Index

A

a (atomman.Box property) A (atomman.defect.Stroh property) a12_to_pos() (atomman.defect.GammaSurface method) a12_to_xy() (atomman.defect.GammaSurface method) a1vect (atomman.defect.GammaSurface property) a1vect_cart (atomman.defect.StackingFault property) a1vect_uvw (atomman.defect.StackingFault property) a2vect (atomman.defect.GammaSurface property) a2vect_cart (atomman.defect.StackingFault property) a2vect_uvw (atomman.defect.StackingFault property) above() (atomman.region.Plane method) abovefault (atomman.defect.StackingFault property) all_indices() (in module atomman.tools.miller) alpha (atomman.Box property) (atomman.defect.SDVPN property) angularvelocity (atomman.defect.Strain property) arccoord (atomman.mep.BasePath property) array_boundary() (atomman.defect.Dislocation method) arrowcenters (atomman.defect.DifferentialDisplacement property) arrowuvectors (atomman.defect.DifferentialDisplacement property) asdict() (atomman.defect.Strain method) aslist() (in module atomman.tools) atomic_mass() (in module atomman.tools) atomic_number() (in module atomman.tools) atomic_symbol() (in module atomman.tools) atomman module atomman.defect module atomman.lammps module

atomman.lammps.Potential module atomman.lammps.style module atomman.mep module atomman.mep.gradient module atomman.mep.integrator module atomman.plot module atomman.region module atomman.tools module atomman.tools.miller module atomman.unitconvert module atoms (atomman.System property) Atoms (class in atomman) Atoms.PropertyDict (class in atomman) atoms_df() (atomman.System method) atoms_extend() (atomman.System method) atoms_ix (atomman.System property) atoms_prop() (atomman.System method) atypes (atomman.Atoms property) (atomman.System property) avect (atomman.Box property) axes_check() (in module atomman.tools) axis (atomman.region.Cylinder property)

B

b (atomman.Box property) base_system (atomman.defect.Dislocation property) BasePath (class in atomman.mep) below() (atomman.region.Plane method) beta (atomman.Box property) (atomman.defect.SDVPN property) BondAngleMap (class in atomman.cluster) boolean() (in module atomman.tools) box (atomman.defect.GammaSurface property) (atomman.System property) Box (class in atomman)

box_boundary() (atomman.defect.Dislocation method) box_set() (atomman.System method) build() (atomman.NeighborList method) build_disl_array() (atomman.defect.Dislocation method) build_lammps_potential() (in module atomman) build_p_vectors() (atomman.defect.Strain method) build_path() (atomman.defect.GammaSurface method) build_unit() (in module atomman.unitconvert) bulk() (atomman.ElasticConstants method) burgers (atomman.defect.SDVPN property) (atomman.defect.VolterraDislocation property) bvect (atomman.Box property)

C

c (atomman.Box property) C (atomman.defect.VolterraDislocation property) cdiffelastic (atomman.defect.SDVPN property) cdiffstress (atomman.defect.SDVPN property) cdiffsurface (atomman.defect.SDVPN property) center (atomman.region.Sphere property) center1 (atomman.region.Cylinder property) center2 (atomman.region.Cylinder property) central_difference() (in module atomman.mep.gradient) characterangle() (atomman.defect.VolterraDislocation method) check_energies() (atomman.defect.SDVPN method) checkversion() (in module atomman.lammps) Cij (atomman.ElasticConstants property) Cij9 (atomman.ElasticConstants property) Cijkl (atomman.ElasticConstants property) clear_properties() (atomman.defect.Strain method) climbrun (atomman.lammps.NEBLog property)

composition (atomman.System property) compositionstr() (in module atomman.tools) conventional_setting (atomman.defect.FreeSurface property) coord (atomman.mep.BasePath property) (atomman.NeighborList property) create_path() (in module atomman.mep) CrystalPrototype (in module atomman.library.record) cubic() (atomman.Box class method) (atomman.ElasticConstants method) cumulative_pdf() (atomman.cluster.BondAngleMap method) cutboxvector (atomman.defect.FreeSurface property) cutindex (atomman.defect.Dislocation property) (atomman.defect.FreeSurface property) cutofflongrange (atomman.defect.SDVPN property) cvect (atomman.Box property) Cylinder (class in atomman.region) cylinder_boundary() (atomman.defect.Dislocation method)

