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Prototype2009

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An overview of the Prototype2009 Design
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An overview of the Prototype2009 Design

The Prototype 2009 is an attempt to get a working chemical simulator in place that can:

  • Explore a wide range of initial conditions, e.g.:
    • Density
    • Temperature
    • Variable atomic types
    • Various atomic type ratios
    • Variable inter-atom forces
    • Simulation length
  • Simulate and record atomic positions and velocities
  • Create bonds between atoms as conditions become favorable
  • Evaluate simulation history to produce statistics about the run (over time), e.g.:
    • Bonds created per second
    • Current average particle speed
    • Current maximum molecule size
    • Current average molecule size
    • Number of molecules matching each molecule structure
  • Evaluate run statistics to produce score (for entire run), e.g.:
    • Total bonds created
    • Average bonds created per second
    • Maximum molecule size
    • Average molecule size

The prototype will use a distributed processing method, by running simulations in parallel, providing different initial conditions to each parallel instance. Additionally, simulation analysis will be performed separately to simulation, allowing for load balancing between data generation and data analysis.

Initial conceptual design indicates that simulation will be performed on controlled machines, due to additional software complexity. Simulation analysis will be distributed to end-user workstation machines, in the form of a BOINC client. The current implementation uses GROMACS (version 3.3) to perform the molecular dynamics simulation, writing and reading the GROMACS specific binary formats. Our code is called before and after the GROMACS executable, to set up initial conditions and to update the simulation state (such as molecular bonding) before resubmitting to the GROMACS binary for the next stage of processing.

Current Milestones

These milestones are aiming for June delivery.

  • Complete storage and loading of simulation state.
    • Missing/currently not working:
      • Bonds.
      • Bounding Box.
      • Pressure Coupling.
      • Random seed(s) used in simulation.
  • Improved in-simulation bonding code.
    • Bond formation based on atom radius.
    • Missing: Redistribution of charge in bonded pairs.
  • Initial condition generation from real-world simulation data.
  • Branching based on "external events" vs numeric mutation.
    • What external events? Ideas:
      • Replacement of random molecules.
      • Localised variation in temperature.
    • Simulation with different random seeds (Monte Carlo).
  • Multiple experiments in Simulation Manager
    • Experiment type #1
      • Continuous simulation without branching
        • This acts as a control
    • Experiment type #2
      • Branching
    • Each type should be spawned from initial conditions multiple times for parallel simulation.
    • Each type should receive equal amounts of simulation time.

Alpha Release

See Prototype2009: Alpha 10-01.

EvoGrid 2009/2010 Prototype Experimental Concept
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EvoGrid 2009/2010 Prototype Experimental Concept

More Pages

List of Documentation Pages

EvoGrid on Sourceforge

Prototype2009: Test Cases

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