from __future__ import annotations
from pathlib import Path
from typing import Iterable, Literal, Sequence
from scm.pisa.block import DriverBlock,EngineBlock,FixedBlock,FreeBlock,InputBlock
from scm.pisa.key import BoolKey,FloatKey,FloatListKey,IntKey,IntListKey,MultipleChoiceKey,PathStringKey,StringKey,BoolType
[docs]class OLEDDepostion(DriverBlock):
r"""
:ivar RestartWorkdir: Uses the data from the working directory of a previously run deposition workflow for restarting. Under the hood this uses the normal rerun-prevention available in PLAMS: it may reuse results from old jobs instead of running them again.
:vartype RestartWorkdir: str | Path | StringKey
:ivar Box: Specifications of the box into which the material is deposited.
:vartype Box: OLEDDepostion._Box
:ivar Deposition: Specifies the details of how molecules are deposited.
:vartype Deposition: OLEDDepostion._Deposition
:ivar LAMMPSOffload: Offload the calculation to LAMMPS via AMSPipe.
:vartype LAMMPSOffload: OLEDDepostion._LAMMPSOffload
:ivar LoadSystem: Block that controls reading the chemical system from a KF file instead of the [System] block.
:vartype LoadSystem: OLEDDepostion._LoadSystem
:ivar Molecule: Specification of the molecule to be deposited.
:vartype Molecule: OLEDDepostion._Molecule
:ivar System: Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
:vartype System: OLEDDepostion._System
"""
[docs] class _Box(FixedBlock):
r"""
Specifications of the box into which the material is deposited.
:ivar Size: Specify the desired size of the box. The final deposited box may have a different size. The x- and y-axis are perpendicular to the direction of deposition, so these may be regarded as the width of the growing layer. The z-axis is the direction along which the deposition happens, so this determines the thickness of the deposited layer. Note that the x- and y-axis will be ignored if a custom substrate is used: the are of the box is then determined by the lattice of the substrate. The z-axis can still be freely chosen, but should be large enough that there is enough space for the substrate itself and to deposit more molecules on top of it.
:vartype Size: Iterable[float] | FloatListKey
:ivar Substrate: The substrate on which to grow the layer.
:vartype Substrate: Literal["Graphene", "Custom"]
:ivar SubstrateSystem: String ID of a named [System] to be used as a substrate. (This is only used when the Substrate key is set to Custom.)
:vartype SubstrateSystem: str | StringKey
"""
def __post_init__(self):
self.Size: Iterable[float] | FloatListKey = FloatListKey(name='Size', comment='Specify the desired size of the box. The final deposited box may have a different size. The x- and y-axis are perpendicular to the direction of deposition, so these may be regarded as the width of the growing layer. The z-axis is the direction along which the deposition happens, so this determines the thickness of the deposited layer. Note that the x- and y-axis will be ignored if a custom substrate is used: the are of the box is then determined by the lattice of the substrate. The z-axis can still be freely chosen, but should be large enough that there is enough space for the substrate itself and to deposit more molecules on top of it.', gui_name='Box size', default=[60.0, 60.0, 120.0], unit='Angstrom', gui_type='nfloat 3')
self.Substrate: Literal["Graphene", "Custom"] = MultipleChoiceKey(name='Substrate', comment='The substrate on which to grow the layer.', default='Graphene', choices=['Graphene', 'Custom'])
self.SubstrateSystem: str | StringKey = StringKey(name='SubstrateSystem', comment='String ID of a named [System] to be used as a substrate. (This is only used when the Substrate key is set to Custom.)', gui_name='Custom substrate:', gui_type='molecule')
[docs] class _Deposition(FixedBlock):
r"""
Specifies the details of how molecules are deposited.
:ivar ConstrainHXBonds: Constrain the bond length for all H-* bonds (i.e. any bond to a hydrogen atom). Doing this allows choosing a larger time step. If this option is disabled, the TimeStep needs to be reduced manually.
:vartype ConstrainHXBonds: BoolType | BoolKey
:ivar Frequency: The frequency in MD steps at which new molecules will be added to the system.
:vartype Frequency: int | IntKey
:ivar NumMolecules: The number of molecules that we will try to deposit. If not specified the number will be determined automatically such that the box becomes approximately full.
:vartype NumMolecules: int | IntKey
:ivar Temperature: The temperature at which the deposition happens.
:vartype Temperature: float | FloatKey
:ivar TimeStep: The time difference per step.
