Index

_

__init__() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.Committee method) (matscipy.calculators.committee.committee.CommitteeMember method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.ewald.calculator.EwaldShortRange method) (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Parameters method) (matscipy.calculators.fitting.Penalty method) (matscipy.calculators.fitting.RotatingFit method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.explicit_forms.harmonic.HarmonicAngle method) (matscipy.calculators.manybody.explicit_forms.harmonic.HarmonicBond method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.manybody.potentials.BornMayerCut method) (matscipy.calculators.manybody.potentials.HarmonicAngle method) (matscipy.calculators.manybody.potentials.HarmonicPair method) (matscipy.calculators.manybody.potentials.KumagaiAngle method) (matscipy.calculators.manybody.potentials.KumagaiPair method) (matscipy.calculators.manybody.potentials.LennardJones method) (matscipy.calculators.manybody.potentials.StillingerWeberAngle method) (matscipy.calculators.manybody.potentials.StillingerWeberPair method) (matscipy.calculators.manybody.potentials.SymPhi method) (matscipy.calculators.manybody.potentials.SymTheta method) (matscipy.calculators.manybody.potentials.TersoffBrennerAngle method) (matscipy.calculators.manybody.potentials.TersoffBrennerPair method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.cluster_data.ClusterData method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_mcfm.NeighbourListMCFM method) (matscipy.calculators.mcfm.qm_cluster.QMCluster method) (matscipy.calculators.mcfm.qm_cluster_tools.base_qm_cluster_tool.BaseQMClusterTool method) (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) (matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool.QMFlaggingTool method) (matscipy.calculators.pair_potential.calculator.BeestKramerSanten method) (matscipy.calculators.pair_potential.calculator.CutoffInteraction method) (matscipy.calculators.pair_potential.calculator.FeneLJCut method) (matscipy.calculators.pair_potential.calculator.LennardJones84 method) (matscipy.calculators.pair_potential.calculator.LennardJonesCut method) (matscipy.calculators.pair_potential.calculator.LennardJonesLinear method) (matscipy.calculators.pair_potential.calculator.LennardJonesQuadratic method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.InversePowerLawPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.cauchy_born.CubicCauchyBorn method) (matscipy.deformation.RemoveSimpleShearDeformation method) (matscipy.dislocation.AnisotropicDislocation method) (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) (matscipy.dislocation.FixedLineAtoms method) (matscipy.drift.RemoveDrift method) (matscipy.elasticity.CubicElasticModuli method) (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.Boundary method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) (matscipy.electrochemistry.steric_correction.DeferredMessage method) (matscipy.fracture_mechanics.crack.ConstantStrainRate method) (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) (matscipy.fracture_mechanics.crack.IsotropicStressField method) (matscipy.fracture_mechanics.crack.RectilinearAnisotropicCrack method) (matscipy.fracture_mechanics.crack.SinclairCrack method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.gamma_surface.GammaSurface method) (matscipy.gamma_surface.StackingFault method) (matscipy.io.lammpsdata.LAMMPSData method) (matscipy.logger.Logger method) (matscipy.molecules.Molecules method) (matscipy.neighbours.CutoffNeighbourhood method) (matscipy.neighbours.MolecularNeighbourhood method) (matscipy.neighbours.Neighbourhood method) (matscipy.opls.AnglesData method) (matscipy.opls.BondData method) (matscipy.opls.CutoffList method) (matscipy.opls.DihedralsData method) (matscipy.opls.LJQData method) (matscipy.opls.OPLSStructure method) (matscipy.precon.HessianPrecon method) (matscipy.pressurecoupling.AutoDamping method) (matscipy.pressurecoupling.FixedDamping method) (matscipy.pressurecoupling.FixedMassCriticalDamping method) (matscipy.pressurecoupling.SlideLog method) (matscipy.pressurecoupling.SlideLogger method) (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell method) (matscipy.socketcalc.AtomsRequestHandler method) (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.SocketCalculator method) (matscipy.socketcalc.VaspClient method) (matscipy.surface_reconstruction.SurfaceReconstruction method) (matscipy.utils.classproperty method)

A

a (matscipy.pressurecoupling.SlideLog attribute) a0 (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) ab() (in module matscipy.calculators.manybody.explicit_forms.kumagai) (in module matscipy.calculators.manybody.explicit_forms.stillinger_weber) add_member() (matscipy.calculators.committee.committee.Committee method) add_name() (matscipy.opls.AnglesData method) (matscipy.opls.DihedralsData method) address_family (matscipy.socketcalc.AtomsServerAsync attribute) (matscipy.socketcalc.AtomsServerSync attribute) adjust_forces() (matscipy.dislocation.FixedLineAtoms method) (matscipy.fracture_mechanics.crack.ConstantStrainRate method) (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell method) adjust_momenta() (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell method) adjust_positions() (matscipy.dislocation.FixedLineAtoms method) (matscipy.fracture_mechanics.crack.ConstantStrainRate method) (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell method) adjust_potential_energy() (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell method) ADstroh (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) alat (matscipy.dislocation.BCCEdge100110Dislocation attribute), [1] (matscipy.dislocation.BCCEdge100Dislocation attribute), [1] (matscipy.dislocation.BCCEdge111barDislocation attribute), [1] (matscipy.dislocation.BCCEdge111Dislocation attribute), [1] (matscipy.dislocation.BCCMixed111Dislocation attribute), [1] (matscipy.dislocation.BCCScrew111Dislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.CubicCrystalDissociatedDislocation property) (matscipy.dislocation.DiamondGlide30degreePartial attribute), [1] (matscipy.dislocation.DiamondGlide60Degree property) (matscipy.dislocation.DiamondGlide90degreePartial attribute), [1] (matscipy.dislocation.DiamondGlideScrew property) (matscipy.dislocation.FCCEdge110Dislocation property) (matscipy.dislocation.FCCEdgeShockleyPartial attribute), [1] (matscipy.dislocation.FCCScrew110Dislocation property) (matscipy.dislocation.FCCScrewShockleyPartial attribute), [1] align() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) ALIGNED (matscipy.surface.MillerIndex attribute) all() (matscipy.surface.MillerIndex method) all_brackets (matscipy.surface.MillerIndex attribute) all_changes (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential attribute) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential attribute) allow_reuse_address (matscipy.socketcalc.AtomsServerAsync attribute) (matscipy.socketcalc.AtomsServerSync attribute) allowed_wave_vectors() (matscipy.calculators.ewald.calculator.Ewald static method) alpha (matscipy.calculators.ewald.calculator.Ewald property) alphas (matscipy.calculators.committee.committee.Committee property) angle() (matscipy.surface.MillerIndex method) angle_between() (in module matscipy.surface) angle_distance_defined() (in module matscipy.calculators.manybody.potentials) angle_distribution() (in module matscipy.angle_distribution) AnglesData (class in matscipy.opls) animate() (matscipy.fracture_mechanics.crack.SinclairCrack method) AnisotropicDislocation (class in matscipy.dislocation) any() (matscipy.surface.MillerIndex method) append() (matscipy.opls.OPLSStructure method) apply() (matscipy.precon.HessianPrecon method) apply_central_reference_concentration_constraint() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_left_concentration_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_left_potential_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_left_potential_robin_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_number_conservation_constraint() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_pandey_111() (matscipy.surface_reconstruction.SurfaceReconstruction method) apply_potential_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_potential_robin_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_right_concentration_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_right_potential_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_right_potential_robin_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) apply_shifts() (matscipy.cauchy_born.CubicCauchyBorn method) apply_si_110() (matscipy.surface_reconstruction.SurfaceReconstruction method) apply_steric_correction() (in module matscipy.electrochemistry.steric_correction) apply_strain() (matscipy.fracture_mechanics.crack.ConstantStrainRate method) apply_surface_shift() (matscipy.surface_reconstruction.SurfaceReconstruction method) arc_length_continuation() (matscipy.fracture_mechanics.crack.SinclairCrack method) argmax() (matscipy.surface.MillerIndex method) argmin() (matscipy.surface.MillerIndex method) argpartition() (matscipy.surface.MillerIndex method) argsort() (matscipy.surface.MillerIndex method) array_inverse() (in module matscipy.atomic_strain) as3() (matscipy.surface.MillerIndex method)

as4() (matscipy.surface.MillerIndex method) asarray() (matscipy.precon.HessianPrecon method) ase_objtype (matscipy.opls.OPLSStructure attribute) astype() (matscipy.surface.MillerIndex method) atm (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) atomic_masses (matscipy.calculators.eam.io.EAMParameters attribute) atomic_numbers (matscipy.calculators.eam.io.EAMParameters attribute) atomic_strain() (in module matscipy.atomic_strain) atomman (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) atoms (matscipy.calculators.committee.committee.Committee property) (matscipy.calculators.committee.committee.CommitteeMember property) (matscipy.calculators.fitting.CombinedFit attribute) (matscipy.calculators.fitting.Fit attribute) (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitDimer attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSinglePoint attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) (matscipy.calculators.fitting.Penalty attribute) atoms_in_unit_cell (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute) AtomsRequestHandler (class in matscipy.socketcalc) AtomsServer (in module matscipy.socketcalc) AtomsServerAsync (class in matscipy.socketcalc) AtomsServerSync (class in matscipy.socketcalc) attach_clustering_module() (matscipy.calculators.mcfm.qm_cluster.QMCluster method) attach_flagging_module() (matscipy.calculators.mcfm.qm_cluster.QMCluster method) attach_hybrid_data() (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) attach_neighbour_list() (matscipy.calculators.mcfm.qm_cluster.QMCluster method) AutoDamping (class in matscipy.pressurecoupling) avail_methods (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) average_potential() (in module matscipy.calculators.eam.average_atom) axes (matscipy.dislocation.BCCEdge100110Dislocation attribute), [1] (matscipy.dislocation.BCCEdge100Dislocation attribute), [1] (matscipy.dislocation.BCCEdge111barDislocation attribute), [1] (matscipy.dislocation.BCCEdge111Dislocation attribute), [1] (matscipy.dislocation.BCCMixed111Dislocation attribute), [1] (matscipy.dislocation.BCCScrew111Dislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.DiamondGlide30degreePartial attribute), [1] (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute), [1] (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute), [1] (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute), [1] axes() (matscipy.dislocation.CubicCrystalDissociatedDislocation method)

B

B() (in module matscipy.electrochemistry.poisson_nernst_planck_solver) band_structure() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) base (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) BaseQMClusterTool (class in matscipy.calculators.mcfm.qm_cluster_tools.base_qm_cluster_tool) basis_factor (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute) basis_function_evaluation() (matscipy.cauchy_born.CubicCauchyBorn method) bcc() (in module matscipy.fracture_mechanics.clusters) BCCEdge100110Dislocation (class in matscipy.dislocation) BCCEdge100Dislocation (class in matscipy.dislocation) BCCEdge111barDislocation (class in matscipy.dislocation) BCCEdge111Dislocation (class in matscipy.dislocation) BCCMixed111Dislocation (class in matscipy.dislocation) BCCScrew111Dislocation (class in matscipy.dislocation) BeestKramerSanten (class in matscipy.calculators.pair_potential.calculator) BEHAVED (matscipy.surface.MillerIndex attribute) betrag() (in module matscipy.spatial_correlation_function) block_on_close (matscipy.socketcalc.AtomsServerAsync attribute) BodyCenteredCubicOctahedralFactory (class in matscipy.dislocation) BodyCenteredCubicTetrahedralFactory (class in matscipy.dislocation) BondData (class in matscipy.opls) BornMayerCut (class in matscipy.calculators.manybody.potentials) Boundary (class in matscipy.electrochemistry.poisson_nernst_planck_solver_fenics) boundary_C() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) boundary_L() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) boundary_R() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) box_constraint() (in module matscipy.electrochemistry.steric_correction) box_constraint_with_gradient() (in module matscipy.electrochemistry.steric_correction) brackets (matscipy.surface.MillerIndex attribute) bravais_basis (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute) brute_force_closest_pair() (in module matscipy.electrochemistry.steric_correction) brute_force_target_function() (in module matscipy.electrochemistry.steric_correction) build_cylinder() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) build_glide_configurations() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) build_glide_quadrupoles() (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) build_impurity_cylinder() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) build_kink_cylinder() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method)

build_kink_from_glide_cyls() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) build_kink_glide_structs() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) build_kink_quadrupole() (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) build_kink_quadrupole_from_glide_structs() (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) build_kink_quadrupole_glide_structs() (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) build_minimal_kink_quadrupole() (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) build_quadrupole() (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) burgers (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100110Dislocation property) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation property) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation property) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation property) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation property) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation property) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocation property) (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.CubicCrystalDissociatedDislocation property) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide30degreePartial property) (matscipy.dislocation.DiamondGlide60Degree property) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlide90degreePartial property) (matscipy.dislocation.DiamondGlideScrew property) (matscipy.dislocation.FCCEdge110Dislocation property) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCEdgeShockleyPartial property) (matscipy.dislocation.FCCScrew110Dislocation property) (matscipy.dislocation.FCCScrewShockleyPartial attribute) (matscipy.dislocation.FCCScrewShockleyPartial property) burgers_dimensionless (matscipy.dislocation.BCCEdge100110Dislocation attribute), [1] (matscipy.dislocation.BCCEdge100Dislocation attribute), [1] (matscipy.dislocation.BCCEdge111barDislocation attribute), [1] (matscipy.dislocation.BCCEdge111Dislocation attribute), [1] (matscipy.dislocation.BCCMixed111Dislocation attribute), [1] (matscipy.dislocation.BCCScrew111Dislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute), [1] (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute), [1] (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute), [1] (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute), [1] byteswap() (matscipy.surface.MillerIndex method)

