Your first simulation
One full loop: create a simulation, edit and check it, run it, look at the results. The example is a Lennard-Jones melt in LAMMPS, which runs in seconds on a laptop.
Before you start
Section titled “Before you start”Open Environments. local should be ready, meaning a verified executable was found on your computer. If it is pending, install the engine and press Rescan, or add a remote machine that has one.
Create the simulation
Section titled “Create the simulation”-
Open Simulations and press New simulation.
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Point verlet at an existing input, or describe the system and press Draft with the agent:
A Lennard-Jones melt in reduced units: fcc lattice at density 0.8442, 4000 atoms, start at T* = 3.0, NVE, 250 steps, thermo every 50 steps.
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The agent looks up what it needs, writes a draft, checks it with your executable and repairs what the check rejects. The result is version 1.
Edit and check
Section titled “Edit and check”Open the simulation’s Script tab. Add a thermostat: type fix 2 all n and the editor offers
nve, nvt and npt with a line on each; after nvt, its keywords with their values. F1 on any
command opens its manual page beside the editor.
Press Save (⌘S or Ctrl+S). verlet checks the input with your executable first and makes a new version only if it passes. A problem is marked on its line and nothing is saved.
- Press Run.
- Pick the version, the environment (local), the executable and the number of MPI ranks.
- Press Run in the sheet. The run opens on its own page.
Overview shows timesteps per second, wall time, CPU, peak memory and time left; Thermo plots every column as it arrives; Logs follows the output.
When it finishes
Section titled “When it finishes”- Artifacts lists the log, dumps and restart files. For a remote run, Download all outputs copies them to your computer.
- Run the same version again with more ranks, select both runs on Executions and press Compare to see the speed difference and the thermo curves overlaid.
Next: run on a remote machine.