:vartype TimeStep: float | FloatKey
"""
def __post_init__(self):
self.ConstrainHXBonds: BoolType | BoolKey = BoolKey(name='ConstrainHXBonds', comment='Constrain the bond length for all H-* bonds (i.e. any bond to a hydrogen atom). Doing this allows choosing a larger time step. If this option is disabled, the TimeStep needs to be reduced manually.', gui_name='Constrain H-* bonds:', default=True)
self.Frequency: int | IntKey = IntKey(name='Frequency', comment='The frequency in MD steps at which new molecules will be added to the system.', default=10000)
self.NumMolecules: int | IntKey = IntKey(name='NumMolecules', comment='The number of molecules that we will try to deposit. If not specified the number will be determined automatically such that the box becomes approximately full.')
self.Temperature: float | FloatKey = FloatKey(name='Temperature', comment='The temperature at which the deposition happens.', default=600.0)
self.TimeStep: float | FloatKey = FloatKey(name='TimeStep', comment='The time difference per step.', default=1.0, unit='Femtoseconds')
[docs] class _LAMMPSOffload(FixedBlock):
r"""
Offload the calculation to LAMMPS via AMSPipe.
:ivar Enabled: Enable offloading the force field evaluation to LAMMPS instead of handling it internally in AMS.
:vartype Enabled: BoolType | BoolKey
:ivar UseGPU: Accelerate LAMMPS calculations using a GPU. Requires a LAMMPS library built with the GPU package.
:vartype UseGPU: BoolType | BoolKey
:ivar UseGPUForKSpace: When UseGPU is enabled, also use the GPU to accelerate reciprocal space electrostatic interactions. Disabling this can improve performance on less powerful GPUs.
:vartype UseGPUForKSpace: BoolType | BoolKey
:ivar UseGPUForNeighbor: When UseGPU is enabled, also use the GPU to accelerate neighbor searches. Disabling this can improve performance on less powerful GPUs.
:vartype UseGPUForNeighbor: BoolType | BoolKey
:ivar UseOpenMP: Parallelize LAMMPS calculations using OpenMP threading. Requires a LAMMPS library built with the OMP package.
:vartype UseOpenMP: BoolType | BoolKey
"""
def __post_init__(self):
self.Enabled: BoolType | BoolKey = BoolKey(name='Enabled', comment='Enable offloading the force field evaluation to LAMMPS instead of handling it internally in AMS.', default=False)
self.UseGPU: BoolType | BoolKey = BoolKey(name='UseGPU', comment='Accelerate LAMMPS calculations using a GPU. Requires a LAMMPS library built with the GPU package.', gui_name='Use GPU:', default=False)
self.UseGPUForKSpace: BoolType | BoolKey = BoolKey(name='UseGPUForKSpace', comment='When UseGPU is enabled, also use the GPU to accelerate reciprocal space electrostatic interactions. Disabling this can improve performance on less powerful GPUs.', default=True)
self.UseGPUForNeighbor: BoolType | BoolKey = BoolKey(name='UseGPUForNeighbor', comment='When UseGPU is enabled, also use the GPU to accelerate neighbor searches. Disabling this can improve performance on less powerful GPUs.', default=True)
self.UseOpenMP: BoolType | BoolKey = BoolKey(name='UseOpenMP', comment='Parallelize LAMMPS calculations using OpenMP threading. Requires a LAMMPS library built with the OMP package.', gui_name='Use OpenMP:', default=False)
[docs] class _LoadSystem(FixedBlock):
r"""
Block that controls reading the chemical system from a KF file instead of the [System] block.
:ivar File: The path of the KF file from which to load the system. It may also be the results directory containing it.
:vartype File: str | Path | StringKey
:ivar Section: The section on the KF file from which to load the system.
:vartype Section: str | StringKey
"""
def __post_init__(self):
self.File: str | Path | StringKey = PathStringKey(name='File', comment='The path of the KF file from which to load the system. It may also be the results directory containing it.', ispath=True)
self.Section: str | StringKey = StringKey(name='Section', comment='The section on the KF file from which to load the system.', default='Molecule')
[docs] class _Molecule(FixedBlock):
r"""
Specification of the molecule to be deposited.
:ivar MoleFraction: The relative occurrence of the molecule with regard to other deposited species. Only relevant for mixed molecule depositions.
:vartype MoleFraction: float | FloatKey
:ivar SystemName: String ID of a named [System] to be inserted. The lattice specified with this System, if any, is ignored and the main system's lattice is used instead.