C

C (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) c0 (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) C_CONTIGUOUS (matscipy.surface.MillerIndex attribute) calc (matscipy.calculators.fitting.CombinedFit attribute) (matscipy.calculators.fitting.Fit attribute) (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitDimer attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSinglePoint attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) (matscipy.calculators.fitting.Penalty attribute) (matscipy.opls.OPLSStructure property) calc_num_atoms() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) calculate() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) calculate_hessian_matrix() (matscipy.calculators.eam.calculator.EAM method) calculate_numerical_forces() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) calculate_numerical_stress() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) calculate_properties() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) calculation_required() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) calculator (matscipy.calculators.committee.committee.CommitteeMember property) calibrate() (matscipy.calculators.committee.committee.Committee method) calibrated_for (matscipy.calculators.committee.committee.Committee property) CARRAY (matscipy.surface.MillerIndex attribute) carve_cluster() (matscipy.calculators.mcfm.qm_cluster.QMCluster method) (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) CastepClient (class in matscipy.socketcalc) cell (matscipy.opls.OPLSStructure property) center() (matscipy.opls.OPLSStructure method) charge_density (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem property) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS property) charge_density() (in module matscipy.electrochemistry.poisson_boltzmann_distribution) check_basis_volume() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) check_duplicates() (in module matscipy.dislocation) check_for_refit() (matscipy.cauchy_born.CubicCauchyBorn method) check_legal_name() (in module matscipy.io.lammpsdata) check_state() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) choose() (matscipy.surface.MillerIndex method) chop_tolerance (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute)

classproperty (class in matscipy.utils) clear() (matscipy.opls.LJQData method) Client (class in matscipy.socketcalc) clip() (matscipy.surface.MillerIndex method) close_request() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) cluster() (in module matscipy.fracture_mechanics.clusters) ClusterData (class in matscipy.calculators.mcfm.cluster_data) coalesce_elastic_constants() (in module matscipy.elasticity) column_size() (in module matscipy.io.lammpsdata) combine_qm_mm_forces() (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) CombinedFit (class in matscipy.calculators.fitting) Committee (class in matscipy.calculators.committee.committee) CommitteeMember (class in matscipy.calculators.committee.committee) CommitteeUncertainty (class in matscipy.calculators.committee.committee) compare_configurations() (in module matscipy.dislocation) compat_cg_parameters() (in module matscipy.compat) complete_aromatic_rings() (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) complete_basis() (in module matscipy.utils) complete_connectivity() (matscipy.neighbours.MolecularNeighbourhood method) compliance() (matscipy.elasticity.CubicElasticModuli method) compress() (matscipy.surface.MillerIndex method) compute_distances() (matscipy.neighbours.CutoffNeighbourhood static method) (matscipy.neighbours.MolecularNeighbourhood static method) (matscipy.neighbours.Neighbourhood static method) compute_stress() (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) concentration (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem property) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS property) concentration() (in module matscipy.electrochemistry.poisson_boltzmann_distribution) conj() (matscipy.surface.MillerIndex method) conjugate() (matscipy.surface.MillerIndex method) connected_triplets() (matscipy.neighbours.CutoffNeighbourhood method) (matscipy.neighbours.MolecularNeighbourhood method) (matscipy.neighbours.Neighbourhood method) constant (matscipy.calculators.fitting.Parameters attribute) ConstantStrainRate (class in matscipy.fracture_mechanics.crack) constraints (matscipy.opls.OPLSStructure property) continuous2discrete() (in module matscipy.electrochemistry) convergence_line_plot() (matscipy.fracture_mechanics.crack.SinclairCrack method) convert_to_natural_basis() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) coordination() (in module matscipy.neighbours) copy() (matscipy.fracture_mechanics.crack.ConstantStrainRate method) (matscipy.opls.LJQData method) (matscipy.opls.OPLSStructure method) (matscipy.precon.HessianPrecon method) (matscipy.surface.MillerIndex method) cosine() (matscipy.surface.MillerIndex method) cost_function() (in module matscipy.dislocation) cost_history (matscipy.calculators.fitting.CombinedFit attribute) (matscipy.calculators.fitting.Fit attribute) (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitDimer attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSinglePoint attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) (matscipy.calculators.fitting.Penalty attribute) count() (matscipy.calculators.eam.io.EAMParameters method) counted() (in module matscipy.fracture_mechanics.crack) crack_tip_position() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) crack_tip_position_y() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) create_buffer_region() (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) create_cluster_around_atom() (matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool.QMFlaggingTool method) create_cluster_from_marks() (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) create_logger() (in module matscipy.calculators.committee.log) cross() (matscipy.surface.MillerIndex method) crystal (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) crystal_structures (matscipy.calculators.eam.io.EAMParameters attribute) crystalstr (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) crystalstructure (matscipy.dislocation.BCCEdge100110Dislocation attribute), [1] (matscipy.dislocation.BCCEdge100Dislocation attribute), [1] (matscipy.dislocation.BCCEdge111barDislocation attribute), [1] (matscipy.dislocation.BCCEdge111Dislocation attribute), [1] (matscipy.dislocation.BCCMixed111Dislocation attribute), [1] (matscipy.dislocation.BCCScrew111Dislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.DiamondGlide30degreePartial attribute), [1] (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute), [1] (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute), [1] (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute), [1] crystalstructure() (matscipy.dislocation.CubicCrystalDissociatedDislocation method) ctypes (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) cubic_to_Voigt_6x6() (in module matscipy.elasticity) CubicCauchyBorn (class in matscipy.cauchy_born) CubicCrystalCrack (class in matscipy.fracture_mechanics.crack) CubicCrystalDislocation (class in matscipy.dislocation) CubicCrystalDislocationQuadrupole (class in matscipy.dislocation) CubicCrystalDissociatedDislocation (class in matscipy.dislocation) CubicElasticModuli (class in matscipy.elasticity) cumprod() (matscipy.surface.MillerIndex method) cumsum() (matscipy.surface.MillerIndex method) cut_at (matscipy.gamma_surface.GammaSurface.self attribute) (matscipy.gamma_surface.StackingFault.self attribute) cutoff (matscipy.calculators.eam.calculator.EAM property) (matscipy.calculators.eam.io.EAMParameters attribute) (matscipy.calculators.ewald.calculator.EwaldShortRange property) (matscipy.calculators.pair_potential.calculator.BeestKramerSanten property) (matscipy.calculators.pair_potential.calculator.CutoffInteraction property) (matscipy.calculators.pair_potential.calculator.FeneLJCut property) (matscipy.calculators.pair_potential.calculator.LennardJones84 property) (matscipy.calculators.pair_potential.calculator.LennardJonesCut property) (matscipy.calculators.pair_potential.calculator.LennardJonesLinear property) (matscipy.calculators.pair_potential.calculator.LennardJonesQuadratic property) CutoffInteraction (class in matscipy.calculators.pair_potential.calculator) CutoffList (class in matscipy.opls) CutoffNeighbourhood (class in matscipy.neighbours)

D

D0 (matscipy.calculators.fitting.FitDimer attribute) daemon_threads (matscipy.socketcalc.AtomsServerAsync attribute) data (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) debye() (in module matscipy.electrochemistry.poisson_boltzmann_distribution) default (matscipy.calculators.fitting.Parameters attribute) default_map (matscipy.opls.OPLSStructure attribute) default_parameters (matscipy.calculators.calculator.MatscipyCalculator attribute) (matscipy.calculators.committee.committee.CommitteeUncertainty attribute) (matscipy.calculators.eam.calculator.EAM attribute) (matscipy.calculators.ewald.calculator.Ewald attribute) (matscipy.calculators.manybody.calculator.Manybody attribute) (matscipy.calculators.manybody.calculator.NiceManybody attribute) (matscipy.calculators.manybody.newmb.Manybody attribute) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential attribute) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential attribute) (matscipy.calculators.pair_potential.calculator.PairPotential attribute) (matscipy.calculators.polydisperse.calculator.Polydisperse attribute) (matscipy.calculators.supercell_calculator.SupercellCalculator attribute) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid attribute) (matscipy.socketcalc.SocketCalculator attribute) DeferredMessage (class in matscipy.electrochemistry.steric_correction) deformation_gradient() (matscipy.dislocation.AnisotropicDislocation method) (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) (matscipy.fracture_mechanics.crack.RectilinearAnisotropicCrack method) deformation_gradient_from_cartesian_coordinates() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) deformation_gradient_from_cylinder_coordinates() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) deformation_gradient_residual() (in module matscipy.fracture_mechanics.crack) deformation_gradient_residuals() (in module matscipy.fracture_mechanics.crack) density_grid_spacing (matscipy.calculators.eam.io.EAMParameters attribute) derivative() (matscipy.calculators.ewald.calculator.EwaldShortRange method) (matscipy.calculators.pair_potential.calculator.BeestKramerSanten method) (matscipy.calculators.pair_potential.calculator.CutoffInteraction method) (matscipy.calculators.pair_potential.calculator.FeneLJCut method) (matscipy.calculators.pair_potential.calculator.LennardJones84 method) (matscipy.calculators.pair_potential.calculator.LennardJonesCut method) (matscipy.calculators.pair_potential.calculator.LennardJonesLinear method) (matscipy.calculators.pair_potential.calculator.LennardJonesQuadratic method) (matscipy.calculators.polydisperse.calculator.InversePowerLawPotential method) derived (matscipy.calculators.fitting.Parameters attribute) determine_alpha() (matscipy.calculators.ewald.calculator.Ewald static method) determine_kc() (matscipy.calculators.ewald.calculator.Ewald static method) determine_nk() (matscipy.calculators.ewald.calculator.Ewald static method) dfk_dk_approx() (matscipy.fracture_mechanics.crack.SinclairCrack method) diagonal() (matscipy.surface.MillerIndex method) diamond() (in module matscipy.fracture_mechanics.clusters) DiamondGlide30degreePartial (class in matscipy.dislocation) DiamondGlide60Degree (class in matscipy.dislocation) DiamondGlide90degreePartial (class in matscipy.dislocation) DiamondGlideScrew (class in matscipy.dislocation) DihedralsData (class in matscipy.opls) dipole_displacement_angle() (in module matscipy.dislocation) directory (matscipy.calculators.calculator.MatscipyCalculator property) (matscipy.calculators.committee.committee.CommitteeUncertainty property) (matscipy.calculators.eam.calculator.EAM property) (matscipy.calculators.ewald.calculator.Ewald property) (matscipy.calculators.manybody.calculator.Manybody property) (matscipy.calculators.manybody.calculator.NiceManybody property) (matscipy.calculators.manybody.newmb.Manybody property) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential property) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential property) (matscipy.calculators.pair_potential.calculator.PairPotential property) (matscipy.calculators.polydisperse.calculator.Polydisperse property) (matscipy.calculators.supercell_calculator.SupercellCalculator property) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid property) (matscipy.socketcalc.SocketCalculator property)

disable_nagle_algorithm (matscipy.socketcalc.AtomsRequestHandler attribute) discard_results_on_any_change (matscipy.calculators.calculator.MatscipyCalculator attribute) (matscipy.calculators.committee.committee.CommitteeUncertainty attribute) (matscipy.calculators.eam.calculator.EAM attribute) (matscipy.calculators.ewald.calculator.Ewald attribute) (matscipy.calculators.manybody.calculator.Manybody attribute) (matscipy.calculators.manybody.calculator.NiceManybody attribute) (matscipy.calculators.manybody.newmb.Manybody attribute) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential attribute) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential attribute) (matscipy.calculators.pair_potential.calculator.PairPotential attribute) (matscipy.calculators.polydisperse.calculator.Polydisperse attribute) (matscipy.calculators.supercell_calculator.SupercellCalculator attribute) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid attribute) (matscipy.socketcalc.SocketCalculator attribute) discretize() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) displacement() (matscipy.dislocation.AnisotropicDislocation method) displacement_residual() (in module matscipy.fracture_mechanics.crack) displacement_residuals() (in module matscipy.fracture_mechanics.crack) displacements() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) (matscipy.fracture_mechanics.crack.RectilinearAnisotropicCrack method) displacements_from_cartesian_coordinates() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) displacements_from_cylinder_coordinates() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) distance_defined() (in module matscipy.calculators.manybody.potentials) distance_grid_spacing (matscipy.calculators.eam.io.EAMParameters attribute) do_update() (matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_mcfm.NeighbourListMCFM method) dot() (matscipy.precon.HessianPrecon method) (matscipy.surface.MillerIndex method) double_connectivity() (matscipy.neighbours.MolecularNeighbourhood static method) double_neighbourhood() (matscipy.neighbours.CutoffNeighbourhood method) (matscipy.neighbours.MolecularNeighbourhood method) (matscipy.neighbours.Neighbourhood method) dtype (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) dump() (matscipy.surface.MillerIndex method) dumps() (matscipy.surface.MillerIndex method)

