Index

Symbols

$ASE_ORCA_COMMAND

_

__add__() (ase.formula.Formula method) __contains__() (ase.formula.Formula method) __divmod__() (ase.formula.Formula method) __eq__() (ase.formula.Formula method)

__format__() (ase.formula.Formula method) __getitem__() (ase.formula.Formula method) __len__() (ase.formula.Formula method) __mul__() (ase.formula.Formula method)

A

acoustic() (ase.phonons.Phonons method) add_adsorbate() (in module ase.build) add_array() (ase.io.ulm.Writer method) add_vacuum() (in module ase.build) adjacency_matrix (ase.geometry.analysis.Analysis property) adjust_forces() (in module ase.constraints) adjust_momenta() (in module ase.constraints) adjust_positions() (in module ase.constraints) adjust_potential_energy() (in module ase.constraints) ag Aims (class in ase.calculators.aims) AimsCube (class in ase.calculators.aims) all_angles (ase.geometry.analysis.Analysis property) all_bonds (ase.geometry.analysis.Analysis property) all_dihedrals (ase.geometry.analysis.Analysis property) Analysis (class in ase.geometry.analysis) analyze_dimensionality() (in module ase.geometry.dimensionality) Andersen (class in ase.md.andersen) angles() (ase.cell.Cell method) (ase.geometry.Cell method) append() (ase.Atoms method) apply_cutoff() (ase.phonons.Phonons method) ascell() (ase.cell.Cell class method) (ase.geometry.Cell class method) asdict() (ase.calculators.vasp.Vasp method) (ase.io.ulm.Reader method) ase module ase-gui ase.atom module ase.atoms module ase.build module ase.calculators module ase.calculators.abinit module ase.calculators.acemolecule module ase.calculators.aims module ase.calculators.amber module ase.calculators.castep module ase.calculators.checkpoint module ase.calculators.cp2k module ase.calculators.crystal module ase.calculators.demon module ase.calculators.demonnano module ase.calculators.dftb module ase.calculators.dftd3 module ase.calculators.dmol module ase.calculators.eam module ase.calculators.emt module ase.calculators.espresso module ase.calculators.exciting module ase.calculators.fleur module ase.calculators.gamess_us module ase.calculators.gaussian module ase.calculators.gromacs module ase.calculators.gulp module ase.calculators.kim module ase.calculators.lammps module ase.calculators.LAMMPSrun module ase.calculators.lj module ase.calculators.loggingcalc module ase.calculators.mixing module ase.calculators.mopac module ase.calculators.morse module ase.calculators.nwchem module ase.calculators.octopus module ase.calculators.onetep module ase.calculators.openmx module ase.calculators.orca module ase.calculators.psi4 module ase.calculators.qchem module ase.calculators.qmmm module ase.calculators.siesta module ase.calculators.socketio module ase.calculators.test module ase.calculators.tip3p module ase.calculators.tip4p module ase.calculators.turbomole module ase.calculators.vasp module ase.cell module ase.cluster module ase.collections module

ase.constraints module ase.data module ase.db module ase.db.core module ase.dft module ase.dft.bandgap module ase.dft.dos module ase.dft.kpoints module ase.dft.wannier module ase.dimer module ase.eos module ase.formula module ase.ga module ase.geometry module ase.gui module ase.io module ase.io.opls module ase.io.trajectory module ase.io.ulm module ase.lattice module ase.md module ase.md.analysis module ase.md.andersen module ase.md.contour_exploration module ase.md.langevin module ase.md.npt module ase.md.nptberendsen module ase.md.nvtberendsen module ase.md.velocitydistribution module ase.md.verlet module ase.neb module ase.neighborlist module ase.optimize module ase.optimize.basin module ase.optimize.precon module ase.parallel module ase.phasediagram module ase.phonons module ase.spacegroup module ase.spacegroup.symmetrize module ase.spectrum module ase.spectrum.doscollection module ase.spectrum.dosdata module ase.symbols module ase.test module ase.thermochemistry module ase.transport module ase.units module ase.utils module ase.utils.xrdebye module ase.vibrations module ase.visualize module ase.visualize.mlab module ase.visualize.nglview module ASE_ABC_COMMAND ASE_DFTB_COMMAND ASE_GAUSSIAN_COMMAND ASE_LAMMPSRUN_COMMAND ASE_NWCHEM_COMMAND ASE_ONETEP_COMMAND ASE_OPENMX_COMMAND ASE_SIESTA_COMMAND ASE_VASP_COMMAND, [1], [2], [3] ASE_VASP_VDW assert() (in module ase.test) Atom (class in ase.atom) atomic_masses (in module ase.data) atomic_masses_iupac2016 (in module ase.data) atomic_masses_legacy (in module ase.data) atomic_names (in module ase.data) atomic_numbers (in module ase.data) Atoms (class in ase) AtomsRow (class in ase.db.row) attach() (ase.md.npt.NPT method) (in module ase.build.attach) attach_randomly() (in module ase.build.attach) attach_randomly_and_broadcast() (in module ase.build.attach) AutoNEB (class in ase.autoneb) AverageCalculator (class in ase.calculators.mixing)

B

band_structure() (ase.calculators.calculator.Calculator method) (ase.phonons.Phonons method) bandgap() (in module ase.dft.bandgap) BandPath (class in ase.dft.kpoints) bandpath() (ase.cell.Cell method) (ase.geometry.Cell method) (ase.lattice.BravaisLattice method) (in module ase.dft.kpoints) BandStructure (class in ase.spectrum.band_structure) bcc100() (in module ase.build) bcc110() (in module ase.build) bcc111() (in module ase.build)

bcc111_root() (in module ase.build) Berny (class in ase.optimize) BFGS (class in ase.optimize) BFGSLineSearch (class in ase.optimize) BravaisLattice (class in ase.lattice) broadcast() (in module ase.parallel) build() (ase.neighborlist.NewPrimitiveNeighborList method) (ase.neighborlist.PrimitiveNeighborList method) build_neighbor_list() (in module ase.neighborlist) Bulk modulus bulk() (in module ase.build) BundleTrajectory (class in ase.io.bundletrajectory)

