mythos.simulators.oxdna

oxDNA simulator module.

Submodules

• mythos.simulators.oxdna.oxdna
• mythos.simulators.oxdna.utils

Attributes

CMAKE_BIN_ENV_VAR
ERR_BUILD_SETUP_FAILED
ERR_INPUT_FILE_NOT_FOUND
ERR_MISSING_REQUIRED_KEYS
MAKE_BIN_ENV_VAR

Classes

oxDNASimulator

A sampler base on running an oxDNA simulation.

Functions

_guess_binary_location(→ pathlib.Path | None)

Guess the location of a binary.

Package Contents

mythos.simulators.oxdna.CMAKE_BIN_ENV_VAR = 'CMAKE_BIN_PATH'

mythos.simulators.oxdna.ERR_BUILD_SETUP_FAILED = 'OXDNA build setup failed wiht return code: {}'

mythos.simulators.oxdna.ERR_INPUT_FILE_NOT_FOUND = 'Input file not found: {}'

mythos.simulators.oxdna.ERR_MISSING_REQUIRED_KEYS = 'Missing required keys: {}'

mythos.simulators.oxdna.MAKE_BIN_ENV_VAR = 'MAKE_BIN_PATH'

mythos.simulators.oxdna._guess_binary_location(bin_name: str, env_var: str) → pathlib.Path | None

Guess the location of a binary.

class mythos.simulators.oxdna.oxDNASimulator

Bases: mythos.simulators.base.InputDirSimulator

A sampler base on running an oxDNA simulation.

This simulator runs an oxDNA simulation in a subprocess, first compiling oxDNA from source with the provided parameters, or by using a precompiled binary (in the case parameter updates are not desired).

Parameters:

• input_dir – Path to the directory containing the oxDNA input file.

• sim_type – The type of oxDNA simulation to run.

• energy_fn – The energy function to use for default parameter updates.

• n_build_threads – Number of threads to use when building oxDNA from source.

• logger_config – Configuration for the logger.

• binary_path – Path to a precompiled oxDNA binary to use. This is mutually exclusive with source_path. When provided, the binary will be called and no recompilation will be performed. In such a case, parameters cannot be updated, and if supplied to the run will result in an error unless ignore_params is set to True.

• source_path – Path to the oxDNA source code to compile. Updating parameters in this simulator requires compiling oxDNA from source with the parameters built into the object code.

• ignore_params – Whether to ignore provided parameters when running the simulation. This argument is required to be True if there is no source_path set and parameters are passed.

• overwrite_input – Whether to overwrite the input directory or copy it. If this is False (default), the contents of the input_dir will be copied to a temporary directory for running the simulation to avoid overwriting input.

• input_overrides – Key-value pairs to override in the input file. The values accept scalar values that can be converted to str. For example: {“T”: “275K”, “steps”: 10000}. WARNING: no validation is performed on the provided key-value pairs.

sim_type: mythos.utils.types.oxDNASimulatorType

energy_fn: mythos.energy.base.EnergyFunction

n_build_threads: int = 4

logger_config: dict[str, Any] | None = None

binary_path: pathlib.Path | None = None

source_path: pathlib.Path | None = None

ignore_params: bool = False

input_overrides: dict[str, Any]

__post_init__(*args, **kwds) → None

Check the validity of the configuration.

with_cached_build(binary_path: pathlib.Path) → None

Switch to use a precompiled binary.

This may be useful when running on a cluster with a shared file system, or running on a single machine, particularly in cases where:

N_simulators * n_build_threads > N_cpu_cores.

Caution: the user is responsible for ensuring that the binary at provided path is pre-built for the appropriate parameter set, there is no check performed at simulation run-time to verify this.

run_simulation(input_dir: pathlib.Path, opt_params: mythos.utils.types.Params | None = None, seed: float | None = None, **_) → mythos.simulators.base.SimulatorOutput

Run an oxDNA simulation.

_read_trajectory(input_dir: pathlib.Path) → mythos.simulators.io.SimulatorTrajectory

build(*, input_dir: pathlib.Path, new_params: mythos.utils.types.Params, input_config: dict | None = None) → None

Update the simulation.

This function will recompile the oxDNA binary with the new parameters.