E

EAM (class in matscipy.calculators.eam.calculator) EAMParameters (class in matscipy.calculators.eam.io) Ec (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) edit() (matscipy.opls.OPLSStructure method) elastic_moduli() (in module matscipy.elasticity) element_basis (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute) energy (matscipy.calculators.fitting.FitSinglePoint attribute) energy_virial_and_forces() (matscipy.calculators.eam.calculator.EAM method) euler_rotate() (matscipy.opls.OPLSStructure method) eval_shift() (matscipy.cauchy_born.CubicCauchyBorn method) evaluate_E() (matscipy.cauchy_born.CubicCauchyBorn method) evaluate_errors() (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) evaluate_F() (matscipy.cauchy_born.CubicCauchyBorn method)

evaluate_F_or_E() (matscipy.cauchy_born.CubicCauchyBorn method) evaluate_qm_cluster_serial() (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) evaluate_shift_gradient_regression() (matscipy.cauchy_born.CubicCauchyBorn method) evaluate_shift_model() (matscipy.cauchy_born.CubicCauchyBorn method) Ewald (class in matscipy.calculators.ewald.calculator) EwaldShortRange (class in matscipy.calculators.ewald.calculator) expand_cluster() (matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool.QMFlaggingTool method) exponential_moving_average() (in module matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool) export_properties() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) extend() (matscipy.opls.OPLSStructure method) extend_strip() (in module matscipy.fracture_mechanics.idealbrittlesolid) extra_args() (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.VaspClient method)

F

F_CONTIGUOUS (matscipy.surface.MillerIndex attribute) FARRAY (matscipy.surface.MillerIndex attribute) fcc() (in module matscipy.fracture_mechanics.clusters) FCCEdge110Dislocation (class in matscipy.dislocation) FCCEdgeShockleyPartial (class in matscipy.dislocation) FCCScrew110Dislocation (class in matscipy.dislocation) FCCScrewShockleyPartial (class in matscipy.dislocation) FeneLJCut (class in matscipy.calculators.pair_potential.calculator) filename (matscipy.calculators.committee.committee.CommitteeMember property) fileno() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) fill() (matscipy.surface.MillerIndex method) find_common_neighbours() (in module matscipy.neighbours) find_condensed_repr() (in module matscipy.utils) find_condensed_repr_along_axis() (in module matscipy.utils) find_crack_tip() (in module matscipy.fracture_mechanics.idealbrittlesolid) find_directions() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) find_indices_of_reversed_pairs() (in module matscipy.neighbours) find_neighbours() (matscipy.calculators.mcfm.qm_cluster_tools.base_qm_cluster_tool.BaseQMClusterTool method) (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) (matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool.QMFlaggingTool method) find_ortho() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) find_surface_energy() (in module matscipy.surface) find_tip_broken_bonds() (in module matscipy.fracture_mechanics.crack) find_tip_coordination() (in module matscipy.fracture_mechanics.crack) find_tip_stress_field() (in module matscipy.fracture_mechanics.crack) find_triangles_2d() (in module matscipy.fracture_mechanics.idealbrittlesolid) find_triplet_types() (matscipy.neighbours.CutoffNeighbourhood method) (matscipy.neighbours.MolecularNeighbourhood method) (matscipy.neighbours.Neighbourhood method) finish() (matscipy.socketcalc.AtomsRequestHandler method) finish_request() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) first_derivative() (matscipy.calculators.ewald.calculator.EwaldShortRange method) (matscipy.calculators.pair_potential.calculator.BeestKramerSanten method) (matscipy.calculators.pair_potential.calculator.CutoffInteraction method) (matscipy.calculators.pair_potential.calculator.FeneLJCut method) (matscipy.calculators.pair_potential.calculator.LennardJones84 method) (matscipy.calculators.pair_potential.calculator.LennardJonesCut method) (matscipy.calculators.pair_potential.calculator.LennardJonesLinear method) (matscipy.calculators.pair_potential.calculator.LennardJonesQuadratic method) (matscipy.calculators.polydisperse.calculator.InversePowerLawPotential method) first_derivative_kspace() (matscipy.calculators.ewald.calculator.Ewald static method) Fit (class in matscipy.calculators.fitting) fit() (matscipy.cauchy_born.RegressionModel method) fit_cle() (matscipy.fracture_mechanics.crack.SinclairCrack method) fit_core_position() (in module matscipy.dislocation) fit_core_position_images() (in module matscipy.dislocation) fit_crack_stress_field() (in module matscipy.fracture_mechanics.crack) fit_elastic_constants() (in module matscipy.elasticity) fit_taylor() (matscipy.cauchy_born.CubicCauchyBorn method) FitB2 (class in matscipy.calculators.fitting) FitBCC (class in matscipy.calculators.fitting) FitCubicCrystal (class in matscipy.calculators.fitting)

FitDiamond (class in matscipy.calculators.fitting) FitDiamond100 (class in matscipy.calculators.fitting) FitDiamond110 (class in matscipy.calculators.fitting) FitDiamond111 (class in matscipy.calculators.fitting) FitDimer (class in matscipy.calculators.fitting) FitFCC (class in matscipy.calculators.fitting) FitGraphene (class in matscipy.calculators.fitting) FitGraphite (class in matscipy.calculators.fitting) FitHexagonalCrystal (class in matscipy.calculators.fitting) FitL1_0 (class in matscipy.calculators.fitting) FitL1_2 (class in matscipy.calculators.fitting) FitSC (class in matscipy.calculators.fitting) FitSinglePoint (class in matscipy.calculators.fitting) FitSurface (class in matscipy.calculators.fitting) FitTetragonalCrystal (class in matscipy.calculators.fitting) FixedDamping (class in matscipy.pressurecoupling) FixedLineAtoms (class in matscipy.dislocation) FixedMassCriticalDamping (class in matscipy.pressurecoupling) flags (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) flat (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) flatten() (in module matscipy.logger) (matscipy.surface.MillerIndex method) flush() (matscipy.logger.Logger method) fmax (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitDimer attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) FNC (matscipy.surface.MillerIndex attribute) FORC (matscipy.surface.MillerIndex attribute) forces (matscipy.calculators.fitting.FitSinglePoint attribute) (matscipy.calculators.mcfm.cluster_data.ClusterData attribute) from_atoms() (matscipy.molecules.Molecules static method) fromdict() (matscipy.opls.OPLSStructure class method) fromkeys() (matscipy.opls.LJQData method) full_3x3_to_Voigt_6_index() (in module matscipy.elasticity) full_3x3_to_Voigt_6_strain() (in module matscipy.elasticity) full_3x3_to_Voigt_6_stress() (in module matscipy.elasticity) full_3x3x3x3_to_Voigt_6x6() (in module matscipy.elasticity) func (matscipy.calculators.fitting.Penalty attribute)

G

G() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) G_to_strain() (in module matscipy.fracture_mechanics.crack) gamma() (in module matscipy.electrochemistry.poisson_boltzmann_distribution) gamma_line() (in module matscipy.dislocation) GammaSurface (class in matscipy.gamma_surface) gcd() (in module matscipy.surface) generate_3D_cubic_111() (in module matscipy.fracture_mechanics.clusters) generate_3D_structure() (in module matscipy.fracture_mechanics.clusters) generate_images() (matscipy.gamma_surface.GammaSurface method) (matscipy.gamma_surface.StackingFault method) generate_strained_configs() (in module matscipy.elasticity) get() (matscipy.calculators.fitting.Parameters method) (matscipy.opls.LJQData method) get_A() (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell method) get_all_distances() (matscipy.opls.OPLSStructure method) get_alpha_period() (in module matscipy.fracture_mechanics.clusters) get_angle() (matscipy.opls.OPLSStructure method) get_angles() (matscipy.molecules.Molecules method) (matscipy.opls.OPLSStructure method) get_angular_momentum() (matscipy.opls.OPLSStructure method) get_array() (matscipy.calculators.fitting.Parameters method) (matscipy.opls.OPLSStructure method) get_atomic_numbers() (matscipy.opls.OPLSStructure method) get_atoms() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) get_birch_coefficients() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) get_bonds() (matscipy.opls.OPLSStructure method) get_born_elastic_constants() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) get_C11() (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) get_C33() (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitTetragonalCrystal method) get_C44() (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitTetragonalCrystal method) get_C66() (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitTetragonalCrystal method) get_calculator() (matscipy.opls.OPLSStructure method) get_cb_error() (matscipy.cauchy_born.CubicCauchyBorn method) get_cell() (matscipy.opls.OPLSStructure method) get_cell_lengths_and_angles() (matscipy.opls.OPLSStructure method) get_celldisp() (matscipy.opls.OPLSStructure method) get_center_of_mass() (matscipy.opls.OPLSStructure method) get_centering_mask() (in module matscipy.dislocation) get_charges() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method) get_chemical_formula() (matscipy.opls.OPLSStructure method) get_chemical_symbols() (matscipy.opls.OPLSStructure method) get_cluster_data() (in module matscipy.calculators.mcfm.mcfm_parallel.mcfm_parallel_control) get_coeffs() (matscipy.calculators.polydisperse.calculator.InversePowerLawPotential method) get_cohesive_energy() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) get_constant() (matscipy.calculators.fitting.Parameters method) get_cost_function() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) get_cost_history() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) get_Cp() (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) get_crack_tip_force() (matscipy.fracture_mechanics.crack.SinclairCrack method) get_cutoff() (matscipy.calculators.ewald.calculator.EwaldShortRange method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.pair_potential.calculator.BeestKramerSanten method) (matscipy.calculators.pair_potential.calculator.CutoffInteraction method) (matscipy.calculators.pair_potential.calculator.FeneLJCut method) (matscipy.calculators.pair_potential.calculator.LennardJones84 method) (matscipy.calculators.pair_potential.calculator.LennardJonesCut method) (matscipy.calculators.pair_potential.calculator.LennardJonesLinear method) (matscipy.calculators.pair_potential.calculator.LennardJonesQuadratic method) (matscipy.calculators.polydisperse.calculator.InversePowerLawPotential method) get_D1() (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitTetragonalCrystal method) get_D2() (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitTetragonalCrystal method) get_D4() (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitTetragonalCrystal method) get_D_square_min() (in module matscipy.atomic_strain) get_data_points() (matscipy.cauchy_born.CubicCauchyBorn method) get_default_parameters() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) get_deformation_gradient() (matscipy.fracture_mechanics.crack.SinclairCrack method) get_delta_plus_epsilon() (in module matscipy.atomic_strain) get_delta_plus_epsilon_dgesv() (in module matscipy.atomic_strain) get_derivative_volume() (in module matscipy.numerical) get_derivative_wave_vector() (in module matscipy.numerical) get_derived() (matscipy.calculators.fitting.Parameters method) get_dict() (matscipy.calculators.fitting.Parameters method) get_dihedral() (matscipy.opls.OPLSStructure method) get_dihedrals() (matscipy.molecules.Molecules method) (matscipy.opls.OPLSStructure method) get_dipole_moment() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method) get_distance() (matscipy.calculators.fitting.FitDimer method) (matscipy.opls.OPLSStructure method) get_distance_from_polygon2D() (in module matscipy.utils) get_distances() (matscipy.molecules.Molecules method) (matscipy.opls.OPLSStructure method) get_dofs() (matscipy.fracture_mechanics.crack.SinclairCrack method) get_dynamical_matrix() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) get_elastic_constants() (in module matscipy.dislocation) (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) get_elastic_moduli() (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) get_energized_list() (matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool.QMFlaggingTool method) get_energy_densities() (matscipy.gamma_surface.GammaSurface method) (matscipy.gamma_surface.StackingFault method) get_energy_release_rate() (in module matscipy.fracture_mechanics.crack) get_forces() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.crack.SinclairCrack method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method) get_global_number_of_atoms() (matscipy.opls.OPLSStructure method) get_hessian() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) get_hessian_from_second_derivative() (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) get_initial_charges() (matscipy.opls.OPLSStructure method) get_initial_magnetic_moments() (matscipy.opls.OPLSStructure method) get_k_force() (matscipy.fracture_mechanics.crack.SinclairCrack method) get_kinetic_energy() (matscipy.opls.OPLSStructure method) get_lattice_constant() (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) get_logfile() (matscipy.logger.Logger method) get_lower_bounds() (matscipy.calculators.fitting.Parameters method) get_M_gamma() (matscipy.pressurecoupling.AutoDamping method) (matscipy.pressurecoupling.FixedDamping method) (matscipy.pressurecoupling.FixedMassCriticalDamping method) get_magnetic_moment() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method) get_magnetic_moments() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method) get_masses() (matscipy.opls.OPLSStructure method) get_maxSize() (matscipy.calculators.polydisperse.calculator.InversePowerLawPotential method) get_minSize() (matscipy.calculators.polydisperse.calculator.InversePowerLawPotential method) get_model() (matscipy.cauchy_born.CubicCauchyBorn method) get_momenta() (matscipy.opls.OPLSStructure method) get_moments_of_inertia() (matscipy.opls.OPLSStructure method) get_name() (matscipy.opls.AnglesData method) (matscipy.opls.BondData method) (matscipy.opls.CutoffList method) (matscipy.opls.DihedralsData method) get_neighbors() (matscipy.opls.OPLSStructure method)

