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An overview of the Prototype2009 Design
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.

Alpha Release

See Prototype2009: Alpha 10-01.


Goal for February Presentation
Goal for February Presentation

Aiming for a February presentation, we want:

  • Control - Randomly generated frames Implemented
    • Linear simulation from randomly generated frames
  • Search - Algorithmic selection of frames
  • Analysis for Algorithmic Selection
    • Molecule size - Number of connections Implemented
    • Molecule occurrence - Number of times the same molecules are formed
  • Scores for Algorithmic Selection
    • Average temperature Implemented
    • Average molecule size Implemented
    • Average molecule occurrence
    • Plateau-ness - Measure of analysis scores rate of change

Breaking this down into milestones:

  • Random frame generation from simulation manager Implemented
    • Random atom placement
      • If Possible - Generation at molecular level vs atomic level
  • Bond destruction in simulator Implemented
  • Submission of completed simulation raw data Implemented
  • Submission of simulation analysis data Implemented
  • Submission of simulation scores Implemented
  • Implementation of analysis algorithms
  • Linear time frame generation
  • Algorithmic frame generation based on hill-climb algorithm
  • Analysis of produced results
    • Hierarchy of simulations
    • Scores of search tree entries
    • Visual samples of contents of search tree entries


Prototype2009: Example Process

EvoGrid on Sourceforge

Prototype2009: Data Formats

Simulation Manager Database Design
Simulation Manager Database Design

Prototype2009: Test Cases

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