Index

Symbols | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W

Symbols

$HOME, [1]
$PATH
$PYTHONPATH

A

add_adsorbate() (in module ase.lattice.surface)
add_vacuum() (in module ase.lattice.surface)
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)
API
append() (ase.atoms.Atoms method)
ASE
ase (module)
ase-gui
ase.atom (module)
ase.atoms (module)
ase.calculators (module)
ase.calculators.abinit (module)
ase.calculators.aims (module)
ase.calculators.ase_qmmm_manyqm (module)
ase.calculators.castep (module)
ase.calculators.dftb (module)
ase.calculators.eam (module)
ase.calculators.emt (module)
ase.calculators.exciting (module)
ase.calculators.fleur (module)
ase.calculators.gromacs (module)
ase.calculators.jacapo (module)
ase.calculators.lammps (module)
ase.calculators.LAMMPSrun (module)
ase.calculators.nwchem (module)
ase.calculators.siesta (module)
ase.calculators.turbomole (module)
ase.calculators.vasp (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.ga (module)
ase.gui (module)
ase.infrared (module)
ase.io (module)
ase.io.opls (module)
ase.io.trajectory (module)
ase.lattice (module)
ase.lattice.spacegroup (module)
ase.lattice.surface (module)
ase.md (module)
ase.md.langevin (module)
ase.md.npt (module)
ase.md.nptberendsen (module)
ase.md.nvtberendsen (module)
ase.md.verlet (module)
ase.neb (module)
ase.optimize (module)
ase.optimize.basin (module)
ase.optimize.bfgslinesearch (module)
ase.optimize.fire (module)
ase.optimize.lbfgs (module)
ase.optimize.mdmin (module)
ase.optimize.qn (module)
ase.optimize.sciopt (module)
ase.parallel (module)
ase.phasediagram (module)
ase.phonons (module)
ase.structure (module)
ase.test (module)
ase.thermochemistry (module)
ase.transport (module)
ase.transport.calculators.TransportCalculator (class in ase.transport)
ase.units (module)
ase.utils (module)
ase.utils.geometry (module)
ase.vibrations (module)
ase.visualize (module)
ase.visualize.mlab (module)
ase.visualize.vtk (module)
ASE2ase
ASE_ABC_COMMAND, [1]
ASE_NWCHEM_COMMAND
assert() (in module ase.test)
Atom (class in ase.atom)
atomic_masses (in module ase.data)
atomic_names (in module ase.data)
atomic_numbers (in module ase.data)
Atoms (class in ase.atoms)
AtomsRow (class in ase.db.row)

B

basics (module)
bcc100() (in module ase.lattice.surface)
bcc110() (in module ase.lattice.surface)
bcc111() (in module ase.lattice.surface)
build() (ase.calculators.neighborlist.NeighborList method)
Bulk modulus
bulk() (in module ase.lattice)
BundleTrajectory (class in ase.io.bundletrajectory)

C

calc (ase.atoms.Atoms attribute)
calculate (module)
calculate() (ase.calculators.calculator.Calculator method)
(ase.calculators.fleur.FLEUR method)
calculate_ldos() (ase.dft.stm.STM method)
calculate_numerical_forces() (ase.calculators.calculator.Calculator method)
calculation_required() (ase.calculators.interface.Calculator method)
Calculator (class in ase.calculators.calculator)
(class in ase.calculators.interface)
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.Atoms attribute)
center() (ase.atoms.Atoms method)
charge (ase.db.row.AtomsRow attribute)
check_state() (ase.calculators.calculator.Calculator method)
chemical_symbols (in module ase.data)
Class
close() (ase.io.bundletrajectory.BundleTrajectory method)
(ase.io.trajectory.PickleTrajectory method)
(ase.io.trajectory.TrajectoryReader method)
(ase.io.trajectory.TrajectoryWriter method)
command (ase.calculators.calculator.FileIOCalculator attribute)
command line tools
connect() (in module ase.db.core)
constrained_forces (ase.db.row.AtomsRow attribute)
constraints (ase.atoms.Atoms attribute)
(ase.db.row.AtomsRow attribute)
Constructor
copy() (ase.atoms.Atoms 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)
CrystalThermo (class in ase.thermochemistry)
cut() (in module ase.utils.geometry)