get_neighbours() (matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_base.NeighbourListBase method) (matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_mcfm.NeighbourListMCFM method) get_non_affine_contribution_to_elastic_constants() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) get_non_affine_forces_from_second_derivative() (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) get_nonaffine_forces() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) get_number_of_atoms() (matscipy.opls.OPLSStructure method) get_pairs() (matscipy.neighbours.CutoffNeighbourhood method) (matscipy.neighbours.MolecularNeighbourhood method) (matscipy.neighbours.Neighbourhood method) get_parameters_at_minimal_cost() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) get_pbc() (matscipy.opls.OPLSStructure method) get_poisson_ratio() (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) get_positions() (matscipy.opls.OPLSStructure method) get_potential_energies() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method) get_potential_energy() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.crack.SinclairCrack method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method) get_precon() (matscipy.fracture_mechanics.crack.SinclairCrack method) get_properties() (matscipy.opls.OPLSStructure method) get_property() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.Boundary method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) get_reciprocal_cell() (matscipy.opls.OPLSStructure method) get_request() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) get_residuals() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) get_residuals_history() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) get_results() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) get_scaled_positions() (matscipy.opls.OPLSStructure method) get_second_derivative() (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) get_SFE() (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitTetragonalCrystal method) get_shear_distance() (in module matscipy.deformation) get_shift_gradients() (matscipy.cauchy_born.CubicCauchyBorn method) get_solvers() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) get_square_residuals() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) get_strain() (in module matscipy.fracture_mechanics.crack) get_stress() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method) get_stress_contribution_to_elastic_constants() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) get_stress_intensity_factor() (in module matscipy.fracture_mechanics.crack) get_stresses() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.crack.IsotropicStressField method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method) get_structure_types() (in module matscipy.utils) get_surface_energy() (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitSurface method) get_tags() (matscipy.opls.OPLSStructure method) get_temperature() (matscipy.opls.OPLSStructure method) get_total_energy() (matscipy.opls.OPLSStructure method) get_triplets() (matscipy.neighbours.CutoffNeighbourhood method) (matscipy.neighbours.MolecularNeighbourhood method) (matscipy.neighbours.Neighbourhood method) get_types() (matscipy.opls.OPLSStructure method) get_u_img() (in module matscipy.dislocation) get_upper_bounds() (matscipy.calculators.fitting.Parameters method) get_value() (matscipy.opls.BondData method) (matscipy.opls.CutoffList method) get_variable() (matscipy.calculators.fitting.Parameters method) get_velocities() (matscipy.opls.OPLSStructure method) get_volume() (matscipy.opls.OPLSStructure method) get_wave_speeds() (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) get_xdot() (matscipy.fracture_mechanics.crack.SinclairCrack method) get_XIJ() (in module matscipy.atomic_strain) get_YIJ() (in module matscipy.atomic_strain) get_youngs_modulus() (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) getfield() (matscipy.surface.MillerIndex method) glide_distance (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100110Dislocation property) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation property) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation property) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation property) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation property) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation property) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocation property) (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.CubicCrystalDissociatedDislocation property) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide30degreePartial property) (matscipy.dislocation.DiamondGlide60Degree property) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlide90degreePartial property) (matscipy.dislocation.DiamondGlideScrew property) (matscipy.dislocation.FCCEdge110Dislocation property) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCEdgeShockleyPartial property) (matscipy.dislocation.FCCScrew110Dislocation property) (matscipy.dislocation.FCCScrewShockleyPartial attribute) (matscipy.dislocation.FCCScrewShockleyPartial property) glide_distance_dimensionless (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) glide_distance_dimensionless() (matscipy.dislocation.CubicCrystalDissociatedDislocation method) grad_basis_function_evaluation() (matscipy.cauchy_born.CubicCauchyBorn method) gradient() (matscipy.calculators.manybody.calculator.NiceManybody.F method) (matscipy.calculators.manybody.calculator.NiceManybody.G method) (matscipy.calculators.manybody.explicit_forms.harmonic.HarmonicAngle method) (matscipy.calculators.manybody.explicit_forms.harmonic.HarmonicBond method) (matscipy.calculators.manybody.explicit_forms.harmonic.ZeroPair method) (matscipy.calculators.manybody.explicit_forms.harmonic.ZeroTriplet method) (matscipy.calculators.manybody.newmb.Manybody.Phi method) (matscipy.calculators.manybody.newmb.Manybody.Theta method) (matscipy.calculators.manybody.potentials.BornMayerCut method) (matscipy.calculators.manybody.potentials.HarmonicAngle method) (matscipy.calculators.manybody.potentials.HarmonicPair method) (matscipy.calculators.manybody.potentials.KumagaiAngle method) (matscipy.calculators.manybody.potentials.KumagaiPair method) (matscipy.calculators.manybody.potentials.LennardJones method) (matscipy.calculators.manybody.potentials.StillingerWeberAngle method) (matscipy.calculators.manybody.potentials.StillingerWeberPair method) (matscipy.calculators.manybody.potentials.SymPhi method) (matscipy.calculators.manybody.potentials.SymTheta method) (matscipy.calculators.manybody.potentials.TersoffBrennerAngle method) (matscipy.calculators.manybody.potentials.TersoffBrennerPair method) (matscipy.calculators.manybody.potentials.ZeroAngle method) (matscipy.calculators.manybody.potentials.ZeroPair method) grid (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem property) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS property)

H

h (matscipy.pressurecoupling.SlideLog attribute) handle() (matscipy.socketcalc.AtomsRequestHandler method) handle_error() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) handle_request() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) handle_sigusr2() (in module matscipy.cli.glasses.quench) handle_timeout() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) HarmonicAngle (class in matscipy.calculators.manybody.explicit_forms.harmonic) (class in matscipy.calculators.manybody.potentials) HarmonicBond (class in matscipy.calculators.manybody.explicit_forms.harmonic) HarmonicPair (class in matscipy.calculators.manybody.potentials) has() (matscipy.opls.OPLSStructure method) has_logfile() (matscipy.logger.Logger method) has_parameter() (in module matscipy) hat() (matscipy.surface.MillerIndex method) hdr_str() (in module matscipy.logger) hdrfmt_str() (in module matscipy.logger) hessian() (matscipy.calculators.manybody.calculator.NiceManybody.F method) (matscipy.calculators.manybody.calculator.NiceManybody.G method) (matscipy.calculators.manybody.explicit_forms.harmonic.HarmonicAngle method) (matscipy.calculators.manybody.explicit_forms.harmonic.HarmonicBond method) (matscipy.calculators.manybody.explicit_forms.harmonic.ZeroPair method) (matscipy.calculators.manybody.explicit_forms.harmonic.ZeroTriplet method) (matscipy.calculators.manybody.newmb.Manybody.Phi method) (matscipy.calculators.manybody.newmb.Manybody.Theta method) (matscipy.calculators.manybody.potentials.BornMayerCut method) (matscipy.calculators.manybody.potentials.HarmonicAngle method) (matscipy.calculators.manybody.potentials.HarmonicPair method) (matscipy.calculators.manybody.potentials.KumagaiAngle method) (matscipy.calculators.manybody.potentials.KumagaiPair method) (matscipy.calculators.manybody.potentials.LennardJones method) (matscipy.calculators.manybody.potentials.StillingerWeberAngle method) (matscipy.calculators.manybody.potentials.StillingerWeberPair method) (matscipy.calculators.manybody.potentials.SymPhi method) (matscipy.calculators.manybody.potentials.SymTheta method) (matscipy.calculators.manybody.potentials.TersoffBrennerAngle method) (matscipy.calculators.manybody.potentials.TersoffBrennerPair method) (matscipy.calculators.manybody.potentials.ZeroAngle method) (matscipy.calculators.manybody.potentials.ZeroPair method)

HessianPrecon (class in matscipy.precon) hidden (matscipy.calculators.fitting.Parameters attribute) hydrogenate() (in module matscipy.hydrogenate) hydrogenate_cluster() (matscipy.calculators.mcfm.qm_cluster_tools.base_qm_cluster_tool.BaseQMClusterTool method) (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) (matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool.QMFlaggingTool method) hydrogenate_dangling_bonds() (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method)

I

id_counter (matscipy.calculators.committee.committee.Committee property) id_to_atoms (matscipy.calculators.committee.committee.Committee property) IdealBrittleSolid (class in matscipy.fracture_mechanics.idealbrittlesolid) identify_layers() (matscipy.surface_reconstruction.SurfaceReconstruction method) identify_pandey_layers() (matscipy.surface_reconstruction.SurfaceReconstruction method) identify_si_110_layers() (matscipy.surface_reconstruction.SurfaceReconstruction method) ids (matscipy.calculators.committee.committee.Committee property) (matscipy.calculators.committee.committee.CommitteeMember property) ignored_changes (matscipy.calculators.calculator.MatscipyCalculator attribute) (matscipy.calculators.committee.committee.CommitteeUncertainty attribute) (matscipy.calculators.eam.calculator.EAM attribute) (matscipy.calculators.ewald.calculator.Ewald attribute) (matscipy.calculators.manybody.calculator.Manybody attribute) (matscipy.calculators.manybody.calculator.NiceManybody attribute) (matscipy.calculators.manybody.newmb.Manybody attribute) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential attribute) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential attribute) (matscipy.calculators.pair_potential.calculator.PairPotential attribute) (matscipy.calculators.polydisperse.calculator.Polydisperse attribute) (matscipy.calculators.supercell_calculator.SupercellCalculator attribute) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid attribute) (matscipy.socketcalc.SocketCalculator attribute) imag (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) images (matscipy.gamma_surface.GammaSurface.self attribute) (matscipy.gamma_surface.StackingFault.self attribute) implemented_properties (matscipy.calculators.calculator.MatscipyCalculator attribute) (matscipy.calculators.committee.committee.CommitteeUncertainty attribute) (matscipy.calculators.eam.calculator.EAM attribute) (matscipy.calculators.ewald.calculator.Ewald attribute) (matscipy.calculators.manybody.calculator.Manybody attribute) (matscipy.calculators.manybody.calculator.NiceManybody attribute) (matscipy.calculators.manybody.newmb.Manybody attribute) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential attribute) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential attribute) (matscipy.calculators.pair_potential.calculator.PairPotential attribute) (matscipy.calculators.polydisperse.calculator.Polydisperse attribute) (matscipy.calculators.supercell_calculator.SupercellCalculator attribute) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid attribute) (matscipy.socketcalc.SocketCalculator attribute) in_range() (matscipy.calculators.fitting.Parameters method) include_special_atom() (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) index() (matscipy.calculators.eam.io.EAMParameters method) init() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) init_adsl() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) init_atomman() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method)

init_solver() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) initial_regression_fit() (matscipy.cauchy_born.CubicCauchyBorn method) initial_values() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) inside() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.Boundary method) int_basis (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute) invariants() (in module matscipy.elasticity) inverse_basis (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute) inverse_basis_factor (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute) InversePowerLawPotential (class in matscipy.calculators.polydisperse.calculator) invert_burgers() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) ionic_strength (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem property) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS property) ionic_strength() (in module matscipy.electrochemistry.poisson_boltzmann_distribution) is_calibrated_for() (matscipy.calculators.committee.committee.Committee method) is_compatible() (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.VaspClient method) is_sample_in_atoms() (matscipy.calculators.committee.committee.CommitteeMember method) isotropic_modeI_crack_tip_displacement_field() (in module matscipy.fracture_mechanics.crack) isotropic_modeI_crack_tip_stress_field() (in module matscipy.fracture_mechanics.crack) isotropic_modeII_crack_tip_displacement_field() (in module matscipy.fracture_mechanics.crack) IsotropicStressField (class in matscipy.fracture_mechanics.crack) item() (matscipy.surface.MillerIndex method) items() (matscipy.opls.LJQData method) itemset() (matscipy.surface.MillerIndex method) itemsize (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) iteration_finished() (matscipy.logger.Logger method) iterimages() (matscipy.opls.OPLSStructure method)