C

calc (ase.Atoms property) calc_pattern() (ase.utils.xrdebye.XrDebye method) calculate() (ase.calculators.calculator.Calculator method) (ase.calculators.calculator.FileIOCalculator method) (ase.calculators.checkpoint.CheckpointCalculator method) (ase.calculators.fleur.FLEUR method) (ase.calculators.test.FreeElectrons method) calculate_eos() (in module ase.eos) calculate_ldos() (ase.dft.stm.STM method) calculate_numerical_forces() (ase.calculators.calculator.Calculator method) calculate_numerical_stress() (ase.calculators.calculator.Calculator method) calculate_properties() (ase.calculators.calculator.Calculator method) calculation_required() (ase.calculators.interface.Calculator method) Calculator (class in ase.calculators.calculator) (class in ase.calculators.interface) cartesian_kpts() (ase.dft.kpoints.BandPath method) cartesian_positions() (ase.cell.Cell method) (ase.geometry.Cell method) Castep (class in ase.calculators.castep) cc12_2x3 (in module ase.dft.kpoints) cc162_1x1 (in module ase.dft.kpoints) cc162_sq3xsq3 (in module ase.dft.kpoints) cc18_1x1 (in module ase.dft.kpoints) cc18_sq3xsq3 (in module ase.dft.kpoints) cc54_1x1 (in module ase.dft.kpoints) cc54_sq3xsq3 (in module ase.dft.kpoints) cc6_1x1 (in module ase.dft.kpoints) cell (ase.Atoms property) (ase.dft.kpoints.BandPath property) Cell (class in ase.cell) (class in ase.geometry) cell_to_cellpar() (in module ase.geometry) CellBounds (class in ase.ga.utilities) cellpar() (ase.cell.Cell method) (ase.geometry.Cell method) (ase.lattice.BravaisLattice method) cellpar_to_cell() (in module ase.geometry) center() (ase.Atoms method) charge (ase.db.row.AtomsRow property) check_eq_forces() (ase.phonons.Phonons method) check_state() (ase.calculators.calculator.Calculator method) check_symmetry() (in module ase.spacegroup.symmetrize) Checkpoint (class in ase.calculators.checkpoint) CheckpointCalculator (class in ase.calculators.checkpoint)

chemical_symbols (in module ase.data) child() (ase.io.ulm.Writer method) clean() (ase.vibrations.Vibrations method) clear_cache() (ase.geometry.analysis.Analysis method) close() (ase.io.bundletrajectory.BundleTrajectory method) (ase.io.trajectory.TrajectoryReader method) (ase.io.trajectory.TrajectoryWriter method) (ase.io.ulm.Writer method) Cluster (class in ase.cluster) Collection (class in ase.collections.collection) combine() (ase.vibrations.Vibrations method) command (ase.calculators.calculator.FileIOCalculator attribute) command line tools compare() (ase.utils.structure_comparator.SymmetryEquivalenceCheck method) complete() (ase.cell.Cell method) (ase.geometry.Cell method) complete_cell() (in module ase.geometry) compute_dynamical_matrix() (ase.phonons.Phonons method) conditional_find_mic() (in module ase.geometry) connect() (in module ase.db.core) connected_atoms() (in module ase.build) connected_indices() (in module ase.build) constrained_forces (ase.db.row.AtomsRow property) constraints (ase.Atoms property) (ase.db.row.AtomsRow property) ContourExploration (class in ase.md.contour_exploration) conventional() (ase.lattice.BravaisLattice method) convert() (ase.formula.Formula method) convert_string_to_fd() (in module ase.utils) copy() (ase.Atoms method) (ase.cell.Cell method) (ase.cluster.Cluster method) (ase.geometry.Cell method) count() (ase.db.core.Database method) (ase.formula.Formula method) count_atoms() (ase.db.row.AtomsRow method) covalent_radii (in module ase.data) CP2K (class in ase.calculators.cp2k) cpk_colors (in module ase.data) create_units() (in module ase.units) crystal() (in module ase.spacegroup) CrystalThermo (class in ase.thermochemistry) custom_colors() (ase.visualize.ngl.NGLDisplay method) cut() (in module ase.build) CutAndSplicePairing (class in ase.ga.cutandsplicepairing)

D

D3 data (ase.db.row.AtomsRow property) Database (class in ase.db.core) dcdft (in module ase.collections) Decahedron() (in module ase.cluster) decompose() (ase.phasediagram.PhaseDiagram method) (ase.phasediagram.Pourbaix method) default_parameters (ase.calculators.calculator.Calculator attribute) (ase.calculators.checkpoint.CheckpointCalculator attribute) (ase.calculators.test.FreeElectrons attribute) delete() (ase.db.core.Database method) delete_bundle() (ase.io.bundletrajectory.BundleTrajectory class method) delta() (in module ase.utils.deltacodesdft) Demon (class in ase.calculators.demon) DemonNano (class in ase.calculators.demonnano) description() (ase.lattice.BravaisLattice method) Dftb (class in ase.calculators.dftb)

DFTB_COMMAND DFTB_PREFIX DFTCalculator (class in ase.calculators.interface) diagram() (ase.phasediagram.Pourbaix method) diamond100() (in module ase.build) diamond111() (in module ase.build) DiffusionCoefficient (class in ase.md.analysis) DimerControl (class in ase.dimer) DimerEigenmodeSearch (class in ase.dimer) discard_results_on_any_change (ase.calculators.calculator.Calculator attribute) distance() (in module ase.geometry) distance_matrix (ase.geometry.analysis.Analysis property) distances() (ase.dft.wannier.Wannier method) DMol3 (class in ase.calculators.dmol) DOS (class in ase.dft.dos) dos() (ase.phonons.Phonons method) download_isotope_data() (in module ase.data.isotopes) DyNEB (class in ase.dyneb)