D

data (ase.db.row.AtomsRow attribute)
Database (class in ase.db.core)
decompose() (ase.phasediagram.PhaseDiagram method)
(ase.phasediagram.Pourbaix method)
default_parameters (ase.calculators.calculator.Calculator attribute)
delete() (ase.db.core.Database method)
delete_bundle() (ase.io.bundletrajectory.BundleTrajectory class method)
DFT
DFTCalculator (class in ase.calculators.interface)
diagram() (ase.phasediagram.Pourbaix method)
diamond100() (in module ase.lattice.surface)
diamond111() (in module ase.lattice.surface)
DimerControl (class in ase.dimer)
DimerEigenmodeSearch (class in ase.dimer)
Docstring
DOS (class in ase.dft.dos)

E

edit (module)
edit() (ase.atoms.Atoms method)
EMT
(class in ase.calculators.emt)
environment variable
$HOME, [1]
$PATH
$PYTHONPATH
ABINIT_PP_PATH
ASE_ABC_COMMAND, [1]
ASE_ABINIT_COMMAND
ASE_NWCHEM_COMMAND
FLEUR
FLEUR_INPGEN
HOME
LAMMPS_COMMAND
PATH, [1], [2], [3]
PYTHONPATH, [1], [2], [3]
PYTHONSTARTUP
SIESTA_PP_PATH
SIESTA_SCRIPT
SVN_EDITOR
VASP_PP_PATH
VASP_SCRIPT
EquationOfState (class in ase.utils.eos)
Exciting (class in ase.calculators.exciting), [1]
extend() (ase.atoms.Atoms method)

F

fcc100() (in module ase.lattice.surface)
fcc110() (in module ase.lattice.surface)
fcc111() (in module ase.lattice.surface)
fcc111_root() (in module ase.lattice.surface)
fcc211() (in module ase.lattice.surface)
FieldPlotter (class in ase.visualize.fieldplotter)
FileIOCalculator (class in ase.calculators.calculator)
Filter (class in ase.constraints)
find_mic() (in module ase.utils.geometry)
FixAtoms (class in ase.constraints)
FixBondLength (class in ase.constraints)
FixBondLengths (class in ase.constraints)
FixedLine (class in ase.constraints)
FixedMode (class in ase.constraints)
FixedPlane (class in ase.constraints)
FLEUR
FLEUR_INPGEN
fmax (ase.db.row.AtomsRow attribute)
fold() (ase.vibrations.Vibrations method)
formula (ase.db.row.AtomsRow attribute)