D

data (atomman.defect.GammaSurface property) Database (class in atomman.library) ddvectors (atomman.defect.DifferentialDisplacement property) default_timestep (atomman.mep.ISMPath property) default_tolerance (atomman.mep.ISMPath property) delta() (atomman.defect.GammaSurface method) delta_line_plot() (atomman.defect.GammaSurface method) delta_surface_plot() (atomman.defect.GammaSurface method) df (atomman.cluster.BondAngleMap property) df() (atomman.Atoms method) differential_displacement() (in module atomman.defect) DifferentialDisplacement (class in atomman.defect) dipole() (atomman.defect.Dislocation method) dipole_displacement() (atomman.defect.Dislocation static method) disl_system (atomman.defect.Dislocation property) disldensity() (atomman.defect.SDVPN method) Dislocation (class in atomman.defect) dislocation_array() (in module atomman.defect) dislocation_system_basis() (in module atomman.defect) dislocation_system_transform() (in module atomman.defect)

dislsol (atomman.defect.Dislocation property) displacement() (atomman.defect.IsotropicVolterraDislocation method) (atomman.defect.Stroh method) (atomman.defect.VolterraDislocation method) (in module atomman) disregistry (atomman.defect.SDVPN property) disregistry() (in module atomman.defect) disregistry_plot() (atomman.defect.SDVPN method) dmag() (atomman.System method) (in module atomman) download_all() (atomman.library.Database method) download_crystal_prototypes() (atomman.library.Database method) download_reference_crystals() (atomman.library.Database method) download_relaxed_crystals() (atomman.library.Database method) dumbbell() (in module atomman.defect) dump() (atomman.NeighborList method) (atomman.System method) (in module atomman) duplicates_allclose() (in module atomman.tools) dvect() (atomman.System method) (in module atomman)

E

E_gsf() (atomman.defect.GammaSurface method) E_gsf_line_plot() (atomman.defect.GammaSurface method) E_gsf_surface_plot() (atomman.defect.GammaSurface method) (atomman.defect.SDVPN method) E_gsf_vs_x_plot() (atomman.defect.SDVPN method) elastic_energy() (atomman.defect.SDVPN method) ElasticConstants (class in atomman)

endcaps (atomman.region.Cylinder property) energy() (atomman.mep.BasePath method) energyfxn (atomman.mep.BasePath property) error_unit() (in module atomman.unitconvert) eta() (atomman.defect.Stroh method) euler() (in module atomman.mep.integrator) extend() (atomman.Atoms method)

F

fault() (atomman.defect.StackingFault method) faultpos_cart (atomman.defect.StackingFault property) faultpos_rel (atomman.defect.StackingFault property) fetch_mp_crystal() (atomman.library.Database method) fetch_mp_crystals() (atomman.library.Database method) fetch_oqmd_crystal() (atomman.library.Database method) fetch_reference_crystal() (atomman.library.Database method) filltemplate() (in module atomman.tools) fit() (atomman.defect.GammaSurface method) flatten() (atomman.lammps.Log method)

force (atomman.mep.BasePath property) free_surface_basis() (in module atomman.defect) FreeSurface (class in atomman.defect) fromdatabase() (atomman.defect.Dislocation class method) (atomman.defect.FreeSurface class method) (atomman.defect.StackingFault class method) fromrecord() (atomman.defect.Dislocation class method) (atomman.defect.FreeSurface class method) (atomman.defect.StackingFault class method) fromstring() (in module atomman.tools.miller) fullstress (atomman.defect.SDVPN property)

G

G (atomman.defect.Strain property) gamma (atomman.Box property) (atomman.defect.SDVPN property) GammaSurface (class in atomman.defect) get_barrier() (atomman.lammps.NEBLog method) get_crystal_prototype() (atomman.library.Database method) get_crystal_prototypes() (atomman.library.Database method) get_in_units() (in module atomman.unitconvert)

get_neb_path() (atomman.lammps.NEBLog method) get_prop_values() (in module atomman.plot) get_reference_crystal() (atomman.library.Database method) get_reference_crystals() (atomman.library.Database method) get_relaxed_crystal() (atomman.library.Database method) get_relaxed_crystals() (atomman.library.Database method) grad_energy() (atomman.mep.BasePath method) gradientfxn (atomman.mep.BasePath property) gradientkwargs (atomman.mep.BasePath property)