J

J_integral() (in module matscipy.fracture_mechanics.energy_release) jacobian() (in module matscipy.electrochemistry.poisson_nernst_planck_solver)

join_all() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) join_clusters() (matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool.QMFlaggingTool method)

K

k (matscipy.fracture_mechanics.crack.SinclairCrack property) k1g() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) (matscipy.fracture_mechanics.crack.RectilinearAnisotropicCrack method) k1gsqG() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) (matscipy.fracture_mechanics.crack.RectilinearAnisotropicCrack method)

keys() (matscipy.opls.LJQData method) kspace_energy() (matscipy.calculators.ewald.calculator.Ewald static method) kspace_properties() (matscipy.calculators.ewald.calculator.Ewald method) Kumagai() (in module matscipy.calculators.manybody.explicit_forms.kumagai) KumagaiAngle (class in matscipy.calculators.manybody.potentials) KumagaiPair (class in matscipy.calculators.manybody.potentials)

L

label (matscipy.calculators.calculator.MatscipyCalculator property) (matscipy.calculators.committee.committee.CommitteeUncertainty property) (matscipy.calculators.eam.calculator.EAM property) (matscipy.calculators.ewald.calculator.Ewald property) (matscipy.calculators.manybody.calculator.Manybody property) (matscipy.calculators.manybody.calculator.NiceManybody property) (matscipy.calculators.manybody.newmb.Manybody property) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential property) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential property) (matscipy.calculators.pair_potential.calculator.PairPotential property) (matscipy.calculators.polydisperse.calculator.Polydisperse property) (matscipy.calculators.supercell_calculator.SupercellCalculator property) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid property) (matscipy.socketcalc.SocketCalculator property) lambda_D (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem property) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS property) LAMMPSData (class in matscipy.io.lammpsdata) latex() (matscipy.surface.MillerIndex method) lattice_constants (matscipy.calculators.eam.io.EAMParameters attribute) left_controlled_volume_scheme_flux_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) left_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) left_dislocation (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute)

left_finite_difference_scheme_flux_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) left_potential_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) left_potential_robin_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) left_robin_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) LennardJones (class in matscipy.calculators.manybody.potentials) LennardJones84 (class in matscipy.calculators.pair_potential.calculator) LennardJonesCut (class in matscipy.calculators.pair_potential.calculator) LennardJonesLinear (class in matscipy.calculators.pair_potential.calculator) LennardJonesQuadratic (class in matscipy.calculators.pair_potential.calculator) lexsort() (matscipy.neighbours.CutoffNeighbourhood static method) (matscipy.neighbours.MolecularNeighbourhood static method) (matscipy.neighbours.Neighbourhood static method) line_intersect_2D() (in module matscipy.utils) LJQData (class in matscipy.opls) load() (matscipy.cauchy_born.RegressionModel method) load_cb_model() (matscipy.fracture_mechanics.crack.SinclairCrack method) load_regression_model() (matscipy.cauchy_born.CubicCauchyBorn method) load_taylor() (matscipy.cauchy_born.CubicCauchyBorn method) loadtbl() (in module matscipy.io.tbl) Logger (class in matscipy.logger)

M

mabincount() (in module matscipy.numpy_tricks) main() (in module matscipy.cli.calculators.average_eam_potential) (in module matscipy.cli.diffusion.rms) (in module matscipy.cli.electrochemistry.continuous2discrete) (in module matscipy.cli.electrochemistry.poisson_nernst_planck_solver) (in module matscipy.cli.electrochemistry.stericify) (in module matscipy.cli.fracture_mechanics.quasistatic_crack) (in module matscipy.cli.fracture_mechanics.sinclair_crack) (in module matscipy.cli.glasses.quench) (in module matscipy.electrochemistry.poisson_boltzmann_distribution) make_barrier_configurations() (in module matscipy.dislocation) make_crystal_basis() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) make_edge_cyl() (in module matscipy.dislocation) make_edge_cyl_001_100() (in module matscipy.dislocation) make_list_of_atoms() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) make_precon() (matscipy.precon.HessianPrecon method) make_result() (matscipy.neighbours.CutoffNeighbourhood static method) (matscipy.neighbours.MolecularNeighbourhood static method) (matscipy.neighbours.Neighbourhood static method) make_screw_cyl() (in module matscipy.dislocation) make_screw_cyl_kink() (in module matscipy.dislocation) make_screw_quadrupole() (in module matscipy.dislocation) make_screw_quadrupole_kink() (in module matscipy.dislocation) make_unit_cell() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) make_unit_slab() (in module matscipy.surface) Manybody (class in matscipy.calculators.manybody.calculator) (class in matscipy.calculators.manybody.newmb) Manybody.Phi (class in matscipy.calculators.manybody.newmb) Manybody.Theta (class in matscipy.calculators.manybody.newmb) map() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.Boundary method) map_pandey_111() (matscipy.surface_reconstruction.SurfaceReconstruction method) map_si_110_3x1() (matscipy.surface_reconstruction.SurfaceReconstruction method) map_surface() (matscipy.surface_reconstruction.SurfaceReconstruction method) mark (matscipy.calculators.mcfm.cluster_data.ClusterData attribute) mark() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.Boundary method) mark_cells() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.Boundary method) mark_facets() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.Boundary method) mask() (matscipy.neighbours.CutoffNeighbourhood static method) (matscipy.neighbours.MolecularNeighbourhood static method) (matscipy.neighbours.Neighbourhood static method) matscipy module matscipy.angle_distribution module matscipy.atomic_strain module matscipy.calculators module matscipy.calculators.calculator module matscipy.calculators.committee module matscipy.calculators.committee.committee module matscipy.calculators.committee.log module matscipy.calculators.committee.utils module matscipy.calculators.eam module matscipy.calculators.eam.average_atom module matscipy.calculators.eam.calculator module matscipy.calculators.eam.io module matscipy.calculators.ewald module matscipy.calculators.ewald.calculator module matscipy.calculators.fitting module matscipy.calculators.manybody module matscipy.calculators.manybody.calculator module matscipy.calculators.manybody.explicit_forms module matscipy.calculators.manybody.explicit_forms.harmonic module matscipy.calculators.manybody.explicit_forms.kumagai module matscipy.calculators.manybody.explicit_forms.stillinger_weber module matscipy.calculators.manybody.explicit_forms.tersoff_brenner module matscipy.calculators.manybody.newmb module matscipy.calculators.manybody.potentials module matscipy.calculators.mcfm module matscipy.calculators.mcfm.calculator module matscipy.calculators.mcfm.cluster_data module matscipy.calculators.mcfm.mcfm_parallel module matscipy.calculators.mcfm.mcfm_parallel.mcfm_parallel_control module matscipy.calculators.mcfm.mcfm_parallel.mcfm_parallel_worker module matscipy.calculators.mcfm.neighbour_list_mcfm module matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_base module matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_mcfm module matscipy.calculators.mcfm.qm_cluster module matscipy.calculators.mcfm.qm_cluster_tools module matscipy.calculators.mcfm.qm_cluster_tools.base_qm_cluster_tool module matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool module matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool module matscipy.calculators.pair_potential module matscipy.calculators.pair_potential.calculator module matscipy.calculators.polydisperse module matscipy.calculators.polydisperse.calculator module matscipy.calculators.supercell_calculator module matscipy.cauchy_born module matscipy.cli module matscipy.cli.calculators module matscipy.cli.calculators.average_eam_potential module matscipy.cli.diffusion module matscipy.cli.diffusion.rms module matscipy.cli.electrochemistry module matscipy.cli.electrochemistry.continuous2discrete module matscipy.cli.electrochemistry.poisson_nernst_planck_solver module matscipy.cli.electrochemistry.stericify module matscipy.cli.fracture_mechanics module matscipy.cli.fracture_mechanics.quasistatic_crack module matscipy.cli.fracture_mechanics.setup_crack module matscipy.cli.fracture_mechanics.sinclair_crack module matscipy.cli.glasses module matscipy.cli.glasses.quench module matscipy.compat module matscipy.deformation module matscipy.dislocation module matscipy.drift module matscipy.elasticity module matscipy.electrochemistry module matscipy.electrochemistry.poisson_boltzmann_distribution module matscipy.electrochemistry.poisson_nernst_planck_solver module matscipy.electrochemistry.poisson_nernst_planck_solver_fenics module matscipy.electrochemistry.steric_correction module matscipy.ffi module matscipy.fracture_mechanics module matscipy.fracture_mechanics.clusters module matscipy.fracture_mechanics.crack module matscipy.fracture_mechanics.crackpathsel module

matscipy.fracture_mechanics.energy_release module matscipy.fracture_mechanics.idealbrittlesolid module matscipy.gamma_surface module matscipy.hydrogenate module matscipy.io module matscipy.io.lammpsdata module matscipy.io.metis module matscipy.io.opls module matscipy.io.tbl module matscipy.logger module matscipy.molecules module matscipy.neighbours module matscipy.numerical module matscipy.numpy_tricks module matscipy.opls module matscipy.optimize module matscipy.precon module matscipy.pressurecoupling module matscipy.rings module matscipy.socketcalc module matscipy.spatial_correlation_function module matscipy.surface module matscipy.surface_reconstruction module matscipy.utils module MatscipyCalculator (class in matscipy.calculators.calculator) max() (matscipy.opls.CutoffList method) (matscipy.surface.MillerIndex method) max_rad() (in module matscipy.spatial_correlation_function) mean() (matscipy.surface.MillerIndex method) measure_triclinic_elastic_constants() (in module matscipy.elasticity) members (matscipy.calculators.committee.committee.Committee property) mic() (in module matscipy.neighbours) middle_mask (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell property) MillerDirection() (in module matscipy.surface) MillerIndex (class in matscipy.surface) MillerPlane() (in module matscipy.surface) min() (matscipy.surface.MillerIndex method) minimal_cost (matscipy.calculators.fitting.CombinedFit attribute) (matscipy.calculators.fitting.Fit attribute) (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitDimer attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSinglePoint attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) (matscipy.calculators.fitting.Penalty attribute) mix() (in module matscipy.calculators.manybody.explicit_forms.tersoff_brenner) mix_arithmetic() (in module matscipy.calculators.manybody.explicit_forms.tersoff_brenner) mix_eam() (in module matscipy.calculators.eam.io) mix_geometric() (in module matscipy.calculators.manybody.explicit_forms.tersoff_brenner) mix_sizes() (matscipy.calculators.polydisperse.calculator.InversePowerLawPotential method) module matscipy matscipy.angle_distribution matscipy.atomic_strain matscipy.calculators matscipy.calculators.calculator matscipy.calculators.committee matscipy.calculators.committee.committee matscipy.calculators.committee.log matscipy.calculators.committee.utils matscipy.calculators.eam matscipy.calculators.eam.average_atom matscipy.calculators.eam.calculator matscipy.calculators.eam.io matscipy.calculators.ewald matscipy.calculators.ewald.calculator matscipy.calculators.fitting matscipy.calculators.manybody matscipy.calculators.manybody.calculator matscipy.calculators.manybody.explicit_forms matscipy.calculators.manybody.explicit_forms.harmonic matscipy.calculators.manybody.explicit_forms.kumagai matscipy.calculators.manybody.explicit_forms.stillinger_weber matscipy.calculators.manybody.explicit_forms.tersoff_brenner matscipy.calculators.manybody.newmb matscipy.calculators.manybody.potentials matscipy.calculators.mcfm matscipy.calculators.mcfm.calculator matscipy.calculators.mcfm.cluster_data matscipy.calculators.mcfm.mcfm_parallel matscipy.calculators.mcfm.mcfm_parallel.mcfm_parallel_control matscipy.calculators.mcfm.mcfm_parallel.mcfm_parallel_worker matscipy.calculators.mcfm.neighbour_list_mcfm matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_base matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_mcfm matscipy.calculators.mcfm.qm_cluster matscipy.calculators.mcfm.qm_cluster_tools matscipy.calculators.mcfm.qm_cluster_tools.base_qm_cluster_tool matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool matscipy.calculators.pair_potential matscipy.calculators.pair_potential.calculator matscipy.calculators.polydisperse matscipy.calculators.polydisperse.calculator matscipy.calculators.supercell_calculator matscipy.cauchy_born matscipy.cli matscipy.cli.calculators matscipy.cli.calculators.average_eam_potential matscipy.cli.diffusion matscipy.cli.diffusion.rms matscipy.cli.electrochemistry matscipy.cli.electrochemistry.continuous2discrete matscipy.cli.electrochemistry.poisson_nernst_planck_solver matscipy.cli.electrochemistry.stericify matscipy.cli.fracture_mechanics matscipy.cli.fracture_mechanics.quasistatic_crack matscipy.cli.fracture_mechanics.setup_crack matscipy.cli.fracture_mechanics.sinclair_crack matscipy.cli.glasses matscipy.cli.glasses.quench matscipy.compat matscipy.deformation matscipy.dislocation matscipy.drift matscipy.elasticity matscipy.electrochemistry matscipy.electrochemistry.poisson_boltzmann_distribution matscipy.electrochemistry.poisson_nernst_planck_solver matscipy.electrochemistry.poisson_nernst_planck_solver_fenics matscipy.electrochemistry.steric_correction matscipy.ffi matscipy.fracture_mechanics matscipy.fracture_mechanics.clusters matscipy.fracture_mechanics.crack matscipy.fracture_mechanics.crackpathsel matscipy.fracture_mechanics.energy_release matscipy.fracture_mechanics.idealbrittlesolid matscipy.gamma_surface matscipy.hydrogenate matscipy.io matscipy.io.lammpsdata matscipy.io.metis matscipy.io.opls matscipy.io.tbl matscipy.logger matscipy.molecules matscipy.neighbours matscipy.numerical matscipy.numpy_tricks matscipy.opls matscipy.optimize matscipy.precon matscipy.pressurecoupling matscipy.rings matscipy.socketcalc matscipy.spatial_correlation_function matscipy.surface matscipy.surface_reconstruction matscipy.utils MolecularNeighbourhood (class in matscipy.neighbours) Molecules (class in matscipy.molecules) molecules (matscipy.neighbours.MolecularNeighbourhood property) MultiClusterForceMixingPotential (class in matscipy.calculators.mcfm) (class in matscipy.calculators.mcfm.calculator)

