fix pairwise(): deprecated implicit dims argument

axsk · Feb 21, 2024 · cd4854c · cd4854c
1 parent 7abdc1b
commit cd4854c
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diff --git a/src/IsoMu/datalink.jl b/src/IsoMu/datalink.jl
@@ -95,7 +95,7 @@ end
 function localpdistinds(traj::AbstractArray{<:Any,3}, radius)
   elmin(x, y) = min.(x, y)
   d = mapreduce(elmin, eachslice(traj, dims=3)) do coords
-    UpperTriangular(pairwise(Euclidean(), coords))
+    UpperTriangular(pairwise(Euclidean(), coords, dims=2))
   end
   inds = findall(0 .< d .<= radius)
   return inds

diff --git a/src/IsoMu/reactionpath.jl b/src/IsoMu/reactionpath.jl
@@ -52,7 +52,7 @@ fromto(f::MaxPath, xi) = (argmin(xi), argmax(xi))
 
 # compute the shortest chain through the samples xs with reaction coordinate xi
 function shortestchain(xs, xi, from, to; sigma=1)
-    dxs = pairwise(Euclidean(), xs)
+    dxs = pairwise(Euclidean(), xs, dims=2)
     d = size(xs, 1)
     logp = onsager_machlup(dxs, xi, sigma, d)