E

edit() (ase.Atoms method) EIQMMM (class in ase.calculators.qmmm) Embedding (class in ase.calculators.qmmm) EMT (class in ase.calculators.emt) energies (ase.spectrum.band_structure.BandStructure property) environment variable $ASE_ORCA_COMMAND ABINIT_PP_PATH ASE_ABC_COMMAND ASE_ABINIT_COMMAND ASE_DFTB_COMMAND ASE_GAUSSIAN_COMMAND ASE_LAMMPSRUN_COMMAND ASE_NWCHEM_COMMAND ASE_ONETEP_COMMAND ASE_OPENMX_COMMAND ASE_SIESTA_COMMAND ASE_VASP_COMMAND, [1], [2], [3] ASE_VASP_VDW DFTB_COMMAND DFTB_PREFIX FLEUR FLEUR_INPGEN OPENMX_DFT_DATA_PATH PATH, [1], [2], [3], [4], [5], [6], [7] PYTHONPATH, [1], [2], [3] SIESTA_PP_PATH VASP_COMMAND, [1] VASP_PP_PATH, [1] VASP_SCRIPT, [1]

EquationOfState (class in ase.eos) Espresso (class in ase.calculators.espresso) euler_rotate() (ase.Atoms method) Exciting (class in ase.calculators.exciting) ExpCellFilter (class in ase.constraints) extend() (ase.Atoms method) ExternalForce (class in ase.constraints)

F

fcc100() (in module ase.build) fcc110() (in module ase.build) fcc111() (in module ase.build) fcc111_root() (in module ase.build) fcc211() (in module ase.build) FileIOCalculator (class in ase.calculators.calculator) fill() (ase.io.ulm.Writer method) Filter (class in ase.constraints) find_current() (ase.dft.stm.STM method) find_mic() (in module ase.geometry) find_optimal_cell_shape() (in module ase.build) FIRE (class in ase.optimize) first_neighbors() (in module ase.neighborlist) fit() (ase.eos.EquationOfState method) FixAtoms (class in ase.constraints) FixBondLength (class in ase.constraints) FixBondLengths (class in ase.constraints) FixCom (class in ase.constraints) FixedLine (class in ase.constraints) FixedMode (class in ase.constraints) FixedPlane (class in ase.constraints)

FixInternals (class in ase.constraints) FixLinearTriatomic (class in ase.constraints) FixSymmetry (class in ase.spacegroup.symmetrize) FLEUR FLEUR_INPGEN flush() (ase.calculators.checkpoint.Checkpoint method) fmax (ase.db.row.AtomsRow property) fold() (ase.vibrations.Vibrations method) ForceQMMM (class in ase.calculators.qmmm) format() (ase.formula.Formula method) formula (ase.db.row.AtomsRow property) Formula (class in ase.formula) formula_hill() (in module ase.utils) formula_metal() (in module ase.utils) free_electron_band_structure() (ase.dft.kpoints.BandPath method) FreeElectrons (class in ase.calculators.test) from_dict() (ase.formula.Formula static method) from_list() (ase.formula.Formula static method) fromcellpar() (ase.cell.Cell class method) (ase.geometry.Cell class method) fromdict() (ase.Atoms class method) (ase.calculators.vasp.Vasp method)

G

g2 (in module ase.collections) GAMESSUS (class in ase.calculators.gamess_us) Gaussian (class in ase.calculators.gaussian) get() (ase.db.core.Database method) (ase.db.row.AtomsRow method) (ase.io.ulm.Reader method) (ase.utils.xrdebye.XrDebye method) get_all_distances() (ase.Atoms method) get_angle() (ase.Atoms method) get_angle_value() (ase.geometry.analysis.Analysis method) get_angles() (ase.Atoms method) (ase.geometry.analysis.Analysis method) (in module ase.geometry) get_angles_derivatives() (in module ase.geometry) get_angular_momentum() (ase.Atoms method) get_array() (ase.Atoms method) get_atomic_numbers() (ase.Atoms method) get_atoms() (ase.db.core.Database method) get_averaged_current() (ase.dft.stm.STM method) get_barrier() (ase.neb.NEBTools method) get_basis() (in module ase.spacegroup) get_bond_value() (ase.geometry.analysis.Analysis method) get_bonds() (ase.geometry.analysis.Analysis method) get_bravais_lattice() (ase.cell.Cell method) (ase.geometry.Cell method) get_bz_k_points() (ase.calculators.interface.DFTCalculator method) get_calculator() (ase.Atoms method) get_cell() (ase.Atoms method) get_cell_lengths_and_angles() (ase.Atoms method) get_celldisp() (ase.Atoms method) get_center_of_mass() (ase.Atoms method) get_centers() (ase.dft.wannier.Wannier method) get_charges() (ase.Atoms method) get_chemical_formula() (ase.Atoms method) get_chemical_symbols() (ase.Atoms method) get_connectivity_matrix() (ase.neighborlist.NeighborList method) (in module ase.neighborlist) get_deviation_from_optimal_cell_shape() (in module ase.build) get_diameter() (ase.cluster.Cluster method) get_dihedral() (ase.Atoms method) get_dihedral_value() (ase.geometry.analysis.Analysis method) get_dihedrals() (ase.Atoms method) (ase.geometry.analysis.Analysis method) (in module ase.geometry) get_dihedrals_derivatives() (in module ase.geometry) get_dipole_moment() (ase.Atoms method) get_distance() (ase.Atoms method) get_distance_indices() (in module ase.neighborlist) get_distance_matrix() (in module ase.neighborlist) get_distances() (ase.Atoms method) (in module ase.geometry) get_distances_derivatives() (in module ase.geometry) get_distribution_moment() (in module ase.dft) get_dos() (ase.dft.dos.DOS method) get_duplicate_atoms() (in module ase.geometry) get_effective_potential() (ase.calculators.interface.DFTCalculator method) get_eigenvalues() (ase.calculators.interface.DFTCalculator method) (ase.calculators.test.FreeElectrons method) get_energies() (ase.dft.dos.DOS method) (ase.vibrations.Vibrations method) get_enthalpy() (ase.thermochemistry.IdealGasThermo method) get_entropy() (ase.thermochemistry.CrystalThermo method) (ase.thermochemistry.HarmonicThermo method) (ase.thermochemistry.HinderedThermo method) (ase.thermochemistry.IdealGasThermo method) get_fermi_level() (ase.calculators.interface.DFTCalculator method) (ase.calculators.test.FreeElectrons method) get_fmax() (ase.neb.NEBTools method) get_force_constant() (ase.phonons.Phonons method) get_forces() (ase.Atoms method) (ase.calculators.interface.Calculator method) get_frequencies() (ase.vibrations.Vibrations method) get_function() (ase.dft.wannier.Wannier method) get_functional_value() (ase.dft.wannier.Wannier method) get_gibbs_energy() (ase.thermochemistry.IdealGasThermo method) get_gibbs_free_energy() (ase.md.npt.NPT method) get_global_number_of_atoms() (ase.Atoms method)

get_hamiltonian() (ase.dft.wannier.Wannier method) get_hamiltonian_kpoint() (ase.dft.wannier.Wannier method) get_helmholtz_energy() (ase.thermochemistry.CrystalThermo method) (ase.thermochemistry.HarmonicThermo method) (ase.thermochemistry.HinderedThermo method) get_hopping() (ase.dft.wannier.Wannier method) get_ibz_k_points() (ase.calculators.interface.DFTCalculator method) (ase.calculators.test.FreeElectrons method) get_initial_charges() (ase.Atoms method) get_initial_magnetic_moments() (ase.Atoms method) get_internal_energy() (ase.thermochemistry.CrystalThermo method) (ase.thermochemistry.HarmonicThermo method) (ase.thermochemistry.HinderedThermo method) get_k_point_weights() (ase.calculators.interface.DFTCalculator method) get_kinetic_energy() (ase.Atoms method) get_labels() (ase.spectrum.band_structure.BandStructure method) get_layers() (ase.cluster.Cluster method) (in module ase.geometry) get_linear_kpoint_axis() (ase.dft.kpoints.BandPath method) get_magnetic_moment() (ase.Atoms method) (ase.calculators.interface.DFTCalculator method) get_magnetic_moments() (ase.Atoms method) get_masses() (ase.Atoms method) get_mode() (ase.vibrations.Vibrations method) get_momenta() (ase.Atoms method) get_moments_of_inertia() (ase.Atoms method) get_monkhorst_pack_size_and_offset() (in module ase.dft.kpoints) get_neighbors() (ase.neighborlist.NeighborList method) (ase.neighborlist.NewPrimitiveNeighborList method) (ase.neighborlist.PrimitiveNeighborList method) get_number_of_atoms() (ase.Atoms method) get_number_of_bands() (ase.calculators.interface.DFTCalculator method) get_number_of_grid_points() (ase.calculators.interface.DFTCalculator method) get_number_of_spins() (ase.calculators.interface.DFTCalculator method) (ase.calculators.test.FreeElectrons method) get_occupation_numbers() (ase.calculators.interface.DFTCalculator method) get_pbc() (ase.Atoms method) get_pdos() (ase.dft.wannier.Wannier method) get_positions() (ase.Atoms method) get_potential_energies() (ase.Atoms method) get_potential_energy() (ase.Atoms method) (ase.calculators.interface.Calculator method) get_properties() (ase.Atoms method) get_property() (ase.calculators.calculator.Calculator method) get_pseudo_density() (ase.calculators.interface.DFTCalculator method) get_pseudo_wave_function() (ase.calculators.interface.DFTCalculator method) get_radii() (ase.dft.wannier.Wannier method) get_rdf() (ase.geometry.analysis.Analysis method) get_reciprocal_cell() (ase.Atoms method) get_scaled_positions() (ase.Atoms method) get_spacegroup() (in module ase.spacegroup) get_special_points() (ase.lattice.BravaisLattice method) (in module ase.dft.kpoints) get_special_points_array() (ase.lattice.BravaisLattice method) get_spectrum() (ase.vibrations.Infrared method) get_spin_polarized() (ase.calculators.interface.DFTCalculator method) get_strain_rate() (ase.md.npt.NPT method) get_stress() (ase.Atoms method) (ase.calculators.interface.Calculator method) get_stresses() (ase.Atoms method) get_surfaces() (ase.cluster.Cluster method) get_tag() (ase.io.ulm.Reader method) get_tags() (ase.Atoms method) get_temperature() (ase.Atoms method) get_time() (ase.md.npt.NPT method) get_total_energy() (ase.Atoms method) get_values() (ase.geometry.analysis.Analysis method) get_velocities() (ase.Atoms method) get_vibrations() (ase.vibrations.Vibrations method) get_volume() (ase.Atoms method) get_waasmaier() (ase.utils.xrdebye.XrDebye method) get_wannier_localization_matrix() (ase.calculators.interface.DFTCalculator method) get_xc_functional() (ase.calculators.interface.DFTCalculator method) get_zero_point_energy() (ase.thermochemistry.HinderedThermo method) GPMin (class in ase.optimize) graphene_nanoribbon() (in module ase.build) Grimme gui

H

handedness (ase.cell.Cell property) (ase.geometry.Cell property) HarmonicThermo (class in ase.thermochemistry) has() (ase.Atoms method)

hcp0001() (in module ase.build) hcp0001_root() (in module ase.build) hcp10m10() (in module ase.build) HinderedThermo (class in ase.thermochemistry)

I

icell (ase.dft.kpoints.BandPath property) Icosahedron() (in module ase.cluster) IdealGasThermo (class in ase.thermochemistry) idpp_interpolate() (in module ase.neb) ignored_changes (ase.calculators.calculator.Calculator attribute) images (ase.geometry.analysis.Analysis property) implemented_properties (ase.calculators.calculator.Calculator attribute) (ase.calculators.checkpoint.CheckpointCalculator attribute) (ase.calculators.test.FreeElectrons attribute) Infrared (class in ase.vibrations) initial_wannier() (ase.calculators.interface.DFTCalculator method) initialize() (ase.dft.wannier.Wannier method) (ase.md.npt.NPT method)

initialize_density() (ase.calculators.fleur.FLEUR method) interpolate() (ase.dft.kpoints.BandPath method) (in module ase.neb) InvalidULMFileError iread() (in module ase.io) is_bundle() (ase.io.bundletrajectory.BundleTrajectory static method) is_empty_bundle() (ase.io.bundletrajectory.BundleTrajectory static method) is_minkowski_reduced() (in module ase.geometry) is_orthorhombic() (in module ase.geometry) isolate_components() (in module ase.geometry.dimensionality) iterdisplace() (ase.vibrations.Vibrations method) iterimages() (ase.vibrations.Vibrations method)

