snap_simulate

snap_simulate is a Python library designed to automate the generation of initial configurations and the construction, execution, and dynamic monitoring of molecular dynamics (MD) simulations in HOOMD-blue (v3+). It is specifically designed to work in tandem with snap_workflow to orchestrate massive parametric sweeps and run computational experiments across local workstations and HPC clusters. It reads structured, parametric configuration dictionaries to place particles/molecules without overlap, configure potentials, manage rigid bodies, compress/shrink boxes, and dynamically run simulations until statistical properties reach equilibrium.

Core Capabilities

  • Parametric System Builder: Place particles and complex molecules without overlap in random or simple cubic layouts. Supported templates include star polymers, linear chains, ring structures, comb polymers, grafted colloids, and patchy particles.

  • Dynamic Simulation Executor: Build HOOMD-blue objects (integrators, pair/bond forces, loggers, and writers) dynamically from modular parameter blocks.

  • Adaptive Box Compression: Dynamically compact simulation boxes to target volume or area fractions using resizing triggers.

  • Equilibrium Monitoring: Automatically monitor and run simulations until physical parameters reach equilibrium via dynamic autocorrelation analysis.

Quick Example

import snap_simulate as ns
from snap_workflow import SystemParams

# 1. Load the parameter sweep configurations from the modular params folder
params = SystemParams("my/work/dir/params")

# 2. Generate the initial configuration snapshot GSD
ns.system.gen_mixture(params, "init.gsd")

# 3. Build and initialize the HOOMD-blue simulation
sim, hoomd_objs = ns.hoomd.build_simulation(params)

# 4. Execute the simulation run steps
sim.run(100000)

See also

For detailed information on the contents, directories, and structural layout of the params configuration dictionary, refer to the Getting Started page and the specific API Reference sections below.

Module Architecture

The package is split into two primary modules:

  • snap_simulate.system: Handles snapshot framing, particle packing, and molecule geometry templates.

  • snap_simulate.hoomd: Drives simulation builds, box shrinking, and equilibrium execution controls.

User Guide:

API Reference: