pydft_qmmm.wrappers package

Submodules

pydft_qmmm.wrappers.logger module

Centralized logging classes based on context management.

class pydft_qmmm.wrappers.logger.Logger(output_directory, system, write_to_log=True, decimal_places=3, log_write_interval=1, write_to_csv=True, csv_write_interval=1, write_to_dcd=True, dcd_write_interval=50, write_to_pdb=True)

Bases: object

Logger for recording system and simulation data.

Parameters:

• output_dir – The directory where records are written.

• system (System) – The system whose data will be reported.

• write_to_log (bool) – Whether or not to write energies to a tree-like log file.

• decimal_places (int) – Number of decimal places to write energies in the log file before truncation.

• log_write_interval (int) – The interval between successive log writes, in simulation steps.

• write_to_csv (bool) – Whether or not to write energies to a CSV file.

• csv_write_interval (int) – The interval between successive CSV writes, in simulation steps.

• write_to_dcd (bool) – Whether or not to write atom positions to a DCD file.

• dcd_write_interval (int) – The interval between successive DCD writes, in simulation steps.

• write_to_pdb (bool) – Whether or not to write atom positions to a PDB file at the end of a simulation.

• output_directory (str)

csv_write_interval: int = 1

dcd_write_interval: int = 50

decimal_places: int = 3

log_write_interval: int = 1

output_directory: str

record(simulation)

Record simulation data into the log files.

Parameters:

simulation (Simulation) – The simulation whose data will be recorded by the logger.

Return type:

None

system: System

write_to_csv: bool = True

write_to_dcd: bool = True

write_to_log: bool = True

write_to_pdb: bool = True

class pydft_qmmm.wrappers.logger.NullLogger

Bases: object

A default logger class which does not perform logging.

record(simulation)

Default record call, which does nothing.

Parameters:

simulation (Simulation) – The simulation whose data will be recorded by the logger.

Return type:

None

pydft_qmmm.wrappers.simulation module

The core object which organizes simulations.

class pydft_qmmm.wrappers.simulation.Simulation(system, integrator, hamiltonian=None, calculator=None, plugins=None, logger=<pydft_qmmm.wrappers.logger.NullLogger object>)

Bases: object

Manages and performs simulations.

Parameters:

• system (System) – The system to simulate.

• integrator (Integrator) – The integrator defining how the system evolves.

• hamiltonian (Hamiltonian | None) – The Hamiltonian defining how calculations will be performed.

• calculator (Calculator | None) – A user-defined calculator, which may be provided in place of a Hamiltonian object.

• plugins (list[Plugin] | None) – A list of plugins to apply to the calculator or integrator objects before simulation.

• logger (Any) – A logger to record data generated during the simulation.

_frame

The current frame of the simulation, defaults to zero upon instantiation.

Type:

int

calculate_energy_forces()

Update total system energy and forces on atoms in the system.

Return type:

None

run_dynamics(steps)

Perform a number of simulation steps.

Parameters:

steps (int) – The number of steps to take.

Return type:

None

set_memory(memory)

Set the amount of memory that calculators can use.

Parameters:

memory (str) – The amount of memory to utilize.

Return type:

None

set_threads(threads)

Set the number of threads that calculators can use.

Parameters:

threads (int) – The number of threads to utilize.

Return type:

None

Module contents

A sub-package containing wrapper classes for the end user.