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atomistic.jl's Issues

ERROR: LoadError: UndefVarError: Atom not defined

After a fresh installation of Julia version 1.7.0 (2021-11-30):

julia> import Pkg
julia> Pkg.add(url="https://github.com/cesmix-mit/Atomistic.jl", rev="v0.3.0")

Result:

Precompiling project...
  ✗ Atomistic
  249 dependencies successfully precompiled in 279 seconds (10 already precompiled)
  1 dependency errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the package

Then

julia> import Pkg; Pkg.precompile()

Result:

Precompiling project...
  ✗ Atomistic
  0 dependencies successfully precompiled in 23 seconds (259 already precompiled)

ERROR: The following 1 direct dependency failed to precompile:

Atomistic [3e762ff9-b8d8-45cf-a902-edcbc7124e71]

Failed to precompile Atomistic [3e762ff9-b8d8-45cf-a902-edcbc7124e71] to /home/elujan/.julia/compiled/v1.7/Atomistic/jl_YYm32C.
WARNING: both InteratomicPotentials and AtomsBase export "Atom"; uses of it in module Atomistic must be qualified
ERROR: LoadError: UndefVarError: Atom not defined
Stacktrace:
  [1] top-level scope
    @ ~/.julia/packages/Atomistic/goFDt/src/implementations/nbodysimulator/nbodysimulator_base.jl:24
  [2] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
  [3] include(x::String)
    @ Atomistic ~/.julia/packages/Atomistic/goFDt/src/Atomistic.jl:1
  [4] top-level scope
    @ ~/.julia/packages/Atomistic/goFDt/src/implementations/nbodysimulator.jl:3
  [5] include(mod::Module, _path::String)
    @ Base ./Base.jl:418
  [6] include(x::String)
    @ Atomistic ~/.julia/packages/Atomistic/goFDt/src/Atomistic.jl:1
  [7] top-level scope
    @ ~/.julia/packages/Atomistic/goFDt/src/Atomistic.jl:47
  [8] include
    @ ./Base.jl:418 [inlined]
  [9] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
    @ Base ./loading.jl:1318
 [10] top-level scope
    @ none:1
 [11] eval
    @ ./boot.jl:373 [inlined]
 [12] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [13] top-level scope
    @ none:1
in expression starting at /home/elujan/.julia/packages/Atomistic/goFDt/src/implementations/nbodysimulator/nbodysimulator_base.jl:24
in expression starting at /home/elujan/.julia/packages/Atomistic/goFDt/src/implementations/nbodysimulator.jl:3
in expression starting at /home/elujan/.julia/packages/Atomistic/goFDt/src/Atomistic.jl:1
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/julia-1.7.0/share/julia/stdlib/v1.7/Pkg/src/Types.jl:68
 [2] precompile(ctx::Pkg.Types.Context; internal_call::Bool, strict::Bool, warn_loaded::Bool, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
   @ Pkg.API /opt/julia-1.7.0/share/julia/stdlib/v1.7/Pkg/src/API.jl:1362
 [3] precompile
   @ /opt/julia-1.7.0/share/julia/stdlib/v1.7/Pkg/src/API.jl:1013 [inlined]
 [4] #precompile#220
   @ /opt/julia-1.7.0/share/julia/stdlib/v1.7/Pkg/src/API.jl:1011 [inlined]
 [5] precompile()
   @ Pkg.API /opt/julia-1.7.0/share/julia/stdlib/v1.7/Pkg/src/API.jl:1011
 [6] top-level scope
   @ REPL[4]:1

TagBot trigger issue

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LAMMPS interfaces

It would be very nice to have interfaces that allow to run an MD simulation in LAMMPS. Currently that can be done using LAMMPS.jl (see AtomistcComposableWorkflows example), but it is not yet integrated into the user-friendly Atomistic.jl interfaces.

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