pychum.engine.orca._dataclasses =============================== .. py:module:: pychum.engine.orca._dataclasses Classes ------- .. autoapisummary:: pychum.engine.orca._dataclasses.BlockType pychum.engine.orca._dataclasses.OrcaBlock pychum.engine.orca._dataclasses.UnitConversion pychum.engine.orca._dataclasses.Atom pychum.engine.orca._dataclasses.Coords pychum.engine.orca._dataclasses.GeomScan pychum.engine.orca._dataclasses.GeomBlock pychum.engine.orca._dataclasses.LBFGSSettings pychum.engine.orca._dataclasses.FIRESettings pychum.engine.orca._dataclasses.ReparamSettings pychum.engine.orca._dataclasses.ConvTolSettings pychum.engine.orca._dataclasses.IDPPSettings pychum.engine.orca._dataclasses.OptimSettings pychum.engine.orca._dataclasses.FreeEndSettings pychum.engine.orca._dataclasses.ZoomSettings pychum.engine.orca._dataclasses.SpringSettings pychum.engine.orca._dataclasses.RestartSettings pychum.engine.orca._dataclasses.TSGuessSettings pychum.engine.orca._dataclasses.FixCenterSettings pychum.engine.orca._dataclasses.NebBlock pychum.engine.orca._dataclasses.OrcaConfig Module Contents --------------- .. py:class:: BlockType Bases: :py:obj:`enum.Enum` Create a collection of name/value pairs. Example enumeration: >>> class Color(Enum): ... RED = 1 ... BLUE = 2 ... GREEN = 3 Access them by: - attribute access: >>> Color.RED - value lookup: >>> Color(1) - name lookup: >>> Color['RED'] Enumerations can be iterated over, and know how many members they have: >>> len(Color) 3 >>> list(Color) [, , ] Methods can be added to enumerations, and members can have their own attributes -- see the documentation for details. .. py:attribute:: NEB :value: 'neb' .. py:attribute:: GEOM :value: 'geom' .. py:class:: OrcaBlock Bases: :py:obj:`abc.ABC` Helper class that provides a standard way to create an ABC using inheritance. .. py:method:: block_type() -> BlockType :abstractmethod: .. py:class:: UnitConversion .. py:attribute:: inp :type: str .. py:attribute:: out :type: str .. py:class:: Atom .. py:attribute:: x :type: float :value: 0.0 .. py:attribute:: y :type: float :value: 0.0 .. py:attribute:: z :type: float :value: 0.0 .. py:attribute:: symbol :type: str :value: None .. py:attribute:: is_ghost :type: bool :value: False .. py:attribute:: embedding_potential :type: bool :value: False .. py:attribute:: is_frozen :type: bool :value: False .. py:attribute:: isotope :type: float | None :value: None .. py:attribute:: nuclear_charge :type: float | None :value: None .. py:attribute:: fragment_number :type: int | None :value: None .. py:attribute:: is_dummy :type: bool :value: False .. py:attribute:: point_charge :type: float | None :value: None .. py:attribute:: bond_atom :type: int | None :value: None .. py:attribute:: bond_length :type: float | None :value: None .. py:attribute:: angle_atom :type: int | None :value: None .. py:attribute:: angle :type: float | None :value: None .. py:attribute:: dihedral_atom :type: int | None :value: None .. py:attribute:: dihedral :type: float | None :value: None .. py:attribute:: is_frozen_x :type: bool :value: False .. py:attribute:: is_frozen_y :type: bool :value: False .. py:attribute:: is_frozen_z :type: bool :value: False .. py:method:: __post_init__() .. py:class:: Coords .. py:attribute:: charge :type: int .. py:attribute:: multiplicity :type: int .. py:attribute:: fmt :type: str .. py:attribute:: filedat :type: str :value: '' .. py:attribute:: atoms :type: list[Atom] :value: [] .. py:class:: GeomScan .. py:attribute:: atoms :type: list[int] .. py:attribute:: range :type: list[float] .. py:attribute:: points :type: int .. py:class:: GeomBlock Bases: :py:obj:`OrcaBlock` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: bonds :type: list[GeomScan] :value: [] .. py:attribute:: dihedrals :type: list[GeomScan] :value: [] .. py:attribute:: angles :type: list[GeomScan] :value: [] .. py:method:: block_type() -> BlockType .. py:class:: LBFGSSettings .. py:attribute:: reparam_on_restart :type: bool :value: False .. py:attribute:: memory :type: int :value: 20 .. py:attribute:: precondition :type: bool :value: True .. py:attribute:: dr :type: float :value: 0.002 .. py:attribute:: restart_on_maxmove :type: bool :value: True .. py:class:: FIRESettings .. py:attribute:: init_damp :type: float :value: 0.1 .. py:attribute:: damp_decr :type: float :value: 0.99 .. py:attribute:: step_incr :type: float :value: 1.1 .. py:attribute:: step_decr :type: float :value: 0.5 .. py:attribute:: max_step :type: float :value: 5.0 .. py:attribute:: retention :type: int :value: 5 .. py:class:: ReparamSettings .. py:attribute:: interp :type: str :value: 'linear' .. py:attribute:: every :type: int :value: 0 .. py:attribute:: tol :type: float :value: 0.0 .. py:method:: __post_init__() .. py:class:: ConvTolSettings .. py:attribute:: units :type: str :value: 'Eh/Bohr' .. py:attribute:: maxfp_i :type: float :value: 0.005 .. py:attribute:: rmsfp_i :type: float :value: 0.003 .. py:attribute:: maxf_ci :type: float :value: 0.0005 .. py:attribute:: rmsf_ci :type: float :value: 0.0003 .. py:attribute:: turn_on_ci :type: float :value: 0.02 .. py:attribute:: scale :type: int :value: 10 .. py:class:: IDPPSettings .. py:attribute:: tol_maxf :type: float :value: 0.01 .. py:attribute:: maxmove :type: float :value: 0.05 .. py:attribute:: alpha :type: float :value: 0.01 .. py:attribute:: nmax :type: int :value: 3000 .. py:attribute:: quatern :type: bool :value: True .. py:attribute:: ksp :type: float :value: 1.0 .. py:attribute:: debug :type: bool :value: False .. py:class:: OptimSettings .. py:attribute:: method :type: str :value: 'LBFGS' .. py:attribute:: maxmove :type: float :value: 0.2 .. py:attribute:: stepsize :type: float :value: 1.0 .. py:attribute:: maxiter :type: float :value: 500 .. py:attribute:: local :type: bool :value: False .. py:method:: __post_init__() .. py:class:: FreeEndSettings .. py:attribute:: use :type: bool :value: False .. py:attribute:: opt_type :type: str :value: 'PERP' .. py:attribute:: ec :type: float :value: 0.0 .. py:attribute:: ec_end :type: float :value: 0.0 .. py:attribute:: kappa :type: float :value: 1.0 .. py:method:: __post_init__() .. py:class:: ZoomSettings .. py:attribute:: tol_turn_on :type: float :value: 0.0 .. py:attribute:: offset :type: int :value: 2 .. py:attribute:: auto :type: bool :value: True .. py:attribute:: tol_scale :type: int :value: 10 .. py:attribute:: alpha :type: float :value: 0.5 .. py:attribute:: interpolation :type: str :value: 'linear' .. py:attribute:: printfulltrj :type: bool :value: True .. py:method:: __post_init__() .. py:class:: SpringSettings .. py:attribute:: spring_kind :type: str :value: 'image' .. py:attribute:: const1 :type: float :value: 0.01 .. py:attribute:: const2 :type: float :value: 0.1 .. py:attribute:: energy_weighted :type: bool :value: True .. py:attribute:: perpspring :type: str :value: 'no' .. py:attribute:: llt_cos :type: bool :value: True .. py:method:: __post_init__() .. py:class:: RestartSettings .. py:attribute:: gbw_basename :type: str :value: None .. py:attribute:: allxyz :type: str :value: None .. py:method:: __post_init__() .. py:class:: TSGuessSettings .. py:attribute:: xyz_struct :type: str :value: None .. py:attribute:: pdb_struct :type: str :value: None .. py:attribute:: ts_img :type: int :value: -1 .. py:method:: __post_init__() .. py:class:: FixCenterSettings .. py:attribute:: active :type: bool :value: True .. py:attribute:: remove_extern_force :type: bool :value: True .. py:class:: NebBlock Bases: :py:obj:`OrcaBlock` Helper class that provides a standard way to create an ABC using inheritance. .. py:attribute:: end_xyz :type: str .. py:attribute:: nimgs :type: int .. py:attribute:: convtype :type: str :value: 'CIONLY' .. py:attribute:: printlevel :type: int :value: 4 .. py:attribute:: neb_ts :type: bool :value: False .. py:attribute:: neb_ci :type: bool :value: False .. py:attribute:: quatern :type: str :value: 'ALWAYS' .. py:attribute:: climbingimage :type: bool :value: True .. py:attribute:: check_scf_conv :type: bool :value: True .. py:attribute:: preopt :type: bool :value: False .. py:attribute:: nsteps_foundintermediate :type: int :value: 30 .. py:attribute:: abortif_foundintermediate :type: bool :value: False .. py:attribute:: npts_interpol :type: int :value: 10 .. py:attribute:: interpolation :type: str :value: 'IDPP' .. py:attribute:: tangent :type: str :value: 'IMPROVED' .. py:attribute:: lbfgs_settings :type: LBFGSSettings .. py:attribute:: fire_settings :type: FIRESettings .. py:attribute:: reparam_settings :type: ReparamSettings .. py:attribute:: idpp_settings :type: IDPPSettings .. py:attribute:: zoom_settings :type: ZoomSettings .. py:attribute:: optim_settings :type: OptimSettings .. py:attribute:: convtol_settings :type: ConvTolSettings .. py:attribute:: free_end_settings :type: FreeEndSettings .. py:attribute:: spring_settings :type: SpringSettings .. py:attribute:: restart_settings :type: RestartSettings .. py:attribute:: tsguess_settings :type: TSGuessSettings .. py:attribute:: fix_center_settings :type: FixCenterSettings .. py:method:: __post_init__() .. py:method:: block_type() -> BlockType .. py:class:: OrcaConfig .. py:attribute:: kwlines :type: str .. py:attribute:: coords :type: Coords .. py:attribute:: blocks :type: dict[BlockType, OrcaBlock] .. py:attribute:: extra_blocks :type: dict[str, str] .. py:method:: add_block(block: OrcaBlock)