dlsimtools 0.1.5

Automation framework for DL_MONTE and DL_POLY molecular simulations

dlsimtools

Automation framework for DL_MONTE and DL_POLY molecular simulations.

Installation

pip install dlsimtools

Overview

dlsimtools provides a high-level automation layer for running and analysing DL_MONTE (Monte Carlo) and DL_POLY (Molecular Dynamics) simulations, including tools for HPC job submission, input file manipulation, and output analysis.

Modules

Simulation control

• tmmc_master_control.Controller — top-level controller for running full TMMC (Transition Matrix Monte Carlo) pipelines, including range-seeking, bias optimisation, and production runs. Supports local execution and HPC job submission (Slurm/Archer2/Isambard3) via the sched parameter.
• MonteCore — low-level automation of DL_MONTE runs: editing CONTROL/CONFIG files, launching serial/parallel jobs, and monitoring convergence.
• LSMC — range-seeking and optimised bin calculation for TMMC simulations.
• PolyCore — equivalent automation utilities for DL_POLY MD runs.

Input/output

• InputConverter — converts between simulation input formats.
• MonteCon — reads and manipulates DL_MONTE CONFIG files.
• FieldTools — handles FIELD file editing.
• CifTools — reads CIF crystallographic files and prepares simulation inputs.
• PolyDataCore, PolyOutput — DL_POLY output parsing and data extraction.
• STATIS — parses DL_POLY STATIS files.
• TrajAnalysis — reads and analyses XYZ trajectory files.

Thermodynamics & sampling

• SwitchBias — switch bias calculation for TMMC.
• LSMC — lattice-switch Monte Carlo utilities.
• CoexistenceMP — coexistence point calculation.
• chempotfind — chemical potential search.
• MetaSurf, MetaUtil — metadynamics surface utilities.

Utilities

• GeneralUtil — common file editing and unit conversion utilities.
• GeneralOptimizer — general-purpose optimisation routines.
• OptimizerScript — scripting interface for optimisation workflows.
• HPCworker — writes and submits job scripts for Slurm, Archer2, and Isambard3.

Quick start

from dlsimtools.tmmc_master_control import Controller

pc = Controller(
    dlm_exec="/path/to/DLMONTE-SRL.X",
    dlm_exec_par="/path/to/DLMONTE-PRL.X",
    nw=16,
    nodes=1,
    sched="archer2",
)

# Run full TMMC pipeline at 300K (requires CONTROL, CONFIG, FIELD in working directory)
pc.master_surf_tmmc(temp=300)

# Or submit jobs for multiple temperatures to HPC
pc.tmmc_looper(temps=[300, 350, 400], timec=24)