cesmix-mit / atomistic.jl Goto Github PK
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License: MIT License
Package that provides a integrated Julia workflow for molecular dyanmics simulations.
License: MIT License
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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
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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