G

gcd() (in module ase.utils)
get() (ase.db.core.Database method)
(ase.db.row.AtomsRow method)
get_all_distances() (ase.atoms.Atoms method)
get_angle() (ase.atoms.Atoms method)
get_angular_momentum() (ase.atoms.Atoms method)
get_array() (ase.atoms.Atoms method)
get_atomic_numbers() (ase.atoms.Atoms method)
get_atoms() (ase.db.core.Database method)
get_averaged_current() (ase.dft.stm.STM method)
get_band_gap() (in module ase.dft.bandgap)
get_bandpath() (in module ase.dft.kpoints)
get_barrier() (ase.neb.NEBtools method)
get_bz_k_points() (ase.calculators.interface.DFTCalculator method)
get_calculator() (ase.atoms.Atoms method)
get_cell() (ase.atoms.Atoms method)
get_celldisp() (ase.atoms.Atoms method)
get_center_of_mass() (ase.atoms.Atoms method)
get_centers() (ase.dft.wannier.Wannier method)
get_charges() (ase.atoms.Atoms method)
get_chemical_formula() (ase.atoms.Atoms method)
get_chemical_symbols() (ase.atoms.Atoms method)
get_dihedral() (ase.atoms.Atoms method)
get_dipole_moment() (ase.atoms.Atoms method)
get_distance() (ase.atoms.Atoms method)
get_distances() (ase.atoms.Atoms method)
get_distribution_moment() (in module ase.dft)
get_dos() (ase.dft.dos.DOS method)
get_effective_potential() (ase.calculators.interface.DFTCalculator method)
get_eigenvalues() (ase.calculators.interface.DFTCalculator 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.IdealGasThermo method)
get_fermi_level() (ase.calculators.interface.DFTCalculator method)
get_fit() (ase.neb.NEBtools method)
get_fmax() (ase.neb.NEBtools method)
get_forces() (ase.atoms.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.HarmonicThermo method)
(ase.thermochemistry.IdealGasThermo method)
get_hamiltonian() (ase.dft.wannier.Wannier method)
get_hamiltonian_kpoint() (ase.dft.wannier.Wannier method)
get_helmholtz_energy() (ase.thermochemistry.CrystalThermo method)
get_hopping() (ase.dft.wannier.Wannier method)
get_ibz_k_points() (ase.calculators.interface.DFTCalculator method)
get_initial_charges() (ase.atoms.Atoms method)
get_initial_magnetic_moments() (ase.atoms.Atoms method)
get_internal_energy() (ase.thermochemistry.CrystalThermo method)
(ase.thermochemistry.HarmonicThermo method)
get_k_point_weights() (ase.calculators.interface.DFTCalculator method)
get_kinetic_energy() (ase.atoms.Atoms method)
get_layers() (in module ase.utils.geometry)
get_magnetic_moment() (ase.atoms.Atoms method)
(ase.calculators.interface.DFTCalculator method)
get_magnetic_moments() (ase.atoms.Atoms method)
get_masses() (ase.atoms.Atoms method)
get_mode() (ase.vibrations.Vibrations method)
get_momenta() (ase.atoms.Atoms method)
get_moments_of_inertia() (ase.atoms.Atoms method)
get_monkhorst_pack_size_and_offset() (in module ase.dft.kpoints)
get_neighbors() (ase.calculators.neighborlist.NeighborList method)
get_number_of_atoms() (ase.atoms.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)
get_occupation_numbers() (ase.calculators.interface.DFTCalculator method)
get_pbc() (ase.atoms.Atoms method)
get_pdos() (ase.dft.wannier.Wannier method)
get_positions() (ase.atoms.Atoms method)
get_potential_energies() (ase.atoms.Atoms method)
get_potential_energy() (ase.atoms.Atoms method)
(ase.calculators.interface.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_reciprocal_cell() (ase.atoms.Atoms method)
get_scaled_positions() (ase.atoms.Atoms method)
get_spectrum() (ase.vibrations.infrared.InfraRed method)
get_spin_polarized() (ase.calculators.interface.DFTCalculator method)
get_stress() (ase.atoms.Atoms method)
(ase.calculators.interface.Calculator method)
get_stresses() (ase.atoms.Atoms method)
get_tags() (ase.atoms.Atoms method)
get_temperature() (ase.atoms.Atoms method)
get_total_energy() (ase.atoms.Atoms method)
get_velocities() (ase.atoms.Atoms method)
get_volume() (ase.atoms.Atoms method)
get_wannier_localization_matrix() (ase.calculators.interface.DFTCalculator method)
get_xc_functional() (ase.calculators.interface.DFTCalculator method)
graphene_nanoribbon() (in module ase.structure)
gui

H

HarmonicThermo (class in ase.thermochemistry)
has() (ase.atoms.Atoms method)
hcp0001() (in module ase.lattice.surface)
hcp10m10() (in module ase.lattice.surface)
HF
HOME

I

IdealGasThermo (class in ase.thermochemistry)
idpp_interpolate() (ase.neb.NEB method)
implemented_properties (ase.calculators.calculator.Calculator attribute)
IncompatibleCellError
InfraRed (class in ase.vibrations.infrared)
initial_wannier() (ase.calculators.interface.DFTCalculator method)
initialize() (ase.dft.wannier.Wannier method)
initialize_density() (ase.calculators.fleur.FLEUR method)
Instance
interpolate() (ase.neb.NEB method), [1]
is_bundle() (ase.io.bundletrajectory.BundleTrajectory static method)
is_empty_bundle() (ase.io.bundletrajectory.BundleTrajectory static method)

J

Jacapo (class in ase.calculators.jacapo)

K

key_value_pairs (ase.db.row.AtomsRow attribute)