:vartype SystemName: str | StringKey
"""
def __post_init__(self):
self.MoleFraction: float | FloatKey = FloatKey(name='MoleFraction', comment='The relative occurrence of the molecule with regard to other deposited species. Only relevant for mixed molecule depositions.', gui_name='Molar fraction:', default=1.0)
self.SystemName: str | StringKey = StringKey(name='SystemName', comment="String ID of a named [System] to be inserted. The lattice specified with this System, if any, is ignored and the main system's lattice is used instead. ", gui_name='Molecule:', gui_type='molecule')
[docs] class _System(FixedBlock):
r"""
Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.
:ivar AllowCloseAtoms: No longer functional. Just here for backwards compatibility.
:vartype AllowCloseAtoms: BoolType | BoolKey
:ivar Charge: The system's total charge in atomic units.
:vartype Charge: float | FloatKey
:ivar FractionalCoords: Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.
:vartype FractionalCoords: BoolType | BoolKey
:ivar GeometryFile: Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz
:vartype GeometryFile: str | Path | StringKey
:ivar GuessBonds: Equivalent to 'Modify%GuessBonds'. Please update input file to use 'Modify' block instead.
:vartype GuessBonds: BoolType | BoolKey
:ivar LatticeStrain: Equivalent to 'Modify%LatticeStrain'. Please update input file to use 'Modify' block instead.
:vartype LatticeStrain: Iterable[float] | FloatListKey
:ivar MapAtomsToUnitCell: Equivalent to 'Modify%MapAtomsToUnitCell'. Please update input file to use 'Modify' block instead.
:vartype MapAtomsToUnitCell: BoolType | BoolKey
:ivar PerturbCoordinates: Equivalent to 'Modify%PerturbCoordinates'. Please update input file to use 'Modify' block instead.
:vartype PerturbCoordinates: float | FloatKey
:ivar PerturbLattice: Equivalent to 'Modify%PerturbLattice'. Please update input file to use 'Modify' block instead.
:vartype PerturbLattice: float | FloatKey
:ivar ShiftCoordinates: Equivalent to 'Modify%Translate', but in the unit of bohr by default. Please update input file to use 'Modify' block instead.
:vartype ShiftCoordinates: Iterable[float] | FloatListKey
:ivar SuperCell: Equivalent to 'Modify%SuperCell'. Please update input file to use 'Modify' block instead.
:vartype SuperCell: Iterable[int] | IntListKey
:ivar SuperCellTrafo: Equivalent to 'Modify%SuperCellTrafo'. Please update input file to use 'Modify' block instead.
:vartype SuperCellTrafo: Iterable[int] | IntListKey
:ivar Symmetrize: Equivalent to 'Modify%Symmetrize'. Please update input file to use 'Modify' block instead.
:vartype Symmetrize: BoolType | BoolKey
:ivar Atoms: The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
:vartype Atoms: str | Sequence[str] | FreeBlock
:ivar BondOrders: Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
:vartype BondOrders: str | Sequence[str] | FreeBlock
:ivar ElectrostaticEmbedding: Container for electrostatic embedding options, which can be combined.
:vartype ElectrostaticEmbedding: OLEDDepostion._System._ElectrostaticEmbedding
:ivar Lattice: Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
:vartype Lattice: str | Sequence[str] | FreeBlock
:ivar Modify: Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
:vartype Modify: OLEDDepostion._System._Modify
"""
[docs] class _Atoms(FreeBlock):
r"""
The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.
"""
def __post_init__(self):
pass
[docs] class _BondOrders(FreeBlock):
r"""
Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.
"""
def __post_init__(self):
pass
[docs] class _ElectrostaticEmbedding(FixedBlock):
r"""
Container for electrostatic embedding options, which can be combined.
:ivar ElectricField: External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.
In atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 ... e11 V/m.
Supported by the engines adf, band, dftb and mopac.
For periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.
:vartype ElectricField: Iterable[float] | FloatListKey
:ivar MultipolePotential: External point charges (and dipoles).
:vartype MultipolePotential: OLEDDepostion._System._ElectrostaticEmbedding._MultipolePotential
"""
[docs] class _MultipolePotential(FixedBlock):
r"""
External point charges (and dipoles).
:ivar ChargeModel: A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.
:vartype ChargeModel: Literal["Point", "Gaussian"]
:ivar ChargeWidth: The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.