K

key_value_pairs (ase.db.row.AtomsRow property) keys() (ase.io.ulm.Reader method)

KIM() (in module ase.calculators.kim.kim) kpts (ase.dft.kpoints.BandPath property)

L

labels_from_kpts() (in module ase.dft.kpoints) LAMMPS (class in ase.calculators.LAMMPSrun) (class in ase.calculators.lammpsrun) LAMMPSlib (class in ase.calculators.lammpslib) Langevin (class in ase.md.langevin) LBFGS (class in ase.optimize) LBFGSLineSearch (class in ase.optimize) lengths() (ase.cell.Cell method) (ase.geometry.Cell method)

LennardJones (class in ase.calculators.lj) linear_tetrahedron_integration() (in module ase.dft.dos) LinearCombinationCalculator (class in ase.calculators.mixing) linescan() (ase.dft.stm.STM method) LJInteractions (class in ase.calculators.qmmm) LJInteractionsGeneral (class in ase.calculators.qmmm) load() (ase.calculators.checkpoint.Checkpoint method) localize() (ase.dft.wannier.Wannier method) log() (ase.io.bundletrajectory.BundleTrajectory method) LoggingCalculator (class in ase.calculators.loggingcalc)

M

make_supercell() (in module ase.build) mass (ase.db.row.AtomsRow property) MaxwellBoltzmannDistribution() (in module ase.md.velocitydistribution) MDLogger (class in ase.md) MDMin (class in ase.optimize) metadata (ase.db.core.Database attribute) mic() (in module ase.neighborlist) minimize_rotation_and_translation() (in module ase.build) minimize_tilt() (in module ase.build) minkowski_reduce() (ase.cell.Cell method) (ase.geometry.Cell method) (in module ase.geometry) MinModeAtoms (class in ase.dimer) MinModeTranslate (class in ase.dimer) module ase ase.atom ase.atoms ase.build ase.calculators ase.calculators.abinit ase.calculators.acemolecule ase.calculators.aims ase.calculators.amber ase.calculators.castep ase.calculators.checkpoint ase.calculators.cp2k ase.calculators.crystal ase.calculators.demon ase.calculators.demonnano ase.calculators.dftb ase.calculators.dftd3 ase.calculators.dmol ase.calculators.eam ase.calculators.emt ase.calculators.espresso ase.calculators.exciting ase.calculators.fleur ase.calculators.gamess_us ase.calculators.gaussian ase.calculators.gromacs ase.calculators.gulp ase.calculators.kim ase.calculators.lammps ase.calculators.LAMMPSrun ase.calculators.lj ase.calculators.loggingcalc ase.calculators.mixing ase.calculators.mopac ase.calculators.morse ase.calculators.nwchem ase.calculators.octopus ase.calculators.onetep ase.calculators.openmx ase.calculators.orca ase.calculators.psi4 ase.calculators.qchem ase.calculators.qmmm ase.calculators.siesta ase.calculators.socketio ase.calculators.test ase.calculators.tip3p ase.calculators.tip4p ase.calculators.turbomole ase.calculators.vasp ase.cell ase.cluster ase.collections ase.constraints ase.data ase.db ase.db.core ase.dft ase.dft.bandgap ase.dft.dos ase.dft.kpoints ase.dft.wannier ase.dimer ase.eos ase.formula ase.ga ase.geometry ase.gui ase.io ase.io.opls ase.io.trajectory ase.io.ulm ase.lattice ase.md ase.md.analysis ase.md.andersen ase.md.contour_exploration ase.md.langevin ase.md.npt ase.md.nptberendsen ase.md.nvtberendsen ase.md.velocitydistribution ase.md.verlet ase.neb ase.neighborlist ase.optimize ase.optimize.basin ase.optimize.precon ase.parallel ase.phasediagram ase.phonons ase.spacegroup ase.spacegroup.symmetrize ase.spectrum ase.spectrum.doscollection ase.spectrum.dosdata ase.symbols ase.test ase.thermochemistry ase.transport ase.units ase.utils ase.utils.xrdebye ase.vibrations ase.visualize ase.visualize.mlab ase.visualize.nglview

molecule() (in module ase.build) monkhorst_pack() (in module ase.dft.kpoints) monkhorst_pack_interpolate() (in module ase.dft.kpoints) MOPAC (class in ase.calculators.mopac) MorsePotential (class in ase.calculators.morse) mx2() (in module ase.build)

N

nanotube() (in module ase.build) natoms (ase.db.row.AtomsRow property) natural_cutoffs() (in module ase.neighborlist) NEB (class in ase.neb) NEBTools (class in ase.neb) neighbor_list() (in module ase.neighborlist) NeighborList (class in ase.neighborlist) new() (ase.cell.Cell class method) (ase.geometry.Cell class method) new_array() (ase.Atoms method) NewPrimitiveNeighborList (class in ase.neighborlist) NGLDisplay (class in ase.visualize.ngl) niggli_reduce() (ase.cell.Cell method) (ase.geometry.Cell method) (in module ase.build)

nImages (ase.geometry.analysis.Analysis property) nl (ase.geometry.analysis.Analysis property) nneighbors (ase.neighborlist.NeighborList property) npbcneighbors (ase.neighborlist.NeighborList property) NPT (class in ase.md.npt) NPTBerendsen (class in ase.md.nptberendsen) number_of_lattice_vectors (ase.Atoms property) numbers (ase.Atoms property) nupdates (ase.neighborlist.NeighborList property) NVTBerendsen (class in ase.md.nvtberendsen) NWChem (class in ase.calculators.nwchem)

