First Example

To demonstrate how UAMMD-structured works in practice, let’s walk through a simple example simulation. This example will showcase a system of four particles configured in a simple rod-like structure, where consecutive particles are bonded by harmonic springs. Additionally, a harmonic angular potential is added between the first three and the last three particles.

Here’s the complete input for this simulation:

system:
  info:
    type: ["Simulation", "Information"]
    parameters:
      name: "ROD"

global:
  units:
    type: ["Units", "None"]
  types:
    type: ["Types", "Basic"]
    labels: ["name", "mass", "radius", "charge"]
    data:
      - ["A", 1.0, 0.5, 0.0]
  ensemble:
    type: ["Ensemble", "NVT"]
    labels: ["box", "temperature"]
    data:
      - [[[10.0, 10.0, 10.0], 1.0]]

integrator:
  lang_bbk:
    type: ["Langevin", "BBK"]
    parameters:
      timeStep: 0.001
      frictionConstant: 1.0
  schedule:
    type: ["Schedule", "Integrator"]
    labels: ["order", "integrator", "steps"]
    data:
      - [1, "lang_bbk", 1000000]

state:
  labels: ["id", "position"]
  data:
    - [0, [0.0, 0.0, 0.0]]
    - [1, [0.0, 0.0, 1.0]]
    - [2, [0.0, 0.0, 2.0]]
    - [3, [0.0, 0.0, 3.0]]

topology:
  structure:
    labels: ["id", "type", "modelId"]
    data:
      - [0, "A", 0]
      - [1, "A", 0]
      - [2, "A", 0]
      - [3, "A", 0]
  forceField:
    bonds:
      type: ["Bond2", "HarmonicCommon_K_r0"]
      parameters:
        K: 100.0
        r0: 1.0
      labels: ["id_i", "id_j"]
      data:
        - [0, 1]
        - [1, 2]
        - [2, 3]
    angles:
      type: ["Bond3", "KratkyPorodCommon_K"]
      parameters:
        K: 50.0
      labels: ["id_i", "id_j", "id_k"]
      data:
        - [0, 1, 2]
        - [1, 2, 3]

simulationStep:
  info:
    type: ["UtilsStep", "InfoStep"]
    parameters:
      intervalStep: 10000
  saveState:
    type: ["WriteStep", "WriteStep"]
    parameters:
      outputFilePath: "test"
      outputFormat: "sp"
      intervalStep: 10000

Let’s break down this example to understand each component:

1. System: Specifies the name of the simulation as “ROD”.

2. Global: Sets up the basic parameters of the simulation:

   • Uses no specific unit system

   • Defines a single particle type “A” with mass 1.0, radius 0.5, and no charge

   • Sets up an NVT ensemble with a cubic box of side length 10.0 and temperature 1.0

3. Integrator: Uses a Langevin BBK integrator with a time step of 0.001 and friction constant of 1.0. The simulation is scheduled to run for 1,000,000 steps.

4. State: Defines the initial positions of the four particles along the z-axis.

5. Topology:

   • Structure: Assigns all particles to type “A” and model 0.

   • Force Field: - Defines harmonic bonds between consecutive particles with spring constant 100.0 and equilibrium distance 1.0. - Adds Kratky-Porod angle potentials with constant 50.0 for the two sets of three consecutive particles.

6. Simulation Step: Sets up two periodic operations:

   • Prints simulation information every 10,000 steps

   • Saves the simulation state every 10,000 steps

This example demonstrates how UAMMD-structured uses a structured input to define all aspects of a molecular dynamics simulation, from system setup to runtime behavior.