Start using Molly.jl: place_atoms not defined in module Molly?

I started looking into Molly.jl and attempting to run one its examples. I get the error described below. Insight would be nice to receive. Thx!

julia> using Molly

julia> n_atoms = 100

100

julia> atom_mass = 10.0u"u"

10.0 u

julia> atoms = [Atom(mass=atom_mass, ฯƒ=0.3u"nm", ฯต=0.2u"kJ * mol^-1") for i in 1:n_atoms]

100-element Vector{Atom{Quantity{Float64, ๐ˆ ๐“, Unitful.FreeUnits{(C,), ๐ˆ ๐“, nothing}}, Quantity{Float64, ๐Œ, Unitful.FreeUnits{(u,), ๐Œ, nothing}}, Quantity{Float64, ๐‹, Unitful.FreeUnits{(nm,), ๐‹, nothing}}, Quantity{Float64, ๐‹ยฒ ๐Œ ๐โปยน ๐“โปยฒ, Unitful.FreeUnits{(kJ, molโปยน), ๐‹ยฒ ๐Œ ๐โปยน ๐“โปยฒ, nothing}}}}:

Atom with index 1, charge=0.0 C, mass=10.0 u, ฯƒ=0.3 nm, ฯต=0.2 kJ molโปยน

โ€ฆ

julia> box_size = SVector(2.0, 2.0, 2.0)u"nm"

3-element SVector{3, Quantity{Float64, ๐‹, Unitful.FreeUnits{(nm,), ๐‹, nothing}}} with indices SOneTo(3):

2.0 nm

2.0 nm

2.0 nm

julia> coords = place_atoms(n_atoms, box_size, 0.3u"nm")

ERROR: UndefVarError: place_atoms not defined

Stacktrace:

[1] top-level scope

@ REPL[6]:1

[2] top-level scope

@ ~/.julia/packages/CUDA/Axzxe/src/initialization.jl:52

Works fine for me - based on your question in the other thread Iโ€™m assuming that youโ€™re just dumping all packages into your default environment, therefore ending up with outdated package versions. Donโ€™t do this, create project-specific environments instead installing only the specific packages required for an analysis.

Whatโ€™s the output of ]st?

True. I am dumping all packages to default.

Output of ]st is below.

I am happy to resort to a less naive approach.

\Status ~/.julia/environments/v1.6/Project.toml
[2169fc97] AlgebraicMultigrid v0.4.2
[6e4b80f9] BenchmarkTools v1.3.1
[159f3aea] Cairo v1.0.5
[39db22c5] ClipData v0.2.2
[a93c6f00] DataFrames v1.3.2
[9fdde737] DiffEqOperators v4.41.0
[0c46a032] DifferentialEquations v7.1.0
[5b8099bc] DomainSets v0.5.9
[587475ba] Flux v0.12.9
[1fa38f19] Format v1.3.2
[713c75ef] Franklin v0.10.69
[e9467ef8] GLMakie v0.5.4
[28b8d3ca] GR v0.64.0
[c91e804a] Gadfly v1.3.4
[705231aa] Gmsh v0.1.1
[7073ff75] IJulia v1.23.2
[40713840] IncompleteLU v0.2.0
[a98d9a8b] Interpolations v0.13.5
[42fd0dbc] IterativeSolvers v0.9.2
[b964fa9f] LaTeXStrings v1.3.0
[ee78f7c6] Makie v0.16.5
[94925ecb] MethodOfLines v0.1.0
[961ee093] ModelingToolkit v8.5.1
[aa0f7f06] Molly v0.5.0
[2774e3e8] NLsolve v4.5.1
[8913a72c] NonlinearSolve v0.3.15
[5fb14364] OhMyREPL v0.5.12
[1dea7af3] OrdinaryDiffEq v6.7.0
[f0f68f2c] PlotlyJS v0.18.8
[91a5bcdd] Plots v1.26.0
[af69fa37] Preconditioners v0.5.0
[47a9eef4] SparseDiffTools v1.20.2
[684fba80] SparsityDetection v0.3.4
[276daf66] SpecialFunctions v1.8.4
[90137ffa] StaticArrays v1.4.1
[c3572dad] Sundials v4.9.2
[0c5d862f] Symbolics v4.3.0
[1986cc42] Unitful v1.11.0
[e88e6eb3] Zygote v0.6.35

The latest release for Molly is 0.8. You are using an outdated version, which is why the examples in the documentation wonโ€™t work. You can either install the latest version of Molly or read an older version of the documentation (in the lower left corner of the docs youโ€™ll find a dropdown menu to select the version).

Have a look at this related thread:

and read the relevant sections of the Pkg.jl manual, e.g.

https://pkgdocs.julialang.org/v1/environments/

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