O

Octahedron() (in module ase.cluster) OFPComparator (class in ase.ga.ofp_comparator) open() (in module ase.io.ulm) opencew() (in module ase.utils)

OpenMX (class in ase.calculators.openmx) OPENMX_DFT_DATA_PATH orthorhombic (ase.cell.Cell property) (ase.geometry.Cell property) orthorhombic() (in module ase.geometry)

P

parallel_function() (in module ase.parallel) parallel_generator() (in module ase.parallel) paropen() (in module ase.parallel) parprint() (in module ase.parallel) parse_path_string() (in module ase.dft.kpoints) PATH, [1], [2], [3], [4], [5], [6] path (ase.dft.kpoints.BandPath property) (ase.spectrum.band_structure.BandStructure property) pbc (ase.Atoms property) PermuStrainMutation (class in ase.ga.standardmutations) permute_axes() (ase.cell.Cell method) (ase.geometry.Cell method) (in module ase.geometry) PhaseDiagram (class in ase.phasediagram) phonon_harmonics() (in module ase.md.velocitydistribution) PhononHarmonics() (in module ase.md.velocitydistribution) Phonons (class in ase.phonons) pip plot() (ase.dft.kpoints.BandPath method) (ase.eos.EquationOfState method) (ase.phasediagram.PhaseDiagram method) (ase.spectrum.band_structure.BandStructure method) (in module ase.visualize.mlab)

plot_band() (ase.neb.NEBTools method) plot_bands() (ase.neb.NEBTools method) plot_bz() (ase.lattice.BravaisLattice method) plot_pattern() (ase.utils.xrdebye.XrDebye method) plural() (in module ase.utils) pointcurrent() (ase.dft.stm.STM method) pop() (ase.Atoms method) positions (ase.Atoms property) post_write_attach() (ase.io.bundletrajectory.BundleTrajectory method) Pourbaix (class in ase.phasediagram) pre_write_attach() (ase.io.bundletrajectory.BundleTrajectory method) primitive_neighbor_list() (in module ase.neighborlist) PrimitiveNeighborList (class in ase.neighborlist) Psi4 (class in ase.calculators.psi4) pubchem_atoms_conformer_search() (in module ase.data.pubchem) pubchem_atoms_search() (in module ase.data.pubchem) pubchem_conformer_search() (in module ase.data.pubchem) pubchem_search() (in module ase.data.pubchem) PYTHONPATH, [1], [2]

Q

QChem (class in ase.calculators.qchem)

QuasiNewton (class in ase.optimize)

R

RamanCalculatorInterface (class in ase.calculators.siesta.siesta_lrtddft) rank (ase.cell.Cell property) (ase.geometry.Cell property) rattle() (ase.Atoms method) RattleRotationalMutation (class in ase.ga.standardmutations) read() (ase.calculators.calculator.Calculator method) (ase.dft.kpoints.BandPath class method) (ase.phonons.Phonons method) (ase.spectrum.band_structure.BandStructure class method) (in module ase.io) read_abinit_in() (in module ase.io.abinit) read_abinit_out() (in module ase.io.abinit) read_acemolecule_input() (in module ase.io.acemolecule) read_acemolecule_out() (in module ase.io.acemolecule) read_aims() (in module ase.io.aims) read_aims_output() (in module ase.io.aims) read_born_charges() (ase.phonons.Phonons method) read_bundletrajectory() (in module ase.io.bundletrajectory) read_castep_castep() (in module ase.io.castep) read_castep_cell() (in module ase.io.castep) read_castep_geom() (in module ase.io.castep) read_castep_md() (in module ase.io.castep) read_castep_phonon() (in module ase.io.castep) read_cfg() (in module ase.io.cfg) read_cif() (in module ase.io.cif) read_cmdft() (in module ase.io.cmdft) read_cml() (in module ase.io.cml) read_cp2k_dcd() (in module ase.io.cp2k) read_cp2k_restart() (in module ase.io.cp2k) read_crystal() (in module ase.io.crystal) read_cube() (in module ase.io.cube) read_cube_data() (in module ase.io) read_dacapo_text() (in module ase.io.dacapo) read_db() (in module ase.io.db) read_dftb() (in module ase.io.dftb) read_dlp4() (in module ase.io.dlp4) read_dlp_history() (in module ase.io.dlp4) read_dmol_arc() (in module ase.io.dmol) read_dmol_car() (in module ase.io.dmol) read_dmol_incoor() (in module ase.io.dmol) read_elk() (in module ase.io.elk) read_eon() (in module ase.io.eon) read_espresso_in() (in module ase.io.espresso) read_espresso_out() (in module ase.io.espresso) read_exciting() (in module ase.io.exciting) read_extra_data() (ase.io.bundletrajectory.BundleTrajectory method) read_extxyz() (in module ase.io.extxyz) read_gamess_us_out() (in module ase.io.gamess_us) read_gamess_us_punch() (in module ase.io.gamess_us) read_gaussian_in() (in module ase.io.gaussian) read_gaussian_out() (in module ase.io.gaussian) read_gen() (in module ase.io.gen) read_gpaw_out() (in module ase.io.gpaw_out) read_gpumd() (in module ase.io.gpumd) read_gpw() (in module ase.io.gpw) read_gromacs() (in module ase.io.gromacs) read_gromos() (in module ase.io.gromos) read_json() (ase.calculators.vasp.Vasp method) (in module ase.io.db)

