| We're looking for more developers. Want to contribute? Join the Mailing List and introduce yourself, or contact Bruce Damer directly. |
| Latest News |
|---|
| Prototype2009: Alpha 10-01 released. Debian Stable packages and images for VMWare available. |
Prototype2009
From The EvoGrid: The Evolution Technology Grid
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.