H

hexagonal() (atomman.Box class method) (atomman.ElasticConstants method)

hkl (atomman.defect.FreeSurface property)

I

iaslist() (in module atomman.tools) identifyfamily() (atomman.Box method) (in module atomman.tools) indexstr() (in module atomman.tools) inside() (atomman.Box method) (atomman.region.Cylinder method) (atomman.region.PlaneSet method) (atomman.region.Shape method) (atomman.region.Sphere method) integratorfxn (atomman.mep.BasePath property) interpolate_contour() (in module atomman.plot) interpolate_path() (atomman.mep.ISMPath method) interstitial() (in module atomman.defect) invariant1 (atomman.defect.Strain property) invariant2 (atomman.defect.Strain property) invariant3 (atomman.defect.Strain property) is_lammps_norm() (atomman.Box method) is_normal() (atomman.ElasticConstants method) isclose() (atomman.region.Plane method)

iscubic() (atomman.Box method) (in module atomman.tools) ishexagonal() (atomman.Box method) (in module atomman.tools) ismonoclinic() (atomman.Box method) (in module atomman.tools) ISMPath (class in atomman.mep) isorthorhombic() (atomman.Box method) (in module atomman.tools) isotropic() (atomman.ElasticConstants method) IsotropicVolterraDislocation (class in atomman.defect) isrhombohedral() (atomman.Box method) (in module atomman.tools) istetragonal() (atomman.Box method) (in module atomman.tools) istriclinic() (atomman.Box method) (in module atomman.tools) itercoords() (atomman.cluster.BondAngleMap method) iterfaultmap() (atomman.defect.StackingFault method) itersystem() (atomman.cluster.BondAngleMap method)

K

k (atomman.defect.Stroh property) K_coeff (atomman.defect.VolterraDislocation property) K_tensor (atomman.defect.IsotropicVolterraDislocation property) (atomman.defect.SDVPN property) (atomman.defect.Stroh property) (atomman.defect.VolterraDislocation property)

L

L (atomman.defect.Stroh property) lammps_date (atomman.lammps.Log property) lammps_version (atomman.lammps.Log property) LammpsError (class in atomman.lammps) lineindex (atomman.defect.Dislocation property) load() (atomman.defect.SDVPN method) (atomman.lammps.NEBLog method) (atomman.NeighborList method) (in module atomman)

load_table() (atomman.cluster.BondAngleMap method) Log (class in atomman.lammps) logs (atomman.lammps.NEBLog property) longrange_energy() (atomman.defect.SDVPN method) lx (atomman.Box property) ly (atomman.Box property) lz (atomman.Box property)

M

m (atomman.defect.VolterraDislocation property) masses (atomman.System property) min_kwargs (atomman.defect.SDVPN property) min_method (atomman.defect.SDVPN property) min_options (atomman.defect.SDVPN property) minrun (atomman.lammps.NEBLog property) misfit_energy() (atomman.defect.SDVPN method) model() (atomman.Atoms method) (atomman.Box method) (atomman.cluster.BondAngleMap method) (atomman.defect.GammaSurface method) (atomman.defect.SDVPN method) (atomman.ElasticConstants method) (atomman.System method) (in module atomman.unitconvert) module atomman atomman.defect atomman.lammps atomman.lammps.Potential atomman.lammps.style atomman.mep atomman.mep.gradient atomman.mep.integrator atomman.plot atomman.region atomman.tools atomman.tools.miller atomman.unitconvert

monoclinic() (atomman.Box class method) (atomman.ElasticConstants method) monopole() (atomman.defect.Dislocation method) motionindex (atomman.defect.Dislocation property) mu (atomman.defect.IsotropicVolterraDislocation property)

N

n (atomman.defect.VolterraDislocation property) natoms (atomman.Atoms property) (atomman.System property) natypes (atomman.Atoms property) (atomman.System property) NEBLog (class in atomman.lammps) NeighborList (class in atomman) neighborlist() (atomman.System method) neighbors (atomman.defect.DifferentialDisplacement property) (atomman.defect.Strain property) nlist (atomman.NeighborList property)

nlist() (in module atomman) nonlocal_energy() (atomman.defect.SDVPN method) normal (atomman.region.Plane property) normalize() (atomman.System method) (in module atomman.lammps) normalized_as() (atomman.ElasticConstants method) nreplicas (atomman.lammps.NEBLog property) nu (atomman.defect.IsotropicVolterraDislocation property) nye (atomman.defect.Strain property) nye_tensor() (in module atomman.defect) nye_tensor_p() (in module atomman.defect)