read_jsv() (in module ase.io.jsv) read_lammps_data() (in module ase.io.lammpsdata) read_lammps_dump_binary() (in module ase.io.lammpsrun) read_lammps_dump_text() (in module ase.io.lammpsrun) read_magres() (in module ase.io.magres) read_mol() (in module ase.io.mol) read_mustem() (in module ase.io.mustem) read_mysql() (in module ase.io.db) read_netcdftrajectory() (in module ase.io.netcdftrajectory) read_nomad_json() (in module ase.io.nomad_json) read_nwchem_in() (in module ase.io.nwchem) read_nwchem_out() (in module ase.io.nwchem) read_octopus_in() (in module ase.io.octopus) read_postgresql() (in module ase.io.db) read_prismatic() (in module ase.io.prismatic) read_proteindatabank() (in module ase.io.proteindatabank) read_qbox() (in module ase.io.qbox) read_res() (in module ase.io.res) read_results() (ase.calculators.calculator.FileIOCalculator method) read_rmc6f() (in module ase.io.rmc6f) read_sdf() (in module ase.io.sdf) read_siesta_xv() (in module ase.io.siesta) read_struct() (in module ase.io.wien2k) read_struct_out() (in module ase.io.siesta) read_sys() (in module ase.io.sys) read_traj() (in module ase.io.trajectory) read_turbomole() (in module ase.io.turbomole) read_turbomole_gradient() (in module ase.io.turbomole) read_v_sim() (in module ase.io.v_sim) read_vasp() (in module ase.io.vasp) read_vasp_out() (in module ase.io.vasp) read_vasp_xdatcar() (in module ase.io.vasp) read_vasp_xml() (in module ase.io.vasp) read_wout() (in module ase.io.wannier90) read_xsd() (in module ase.io.xsd) read_xsf() (in module ase.io.xsf) read_xtd() (in module ase.io.xtd) read_xyz() (in module ase.io.xyz) Reader (class in ase.io.ulm) reciprocal() (ase.cell.Cell method) (ase.geometry.Cell method) reduce() (ase.formula.Formula method) reference (ase.spectrum.band_structure.BandStructure property) reference_states (in module ase.data) refine_symmetry() (in module ase.spacegroup.symmetrize) relax() (ase.calculators.fleur.FLEUR method) repeat() (ase.Atoms method) repeat_poll() (ase.gui.gui.GUI method) reserve() (ase.db.core.Database method) reset() (ase.calculators.calculator.Calculator method) ResonantRamanCalculator (class in ase.vibrations.resonant_raman) root_surface() (in module ase.build) root_surface_analysis() (in module ase.build) rotate() (ase.Atoms method) (in module ase.build) rotate_dihedral() (ase.Atoms method) RotationalMutation (class in ase.ga.standardmutations) run() (ase.md.npt.NPT method) (ase.vibrations.Vibrations method)

S

s22 (in module ase.collections) save() (ase.calculators.checkpoint.Checkpoint method) (ase.dft.wannier.Wannier method) scaled_positions() (ase.cell.Cell method) (ase.geometry.Cell method) scan() (ase.dft.stm.STM method) scan2() (ase.dft.stm.STM method) SciPyFminBFGS (class in ase.optimize.sciopt) SciPyFminCG (class in ase.optimize.sciopt) select() (ase.db.core.Database method) select_data() (ase.io.bundletrajectory.BundleTrajectory method) separate() (in module ase.build) set() (ase.calculators.calculator.Calculator method) (in module ase.calculators) set_angle() (ase.Atoms method) set_array() (ase.Atoms method) set_atomic_numbers() (ase.Atoms method) set_calculator() (ase.Atoms method) set_cell() (ase.Atoms method) set_celldisp() (ase.Atoms method) set_center_of_mass() (ase.Atoms method) set_chemical_symbols() (ase.Atoms method) set_constraint() (ase.Atoms method) set_damping() (ase.utils.xrdebye.XrDebye method) set_dihedral() (ase.Atoms method) set_distance() (ase.Atoms method) set_extra_data() (ase.io.bundletrajectory.BundleTrajectory method) set_fraction_traceless() (ase.md.npt.NPT method) set_initial_charges() (ase.Atoms method) set_initial_magnetic_moments() (ase.Atoms method) set_label() (ase.calculators.calculator.Calculator method) set_mask() (ase.md.npt.NPT method) set_masses() (ase.Atoms method) set_momenta() (ase.Atoms method) set_pbc() (ase.Atoms method) set_positions() (ase.Atoms method) set_scaled_positions() (ase.Atoms method) set_strain_rate() (ase.md.npt.NPT method) set_stress() (ase.md.npt.NPT method) set_tags() (ase.Atoms method)

set_temperature() (ase.md.npt.NPT method) set_velocities() (ase.Atoms method) seterr() (in module ase.utils) Siesta (class in ase.calculators.siesta.siesta) SIESTA_PP_PATH SiestaLRTDDFT (class in ase.calculators.siesta.siesta_lrtddft) SimpleQMMM (class in ase.calculators.qmmm) smax (ase.db.row.AtomsRow property) SocketClient (class in ase.calculators.socketio) SocketIOCalculator (class in ase.calculators.socketio) SocketServer (class in ase.calculators.socketio) SoftMutation (class in ase.ga.soft_mutation) solvated() (in module ase.phasediagram) sort() (in module ase.build) Spacegroup (class in ase.spacegroup) special_path (ase.lattice.BravaisLattice property) special_paths (in module ase.dft.kpoints) special_point_names (ase.lattice.BravaisLattice property) special_points (ase.dft.kpoints.BandPath property) (in module ase.dft.kpoints) split() (ase.vibrations.Vibrations method) split_bond() (in module ase.build) stack() (in module ase.build) standard_form() (ase.cell.Cell method) (ase.geometry.Cell method) StartGenerator (class in ase.ga.startgenerator) Stationary() (in module ase.md.velocitydistribution) STM (class in ase.dft.stm) stoichiometry() (ase.formula.Formula method) StrainFilter (class in ase.constraints) StrainMutation (class in ase.ga.standardmutations) sts() (ase.dft.stm.STM method) subtract_reference() (ase.spectrum.band_structure.BandStructure method) SumCalculator (class in ase.calculators.mixing) surface() (in module ase.build) symbols (ase.Atoms property) (ase.db.row.AtomsRow property) Symbols (class in ase.symbols) symmetrize() (ase.phonons.Phonons method) SymmetryEquivalenceCheck (class in ase.utils.structure_comparator) sync() (ase.io.ulm.Writer method)

