Examples¶
Here are some examples of how to use Asap. Running and modifying these is probably the best way to familiarize yourself with Asap.
These examples have been tested and updated in April 2016, using Asap version 3.8.18.
Simple molecular dynamics simulation
A simple example of how to set up a block of atoms, and run a short simulation. Nothing fancy.
Writing output to a Trajectory file
How to save the output from a simulation.
Constant temperature molecular dynamics
Langevin dynamics makes it possible to do simulations with constant temperature rather than constant energy.
Plotting while the simulation runs
On the fly plotting.
Ramping up the temperature while plotting.
A simple example of a more complicated simulation.
Running Common Neighbor Analysis
How to run Common Neighbor Analysis (CNA) on a running simulation.
Running Polyhedral Template Matching
Same script as above, but using the more robust PTM algorithm instead of CNA.
Creating a dislocation in a slab
Inspiration on how to set up complicated structures.
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An example illustrating some of the tricks to run Asap in parallel.
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