O

operate() (atomman.region.Plane method) origin (atomman.Box property)

orthorhombic() (atomman.Box class method) (atomman.ElasticConstants method) outside() (atomman.region.Shape method)

P

p (atomman.defect.Stroh property) p_vectors (atomman.defect.Strain property) parse() (in module atomman.unitconvert) path() (atomman.defect.GammaSurface method) pbc (atomman.System property) pdf() (atomman.cluster.BondAngleMap method) periodicarray() (atomman.defect.Dislocation method) Plane (class in atomman.region) plane3to4() (in module atomman.tools.miller) plane4to3() (in module atomman.tools.miller) plane_crystal_to_cartesian() (atomman.Box method) (in module atomman.tools.miller) planenormal (atomman.defect.GammaSurface property) planes (atomman.Box property) (atomman.region.PlaneSet property) PlaneSet (class in atomman.region)

plot() (atomman.defect.DifferentialDisplacement method) plot_cumulative_pdf() (atomman.cluster.BondAngleMap method) plot_energy() (atomman.mep.BasePath method) plot_force() (atomman.mep.BasePath method) plot_pdf() (atomman.cluster.BondAngleMap method) plot_with_nye() (atomman.defect.DifferentialDisplacement method) pn_arctan_disregistry() (in module atomman.defect) point (atomman.region.Plane property) point() (in module atomman.defect) pos_to_a12() (atomman.defect.GammaSurface method) pos_to_xy() (atomman.defect.GammaSurface method) position_cartesian_to_relative() (atomman.Box method) position_relative_to_cartesian() (atomman.Box method) Potential() (in module atomman.lammps.Potential) preln (atomman.defect.VolterraDislocation property) prop() (atomman.Atoms method) prop_atype() (atomman.Atoms method)

R

r0() (atomman.System method) radius (atomman.region.Cylinder property) (atomman.region.Sphere property) rcell (atomman.defect.Dislocation property) (atomman.defect.FreeSurface property) rcellwidth (atomman.defect.FreeSurface property) read() (atomman.lammps.Log method) reciprocal_vects (atomman.Box property) reduce_indices() (in module atomman.tools.miller) reference (atomman.defect.DifferentialDisplacement property) ReferenceCrystal (in module atomman.library.record) relax() (atomman.mep.BasePath method) (atomman.mep.ISMPath method)

RelaxedCrystal (in module atomman.library.record) res (atomman.defect.SDVPN property) reset_units() (in module atomman.unitconvert) retrieve_crystal_prototype() (atomman.library.Database method) retrieve_reference_crystal() (atomman.library.Database method) retrieve_relaxed_crystal() (atomman.library.Database method) rhombohedral() (atomman.ElasticConstants method) rmax (atomman.cluster.BondAngleMap property) rmin (atomman.cluster.BondAngleMap property) rnum (atomman.cluster.BondAngleMap property) rotate() (atomman.System method) rotation (atomman.defect.Strain property) run() (in module atomman.lammps) rungekutta() (in module atomman.mep.integrator)

S

save_table() (atomman.cluster.BondAngleMap method) save_to_system() (atomman.defect.Strain method) scale() (atomman.System method) screen_input() (in module atomman.tools) SDVPN (class in atomman.defect) set() (atomman.Box method) (atomman.cluster.BondAngleMap method) (atomman.defect.GammaSurface method) set_abc() (atomman.Box method) set_hi_los() (atomman.Box method) set_in_units() (in module atomman.unitconvert) set_lengths() (atomman.Box method) set_literal() (in module atomman.unitconvert) set_p_vectors() (atomman.defect.Strain method) set_shift() (atomman.defect.Dislocation method) (atomman.defect.FreeSurface method) set_systems() (atomman.defect.Dislocation method) set_vectors() (atomman.Box method) Shape (class in atomman.region) shear() (atomman.ElasticConstants method) shift (atomman.defect.Dislocation property) (atomman.defect.FreeSurface property) shifts (atomman.defect.Dislocation property) (atomman.defect.FreeSurface property) Sij (atomman.ElasticConstants property) Sijkl (atomman.ElasticConstants property) simulations (atomman.lammps.Log property) slip_vector() (in module atomman.defect) solve() (atomman.defect.DifferentialDisplacement method) (atomman.defect.IsotropicVolterraDislocation method) (atomman.defect.SDVPN method) (atomman.defect.Stroh method) (atomman.defect.VolterraDislocation method)

