ichor.core.molecular_dynamics package

Submodules

ichor.core.molecular_dynamics.amber module

class AmberMDIn(path: Path, nsteps: int = FileContents, dt: float = FileContents, temperature: int = FileContents, force_evaluation: ForceEvaluation = FileContents, bond_constraint: BondLengthConstraint = FileContents, write_coordinates_every: int = FileContents, write_velocities_every: int = FileContents, write_forces_every: int = FileContents, periodic_boundary_condition: PeriodicBoundaryCondition = FileContents, thermostat: AmberThermostat = FileContents, ln_gamma: float = FileContents)

Bases: WriteFile, ReadFile

Class that handles amber input files mdin.d

Parameters:

  • mdin_file – File where to write data

  • nsteps – Number of timesteps to run simulation for

  • dt – Timestep time in picoseconds, default is 0.001

  • temperature – Temperature to perform simulation at, default is 300

  • force_evaluation – _description_, defaults to ForceEvaluation.Complete

  • bond_constraint – _description_, defaults to BondLengthConstraint.NoConstraint

  • write_coordinates_every – Write coordinates every nth timestep, defaults to 1

  • write_velocities_every – Write velocities out to mdcrd even nth step Note that these should not be written out as output format ioutfm is set to 0 (meaning output is not in binary format), optional

  • write_forces_every – Write atomic forces out to mdcrd every nth step Note that output file is not NETCDF (binary format), defaults to -1

  • periodic_boundary_condition – Whether to use periodic boundary conditions or not, defaults to PeriodicBoundaryCondition.NoPeriodicBoundary

  • thermostat – The thermostat to use for the simulation, defaults to AmberThermostat.Langevin

  • ln_gamma – The collision frequency in picoseconds, defaults to 0.5

path: Path | str
class AmberThermostat(value)

Bases: Enum

An enumeration.

Andersen = 2
ConstantEnergy = 0
ConstantTemperature = 1
Langevin = 3
OptimisedIsokineticNoseHoover = 9
StochasticIsokineticNoseHoover = 10
class BondLengthConstraint(value)

Bases: Enum

An enumeration.

AllBonds = 3
HydrogenBonds = 2
NoConstraint = 1
class ForceEvaluation(value)

Bases: Enum

An enumeration.

Complete = 1
OmitAll = 8
OmitAngle = 5
OmitBonds = 3
OmitDihedral = 7
OmitHAngle = 4
OmitHBonds = 2
OmitHDihedral = 6
class PeriodicBoundaryCondition(value)

Bases: Enum

An enumeration.

ConstantPressure = 2
ConstantVolume = 1
NoPeriodicBoundary = 0
mdcrd_to_xyz(mdcrd: str | Path, prmtop: str | Path, mdin: str | Path, system_name: str, every: int = 1)
write_mdin(mdin_file: Path, nsteps: int, dt: float = 0.001, temperature: int = 300, force_evaluation: ForceEvaluation = ForceEvaluation.Complete, bond_constraint: BondLengthConstraint = BondLengthConstraint.NoConstraint, write_coordinates_every: int = 1, write_velocities_every: int = 0, write_forces_every: int = 0, periodic_boundary_condition: PeriodicBoundaryCondition = PeriodicBoundaryCondition.NoPeriodicBoundary, thermostat: AmberThermostat = AmberThermostat.Langevin, ln_gamma: float = 0.5)

Writes an AMBER md.in file with the given settings

Parameters:

  • mdin_file – File where to write data

  • nsteps – Number of timesteps to run simulation for

  • dt – Timestep time in picoseconds, default is 0.001

  • temperature – Temperature to perform simulation at, default is 300

  • force_evaluation – _description_, defaults to ForceEvaluation.Complete

  • bond_constraint – _description_, defaults to BondLengthConstraint.NoConstraint

  • write_coordinates_every – Write coordinates every nth timestep, defaults to 1

  • write_velocities_every – Write velocities out to mdcrd even nth step Note that these should not be written out as output format ioutfm is set to 0 (meaning output is not in binary format), optional

  • write_forces_every – Write atomic forces out to mdcrd every nth step Note that output file is not NETCDF (binary format), defaults to -1

  • periodic_boundary_condition – Whether to use periodic boundary conditions or not, defaults to PeriodicBoundaryCondition.NoPeriodicBoundary

  • thermostat – The thermostat to use for the simulation, defaults to AmberThermostat.Langevin

  • ln_gamma – The collision frequency in picoseconds, defaults to 0.5

ichor.core.molecular_dynamics.cp2k module

class CP2KInput(path: Path, atoms: Atoms | None = None, temperature: float = FileContents, nsteps: int = FileContents, datafile_location: Path = FileContents, project_name: str = FileContents, method: str = 'BLYP', basis_set: str = '6-31G*', molecular_charge: int = 0, spin_multiplicity: int = 1, solver: str = 'periodic', n_molecules: int = 1, box_size: float = 25.0)

Bases: ReadFile, WriteFile, HasAtoms

CP2K inpuit file reading/writing class.

Parameters:

  • path – path of CP2K .inp file

  • atoms – Atoms instance which is the starting geometry, defaults to None

  • temperature – Temperature of CP2K simulation, defaults to FileContents

  • nsteps – Timesteps of simulation, defaults to FileContents

  • datafile_location – The location of a file containing CP2K data. This has nothing to do with the datafile that ICHOR uses to submit jobs , defaults to FileContents

  • project_name – The name of the system/project, defaults to FileContents

  • method – The method to use for the DFT simulation, defaults to “BLYP”

  • basis_set – Basis set to use for simulation, defaults to “6-31G*”

  • molecular_charge – Charge of system, defaults to 0

  • n_molecules – Number of molecules, defaults to 1

  • box_size – Box size of simulation, defaults to 25.0

path: Path | str
write_cp2k_input(cp2k_input_file: Path, atoms: Atoms, temperature: int, nsteps: int, datafile_location: Path, system_name: str, method: str = 'BLYP', basis_set: str = '6-31G*', molecular_charge: int = 0, spin_multiplicity: int = 1, solver: str = 'periodic', n_molecules: int = 1, box_size: float = 25.0)

Module contents