:vartype ChargeWidth: float | FloatKey
:ivar Coordinates: Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or
x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
:vartype Coordinates: str | Sequence[str] | FreeBlock
"""
[docs] class _Coordinates(FreeBlock):
r"""
Positions and values of the multipoles, one per line. Each line has the following format:
x y z q, or
x y z q µx µy µz.
Here x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr).
Periodic systems are not supported.
"""
def __post_init__(self):
pass
def __post_init__(self):
self.ChargeModel: Literal["Point", "Gaussian"] = MultipleChoiceKey(name='ChargeModel', comment='A multipole may be represented by a point (with a singular potential at its location) or by a spherical Gaussian distribution.', default='Point', choices=['Point', 'Gaussian'])
self.ChargeWidth: float | FloatKey = FloatKey(name='ChargeWidth', comment='The width parameter in a.u. in case a Gaussian charge model is chosen. A negative value means that the width will be chosen automatically.', default=-1.0)
self.Coordinates: str | Sequence[str] | FreeBlock = self._Coordinates(name='Coordinates', comment='Positions and values of the multipoles, one per line. Each line has the following format:\n\nx y z q, or\nx y z q µx µy µz.\n\nHere x, y, z are the coordinates in Å, q is the charge (in atomic units of charge) and µx, µy, µz are the (optional) dipole moment components (in atomic units, i.e. e*Bohr). \n\nPeriodic systems are not supported.', header=True)
def __post_init__(self):
self.ElectricField: Iterable[float] | FloatListKey = FloatListKey(name='ElectricField', comment='External homogeneous electric field with three Cartesian components: ex, ey, ez, the default unit being V/Å.\n\nIn atomic units: Hartree/(e bohr) = 51.422 V/Angstrom; the relation to SI units is: 1 Hartree/(e bohr) = 5.14 ... e11 V/m.\n\nSupported by the engines adf, band, dftb and mopac.\n\nFor periodic systems the field may only have nonzero components orthogonal to the direction(s) of periodicity (i.e. for 1D periodic system the x-component of the electric field should be zero, while for 2D periodic systems both the x and y components should be zero. This options cannot be used for 3D periodic systems.', unit='V/Angstrom')
self.MultipolePotential: OLEDDepostion._System._ElectrostaticEmbedding._MultipolePotential = self._MultipolePotential(name='MultipolePotential', comment='External point charges (and dipoles).')
[docs] class _Lattice(FreeBlock):
r"""
Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.
"""
def __post_init__(self):
pass
[docs] class _Modify(FixedBlock):
r"""
Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.
:ivar EnableAtomicProperties: Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.
:vartype EnableAtomicProperties: Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"]
:ivar GuessBonds: Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.
:vartype GuessBonds: BoolType | BoolKey
:ivar LatticeStrain: Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.
:vartype LatticeStrain: Iterable[float] | FloatListKey
:ivar MapAtomsToUnitCell: For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.
:vartype MapAtomsToUnitCell: Iterable[float] | FloatListKey
:ivar PerturbCoordinates: Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).
:vartype PerturbCoordinates: float | FloatKey
:ivar PerturbLattice: Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.
:vartype PerturbLattice: float | FloatKey
:ivar SuperCell: Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).
:vartype SuperCell: Iterable[int] | IntListKey
:ivar SuperCellTrafo: Create a supercell of the input system (only possible for periodic systems) :math:`\vec{a}_i' = \sum_j T_{ij} \vec{a}_j`. The integer numbers represent the supercell transformation :math:`T_{ij}`: 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).
:vartype SuperCellTrafo: Iterable[int] | IntListKey
:ivar Symmetrize: Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system's symmetry for calculations with the AMS driver and its engines.
:vartype Symmetrize: BoolType | BoolKey
:ivar Translate: Translate all atoms by a vector.