solve_G() (atomman.defect.Strain method) solve_nye() (atomman.defect.Strain method) solve_volterra_dislocation() (in module atomman.defect) Sphere (class in atomman.region) StackingFault (class in atomman.defect) step() (atomman.mep.BasePath method) (atomman.mep.ISMPath method) strain (atomman.defect.Strain property) Strain (class in atomman.defect) strain() (atomman.defect.IsotropicVolterraDislocation method) (atomman.defect.Stroh method) (atomman.defect.VolterraDislocation method) stress() (atomman.defect.IsotropicVolterraDislocation method) (atomman.defect.Stroh method) (atomman.defect.VolterraDislocation method) stress_energy() (atomman.defect.SDVPN method) Stroh (class in atomman.defect) substitutional() (in module atomman.defect) supersize() (atomman.System method) surface() (atomman.defect.FreeSurface method) (atomman.defect.StackingFault method) surface_energy() (atomman.defect.SDVPN method) surfacearea (atomman.defect.FreeSurface property) symbols (atomman.cluster.BondAngleMap property) (atomman.System property) system (atomman.defect.FreeSurface property) (atomman.defect.Strain property) System (class in atomman) system0 (atomman.defect.DifferentialDisplacement property) system1 (atomman.defect.DifferentialDisplacement property)

T

tau (atomman.defect.SDVPN property) tetragonal() (atomman.Box class method) (atomman.ElasticConstants method) theta() (atomman.defect.IsotropicVolterraDislocation method) theta_max (atomman.defect.Strain property) thetamax (atomman.cluster.BondAngleMap property) thetamin (atomman.cluster.BondAngleMap property) thetanum (atomman.cluster.BondAngleMap property) timestep() (in module atomman.lammps.style)

tol (atomman.defect.VolterraDislocation property) total_energy() (atomman.defect.SDVPN method) transform (atomman.defect.Dislocation property) (atomman.defect.FreeSurface property) (atomman.defect.SDVPN property) (atomman.defect.VolterraDislocation property) transform() (atomman.ElasticConstants method) triclinic() (atomman.Box class method) (atomman.ElasticConstants method) trigonal() (atomman.Box class method)

U

uber_open_rmode() (in module atomman.tools) ucell (atomman.defect.Dislocation property) (atomman.defect.FreeSurface property) ucell_prim (atomman.defect.Dislocation property) unique_shifts() (atomman.defect.FreeSurface method) unit() (in module atomman.lammps.style)

unittangent (atomman.mep.BasePath property) (atomman.mep.ISMPath property) unscale() (atomman.System method) uvws (atomman.defect.Dislocation property) (atomman.defect.FreeSurface property) uvws_prim (atomman.defect.Dislocation property)

V

vacancy() (in module atomman.defect) value_unit() (in module atomman.unitconvert) values_to_hexcolors() (in module atomman.plot) vect_angle() (in module atomman.tools) vector3to4() (in module atomman.tools.miller) vector4to3() (in module atomman.tools.miller) vector_conventional_to_primitive() (in module atomman.tools.miller)

vector_crystal_to_cartesian() (atomman.Box method) (in module atomman.tools.miller) vector_primitive_to_conventional() (in module atomman.tools.miller) vects (atomman.Box property) view (atomman.Atoms property) VolterraDislocation (class in atomman.defect) volume (atomman.Box property)

W

wrap() (atomman.System method)

X

x (atomman.defect.SDVPN property) xhi (atomman.Box property) xlo (atomman.Box property)

xy (atomman.Box property) xy_to_a12() (atomman.defect.GammaSurface method) xy_to_pos() (atomman.defect.GammaSurface method) xz (atomman.Box property)

Y

yhi (atomman.Box property)

ylo (atomman.Box property) yz (atomman.Box property)

Z

zhi (atomman.Box property)

zlo (atomman.Box property)

Ξ

ξ (atomman.defect.VolterraDislocation property)