L

LAMMPS (class in ase.calculators.LAMMPSrun)
LAMMPS_COMMAND
Langevin (class in ase.md.langevin)
LAPW
linescan() (ase.dft.stm.STM method)
localize() (ase.dft.wannier.Wannier method)
log() (ase.io.bundletrajectory.BundleTrajectory method)
(ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)

M

mass (ase.db.row.AtomsRow attribute)
max_spread() (ase.dft.wannier.Wannier method)
Method
minimize_tilt() (in module ase.utils.geometry)
minimize_tilt_ij() (in module ase.utils.geometry)
MinModeAtoms (class in ase.dimer)
MinModeTranslate (class in ase.dimer)
molecule() (in module ase.structure)
monkhorst_pack() (in module ase.dft.kpoints)
mx2() (in module ase.lattice.surface)

N

Namespace
nanotube() (in module ase.structure)
natoms (ase.db.row.AtomsRow attribute)
ndarray
NEB (class in ase.neb)
NEBtools (class in ase.neb)
NeighborList (class in ase.calculators.neighborlist)
new_array() (ase.atoms.Atoms method)
niggli_reduce() (in module ase.utils.geometry)
NPT (class in ase.md.npt)
NPTBerendsen (class in ase.md.nptberendsen)
numbers (ase.atoms.Atoms attribute)
NumPy
NVTBerendsen (class in ase.md.nvtberendsen)

O

open() (ase.io.trajectory.PickleTrajectory method)
opencew() (in module ase.utils)

P

paropen() (in module ase.parallel)
parprint() (in module ase.parallel)
PATH, [1], [2], [3]
pbc (ase.atoms.Atoms attribute)
PhaseDiagram (class in ase.phasediagram)
PickleTrajectory (class in ase.io.trajectory)
plot() (ase.phasediagram.PhaseDiagram method)
(ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)
(in module ase.visualize.mlab)
plot_band() (ase.neb.NEBtools method)
pop() (ase.atoms.Atoms method)
positions (ase.atoms.Atoms attribute)
post_write_attach() (ase.io.bundletrajectory.BundleTrajectory method)
(ase.io.trajectory.PickleTrajectory method)
Pourbaix (class in ase.phasediagram)
pre_write_attach() (ase.io.bundletrajectory.BundleTrajectory method)
(ase.io.trajectory.PickleTrajectory method)
PrimiPlotter (class in ase.visualize.primiplotter)
Python
PYTHONPATH, [1], [2], [3]
PYTHONSTARTUP

R

rattle() (ase.atoms.Atoms method)
read() (ase.calculators.calculator.Calculator method)
(in module ase.io)
read_cube_data() (in module ase.io)
read_extra_data() (ase.io.bundletrajectory.BundleTrajectory method)
read_results() (ase.calculators.calculator.FileIOCalculator method)
reference_states (in module ase.data)
relax() (ase.calculators.fleur.FLEUR method)
repeat() (ase.atoms.Atoms method)
reserve() (ase.db.core.Database method)
reset() (ase.calculators.calculator.Calculator method)
rotate() (ase.atoms.Atoms method)
(in module ase.utils.geometry)
rotate_dihedral() (ase.atoms.Atoms method)
rotate_euler() (ase.atoms.Atoms method)
rotation_matrix() (in module ase.utils.geometry)
run() (ase.vibrations.Vibrations method)

