From cd4854c35ea923db1b612011c105814493d5cf2e Mon Sep 17 00:00:00 2001 From: Sikorski Date: Wed, 21 Feb 2024 18:55:55 +0100 Subject: [PATCH] fix pairwise(): deprecated implicit dims argument --- src/IsoMu/datalink.jl | 2 +- src/IsoMu/reactionpath.jl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/IsoMu/datalink.jl b/src/IsoMu/datalink.jl index 0224bb2..7cd1935 100644 --- 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 index 5df8770..36f41c6 100644 --- 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)