T

test testase Timer (class in ase.utils.timing) timer (class in ase.utils.timing) TIP3P (class in ase.calculators.tip3p) TIP4P (class in ase.calculators.tip4p) toatoms() (ase.db.row.AtomsRow method) tocell() (ase.lattice.BravaisLattice method) todict() (ase.Atoms method)

Trajectory() (in module ase.io) TrajectoryReader (class in ase.io.trajectory) TrajectoryWriter (class in ase.io.trajectory) transform() (ase.dft.kpoints.BandPath method) translate() (ase.Atoms method) (ase.dft.wannier.Wannier method) translate_all_to_cell() (ase.dft.wannier.Wannier method) translate_to_cell() (ase.dft.wannier.Wannier method) TransportCalculator (class in ase.transport) type_description() (ase.lattice.BravaisLattice class method)

U

uncomplete() (ase.cell.Cell method) (ase.geometry.Cell method) unique_angles (ase.geometry.analysis.Analysis property) unique_bonds (ase.geometry.analysis.Analysis property) unique_dihedrals (ase.geometry.analysis.Analysis property)

UnitCellFilter (class in ase.constraints) update() (ase.db.core.Database method) (ase.neighborlist.NeighborList method) (ase.neighborlist.NewPrimitiveNeighborList method) (ase.neighborlist.PrimitiveNeighborList method)

V

variant (ase.lattice.BravaisLattice property) vars() (ase.lattice.BravaisLattice method) Vasp (class in ase.calculators.vasp) VASP_COMMAND, [1] VASP_PP_PATH, [1] VASP_SCRIPT, [1] vdw_radii (in module ase.data)

VelocityVerlet (class in ase.md.verlet) Vibrations (class in ase.vibrations) view() (in module ase.visualize) view_ngl() (in module ase.visualize.ngl) volume (ase.cell.Cell property) (ase.db.row.AtomsRow property) (ase.geometry.Cell property)

W

Wannier (class in ase.dft.wannier) workdir() (in module ase.utils) wrap() (ase.Atoms method) wrap_positions() (in module ase.geometry) write() (ase.Atoms method) (ase.db.core.Database method) (ase.dft.kpoints.BandPath method) (ase.dft.stm.STM method) (ase.io.bundletrajectory.BundleTrajectory method) (ase.io.trajectory.TrajectoryWriter method) (ase.io.ulm.Writer method) (ase.spectrum.band_structure.BandStructure method) (in module ase.io) write_abinit_in() (in module ase.io.abinit) write_aims() (in module ase.io.aims) write_bundletrajectory() (in module ase.io.bundletrajectory) write_castep_cell() (in module ase.io.castep) write_cfg() (in module ase.io.cfg) write_cif() (in module ase.io.cif) write_crystal() (in module ase.io.crystal) write_cube() (ase.dft.wannier.Wannier method) (in module ase.io.cube) write_db() (in module ase.io.db) write_dftb() (in module ase.io.dftb) write_dlp4() (in module ase.io.dlp4) write_dmol_arc() (in module ase.io.dmol) write_dmol_car() (in module ase.io.dmol) write_dmol_incoor() (in module ase.io.dmol) write_dos() (ase.vibrations.Vibrations method) write_elk_in() (in module ase.io.elk) write_eon() (in module ase.io.eon) write_eps() (in module ase.io.eps) write_espresso_in() (in module ase.io.espresso) write_exciting() (in module ase.io.exciting) write_extxyz() (in module ase.io.extxyz) write_findsym() (in module ase.io.findsym) write_gamess_us_in() (in module ase.io.gamess_us) write_gaussian_in() (in module ase.io.gaussian) write_gen() (in module ase.io.gen) write_gif() (in module ase.io.animation) write_gpumd() (in module ase.io.gpumd) write_gromacs() (in module ase.io.gromacs)

write_gromos() (in module ase.io.gromos) write_html() (in module ase.io.x3d) write_inp() (ase.calculators.fleur.FLEUR method) write_input() (ase.calculators.calculator.FileIOCalculator method) write_jmol() (ase.vibrations.Vibrations method) write_json() (ase.calculators.vasp.Vasp method) (in module ase.io.db) write_jsv() (in module ase.io.jsv) write_lammps_data() (in module ase.io.lammpsdata) write_magres() (in module ase.io.magres) write_mode() (ase.vibrations.Vibrations method) write_modes() (ase.phonons.Phonons method) write_mp4() (in module ase.io.animation) write_mustem() (in module ase.io.mustem) write_mysql() (in module ase.io.db) write_netcdftrajectory() (in module ase.io.netcdftrajectory) write_nwchem_in() (in module ase.io.nwchem) write_pattern() (ase.utils.xrdebye.XrDebye method) write_png() (in module ase.io.png) write_postgresql() (in module ase.io.db) write_pov() (in module ase.io.pov) write_prismatic() (in module ase.io.prismatic) write_proteindatabank() (in module ase.io.proteindatabank) write_py() (in module ase.io.py) write_res() (in module ase.io.res) write_rmc6f() (in module ase.io.rmc6f) write_spectra() (ase.vibrations.Infrared method) write_struct() (in module ase.io.wien2k) write_sys() (in module ase.io.sys) write_traj() (in module ase.io.trajectory) write_turbomole() (in module ase.io.turbomole) write_v_sim() (in module ase.io.v_sim) write_vasp() (in module ase.io.vasp) write_vasp_xdatcar() (in module ase.io.vasp) write_vti() (in module ase.io.vtkxml) write_vtu() (in module ase.io.vtkxml) write_x3d() (in module ase.io.x3d) write_xsd() (in module ase.io.xsd) write_xsf() (in module ase.io.xsf) write_xtd() (in module ase.io.xtd) write_xyz() (in module ase.io.xyz) Writer (class in ase.io.ulm) wulff_construction() (in module ase.cluster)

X

XrDebye (class in ase.utils.xrdebye)

Z

zero_center_of_mass_momentum() (ase.md.npt.NPT method)

ZeroRotation() (in module ase.md.velocitydistribution)