantFeature (class in matlantis_features.features.phonon.force_constant) ForceConstantFeatureResult (class in matlantis_features.features.phonon.force_constant) formation_enthalpy (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeatureResult attribute) frequencies (matlantis_features.features.common.vibration.FastVibrationsResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult attribute) frequency (matlantis_features.features.phonon.band.PostPhononBandFeatureResult attribute) frequency_converter() (in module matlantis_features.utils.units_util) from_ase_atoms() (matlantis_features.atoms.MatlantisAtoms class method) from_dict() (matlantis_features.atoms.MatlantisAtoms class method) (matlantis_features.features.base.FeatureBase class method) (matlantis_features.features.base.FeatureBaseOutput class method) (matlantis_features.features.base.FeatureBaseResult class method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature class method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature class method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature class method) (matlantis_features.features.common.hessian.HessianFeature class method) (matlantis_features.features.common.neb.NEBFeature class method) (matlantis_features.features.common.neb.NEBFeatureOutput class method) (matlantis_features.features.common.neb.NEBFeatureResult class method) (matlantis_features.features.common.opt.ASEOptFeature class method) (matlantis_features.features.common.opt.BFGSASEOptFeature class method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature class method) (matlantis_features.features.common.opt.FireASEOptFeature class method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature class method) (matlantis_features.features.common.opt.LBFGSASEOptFeature class method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature class method) (matlantis_features.features.common.opt.MDMinASEOptFeature class method) (matlantis_features.features.common.opt.OptFeatureBase class method) (matlantis_features.features.common.opt.OptFeatureOutput class method) (matlantis_features.features.common.opt.OptFeatureResult class method) (matlantis_features.features.common.vibration.VibrationFeature class method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature class method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature class method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature class method) (matlantis_features.features.md.md.MDFeature class method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature class method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature class method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity class method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature class method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature class method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature class method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature class method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity class method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature class method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature class method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature class method) (matlantis_features.features.phonon.band.PostPhononBandFeature class method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature class method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature class method) (matlantis_features.features.phonon.mode.PostPhononModeFeature class method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature class method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature class method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature class method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureOutput class method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult class method) (matlantis_features.features.reaction.rest_scan.RestScanFeature class method) (matlantis_features.filters.MatlantisFilter class method) from_elastic_tensor() (matlantis_features.features.elasticity.elastic_properties.ElasticProperties class method) from_file() (matlantis_features.atoms.MatlantisAtoms class method) (matlantis_features.features.md.ase_md_system.ASEMDState static method) from_fit() (matlantis_features.functions.eos.BirchMurnaghanEOS class method) from_rdkit_mol() (matlantis_features.atoms.MatlantisAtoms class method) from_smiles() (matlantis_features.atoms.MatlantisAtoms class method) from_strain_tensors() (matlantis_features.features.elasticity.tensors.DeformTensorList class method) from_strains() (matlantis_features.features.elasticity.tensors.StrainTensorList class method) from_stress_strain() (matlantis_features.features.elasticity.elastic_tensor.ElasticTensor class method) from_traj_obj() (matlantis_features.features.md.md.MDFeatureResult class method) from_trajectory() (matlantis_features.features.reaction.rest_scan.RestScanFeatureResult class method) G GasStandardFormationEnthalpyFeature (class in matlantis_features.features.common.gas_formation_enthalpy) GasStandardFormationEnthalpyFeatureResult (class in matlantis_features.features.common.gas_formation_enthalpy) get_brillouin_zone_3d() (in module matlantis_features.utils.visual_utils.brillouin_zone) get_by_voigt() (matlantis_features.features.elasticity.tensors.DeformTensor