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document (using ACE in Molly) update #43

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document (using ACE in Molly) update #43

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19fe30c
first update on ace-molly example
YangshuaiWang Sep 12, 2023
d3646fe
export temperature plot and MD movie
YangshuaiWang Sep 12, 2023
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34 changes: 32 additions & 2 deletions docs/src/molly.md
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ vel = random_velocities(sys, temp)
sys = Molly.System(
sys;
velocities = vel,
loggers=(temp=TemperatureLogger(100),)
loggers=(temp=TemperatureLogger(100),coords=CoordinateLogger(100))
)

# Set up simulator
Expand All @@ -48,5 +48,35 @@ simulator = VelocityVerlet(


# Perform MD
simulate!(sys, simulator, 1000)
@time simulate!(sys, simulator, 30_000)
```

7775.936176 seconds (90.90 G allocations: 4.037 TiB, 9.11% gc time, 0.02% compilation time)

```julia
# Plot temperature
using Plots
plot(ustrip.(sys.loggers.temp.history)[end-175:end], c="blue", linewidth=3, label=:none, ylabel="Temperature", xlabel="Steps")
savefig("Temp_TiAl_ace_md.png")
```

<img src="../../data/Temp_TiAl_ace_md.png" width = "360" height = "270" />


```julia
# Save the trajectory to the .xyz file
using JuLIP
at0 = read_extxyz(fname_xyz)[1]
AT = JuLIP.Atoms{Float64}[];
for X in sys.loggers.coords.history
# units transform
Xn = ustrip.(X) * 10
at = JuLIP.Atoms(:X, Xn, cell=copy(at0.cell), pbc=true, M=copy(at0.M), Z=copy(at0.Z))
push!(AT, at)
end
write_extxyz("TiAl_ace_md.xyz", AT)
```

Open this .xyz file in [Ovito](https://www.ovito.org/) and then export the following animation.

<img src="../../data/TiAl_ace_md.gif" width = "300" height = "400" />