:vartype Translate: Iterable[float] | FloatListKey
"""
def __post_init__(self):
self.EnableAtomicProperties: Literal["gui", "adf", "band", "forcefield", "dftb", "reaxff", "qe"] = MultipleChoiceKey(name='EnableAtomicProperties', comment='Enables an atomic property group. This is only necessary if you want a group enabled, but no atom in the input is using any property from that group.', unique=False, choices=['gui', 'adf', 'band', 'forcefield', 'dftb', 'reaxff', 'qe'])
self.GuessBonds: BoolType | BoolKey = BoolKey(name='GuessBonds', comment='Guesses bonds based on the atomic elements and the geometry. Keeps existing bonds.', unique=False)
self.LatticeStrain: Iterable[float] | FloatListKey = FloatListKey(name='LatticeStrain', comment='Deform the input system by the specified strain. The strain elements are in Voigt notation, so one should specify 6 numbers for 3D periodic system (order: xx,yy,zz,yz,xz,xy), 3 numbers for 2D periodic systems (order: xx,yy,xy) or 1 number for 1D periodic systems.', unique=False)
self.MapAtomsToUnitCell: Iterable[float] | FloatListKey = FloatListKey(name='MapAtomsToUnitCell', comment='For periodic systems the atoms will be moved to the central unit cell where all their fractional coordinates are in the range [start_range,start_range+1). No mapping will take place along non-periodic directions. If just a single number is given, it corresponds to start_range. If multiple numbers are given, they should match the number of lattice vectors and will be used as start ranges along the individual lattice vectors. If no number is given at all, the mapping will be done to the [-0.5:0.5) cell.', unique=False)
self.PerturbCoordinates: float | FloatKey = FloatKey(name='PerturbCoordinates', comment='Perturb the atomic coordinates by adding random numbers between [-PerturbCoordinates,PerturbCoordinates] to each Cartesian component. This can be useful if you want to break the symmetry of your system (e.g. for a geometry optimization).', unique=False, unit='angstrom')
self.PerturbLattice: float | FloatKey = FloatKey(name='PerturbLattice', comment='Perturb the lattice vectors by applying random strain with matrix elements between [-PerturbLattice,PerturbLattice]. This can be useful if you want to deviate from an ideal symmetric geometry, for example if you look for a phase change due to high pressure.', unique=False)
self.SuperCell: Iterable[int] | IntListKey = IntListKey(name='SuperCell', comment='Create a supercell of the input system (only possible for periodic systems). The integer numbers represent the diagonal elements of the supercell transformation; you should specify as many numbers as lattice vectors (i.e. 1 number for 1D, 2 numbers for 2D and 3 numbers for 3D periodic systems).', unique=False)
self.SuperCellTrafo: Iterable[int] | IntListKey = IntListKey(name='SuperCellTrafo', comment="Create a supercell of the input system (only possible for periodic systems) :math:`\\vec{a}_i' = \\sum_j T_{ij} \\vec{a}_j`. The integer numbers represent the supercell transformation :math:`T_{ij}`: 1 number for 1D PBC, 4 numbers for 2D PBC corresponding to a 2x2 matrix (order: (1,1),(1,2),(2,1),(2,2)) and 9 numbers for 3D PBC corresponding to a 3x3 matrix (order: (1,1),(1,2),(1,3),(2,1),(2,2),(2,3),(3,1),(3,2),(3,3)).", unique=False)
self.Symmetrize: BoolType | BoolKey = BoolKey(name='Symmetrize', comment="Symmetrizes the atomic coordinates to machine precision and rototranslates the molecule to the AMS standard orientation. This allows optimal use of the system's symmetry for calculations with the AMS driver and its engines.", unique=False, default=False)
self.Translate: Iterable[float] | FloatListKey = FloatListKey(name='Translate', comment='Translate all atoms by a vector.', unique=False, unit='angstrom')
def __post_init__(self):
self.AllowCloseAtoms: BoolType | BoolKey = BoolKey(name='AllowCloseAtoms', comment='No longer functional. Just here for backwards compatibility.', hidden=True, default=True)
self.Charge: float | FloatKey = FloatKey(name='Charge', comment="The system's total charge in atomic units.", gui_name='Total charge:', default=0.0, engines='-forcefield')
self.FractionalCoords: BoolType | BoolKey = BoolKey(name='FractionalCoords', comment='Whether the atomic coordinates in the Atoms block are given in fractional coordinates of the lattice vectors. Requires the presence of the Lattice block.', default=False)
self.GeometryFile: str | Path | StringKey = PathStringKey(name='GeometryFile', comment='Read the geometry from a file (instead of from Atoms and Lattice blocks). Supported formats: .xyz', ispath=True)
self.GuessBonds: BoolType | BoolKey = BoolKey(name='GuessBonds', comment="Equivalent to 'Modify%GuessBonds'. Please update input file to use 'Modify' block instead.", hidden=True)