method) (matlantis_features.features.elasticity.tensors.StrainTensor method) (matlantis_features.features.elasticity.tensors.StressTensor method) get_calculator() (in module matlantis_features.utils.calculators.pfp_api_calculator) get_coefficient() (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) (matlantis_features.features.reaction.rest_scan.ScanRestraint method) get_colvar() (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) (matlantis_features.features.reaction.rest_scan.ScanRestraint method) get_colvar_forces() (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) (matlantis_features.features.reaction.rest_scan.ScanRestraint method) get_directional_linear_compressibility() (matlantis_features.features.elasticity.elastic_properties.ElasticProperties method) get_directional_poisson_ratio() (matlantis_features.features.elasticity.elastic_properties.ElasticProperties method) get_directional_shear_modulus() (matlantis_features.features.elasticity.elastic_properties.ElasticProperties method) get_directional_young_modulus() (matlantis_features.features.elasticity.elastic_properties.ElasticProperties method) get_frequency() (matlantis_features.features.phonon.utils.PhononFrequency method) get_frequency_mode() (matlantis_features.features.phonon.utils.PhononFrequency method) get_global_number_of_atoms() (matlantis_features.filters.IsotropicFilter method) get_images() (matlantis_features.features.reaction.rest_scan.RestScanFeatureResult method) get_inertia_tensor() (in module matlantis_features.utils.atoms_util) get_k_mesh() (in module matlantis_features.features.phonon.utils) get_kinetic_energy() (matlantis_features.filters.IsotropicFilter method) get_least_displacements_from_symmetry() (in module matlantis_features.features.phonon.symmetry) get_msd() (in module matlantis_features.features.md.post_features.diffusion) get_number_of_steps() (matlantis_features.ase_ext.optimize.FIRELBFGS method) get_permutations() (in module matlantis_features.features.phonon.symmetry) (matlantis_features.features.phonon.symmetry.SymmetryOperations method) get_permutations_on_atom() (matlantis_features.features.phonon.symmetry.SymmetryOperations method) get_primitive_structure() (in module matlantis_features.features.phonon.utils) get_primitive_structure_auto() (in module matlantis_features.features.phonon.utils) get_primitive_structure_from_primitive_matrix() (in module matlantis_features.features.phonon.utils) get_prop_results() (matlantis_features.features.elasticity.elastic_properties.ElasticProperties method) get_removed_dof() (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) (matlantis_features.features.reaction.rest_scan.ScanRestraint method) get_rotation_on_atom() (matlantis_features.features.phonon.symmetry.SymmetryOperations method) get_rotations_coord() (matlantis_features.features.phonon.symmetry.SymmetryOperations method) get_samples() (matlantis_features.features.elasticity.tensors.StrainTensorList method) (matlantis_features.features.elasticity.tensors.StressTensorList method) get_savedir_from_ctx() (matlantis_features.features.base.FeatureBase method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature method) (matlantis_features.features.common.hessian.HessianFeature method) (matlantis_features.features.common.neb.NEBFeature method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) (matlantis_features.features.common.opt.OptFeatureBase method) (matlantis_features.features.common.vibration.VibrationFeature method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) (matlantis_features.features.md.md.MDFeature method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature method) (matlantis_features.features.phonon.band.PostPhononBandFeature method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature method) (matlantis_features.features.phonon.mode.PostPhononModeFeature method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature method) (matlantis_features.features.reaction.rest_scan.RestScanFeature method) get_stress() (matlantis_features.filters.IsotropicFilter method) get_symmetry_lattice() (in module matlantis_features.features.elasticity.utils) get_temp_dir() (matlantis_features.features.md.md.MDFeature method) get_temperature() (matlantis_features.filters.IsotropicFilter method) get_total_energy() (matlantis_features.filters.IsotropicFilter method) get_total_inertia() (in module matlantis_features.utils.atoms_util) get_traj_obj() (matlantis_features.features.md.md.MDFeatureResult method) get_translations_on_atom() (matlantis_features.features.phonon.symmetry.SymmetryOperations method) get_volume_under_pressure() (matlantis_features.functions.eos.BirchMurnaghanEOS method) gibbs_free_energy (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeatureResult attribute) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult attribute) H H (matlantis_features.features.common.hessian.HessianFeatureResult attribute) (matlantis_features.features.common.vibration.FastVibrationsResult attribute) helmholtz_free_energy (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult attribute) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) helmholtz_free_energy_converter() (in module matlantis_features.utils.units_util) HessianFeature (class in matlantis_features.features.common.hessian) HessianFeatureResult (class in matlantis_features.features.common.hessian) I