N

N_cores (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) n_planes (matscipy.dislocation.BCCEdge100110Dislocation attribute), [1] (matscipy.dislocation.BCCEdge100Dislocation attribute), [1] (matscipy.dislocation.BCCEdge111barDislocation attribute), [1] (matscipy.dislocation.BCCEdge111Dislocation attribute), [1] (matscipy.dislocation.BCCMixed111Dislocation attribute), [1] (matscipy.dislocation.BCCScrew111Dislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.DiamondGlide30degreePartial attribute), [1] (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute), [1] (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute), [1] (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute), [1] n_planes() (matscipy.dislocation.CubicCrystalDissociatedDislocation method) name (matscipy.calculators.calculator.MatscipyCalculator property) (matscipy.calculators.committee.committee.CommitteeUncertainty property) (matscipy.calculators.eam.calculator.EAM attribute) (matscipy.calculators.ewald.calculator.Ewald attribute) (matscipy.calculators.manybody.calculator.Manybody attribute) (matscipy.calculators.manybody.calculator.NiceManybody attribute) (matscipy.calculators.manybody.newmb.Manybody property) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential property) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential property) (matscipy.calculators.pair_potential.calculator.PairPotential attribute) (matscipy.calculators.polydisperse.calculator.Polydisperse attribute) (matscipy.calculators.supercell_calculator.SupercellCalculator attribute) (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid property) (matscipy.socketcalc.SocketCalculator attribute) name_value() (matscipy.opls.AnglesData method) (matscipy.opls.BondData method) (matscipy.opls.CutoffList method) (matscipy.opls.DihedralsData method)

nbytes (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) ndim (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) neigh_list_based_target_function() (in module matscipy.electrochemistry.steric_correction) neighbour_list() (in module matscipy.neighbours) Neighbourhood (class in matscipy.neighbours) NeighbourListBase (class in matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_base) NeighbourListMCFM (class in matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_mcfm) nernst_planck_pde() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) new_array() (matscipy.opls.OPLSStructure method) new_bulk() (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitTetragonalCrystal method) new_dimer() (matscipy.calculators.fitting.FitDimer method) new_left_burgers (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) new_right_burgers (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) new_surface() (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) newbyteorder() (matscipy.surface.MillerIndex method) newton() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) NiceManybody (class in matscipy.calculators.manybody.calculator) NiceManybody.F (class in matscipy.calculators.manybody.calculator) NiceManybody.G (class in matscipy.calculators.manybody.calculator) nonaffine_elastic_contribution() (in module matscipy.elasticity) nonzero() (matscipy.surface.MillerIndex method) norm() (matscipy.precon.HessianPrecon method) (matscipy.surface.MillerIndex method) normalised() (matscipy.surface.MillerIndex method) number (matscipy.calculators.committee.committee.Committee property) number_conservation_constraint() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) number_of_density_grid_points (matscipy.calculators.eam.io.EAMParameters attribute) number_of_distance_grid_points (matscipy.calculators.eam.io.EAMParameters attribute) number_of_lattice_vectors (matscipy.opls.OPLSStructure property) numbers (matscipy.opls.OPLSStructure property) numerical_forces() (in module matscipy.numerical) numerical_hessian() (in module matscipy.numerical) numerical_nonaffine_forces() (in module matscipy.numerical) numerical_nonaffine_forces_reference() (in module matscipy.numerical) numerical_stress() (in module matscipy.numerical) numfmt_str() (in module matscipy.logger) numpy_only_target_function() (in module matscipy.electrochemistry.steric_correction)

O

ode12r() (in module matscipy.optimize) OPLSStructure (class in matscipy.opls) optimize() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) (matscipy.calculators.fitting.RotatingFit method) (matscipy.fracture_mechanics.crack.SinclairCrack method) optimize_anneal() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) optimize_brute() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method)

optimize_leastsq() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) optimize_openopt() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) other (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute) ovito_dxa() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) ovito_dxa_straight_dislo_info() (in module matscipy.dislocation) OWNDATA (matscipy.surface.MillerIndex attribute)

P

P_bottom (matscipy.pressurecoupling.SlideLog attribute) P_top (matscipy.pressurecoupling.SlideLog attribute) pack() (matscipy.fracture_mechanics.crack.SinclairCrack method) pack_atoms_to_reftraj_str() (in module matscipy.socketcalc) pack_atoms_to_xyz_str() (in module matscipy.socketcalc) pack_results_to_reftraj_output_str() (in module matscipy.socketcalc) pair_index() (in module matscipy.calculators.manybody.explicit_forms.tersoff_brenner) pair_type (matscipy.neighbours.MolecularNeighbourhood property) PairPotential (class in matscipy.calculators.pair_potential.calculator) par (matscipy.calculators.fitting.CombinedFit attribute) (matscipy.calculators.fitting.Fit attribute) (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitDimer attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSinglePoint attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) (matscipy.calculators.fitting.Penalty attribute) (matscipy.calculators.fitting.RotatingFit attribute) par_at_minimal_cost (matscipy.calculators.fitting.CombinedFit attribute) (matscipy.calculators.fitting.Fit attribute) (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitDimer attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSinglePoint attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) (matscipy.calculators.fitting.Penalty attribute) parameter() (in module matscipy) Parameters (class in matscipy.calculators.fitting) parameters (matscipy.calculators.fitting.Parameters attribute) parity (matscipy.dislocation.BCCEdge100110Dislocation attribute), [1] (matscipy.dislocation.BCCEdge100Dislocation attribute), [1] (matscipy.dislocation.BCCEdge111barDislocation attribute), [1] (matscipy.dislocation.BCCEdge111Dislocation attribute), [1] (matscipy.dislocation.BCCMixed111Dislocation attribute), [1] (matscipy.dislocation.BCCScrew111Dislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.DiamondGlide30degreePartial attribute), [1] (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute), [1] (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute), [1] (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute), [1] parity() (matscipy.dislocation.CubicCrystalDissociatedDislocation method) parse() (matscipy.surface.MillerIndex class method) partition() (matscipy.surface.MillerIndex method) pbc (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) (matscipy.opls.OPLSStructure property)

Pdot() (matscipy.precon.HessianPrecon method) Penalty (class in matscipy.calculators.fitting) periodic_displacements() (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) permutation() (matscipy.cauchy_born.CubicCauchyBorn method) planar_closest_pair() (in module matscipy.electrochemistry.steric_correction) plane_spacing() (matscipy.surface.MillerIndex method) plot() (matscipy.fracture_mechanics.crack.SinclairCrack method) plot_bulk() (in module matscipy.dislocation) plot_energy_densities() (matscipy.gamma_surface.GammaSurface method) (matscipy.gamma_surface.StackingFault method) plot_stress_fields() (in module matscipy.fracture_mechanics.crack) plot_unit_cell() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) plot_vitek() (in module matscipy.dislocation) points_in_polygon2D() (in module matscipy.utils) poisson_pde() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) poisson_ratio() (in module matscipy.elasticity) PoissonNernstPlanckSystem (class in matscipy.electrochemistry.poisson_nernst_planck_solver) PoissonNernstPlanckSystemFEniCS (class in matscipy.electrochemistry.poisson_nernst_planck_solver_fenics) Polydisperse (class in matscipy.calculators.polydisperse.calculator) pop() (matscipy.opls.LJQData method) (matscipy.opls.OPLSStructure method) popitem() (matscipy.opls.LJQData method) positions (matscipy.opls.OPLSStructure property) postprocess() (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.VaspClient method) potential (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem property) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS property) potential() (in module matscipy.electrochemistry.poisson_boltzmann_distribution) pr() (matscipy.logger.Logger method) predict() (matscipy.cauchy_born.RegressionModel method) predict_gradient() (matscipy.cauchy_born.RegressionModel method) predict_shifts() (matscipy.cauchy_born.CubicCauchyBorn method) preprocess() (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.VaspClient method) print_crack_system() (in module matscipy.fracture_mechanics.crack) print_directions_and_miller() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) print_message() (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) process_element() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method) process_request() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) process_request_thread() (matscipy.socketcalc.AtomsServerAsync method) prod() (matscipy.surface.MillerIndex method) produce_classical_results() (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) produce_qm_clusters() (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) ptp() (matscipy.surface.MillerIndex method) put() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) (matscipy.surface.MillerIndex method) put_atom() (matscipy.dislocation.BodyCenteredCubicOctahedralFactory method) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory method)

Q

qm_list (matscipy.calculators.mcfm.cluster_data.ClusterData attribute) QMClient (class in matscipy.socketcalc) QMCluster (class in matscipy.calculators.mcfm.qm_cluster)

QMClusteringTool (class in matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool) QMFlaggingTool (class in matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool) Quadrupole (in module matscipy.dislocation) QUIPClient (class in matscipy.socketcalc)

R

r0 (matscipy.calculators.fitting.FitDimer attribute) radial_mask_from_polygon2D() (in module matscipy.utils) random_solid() (in module matscipy.cli.glasses.quench) range_mapping (matscipy.calculators.fitting.Parameters attribute) ranges (matscipy.calculators.fitting.Parameters attribute) rattle() (matscipy.opls.OPLSStructure method) ravel() (matscipy.surface.MillerIndex method) rbufsize (matscipy.socketcalc.AtomsRequestHandler attribute) read() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.io.lammpsdata.LAMMPSData method) (matscipy.socketcalc.SocketCalculator method) read_atoms() (matscipy.calculators.calculator.MatscipyCalculator class method) (matscipy.calculators.committee.committee.CommitteeUncertainty class method) (matscipy.calculators.eam.calculator.EAM class method) (matscipy.calculators.ewald.calculator.Ewald class method) (matscipy.calculators.manybody.calculator.Manybody class method) (matscipy.calculators.manybody.calculator.NiceManybody class method) (matscipy.calculators.manybody.newmb.Manybody class method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential class method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential class method) (matscipy.calculators.pair_potential.calculator.PairPotential class method) (matscipy.calculators.polydisperse.calculator.Polydisperse class method) (matscipy.calculators.supercell_calculator.SupercellCalculator class method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid class method) (matscipy.socketcalc.SocketCalculator class method) read_block() (in module matscipy.io.opls) read_cutoffs() (in module matscipy.io.opls) read_dislo_QMMM() (in module matscipy.dislocation) read_eam() (in module matscipy.calculators.eam.io) read_extended_xyz() (in module matscipy.io.opls) read_lammps_data() (in module matscipy.io.opls) read_lammps_definitions() (in module matscipy.io.opls) read_molecules_from_lammps_data() (in module matscipy.io.lammpsdata) read_parameter_file() (in module matscipy.io.opls) real (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) RectilinearAnisotropicCrack (class in matscipy.fracture_mechanics.crack) recursive_closest_pair() (in module matscipy.electrochemistry.steric_correction) refit_regression() (matscipy.cauchy_born.CubicCauchyBorn method) RegressionModel (class in matscipy.cauchy_born) relax_images() (matscipy.gamma_surface.GammaSurface method) (matscipy.gamma_surface.StackingFault method) RemoveDrift (class in matscipy.drift) RemoveSimpleShearDeformation (class in matscipy.deformation) repeat() (matscipy.opls.OPLSStructure method) (matscipy.surface.MillerIndex method) replace_double_bond() (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) replace_single_bond() (matscipy.calculators.mcfm.qm_cluster_tools.qm_clustering_tool.QMClusteringTool method) request_queue_size (matscipy.socketcalc.AtomsServerAsync attribute) (matscipy.socketcalc.AtomsServerSync attribute) rescale_k() (matscipy.fracture_mechanics.crack.SinclairCrack method) reset() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method)

reset_energized_list() (matscipy.calculators.mcfm.qm_cluster.QMCluster method) reset_kspace() (matscipy.calculators.ewald.calculator.Ewald method) reshape() (matscipy.surface.MillerIndex method) residuals_history (matscipy.calculators.fitting.CombinedFit attribute) (matscipy.calculators.fitting.Fit attribute) (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitDimer attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSinglePoint attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) (matscipy.calculators.fitting.Penalty attribute) resize() (matscipy.surface.MillerIndex method) reverse_pair_indices() (matscipy.neighbours.CutoffNeighbourhood method) (matscipy.neighbours.MolecularNeighbourhood method) (matscipy.neighbours.Neighbourhood method) right_controlled_volume_scheme_flux_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) right_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) right_dislocation (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) right_finite_difference_scheme_flux_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) right_potential_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) right_potential_robin_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) right_robin_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) ring_statistics() (in module matscipy.rings) rms_kspace() (matscipy.calculators.ewald.calculator.Ewald static method) rms_rspace() (matscipy.calculators.ewald.calculator.Ewald static method) rotate() (matscipy.elasticity.CubicElasticModuli method) (matscipy.opls.OPLSStructure method) rotate_cubic_elastic_constants() (in module matscipy.elasticity) rotate_dihedral() (matscipy.opls.OPLSStructure method) rotate_elastic_constants() (in module matscipy.elasticity) RotatingFit (class in matscipy.calculators.fitting) round() (matscipy.surface.MillerIndex method) rows (matscipy.pressurecoupling.SlideLog attribute) rtheta() (matscipy.fracture_mechanics.crack.RectilinearAnisotropicCrack method)