S

save() (ase.dft.wannier.Wannier method)
scan() (ase.dft.stm.STM method)
SciPyFminBFGS (class in ase.optimize.sciopt)
SciPyFminCG (class in ase.optimize.sciopt)
Scope
select() (ase.db.core.Database method)
select_data() (ase.io.bundletrajectory.BundleTrajectory method)
set() (ase.calculators.calculator.Calculator method)
(in module ase.calculators)
set_angle() (ase.atoms.Atoms method)
set_array() (ase.atoms.Atoms method)
set_atomic_numbers() (ase.atoms.Atoms method)
set_atoms() (ase.io.trajectory.PickleTrajectory method)
set_background() (ase.visualize.fieldplotter.FieldPlotter method)
set_background_color() (ase.visualize.fieldplotter.FieldPlotter method)
set_black_white_colors() (ase.visualize.fieldplotter.FieldPlotter method)
set_calculator() (ase.atoms.Atoms method)
set_cell() (ase.atoms.Atoms method)
set_celldisp() (ase.atoms.Atoms method)
set_chemical_symbols() (ase.atoms.Atoms method)
set_color_function() (ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)
set_colors() (ase.visualize.primiplotter.PrimiPlotter method)
set_constraint() (ase.atoms.Atoms method)
set_data_range() (ase.visualize.fieldplotter.FieldPlotter method)
set_dihedral() (ase.atoms.Atoms method)
set_dimensions() (ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)
set_distance() (ase.atoms.Atoms method)
set_extra_data() (ase.io.bundletrajectory.BundleTrajectory method)
set_initial_charges() (ase.atoms.Atoms method)
set_initial_magnetic_moments() (ase.atoms.Atoms method)
set_invisibility_function() (ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)
set_invisible() (ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)
set_label() (ase.calculators.calculator.Calculator method)
set_log() (ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)
set_masses() (ase.atoms.Atoms method)
set_momenta() (ase.atoms.Atoms method)
set_output() (ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)
set_pbc() (ase.atoms.Atoms method)
set_plot_plane() (ase.visualize.fieldplotter.FieldPlotter method)
set_positions() (ase.atoms.Atoms method)
set_radii() (ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)
set_red_yellow_colors() (ase.visualize.fieldplotter.FieldPlotter method)
set_rotation() (ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)
set_scaled_positions() (ase.atoms.Atoms method)
set_tags() (ase.atoms.Atoms method)
set_velocities() (ase.atoms.Atoms method)
setup (module)
Siesta (class in ase.calculators.siesta)
SIESTA_PP_PATH
SIESTA_SCRIPT
smax (ase.db.row.AtomsRow attribute)
solvated() (in module ase.phasediagram)
sort() (in module ase.utils.geometry)
stack() (in module ase.utils.geometry)
STM (class in ase.dft.stm)
StrainFilter (class in ase.constraints)
summary() (ase.vibrations.Vibrations method)
surface() (in module ase.lattice.surface)
SVN_EDITOR
symbols (ase.db.row.AtomsRow attribute)

T

test
test.test() (in module ase.test)
testase
Timer (class in ase.utils.timing)
timer (class in ase.utils.timing)
toatoms() (ase.db.row.AtomsRow method)
tools (module)
Trajectory() (in module ase.io)
TrajectoryReader (class in ase.io.trajectory)
TrajectoryWriter (class in ase.io.trajectory)
translate() (ase.atoms.Atoms method)
(ase.dft.wannier.Wannier method)
translate_all_to_cell() (ase.dft.wannier.Wannier method)
translate_to_cell() (ase.dft.wannier.Wannier method)

U

UnitCellFilter (class in ase.constraints)
update() (ase.calculators.neighborlist.NeighborList method)
(ase.db.core.Database method)
(ase.visualize.fieldplotter.FieldPlotter method)
(ase.visualize.primiplotter.PrimiPlotter method)

V

Vasp (class in ase.calculators.vasp)
VASP_PP_PATH
VASP_SCRIPT
vdw_radii (in module ase.data)
VelocityVerlet (class in ase.md.verlet)
Vibrations (class in ase.vibrations)
view (module)
view() (in module ase.visualize)
volume (ase.db.row.AtomsRow attribute)
vtk
(module)

W

Wannier (class in ase.dft.wannier)
wrap() (ase.atoms.Atoms method)
wrap_positions() (in module ase.utils.geometry)
write() (ase.atoms.Atoms method)
(ase.db.core.Database method)
(ase.dft.stm.STM method)
(ase.io.bundletrajectory.BundleTrajectory method)
(ase.io.trajectory.PickleTrajectory method)
(ase.io.trajectory.TrajectoryWriter method)
(in module ase.io)
write_cube() (ase.dft.wannier.Wannier method)
write_dos() (ase.vibrations.Vibrations method)
write_inp() (ase.calculators.fleur.FLEUR method)
write_input() (ase.calculators.calculator.FileIOCalculator method)
write_jmol() (ase.vibrations.Vibrations method)
write_mode() (ase.vibrations.Vibrations method)
write_spectra() (ase.vibrations.infrared.InfraRed method)