ij_to_voigt() (in module matlantis_features.features.elasticity.utils) image_frequencies (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) include_lattice_energy (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) index_shuffle() (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) indices (matlantis_features.features.common.hessian.HessianFeatureResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) init_scope() (matlantis_features.features.base.FeatureBase method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature method) (matlantis_features.features.common.hessian.HessianFeature method) (matlantis_features.features.common.neb.NEBFeature method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) (matlantis_features.features.common.opt.OptFeatureBase method) (matlantis_features.features.common.vibration.VibrationFeature method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) (matlantis_features.features.md.md.MDFeature method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature method) (matlantis_features.features.phonon.band.PostPhononBandFeature method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature method) (matlantis_features.features.phonon.mode.PostPhononModeFeature method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature method) (matlantis_features.features.reaction.rest_scan.RestScanFeature method) init_temperature() (matlantis_features.features.md.ase_md_system.ASEMDSystem method) init_time (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) initialize() (matlantis_features.ase_ext.optimize.FIRELBFGS method) insert_observer() (matlantis_features.ase_ext.optimize.FIRELBFGS method) internal_energy (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) irun() (matlantis_features.ase_ext.optimize.FIRELBFGS method) is_voigt_diag() (in module matlantis_features.features.elasticity.utils) IsotropicASEFilter (class in matlantis_features.filters) IsotropicFilter (class in matlantis_features.filters) K k_point (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult attribute) KptPath (class in matlantis_features.features.phonon.utils) kpts (matlantis_features.features.phonon.band.PostPhononBandFeatureResult attribute) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult attribute) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) L labels (matlantis_features.features.phonon.band.PostPhononBandFeatureResult attribute) LangevinIntegrator (class in matlantis_features.features.md.ase_integrators) LBFGSASEOptFeature (class in matlantis_features.features.common.opt) LBFGSLineSearchASEOptFeature (class in matlantis_features.features.common.opt) length_x (matlantis_features.features.md.post_features.thermal_expansion.VolumeResult attribute) length_y (matlantis_features.features.md.post_features.thermal_expansion.VolumeResult attribute) length_z (matlantis_features.features.md.post_features.thermal_expansion.VolumeResult attribute) linear_expansion_coeffcient (matlantis_features.features.md.post_features.thermal_expansion.ThermalExpansionResult attribute) linear_expansion_coeffcient_x (matlantis_features.features.md.post_features.thermal_expansion.ThermalExpansionResult attribute) linear_expansion_coeffcient_y (matlantis_features.features.md.post_features.thermal_expansion.ThermalExpansionResult attribute) linear_expansion_coeffcient_z (matlantis_features.features.md.post_features.thermal_expansion.ThermalExpansionResult attribute) load() (matlantis_features.ase_ext.optimize.FIRELBFGS method) (matlantis_features.features.base.FeatureBaseResult class method) (matlantis_features.features.common.neb.NEBFeatureResult class method) (matlantis_features.features.common.opt.OptFeatureResult class method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult class method) log() (matlantis_features.ase_ext.optimize.FIRELBFGS method) M make_deformed_atoms() (in module matlantis_features.features.elasticity.elastic_tensor) map2d() (in module matlantis_features.features.elasticity.utils) matlantis_features.ase_ext.optimize module matlantis_features.atoms module matlantis_features.features.base module matlantis_features.features.common.gas_formation_enthalpy module matlantis_features.features.common.gas_thermo module matlantis_features.features.common.hessian module matlantis_features.features.common.neb module matlantis_features.features.common.opt module matlantis_features.features.common.vibration module matlantis_features.features.elasticity.complex_elastic_feature module matlantis_features.features.elasticity.elastic_properties module matlantis_features.features.elasticity.elastic_tensor module matlantis_features.features.elasticity.tensors module matlantis_features.features.elasticity.utils module matlantis_features.features.md.ase_integrators module matlantis_features.features.md.ase_md_system module matlantis_features.features.md.ase_simulation module matlantis_features.features.md.md module matlantis_features.features.md.md_extensions module matlantis_features.features.md.md_integrator_base module matlantis_features.features.md.md_simulation_base module matlantis_features.features.md.md_system_base module matlantis_features.features.md.post_features.diffusion module matlantis_features.features.md.post_features.emd_viscosity module matlantis_features.features.md.post_features.nemd_thermal_conductivity module matlantis_features.features.md.post_features.nemd_viscosity module matlantis_features.features.md.post_features.rnemd_extension module matlantis_features.features.md.post_features.specific_heat module matlantis_features.features.md.post_features.thermal_expansion module matlantis_features.features.phonon.band module matlantis_features.features.phonon.dos module matlantis_features.features.phonon.force_constant module matlantis_features.features.phonon.mode module matlantis_features.features.phonon.qha_gibbs_free_energy module matlantis_features.features.phonon.symmetry module matlantis_features.features.phonon.thermo module matlantis_features.features.phonon.utils module matlantis_features.features.reaction.reaction_string module matlantis_features.features.reaction.rest_scan module matlantis_features.filters module matlantis_features.functions.eos module matlantis_features.utils.atoms_util module matlantis_features.utils.calculators.pfp_api_calculator module matlantis_features.utils.units_util module matlantis_features.utils.visual_utils module matlantis_features.utils.visual_utils.brillouin_zone module MatlantisASEFilter (class in matlantis_features.filters) MatlantisAtoms (class in matlantis_features.atoms) MatlantisFilter (class in matlantis_features.filters) MDExtensionBase (class in matlantis_features.features.md.md_extensions) MDFeature (class in matlantis_features.features.md.md) MDFeatureResult (class in matlantis_features.features.md.md) MDIntegratorBase (class in matlantis_features.features.md.md_integrator_base) MDMinASEOptFeature (class in matlantis_features.features.common.opt) MDSimulationBase (class in matlantis_features.features.md.md_simulation_base) MDSystemBase (class in matlantis_features.features.md.md_system_base) mean_squared_displacement (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) mean_squared_displacement_molecule (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) method (matlantis_features.features.common.hessian.HessianFeatureResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) mode (matlantis_features.features.common.vibration.FastVibrationsResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) mode_indices (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult attribute) module matlantis_features.ase_ext.optimize matlantis_features.atoms matlantis_features.features.base matlantis_features.features.common.gas_formation_enthalpy matlantis_features.features.common.gas_thermo matlantis_features.features.common.hessian matlantis_features.features.common.neb matlantis_features.features.common.opt matlantis_features.features.common.vibration matlantis_features.features.elasticity.complex_elastic_feature matlantis_features.features.elasticity.elastic_properties matlantis_features.features.elasticity.elastic_tensor matlantis_features.features.elasticity.tensors matlantis_features.features.elasticity.utils matlantis_features.features.md.ase_integrators matlantis_features.features.md.ase_md_system matlantis_features.features.md.ase_simulation matlantis_features.features.md.md matlantis_features.features.md.md_extensions matlantis_features.features.md.md_integrator_base matlantis_features.features.md.md_simulation_base matlantis_features.features.md.md_system_base matlantis_features.features.md.post_features.diffusion matlantis_features.features.md.post_features.emd_viscosity matlantis_features.features.md.post_features.nemd_thermal_conductivity matlantis_features.features.md.post_features.nemd_viscosity matlantis_features.features.md.post_features.rnemd_extension matlantis_features.features.md.post_features.specific_heat matlantis_features.features.md.post_features.thermal_expansion matlantis_features.features.phonon.band matlantis_features.features.phonon.dos matlantis_features.features.phonon.force_constant matlantis_features.features.phonon.mode matlantis_features.features.phonon.qha_gibbs_free_energy matlantis_features.features.phonon.symmetry matlantis_features.features.phonon.thermo matlantis_features.features.phonon.utils matlantis_features.features.reaction.reaction_string matlantis_features.features.reaction.rest_scan matlantis_features.filters matlantis_features.functions.eos matlantis_features.utils.atoms_util matlantis_features.utils.calculators.pfp_api_calculator matlantis_features.utils.units_util matlantis_features.utils.visual_utils matlantis_features.utils.visual_utils.brillouin_zone molecule (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) MoleculeLinearity (class in matlantis_features.utils.atoms_util) mro() (matlantis_features.features.base.FeatureBaseCaller method) N n_images (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult attribute) name (matlantis_features.features.phonon.force_constant.ForceConstantFeatureResult attribute) NEBFeature (class in matlantis_features.features.common.neb) NEBFeatureOutput (class in matlantis_features.features.common.neb) NEBFeatureResult (class in matlantis_features.features.common.neb) nfree (matlantis_features.features.common.hessian.HessianFeatureResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) NPTBerendsenIntegrator (class in matlantis_features.features.md.ase_integrators) NPTIntegrator (class in matlantis_features.features.md.ase_integrators) num_effective_modes (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) num_modes (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) num_of_segments (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult attribute) number_of_segments (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) numbers (matlantis_features.atoms.MatlantisAtoms property) NVTBerendsenIntegrator (class in matlantis_features.features.md.ase_integrators) O observe() (matlantis_features.features.reaction.rest_scan.ScanDihedral method) OldPostMDDiffusionFeature (class in matlantis_features.features.md.post_features.diffusion) OldPostMDDiffusionFeatureResult (class in matlantis_features.features.md.post_features.diffusion) openfile() (matlantis_features.ase_ext.optimize.FIRELBFGS method) OptFeatureBase (class in matlantis_features.features.common.opt) OptFeatureOutput (class in matlantis_features.features.common.opt) OptFeatureResult (class in matlantis_features.features.common.opt) output (matlantis_features.features.base.FeatureBaseResult attribute) (matlantis_features.features.common.neb.NEBFeatureResult attribute) (matlantis_features.features.common.opt.OptFeatureResult attribute) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult attribute) P pfp_estimator_fn() (in module matlantis_features.utils.calculators.pfp_api_calculator) PhononFrequency (class in matlantis_features.features.phonon.utils) plot() (matlantis_features.features.common.neb.NEBFeatureResult method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeatureResult method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeatureResult method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeatureResult method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeatureResult method) (matlantis_features.features.phonon.band.PostPhononBandFeatureResult method) (matlantis_features.features.phonon.dos.PostPhononDOSFeatureResult method) (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult method) (matlantis_features.features.reaction.rest_scan.RestScanFeatureResult method) plot_3d() (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult method) plot_band_dos() (in module matlantis_features.features.phonon.band) plot_energy() (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult method) positions (matlantis_features.atoms.MatlantisAtoms property) post_nemd_thermal_conductivity_result (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeatureResult attribute) post_nemd_viscosity_result (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeatureResult attribute) PostElasticPropertiesFeature (class in matlantis_features.features.elasticity.elastic_properties) PostEMDViscosity (class in matlantis_features.features.md.post_features.emd_viscosity) PostEMDViscosityFeature (class in matlantis_features.features.md.post_features.emd_viscosity) PostEMDViscosityFeatureResult (class in matlantis_features.features.md.post_features.emd_viscosity) PostMDDiffusionFeature (class in matlantis_features.features.md.post_features.diffusion) PostMDDiffusionFeatureResult (class in matlantis_features.features.md.post_features.diffusion) PostMDSpecificHeatFeature (class in matlantis_features.features.md.post_features.specific_heat) PostMDSpecificHeatFeatureResult (class in matlantis_features.features.md.post_features.specific_heat) PostMDThermalExpansionFeature (class in matlantis_features.features.md.post_features.thermal_expansion) PostMDThermalExpansionFeatureResult (class in matlantis_features.features.md.post_features.thermal_expansion) PostNEMDThermalConductivityFeature (class in matlantis_features.features.md.post_features.nemd_thermal_conductivity) PostNEMDThermalConductivityFeatureResult (class in matlantis_features.features.md.post_features.nemd_thermal_conductivity) PostNEMDViscosity (class in matlantis_features.features.md.post_features.nemd_viscosity) PostNEMDViscosityFeature (class in matlantis_features.features.md.post_features.nemd_viscosity) PostNEMDViscosityFeatureResult (class in matlantis_features.features.md.post_features.nemd_viscosity) PostPhononBandFeature (class in matlantis_features.features.phonon.band) PostPhononBandFeatureResult (class in matlantis_features.features.phonon.band) PostPhononDOSFeature (class in matlantis_features.features.phonon.dos) PostPhononDOSFeatureResult (class in matlantis_features.features.phonon.dos) PostPhononModeFeature (class in matlantis_features.features.phonon.mode) PostPhononModeFeatureResult (class in matlantis_features.features.phonon.mode) PostPhononQHAGibbsFeature (class in matlantis_features.features.phonon.qha_gibbs_free_energy) PostPhononQHAGibbsFeatureResult (class in matlantis_features.features.phonon.qha_gibbs_free_energy) PostPhononThermochemistryFeature (class in matlantis_features.features.phonon.thermo) PostPhononThermochemistryFeatureResult (class in matlantis_features.features.phonon.thermo) PostVibrationGasThermoFeature (class in matlantis_features.features.common.gas_thermo) PostVibrationGasThermoFeatureResult (class in matlantis_features.features.common.gas_thermo) potential_energy (matlantis_features.features.common.vibration.VibrationFeatureResult attribute) pressure (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeatureResult attribute) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeatureResult attribute) pressure_converter() (in module matlantis_features.utils.units_util) pressures (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult attribute) Q q_point (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult attribute) R ReactionStringFeature (class in matlantis_features.features.reaction.reaction_string) ReactionStringFeatureOutput (class in matlantis_features.features.reaction.reaction_string) ReactionStringFeatureResult (class in matlantis_features.features.reaction.reaction_string) read() (matlantis_features.ase_ext.optimize.FIRELBFGS method) repeat() (matlantis_features.features.base.FeatureBase method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature method) (matlantis_features.features.common.hessian.HessianFeature method) (matlantis_features.features.common.neb.NEBFeature method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) (matlantis_features.features.common.opt.OptFeatureBase method) (matlantis_features.features.common.vibration.VibrationFeature method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) (matlantis_features.features.md.md.MDFeature method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature method) (matlantis_features.features.phonon.band.PostPhononBandFeature method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature method) (matlantis_features.features.phonon.mode.PostPhononModeFeature method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature method) (matlantis_features.features.reaction.rest_scan.RestScanFeature method) repeat_of_cell (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult attribute) resolve_force_constants() (in module matlantis_features.features.phonon.symmetry) restore_to() (matlantis_features.features.md.ase_md_system.ASEMDState method) RestScanFeature (class in matlantis_features.features.reaction.rest_scan) RestScanFeatureResult (class in matlantis_features.features.reaction.rest_scan) RNEMDExtension (class in matlantis_features.features.md.post_features.rnemd_extension) rotate_atoms_to_upper() (matlantis_features.atoms.MatlantisAtoms method) run() (matlantis_features.ase_ext.optimize.FIRELBFGS method) (matlantis_features.features.common.vibration.FastVibrations method) (matlantis_features.features.md.ase_simulation.ASESimulation method) (matlantis_features.features.md.md_simulation_base.MDSimulationBase method) (matlantis_features.features.phonon.force_constant.FastPhonons method) run_md_feature_result (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeatureResult attribute) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeatureResult attribute) run_opt_feature_result (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeatureResult attribute) S save() (matlantis_features.features.base.FeatureBaseResult method) (matlantis_features.features.common.neb.NEBFeatureResult method) (matlantis_features.features.common.opt.OptFeatureResult method) (matlantis_features.features.md.md.MDFeatureResult method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult method) ScanDihedral (class in matlantis_features.features.reaction.rest_scan) ScanDistance (class in matlantis_features.features.reaction.rest_scan) ScanRestraint (class in matlantis_features.features.reaction.rest_scan) select() (in module matlantis_features.features.elasticity.utils) set_by_voigt() (matlantis_features.features.elasticity.tensors.DeformTensor method) (matlantis_features.features.elasticity.tensors.StrainTensor method) (matlantis_features.features.elasticity.tensors.StressTensor method) set_cell() (matlantis_features.filters.IsotropicFilter method) set_temperature() (matlantis_features.features.md.ase_integrators.AndersenIntegrator method) (matlantis_features.features.md.ase_integrators.ASEIntegrator method) (matlantis_features.features.md.ase_integrators.LangevinIntegrator method) (matlantis_features.features.md.ase_integrators.NPTBerendsenIntegrator method) (matlantis_features.features.md.ase_integrators.NPTIntegrator method) (matlantis_features.features.md.ase_integrators.NVTBerendsenIntegrator method) (matlantis_features.features.md.ase_integrators.VelocityVerletIntegrator method) (matlantis_features.features.md.md_integrator_base.MDIntegratorBase method) similarity_transformation() (in module matlantis_features.features.phonon.symmetry) slab_T (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeatureResult attribute) slab_velocity_x (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeatureResult attribute) slab_z (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeatureResult attribute) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeatureResult attribute) special_kpt_indices (matlantis_features.features.phonon.band.PostPhononBandFeatureResult attribute) specific_heat (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeatureResult attribute) (matlantis_features.features.md.post_features.specific_heat.SpecificHeatResult attribute) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) specific_heat_converter() (in module matlantis_features.utils.units_util) SpecificHeatResult (class in matlantis_features.features.md.post_features.specific_heat) standard_formation_enthalpy (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeatureResult attribute) step() (matlantis_features.ase_ext.optimize.FIRELBFGS method) StrainASEFilter (class in matlantis_features.filters) StrainTensor (class in matlantis_features.features.elasticity.tensors) StrainTensorList (class in matlantis_features.features.elasticity.tensors) stress_from_deform() (in module matlantis_features.features.elasticity.elastic_tensor) StressTensor (class in