S

save() (matscipy.cauchy_born.RegressionModel method) save_cb_model() (matscipy.fracture_mechanics.crack.SinclairCrack method) save_metis() (in module matscipy.io.metis) save_regression_model() (matscipy.cauchy_born.CubicCauchyBorn method) save_taylor() (matscipy.cauchy_born.CubicCauchyBorn method) savetbl() (in module matscipy.io.tbl) sc() (in module matscipy.fracture_mechanics.clusters) scale_displacements() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) scale_uncertainty() (matscipy.calculators.committee.committee.Committee method) scipy_distance_based_closest_pair() (in module matscipy.electrochemistry.steric_correction) scipy_distance_based_target_function() (in module matscipy.electrochemistry.steric_correction) screw_cyl_octahedral() (in module matscipy.dislocation) screw_cyl_tetrahedral() (in module matscipy.dislocation) searchsorted() (matscipy.surface.MillerIndex method) second_derivative() (matscipy.calculators.ewald.calculator.EwaldShortRange method) (matscipy.calculators.pair_potential.calculator.BeestKramerSanten method) (matscipy.calculators.pair_potential.calculator.CutoffInteraction method) (matscipy.calculators.pair_potential.calculator.FeneLJCut method) (matscipy.calculators.pair_potential.calculator.LennardJones84 method) (matscipy.calculators.pair_potential.calculator.LennardJonesCut method) (matscipy.calculators.pair_potential.calculator.LennardJonesLinear method) (matscipy.calculators.pair_potential.calculator.LennardJonesQuadratic method) (matscipy.calculators.polydisperse.calculator.InversePowerLawPotential method) self_consistent (matscipy.dislocation.BCCEdge100110Dislocation attribute), [1] (matscipy.dislocation.BCCEdge100Dislocation attribute), [1] (matscipy.dislocation.BCCEdge111barDislocation attribute), [1] (matscipy.dislocation.BCCEdge111Dislocation attribute), [1] (matscipy.dislocation.BCCMixed111Dislocation attribute), [1] (matscipy.dislocation.BCCScrew111Dislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.DiamondGlide30degreePartial attribute), [1] (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute), [1] (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute), [1] (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute), [1] self_consistent() (matscipy.dislocation.CubicCrystalDissociatedDislocation method) self_consistent_displacements() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) self_energy() (matscipy.calculators.ewald.calculator.Ewald static method) serve_forever() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) server_activate() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) server_bind() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) server_close() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) service_actions() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) set() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.fitting.Parameters method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) set_angle() (matscipy.opls.OPLSStructure method) set_array() (matscipy.calculators.fitting.Parameters method) (matscipy.opls.OPLSStructure method) set_atom_data() (matscipy.opls.OPLSStructure method) set_atomic_numbers() (matscipy.opls.OPLSStructure method) set_atoms() (matscipy.fracture_mechanics.crack.SinclairCrack method) set_burgers() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method) set_calculator() (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) (matscipy.opls.OPLSStructure method) set_calculator_class() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) set_cell() (matscipy.opls.OPLSStructure method) set_celldisp() (matscipy.opls.OPLSStructure method) set_center_of_mass() (matscipy.opls.OPLSStructure method) set_chemical_symbols() (matscipy.opls.OPLSStructure method) set_constant() (matscipy.calculators.fitting.Parameters method) set_constraint() (matscipy.opls.OPLSStructure method) set_constraints() (in module matscipy.fracture_mechanics.idealbrittlesolid) set_cutoffs() (matscipy.opls.OPLSStructure method) set_derived() (matscipy.calculators.fitting.Parameters method) set_dict() (matscipy.calculators.fitting.Parameters method) set_dihedral() (matscipy.opls.OPLSStructure method) set_distance() (matscipy.opls.OPLSStructure method) set_dofs() (matscipy.fracture_mechanics.crack.SinclairCrack method) set_groups() (in module matscipy.fracture_mechanics.clusters) set_initial_charges() (matscipy.opls.OPLSStructure method) set_initial_magnetic_moments() (matscipy.opls.OPLSStructure method) set_initial_velocities() (in module matscipy.fracture_mechanics.idealbrittlesolid) set_internal_validation_set() (matscipy.calculators.committee.committee.Committee method) set_label() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.socketcalc.SocketCalculator method) set_logfile() (matscipy.logger.Logger method) set_logging() (in module matscipy.calculators.committee.log) set_masses() (matscipy.opls.OPLSStructure method)

set_model() (matscipy.cauchy_born.CubicCauchyBorn method) set_momenta() (matscipy.opls.OPLSStructure method) set_names() (matscipy.opls.AnglesData method) (matscipy.opls.BondData method) (matscipy.opls.CutoffList method) (matscipy.opls.DihedralsData method) set_outevery() (matscipy.logger.Logger method) set_parameters() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) set_parameters_from_array() (matscipy.calculators.fitting.CombinedFit method) (matscipy.calculators.fitting.Fit method) (matscipy.calculators.fitting.FitB2 method) (matscipy.calculators.fitting.FitBCC method) (matscipy.calculators.fitting.FitCubicCrystal method) (matscipy.calculators.fitting.FitDiamond method) (matscipy.calculators.fitting.FitDiamond100 method) (matscipy.calculators.fitting.FitDiamond110 method) (matscipy.calculators.fitting.FitDiamond111 method) (matscipy.calculators.fitting.FitDimer method) (matscipy.calculators.fitting.FitFCC method) (matscipy.calculators.fitting.FitGraphene method) (matscipy.calculators.fitting.FitGraphite method) (matscipy.calculators.fitting.FitHexagonalCrystal method) (matscipy.calculators.fitting.FitL1_0 method) (matscipy.calculators.fitting.FitL1_2 method) (matscipy.calculators.fitting.FitSC method) (matscipy.calculators.fitting.FitSinglePoint method) (matscipy.calculators.fitting.FitSurface method) (matscipy.calculators.fitting.FitTetragonalCrystal method) (matscipy.calculators.fitting.Penalty method) set_pbc() (matscipy.opls.OPLSStructure method) set_plane_strain() (matscipy.fracture_mechanics.crack.RectilinearAnisotropicCrack method) set_plane_stress() (matscipy.fracture_mechanics.crack.RectilinearAnisotropicCrack method) set_positions() (matscipy.opls.OPLSStructure method) set_property() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.Boundary method) set_qm_atoms() (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) set_range_derived() (matscipy.calculators.fitting.Parameters method) set_reference_crystal() (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) set_regions() (in module matscipy.fracture_mechanics.clusters) set_scaled_positions() (matscipy.opls.OPLSStructure method) set_shiftmask() (matscipy.fracture_mechanics.crack.SinclairCrack method) set_sublattices() (matscipy.cauchy_born.CubicCauchyBorn method) set_tags() (matscipy.opls.OPLSStructure method) set_training_data() (matscipy.calculators.committee.committee.CommitteeMember method) set_types() (matscipy.opls.OPLSStructure method) set_variable() (matscipy.calculators.fitting.Parameters method) set_velocities() (matscipy.opls.OPLSStructure method) setdefault() (matscipy.opls.LJQData method) setfield() (matscipy.surface.MillerIndex method) setflags() (matscipy.surface.MillerIndex method) setup() (matscipy.socketcalc.AtomsRequestHandler method) setup_crack() (in module matscipy.cli.fracture_mechanics.setup_crack) shape (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) short_range (matscipy.calculators.ewald.calculator.Ewald property) show() (matscipy.gamma_surface.GammaSurface method) (matscipy.gamma_surface.StackingFault method) show_configuration() (in module matscipy.dislocation) show_NEB_configurations() (in module matscipy.dislocation) shutdown() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.SocketCalculator method) (matscipy.socketcalc.VaspClient method) shutdown_clients() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) shutdown_request() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) simplified() (matscipy.surface.MillerIndex method) simplify() (matscipy.surface.MillerIndex method) SinclairCrack (class in matscipy.fracture_mechanics.crack) size (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) slice_long_dislo() (in module matscipy.dislocation) SlideLog (class in matscipy.pressurecoupling) SlideLogger (class in matscipy.pressurecoupling) SlideWithNormalPressureCuboidCell (class in matscipy.pressurecoupling) snap() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.Boundary method) socket_type (matscipy.socketcalc.AtomsServerAsync attribute) (matscipy.socketcalc.AtomsServerSync attribute) SocketCalculator (class in matscipy.socketcalc) solve() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) (matscipy.precon.HessianPrecon method) solver_callback() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) sort() (matscipy.surface.MillerIndex method) spatial_correlation_function() (in module matscipy.spatial_correlation_function) spatial_correlation_function_near() (in module matscipy.spatial_correlation_function) squeeze() (matscipy.surface.MillerIndex method) st() (matscipy.logger.Logger method) StackingFault (class in matscipy.gamma_surface) start() (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.VaspClient method) start_or_restart() (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.VaspClient method) std() (matscipy.surface.MillerIndex method) step (matscipy.pressurecoupling.SlideLog attribute) stiffness() (matscipy.elasticity.CubicElasticModuli method) StillingerWeber() (in module matscipy.calculators.manybody.explicit_forms.stillinger_weber) StillingerWeberAngle (class in matscipy.calculators.manybody.potentials) StillingerWeberPair (class in matscipy.calculators.manybody.potentials) strain_err() (matscipy.fracture_mechanics.crack.SinclairCrack method) strain_to_G() (in module matscipy.fracture_mechanics.crack) stress (matscipy.calculators.fitting.FitSinglePoint attribute) stress_kspace() (matscipy.calculators.ewald.calculator.Ewald static method) stresses() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) (matscipy.fracture_mechanics.crack.RectilinearAnisotropicCrack method) stresses_from_cartesian_coordinates() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) stresses_from_cylinder_coordinates() (matscipy.fracture_mechanics.crack.CubicCrystalCrack method) strides (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) stroh (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) subsample() (in module matscipy.calculators.committee.utils) sum() (matscipy.surface.MillerIndex method) sum_ij_pi_ij_n() (matscipy.calculators.manybody.newmb.Manybody class method) sum_ij_sum_X_pi_X_n() (matscipy.calculators.manybody.newmb.Manybody class method) sum_ijk_tau_XY_mn() (matscipy.calculators.manybody.newmb.Manybody class method) sum_X_sum_ijk_tau_ij_XOR_X_mn() (matscipy.calculators.manybody.newmb.Manybody class method) sum_X_sum_ijk_tau_ijX_mn() (matscipy.calculators.manybody.newmb.Manybody class method) sum_XX_sum_ijk_tau_XX_mn() (matscipy.calculators.manybody.newmb.Manybody class method) sum_XY_sum_ijk_tau_XY_mn() (matscipy.calculators.manybody.newmb.Manybody class method) SupercellCalculator (class in matscipy.calculators.supercell_calculator) surf_directions (matscipy.gamma_surface.GammaSurface.self attribute) (matscipy.gamma_surface.StackingFault.self attribute) SurfaceReconstruction (class in matscipy.surface_reconstruction) surfstr (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) swapaxes() (matscipy.surface.MillerIndex method) switch_sublattices() (matscipy.cauchy_born.CubicCauchyBorn method) symbols (matscipy.calculators.eam.io.EAMParameters attribute) (matscipy.opls.OPLSStructure property) SymPhi (class in matscipy.calculators.manybody.potentials) SymTheta (class in matscipy.calculators.manybody.potentials)

