clean up scripts folder

axsk · Aug 22, 2024 · b2e0bf7 · b2e0bf7
1 parent 7cf78d6
commit b2e0bf7
Show file tree

Hide file tree

Showing 11 changed files with 7 additions and 30 deletions.
diff --git a/scripts/0 - trajectories.ipynb → scripts/archive/0 - trajectories.ipynb b/scripts/0 - trajectories.ipynb → scripts/archive/0 - trajectories.ipynb
diff --git a/scripts/adaptivesampling.jl → scripts/archive/adaptivesampling.jl b/scripts/adaptivesampling.jl → scripts/archive/adaptivesampling.jl
diff --git a/scripts/cmp_openmm_molly.jl → scripts/archive/cmp_openmm_molly.jl b/scripts/cmp_openmm_molly.jl → scripts/archive/cmp_openmm_molly.jl
diff --git a/scripts/dataconvergence.jl → scripts/archive/dataconvergence.jl b/scripts/dataconvergence.jl → scripts/archive/dataconvergence.jl
diff --git a/scripts/dataconvergence.png → scripts/archive/dataconvergence.png b/scripts/dataconvergence.png → scripts/archive/dataconvergence.png
diff --git a/scripts/eigenvalues.ipynb → scripts/archive/eigenvalues.ipynb b/scripts/eigenvalues.ipynb → scripts/archive/eigenvalues.ipynb
diff --git a/scripts/macro.jl → scripts/archive/macro.jl b/scripts/macro.jl → scripts/archive/macro.jl
diff --git a/scripts/runs.jl → scripts/archive/runs.jl b/scripts/runs.jl → scripts/archive/runs.jl
diff --git a/scripts/thesis.jl b/scripts/thesis.jl
diff --git a/scripts/trpcage.jl b/scripts/trpcage.jl
@@ -0,0 +1,7 @@
+sim = OpenMMSimulation(pdb="data/2jof-processed.pdb", forcefields=ISOKANN.OpenMM.FORCE_AMBER_IMPLICIT, features=ISOKANN.OpenMM.noHatoms("data/2jof-processed.pdb"), steps=100, temp=360)
+
+data = SimulationData(sim, nx=100, nk=8)
+
+iso = Iso2(data, model=pairnet(data, activation=Flux.swish, layers=4), gpu=true, opt=AdamRegularized(1e-4, 1e-5), minibatch=100, loggers=[ISOKANN.autoplot(10)])
+
+runadaptive!(iso, generations=1000, nx=3, cutoff=2000, iter=500, keepedges=true)
diff --git a/scripts/vgvadapt.jl → scripts/vgvapg.jl b/scripts/vgvadapt.jl → scripts/vgvapg.jl