matlantis_features.features.elasticity.tensors) StressTensorList (class in matlantis_features.features.elasticity.tensors) stride (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) supercell (matlantis_features.features.phonon.force_constant.ForceConstantFeatureResult attribute) swap_ij() (in module matlantis_features.features.elasticity.utils) SymmetryOperations (class in matlantis_features.features.phonon.symmetry) T temp_dir (matlantis_features.features.md.md.MDFeatureResult attribute) temperature (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeatureResult attribute) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeatureResult attribute) (matlantis_features.features.md.post_features.specific_heat.EnthalpyResult attribute) (matlantis_features.features.md.post_features.specific_heat.SpecificHeatResult attribute) (matlantis_features.features.md.post_features.thermal_expansion.ThermalExpansionResult attribute) (matlantis_features.features.md.post_features.thermal_expansion.VolumeResult attribute) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult attribute) temperatures (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult attribute) TemperatureScheduler (class in matlantis_features.features.md.md_extensions) thermal_conductivity (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeatureResult attribute) thermal_conductivity_converter() (in module matlantis_features.utils.units_util) thermal_conductivity_std (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeatureResult attribute) thermal_expansion (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeatureResult attribute) thermal_expansion_converter() (in module matlantis_features.utils.units_util) ThermalExpansionResult (class in matlantis_features.features.md.post_features.thermal_expansion) thermochemistry (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult attribute) time (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult attribute) timestep (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeatureResult attribute) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeatureResult attribute) to_3x3_ndarray() (matlantis_features.features.elasticity.tensors.DeformTensor method) (matlantis_features.features.elasticity.tensors.StrainTensor method) (matlantis_features.features.elasticity.tensors.StressTensor method) to_dataframe() (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeatureResult method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeatureResult method) (matlantis_features.features.common.neb.NEBFeatureResult method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeatureResult method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeatureResult method) (matlantis_features.features.phonon.band.PostPhononBandFeatureResult method) (matlantis_features.features.phonon.dos.PostPhononDOSFeatureResult method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeatureResult method) to_dict() (matlantis_features.atoms.MatlantisAtoms method) (matlantis_features.features.base.FeatureBase method) (matlantis_features.features.base.FeatureBaseOutput method) (matlantis_features.features.base.FeatureBaseResult method) (matlantis_features.features.common.gas_formation_enthalpy.ComplexGasFormationEnthalpyFeature method) (matlantis_features.features.common.gas_formation_enthalpy.GasStandardFormationEnthalpyFeature method) (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeature method) (matlantis_features.features.common.hessian.HessianFeature method) (matlantis_features.features.common.neb.NEBFeature method) (matlantis_features.features.common.neb.NEBFeatureOutput method) (matlantis_features.features.common.neb.NEBFeatureResult method) (matlantis_features.features.common.opt.ASEOptFeature method) (matlantis_features.features.common.opt.BFGSASEOptFeature method) (matlantis_features.features.common.opt.BFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.FireASEOptFeature method) (matlantis_features.features.common.opt.FireLBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSASEOptFeature method) (matlantis_features.features.common.opt.LBFGSLineSearchASEOptFeature method) (matlantis_features.features.common.opt.MDMinASEOptFeature method) (matlantis_features.features.common.opt.OptFeatureBase method) (matlantis_features.features.common.opt.OptFeatureOutput method) (matlantis_features.features.common.opt.OptFeatureResult method) (matlantis_features.features.common.vibration.VibrationFeature method) (matlantis_features.features.elasticity.complex_elastic_feature.ComplexElasticFeature method) (matlantis_features.features.elasticity.elastic_properties.PostElasticPropertiesFeature method) (matlantis_features.features.elasticity.elastic_tensor.ElasticTensorFeature method) (matlantis_features.features.md.md.MDFeature method) (matlantis_features.features.md.post_features.diffusion.OldPostMDDiffusionFeature method) (matlantis_features.features.md.post_features.diffusion.PostMDDiffusionFeature method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosity method) (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.ComplexNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_thermal_conductivity.PostNEMDThermalConductivityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.ComplexNEMDViscosityFeature method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosity method) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeature method) (matlantis_features.features.md.post_features.specific_heat.PostMDSpecificHeatFeature method) (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeature method) (matlantis_features.features.phonon.band.PostPhononBandFeature method) (matlantis_features.features.phonon.dos.PostPhononDOSFeature method) (matlantis_features.features.phonon.force_constant.ForceConstantFeature method) (matlantis_features.features.phonon.mode.PostPhononModeFeature method) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeature method) (matlantis_features.features.phonon.thermo.PostPhononThermochemistryFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeature method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureOutput method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult method) (matlantis_features.features.reaction.rest_scan.RestScanFeature method) (matlantis_features.filters.ExpCellASEFilter method) (matlantis_features.filters.IsotropicASEFilter method) (matlantis_features.filters.MatlantisFilter method) (matlantis_features.filters.StrainASEFilter method) (matlantis_features.filters.UnitCellASEFilter method) to_gif() (matlantis_features.features.common.neb.NEBFeatureResult method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult method) to_traj() (matlantis_features.features.common.neb.NEBFeatureResult method) (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult method) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult method) to_unit_vec() (in module matlantis_features.features.elasticity.utils) to_voigt_ndarray() (matlantis_features.features.elasticity.tensors.DeformTensor method) (matlantis_features.features.elasticity.tensors.StrainTensor method) (matlantis_features.features.elasticity.tensors.StressTensor method) todict() (matlantis_features.ase_ext.optimize.FIRELBFGS method) (matlantis_features.features.reaction.rest_scan.ScanDihedral method) (matlantis_features.features.reaction.rest_scan.ScanDistance method) traj_path (matlantis_features.features.md.md.MDFeatureResult attribute) (matlantis_features.features.reaction.rest_scan.RestScanFeatureResult attribute) trajectories (matlantis_features.features.phonon.mode.PostPhononModeFeatureResult attribute) trajectory_logger (matlantis_features.features.reaction.rest_scan.RestScanFeatureResult attribute) U unit (matlantis_features.features.phonon.band.PostPhononBandFeatureResult attribute) (matlantis_features.features.phonon.dos.PostPhononDOSFeatureResult attribute) unit_cell_atoms (matlantis_features.features.phonon.band.PostPhononBandFeatureResult attribute) (matlantis_features.features.phonon.force_constant.ForceConstantFeatureResult attribute) (matlantis_features.features.phonon.qha_gibbs_free_energy.PostPhononQHAGibbsFeatureResult attribute) unit_cell_potential_energy (matlantis_features.features.phonon.force_constant.ForceConstantFeatureResult attribute) UnitCellASEFilter (class in matlantis_features.filters) user_info (matlantis_features.features.base.FeatureBaseResult attribute) (matlantis_features.features.common.neb.NEBFeatureResult attribute) (matlantis_features.features.common.opt.OptFeatureResult attribute) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult attribute) V VelocityVerletIntegrator (class in matlantis_features.features.md.ase_integrators) version_info (matlantis_features.features.base.FeatureBaseResult attribute) (matlantis_features.features.common.neb.NEBFeatureResult attribute) (matlantis_features.features.common.opt.OptFeatureResult attribute) (matlantis_features.features.reaction.reaction_string.ReactionStringFeatureResult attribute) VibrationFeature (class in matlantis_features.features.common.vibration) VibrationFeatureResult (class in matlantis_features.features.common.vibration) vis_avg (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult attribute) vis_segment (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult attribute) viscosity (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult attribute) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeatureResult attribute) viscosity_converter() (in module matlantis_features.utils.units_util) viscosity_std (matlantis_features.features.md.post_features.emd_viscosity.PostEMDViscosityFeatureResult attribute) (matlantis_features.features.md.post_features.nemd_viscosity.PostNEMDViscosityFeatureResult attribute) visual_k_path() (matlantis_features.features.phonon.band.PostPhononBandFeatureResult method) voigt_to_ij() (in module matlantis_features.features.elasticity.utils) volume (matlantis_features.features.md.post_features.thermal_expansion.PostMDThermalExpansionFeatureResult attribute) (matlantis_features.features.md.post_features.thermal_expansion.VolumeResult attribute) VolumeResult (class in matlantis_features.features.md.post_features.thermal_expansion) volumetric_expansion_coeffcient (matlantis_features.features.md.post_features.thermal_expansion.ThermalExpansionResult attribute) W warnflag (matlantis_features.features.reaction.rest_scan.RestScanFeatureResult attribute) Z zero_point_energy (matlantis_features.features.common.gas_thermo.PostVibrationGasThermoFeatureResult attribute) (matlantis_features.features.common.vibration.FastVibrationsResult attribute) (matlantis_features.features.common.vibration.VibrationFeatureResult attribute)
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