self.LatticeStrain: Iterable[float] | FloatListKey = FloatListKey(name='LatticeStrain', comment="Equivalent to 'Modify%LatticeStrain'. Please update input file to use 'Modify' block instead.", hidden=True)
self.MapAtomsToUnitCell: BoolType | BoolKey = BoolKey(name='MapAtomsToUnitCell', comment="Equivalent to 'Modify%MapAtomsToUnitCell'. Please update input file to use 'Modify' block instead.", hidden=True)
self.PerturbCoordinates: float | FloatKey = FloatKey(name='PerturbCoordinates', comment="Equivalent to 'Modify%PerturbCoordinates'. Please update input file to use 'Modify' block instead.", hidden=True, unit='angstrom')
self.PerturbLattice: float | FloatKey = FloatKey(name='PerturbLattice', comment="Equivalent to 'Modify%PerturbLattice'. Please update input file to use 'Modify' block instead.", hidden=True)
self.ShiftCoordinates: Iterable[float] | FloatListKey = FloatListKey(name='ShiftCoordinates', comment="Equivalent to 'Modify%Translate', but in the unit of bohr by default. Please update input file to use 'Modify' block instead.", hidden=True, unit='bohr')
self.SuperCell: Iterable[int] | IntListKey = IntListKey(name='SuperCell', comment="Equivalent to 'Modify%SuperCell'. Please update input file to use 'Modify' block instead.", hidden=True)
self.SuperCellTrafo: Iterable[int] | IntListKey = IntListKey(name='SuperCellTrafo', comment="Equivalent to 'Modify%SuperCellTrafo'. Please update input file to use 'Modify' block instead.", hidden=True)
self.Symmetrize: BoolType | BoolKey = BoolKey(name='Symmetrize', comment="Equivalent to 'Modify%Symmetrize'. Please update input file to use 'Modify' block instead.", hidden=True, default=False)
self.Atoms: str | Sequence[str] | FreeBlock = self._Atoms(name='Atoms', comment='The atom types and coordinates. Unit can be specified in the header. Default unit is Angstrom.', header=True)
self.BondOrders: str | Sequence[str] | FreeBlock = self._BondOrders(name='BondOrders', comment='Defined bond orders. Each line should contain two atom indices, followed by the bond order (1, 1.5, 2, 3 for single, aromatic, double and triple bonds) and (optionally) the cell shifts for periodic systems. May be used by MM engines and for defining constraints. If the system is periodic and none of the bonds have the cell shift defined then AMS will attempt to determine them following the minimum image convention.')
self.ElectrostaticEmbedding: OLEDDepostion._System._ElectrostaticEmbedding = self._ElectrostaticEmbedding(name='ElectrostaticEmbedding', comment='Container for electrostatic embedding options, which can be combined.')
self.Lattice: str | Sequence[str] | FreeBlock = self._Lattice(name='Lattice', comment='Up to three lattice vectors. Unit can be specified in the header. Default unit is Angstrom.', header=True)
self.Modify: OLEDDepostion._System._Modify = self._Modify(name='Modify', comment='Modifications to make to the chemical system after construction. This block is read like a script and the modifications applied top to bottom.', ordered=True)
def __post_init__(self):
self.RestartWorkdir: str | Path | StringKey = PathStringKey(name='RestartWorkdir', comment='Uses the data from the working directory of a previously run deposition workflow for restarting. Under the hood this uses the normal rerun-prevention available in PLAMS: it may reuse results from old jobs instead of running them again.', ispath=True, gui_type='directory')
self.Box: OLEDDepostion._Box = self._Box(name='Box', comment='Specifications of the box into which the material is deposited.')
self.Deposition: OLEDDepostion._Deposition = self._Deposition(name='Deposition', comment='Specifies the details of how molecules are deposited.')
self.LAMMPSOffload: OLEDDepostion._LAMMPSOffload = self._LAMMPSOffload(name='LAMMPSOffload', comment='Offload the calculation to LAMMPS via AMSPipe.')
self.LoadSystem: OLEDDepostion._LoadSystem = self._LoadSystem(name='LoadSystem', comment='Block that controls reading the chemical system from a KF file instead of the [System] block.', unique=False, header=True, extra_info='not_in_fragment', shared_id='AMSLoadSystem')
self.Molecule: OLEDDepostion._Molecule = self._Molecule(name='Molecule', comment='Specification of the molecule to be deposited.', unique=False, gui_name='Molecules', gui_type='Repeat at least once')
self.System: OLEDDepostion._System = self._System(name='System', comment='Specification of the chemical system. For some applications more than one system may be present in the input. In this case, all systems except one must have a non-empty string ID specified after the System keyword. The system without an ID is considered the main one.', unique=False, header=True, gui_type='Repeat at least once', shared_id='AMSSystem')