T

T (matscipy.dislocation.CubicCrystalDislocationQuadrupole attribute) (matscipy.dislocation.CubicCrystalDissociatedDislocation attribute) (matscipy.surface.MillerIndex attribute) T_thermostat (matscipy.pressurecoupling.SlideLog attribute) take() (matscipy.surface.MillerIndex method) targets (matscipy.calculators.fitting.CombinedFit attribute) (matscipy.calculators.fitting.RotatingFit attribute) tau_bottom (matscipy.pressurecoupling.SlideLog attribute) tau_top (matscipy.pressurecoupling.SlideLog attribute) Tdir (matscipy.pressurecoupling.SlideWithNormalPressureCuboidCell property) tensor_field_3D_from_atoms() (matscipy.cauchy_born.CubicCauchyBorn method) TersoffBrenner() (in module matscipy.calculators.manybody.explicit_forms.tersoff_brenner) TersoffBrennerAngle (class in matscipy.calculators.manybody.potentials) TersoffBrennerPair (class in matscipy.calculators.manybody.potentials) test() (in module matscipy.electrochemistry.poisson_boltzmann_distribution) thin_strip_displacement_y() (in module matscipy.fracture_mechanics.crack) time (matscipy.pressurecoupling.SlideLog attribute) timeout (matscipy.socketcalc.AtomsRequestHandler attribute) (matscipy.socketcalc.AtomsServerAsync attribute) (matscipy.socketcalc.AtomsServerSync attribute) tobytes() (matscipy.surface.MillerIndex method) todict() (matscipy.calculators.calculator.MatscipyCalculator method) (matscipy.calculators.committee.committee.CommitteeUncertainty method) (matscipy.calculators.eam.calculator.EAM method) (matscipy.calculators.ewald.calculator.Ewald method) (matscipy.calculators.manybody.calculator.Manybody method) (matscipy.calculators.manybody.calculator.NiceManybody method) (matscipy.calculators.manybody.newmb.Manybody method) (matscipy.calculators.mcfm.calculator.MultiClusterForceMixingPotential method) (matscipy.calculators.mcfm.MultiClusterForceMixingPotential method) (matscipy.calculators.pair_potential.calculator.PairPotential method) (matscipy.calculators.polydisperse.calculator.Polydisperse method) (matscipy.calculators.supercell_calculator.SupercellCalculator method) (matscipy.fracture_mechanics.idealbrittlesolid.IdealBrittleSolid method) (matscipy.opls.OPLSStructure method) (matscipy.socketcalc.SocketCalculator method)

tofile() (matscipy.surface.MillerIndex method) tol (matscipy.elasticity.CubicElasticModuli attribute) tolist() (matscipy.surface.MillerIndex method) tostring() (matscipy.surface.MillerIndex method) trace() (matscipy.surface.MillerIndex method) translate() (matscipy.opls.OPLSStructure method) transpose() (matscipy.surface.MillerIndex method) triangular_lattice_slab() (in module matscipy.fracture_mechanics.idealbrittlesolid) triplet_index() (in module matscipy.calculators.manybody.explicit_forms.tersoff_brenner) triplet_list() (in module matscipy.neighbours) triplet_to_numbers() (matscipy.neighbours.CutoffNeighbourhood method) (matscipy.neighbours.MolecularNeighbourhood method) (matscipy.neighbours.Neighbourhood method) triplet_type (matscipy.neighbours.MolecularNeighbourhood property) twochar() (in module matscipy.opls)

U

u_cle() (matscipy.fracture_mechanics.crack.SinclairCrack method) unit_cell (matscipy.dislocation.BCCEdge100110Dislocation attribute), [1] (matscipy.dislocation.BCCEdge100Dislocation attribute), [1] (matscipy.dislocation.BCCEdge111barDislocation attribute), [1] (matscipy.dislocation.BCCEdge111Dislocation attribute), [1] (matscipy.dislocation.BCCMixed111Dislocation attribute), [1] (matscipy.dislocation.BCCScrew111Dislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocation attribute), [1] (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.CubicCrystalDissociatedDislocation property) (matscipy.dislocation.DiamondGlide30degreePartial attribute), [1] (matscipy.dislocation.DiamondGlide60Degree property) (matscipy.dislocation.DiamondGlide90degreePartial attribute), [1] (matscipy.dislocation.DiamondGlideScrew property) (matscipy.dislocation.FCCEdge110Dislocation property) (matscipy.dislocation.FCCEdgeShockleyPartial attribute), [1] (matscipy.dislocation.FCCScrew110Dislocation property) (matscipy.dislocation.FCCScrewShockleyPartial attribute), [1] unit_cell_core_position (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100110Dislocation property) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation property) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation property) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation property) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation property) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation property) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocation property) (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.CubicCrystalDissociatedDislocation property) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide30degreePartial property) (matscipy.dislocation.DiamondGlide60Degree property) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlide90degreePartial property) (matscipy.dislocation.DiamondGlideScrew property) (matscipy.dislocation.FCCEdge110Dislocation property) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCEdgeShockleyPartial property) (matscipy.dislocation.FCCScrew110Dislocation property) (matscipy.dislocation.FCCScrewShockleyPartial attribute) (matscipy.dislocation.FCCScrewShockleyPartial property)

unit_cell_core_position_dimensionless (matscipy.dislocation.BCCEdge100110Dislocation attribute) (matscipy.dislocation.BCCEdge100Dislocation attribute) (matscipy.dislocation.BCCEdge111barDislocation attribute) (matscipy.dislocation.BCCEdge111Dislocation attribute) (matscipy.dislocation.BCCMixed111Dislocation attribute) (matscipy.dislocation.BCCScrew111Dislocation attribute) (matscipy.dislocation.CubicCrystalDislocation attribute) (matscipy.dislocation.CubicCrystalDislocationQuadrupole property) (matscipy.dislocation.DiamondGlide30degreePartial attribute) (matscipy.dislocation.DiamondGlide60Degree attribute) (matscipy.dislocation.DiamondGlide90degreePartial attribute) (matscipy.dislocation.DiamondGlideScrew attribute) (matscipy.dislocation.FCCEdge110Dislocation attribute) (matscipy.dislocation.FCCEdgeShockleyPartial attribute) (matscipy.dislocation.FCCScrew110Dislocation attribute) (matscipy.dislocation.FCCScrewShockleyPartial attribute) unit_cell_core_position_dimensionless() (matscipy.dislocation.CubicCrystalDissociatedDislocation method) unpack() (matscipy.fracture_mechanics.crack.SinclairCrack method) unpack_reftraj_output_str_to_results() (in module matscipy.socketcalc) unpack_reftraj_str_to_atoms() (in module matscipy.socketcalc) unpack_xyz_str_to_results() (in module matscipy.socketcalc) update() (matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_base.NeighbourListBase method) (matscipy.calculators.mcfm.neighbour_list_mcfm.neighbour_list_mcfm.NeighbourListMCFM method) (matscipy.opls.LJQData method) update_atoms() (matscipy.fracture_mechanics.crack.SinclairCrack method) update_avg_property_per_atom() (in module matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool) update_from_lammps_dump() (in module matscipy.io.opls) update_precon() (matscipy.fracture_mechanics.crack.SinclairCrack method) update_qm_region() (matscipy.calculators.mcfm.qm_cluster.QMCluster method) (matscipy.calculators.mcfm.qm_cluster_tools.qm_flagging_tool.QMFlaggingTool method) use_central_reference_concentration_based_cell_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) use_standard_cell_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) use_standard_dirichlet_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) use_standard_interface_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method) use_stern_layer_cell_bc() (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem method) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS method)

V

v (matscipy.pressurecoupling.SlideLog attribute) validate_cubic_cell() (in module matscipy.utils) validation_set (matscipy.calculators.committee.committee.Committee property) values() (matscipy.opls.LJQData method) var() (matscipy.surface.MillerIndex method) variable (matscipy.calculators.fitting.Parameters attribute) VaspClient (class in matscipy.socketcalc) vdot() (matscipy.precon.HessianPrecon method) verify_request() (matscipy.socketcalc.AtomsServerAsync method) (matscipy.socketcalc.AtomsServerSync method) view() (matscipy.surface.MillerIndex method) view_cyl() (matscipy.dislocation.BCCEdge100110Dislocation method) (matscipy.dislocation.BCCEdge100Dislocation method) (matscipy.dislocation.BCCEdge111barDislocation method) (matscipy.dislocation.BCCEdge111Dislocation method) (matscipy.dislocation.BCCMixed111Dislocation method) (matscipy.dislocation.BCCScrew111Dislocation method) (matscipy.dislocation.CubicCrystalDislocation method) (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) (matscipy.dislocation.CubicCrystalDissociatedDislocation method) (matscipy.dislocation.DiamondGlide30degreePartial method) (matscipy.dislocation.DiamondGlide60Degree method) (matscipy.dislocation.DiamondGlide90degreePartial method) (matscipy.dislocation.DiamondGlideScrew method) (matscipy.dislocation.FCCEdge110Dislocation method) (matscipy.dislocation.FCCEdgeShockleyPartial method) (matscipy.dislocation.FCCScrew110Dislocation method) (matscipy.dislocation.FCCScrewShockleyPartial method)

view_quad() (matscipy.dislocation.CubicCrystalDislocationQuadrupole method) Voigt_6_to_full_3x3_strain() (in module matscipy.elasticity) Voigt_6_to_full_3x3_stress() (in module matscipy.elasticity) Voigt_6x6_to_cubic() (in module matscipy.elasticity) Voigt_6x6_to_full_3x3x3x3() (in module matscipy.elasticity)

W

w_a0 (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) w_c0 (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute) w_D0 (matscipy.calculators.fitting.FitDimer attribute) w_Ec (matscipy.calculators.fitting.FitB2 attribute) (matscipy.calculators.fitting.FitBCC attribute) (matscipy.calculators.fitting.FitCubicCrystal attribute) (matscipy.calculators.fitting.FitDiamond attribute) (matscipy.calculators.fitting.FitDiamond100 attribute) (matscipy.calculators.fitting.FitDiamond110 attribute) (matscipy.calculators.fitting.FitDiamond111 attribute) (matscipy.calculators.fitting.FitFCC attribute) (matscipy.calculators.fitting.FitGraphene attribute) (matscipy.calculators.fitting.FitGraphite attribute) (matscipy.calculators.fitting.FitHexagonalCrystal attribute) (matscipy.calculators.fitting.FitL1_0 attribute) (matscipy.calculators.fitting.FitL1_2 attribute) (matscipy.calculators.fitting.FitSC attribute) (matscipy.calculators.fitting.FitSurface attribute) (matscipy.calculators.fitting.FitTetragonalCrystal attribute)

w_energy (matscipy.calculators.fitting.FitSinglePoint attribute) w_forces (matscipy.calculators.fitting.FitSinglePoint attribute) w_r0 (matscipy.calculators.fitting.FitDimer attribute) w_stress (matscipy.calculators.fitting.FitSinglePoint attribute) wait_for_shutdown() (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.VaspClient method) warn() (matscipy.logger.Logger method) wbufsize (matscipy.socketcalc.AtomsRequestHandler attribute) worker_populate_cluster_data() (in module matscipy.calculators.mcfm.mcfm_parallel.mcfm_parallel_worker) wrap() (matscipy.opls.OPLSStructure method) write() (matscipy.io.lammpsdata.LAMMPSData method) (matscipy.opls.OPLSStructure method) write_atoms_to_file() (matscipy.fracture_mechanics.crack.SinclairCrack method) write_eam() (in module matscipy.calculators.eam.io) write_header() (matscipy.pressurecoupling.SlideLogger method) write_input_files() (matscipy.socketcalc.CastepClient method) (matscipy.socketcalc.Client method) (matscipy.socketcalc.QMClient method) (matscipy.socketcalc.QUIPClient method) (matscipy.socketcalc.VaspClient method) write_lammps() (in module matscipy.io.opls) write_lammps_atoms() (in module matscipy.io.opls) write_lammps_definitions() (in module matscipy.io.opls) write_lammps_in() (in module matscipy.io.opls) WRITEABLE (matscipy.surface.MillerIndex attribute) WRITEBACKIFCOPY (matscipy.surface.MillerIndex attribute)

X

X (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS property) x1_scaled (matscipy.electrochemistry.poisson_nernst_planck_solver.PoissonNernstPlanckSystem property) (matscipy.electrochemistry.poisson_nernst_planck_solver_fenics.PoissonNernstPlanckSystemFEniCS property)

xtal_name (matscipy.dislocation.BodyCenteredCubicOctahedralFactory attribute) (matscipy.dislocation.BodyCenteredCubicTetrahedralFactory attribute)

Y

youngs_modulus() (in module matscipy.elasticity)

Z

ZeroAngle (class in matscipy.calculators.manybody.potentials) ZeroPair (class in matscipy.calculators.manybody.explicit_forms.harmonic) (class in matscipy.calculators.manybody.potentials)

ZeroTriplet (class in matscipy.calculators.manybody.explicit_forms.harmonic)