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Dependency-Bump (#53)
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Co-authored-by: Valentin Churavy <[email protected]>
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@Joroks @vchuravy
Joroks and vchuravy authored Jun 27, 2024
1 parent cdad665 commit 913e7c3
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4 changes: 2 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "LAMMPS"
uuid = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d"
authors = ["Valentin Churavy <[email protected]>"]
version = "0.4.1"
version = "0.4.2"

[deps]
CEnum = "fa961155-64e5-5f13-b03f-caf6b980ea82"
Expand All @@ -12,7 +12,7 @@ MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"

[compat]
CEnum = "0.4, 0.5"
LAMMPS_jll = "2.4"
LAMMPS_jll = "2.5"
Preferences = "1"
MPI = "0.20"
julia = "1.8"
89 changes: 50 additions & 39 deletions res/Manifest.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,28 +11,28 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[CEnum]]
git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90"
git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc"
uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
version = "0.4.2"
version = "0.5.0"

[[Clang]]
deps = ["CEnum", "Clang_jll", "Downloads", "Pkg", "TOML"]
git-tree-sha1 = "7f30e6c4197f8576bc3873f095055d24c2baec25"
git-tree-sha1 = "c67b4867f04eba5b202e010fa4cdff817549d69c"
repo-rev = "master"
repo-url = "https://github.com/JuliaInterop/Clang.jl.git"
uuid = "40e3b903-d033-50b4-a0cc-940c62c95e31"
version = "0.17.3"
version = "0.18.3"

[[Clang_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "TOML", "Zlib_jll", "libLLVM_jll"]
git-tree-sha1 = "b88c99c9093f9db49a40d0715ea0e3ae5bbd91f7"
deps = ["Artifacts", "JLLWrappers", "Libdl", "TOML", "Zlib_jll", "libLLVM_jll"]
git-tree-sha1 = "de2204d98741f57e7ddb9a6a738db74ba8a608cb"
uuid = "0ee61d77-7f21-5576-8119-9fcc46b10100"
version = "14.0.6+2"
version = "15.0.7+10"

[[CompilerSupportLibraries_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "1.0.2+0"
version = "1.1.1+0"

[[Dates]]
deps = ["Printf"]
Expand All @@ -46,21 +46,27 @@ version = "1.6.0"
[[FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"

[[Hwloc_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "ca0f6bf568b4bfc807e7537f081c81e35ceca114"
uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
version = "2.10.0+0"

[[InteractiveUtils]]
deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[JLLWrappers]]
deps = ["Preferences"]
git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1"
deps = ["Artifacts", "Preferences"]
git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca"
uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
version = "1.4.1"
version = "1.5.0"

[[LAMMPS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "TOML"]
git-tree-sha1 = "73612e0bc12813b3e333fe668e5ce4cccca8f6a0"
git-tree-sha1 = "f3437b3282fa653f1abb9632cdeca53013194bc8"
uuid = "5b3ab26d-9607-527c-88ea-8fe5ba57cafe"
version = "2.4.0+0"
version = "2.5.0+0"

[[LazyArtifacts]]
deps = ["Artifacts", "Pkg"]
Expand All @@ -69,21 +75,26 @@ uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
[[LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
version = "0.6.3"
version = "0.6.4"

[[LibCURL_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
version = "7.84.0+0"
version = "8.4.0+0"

[[LibGit2]]
deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"]
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"

[[LibGit2_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"]
uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5"
version = "1.6.4+0"

[[LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
version = "1.10.2+0"
version = "1.11.0+1"

[[Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
Expand All @@ -92,22 +103,22 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

[[MPICH_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
git-tree-sha1 = "d790fbd913f85e8865c55bf4725aff197c5155c8"
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
git-tree-sha1 = "4099bb6809ac109bfc17d521dad33763bcf026b7"
uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
version = "4.1.1+1"
version = "4.2.1+1"

[[MPIPreferences]]
deps = ["Libdl", "Preferences"]
git-tree-sha1 = "71f937129731a29eabe6969db2c90368a4408933"
git-tree-sha1 = "c105fe467859e7f6e9a852cb15cb4301126fac07"
uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
version = "0.1.7"
version = "0.1.11"

[[MPItrampoline_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
git-tree-sha1 = "ad88f863a5a16b3e26d14446afd3cd746266281b"
git-tree-sha1 = "8c35d5420193841b2f367e658540e8d9e0601ed0"
uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748"
version = "5.2.1+3"
version = "5.4.0+0"

[[Markdown]]
deps = ["Base64"]
Expand All @@ -116,38 +127,38 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
[[MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
version = "2.28.0+0"
version = "2.28.2+1"

[[MicrosoftMPI_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "a16aa086d335ed7e0170c5265247db29172af2f9"
git-tree-sha1 = "f12a29c4400ba812841c6ace3f4efbb6dbb3ba01"
uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf"
version = "10.1.3+2"
version = "10.1.4+2"

[[MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
version = "2022.10.11"
version = "2023.1.10"

[[NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
version = "1.2.0"

[[OpenMPI_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
git-tree-sha1 = "f3080f4212a8ba2ceb10a34b938601b862094314"
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
git-tree-sha1 = "a9de2f1fc98b92f8856c640bf4aec1ac9b2a0d86"
uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
version = "4.1.5+0"
version = "5.0.3+0"

[[Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
version = "1.9.0"
version = "1.10.0"

[[Preferences]]
deps = ["TOML"]
git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d"
git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6"
uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.3.0"
version = "1.4.3"

[[Printf]]
deps = ["Unicode"]
Expand All @@ -158,7 +169,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[Random]]
deps = ["SHA", "Serialization"]
deps = ["SHA"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

[[SHA]]
Expand Down Expand Up @@ -191,19 +202,19 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
[[Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
version = "1.2.13+0"
version = "1.2.13+1"

[[libLLVM_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8f36deef-c2a5-5394-99ed-8e07531fb29a"
version = "14.0.6+0"
version = "15.0.7+10"

[[nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.48.0+0"
version = "1.52.0+1"

[[p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+0"
version = "17.4.0+2"
6 changes: 2 additions & 4 deletions src/LAMMPS.jl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -58,10 +58,8 @@ mutable struct LMP
@atomic handle::Ptr{Cvoid}

function LMP(args::Vector{String}=String[], comm::Union{Nothing, MPI.Comm}=nothing)
if !isempty(args)
args = copy(args)
pushfirst!(args, "lammps")
end
args = copy(args)
pushfirst!(args, "lammps")

GC.@preserve args begin
if comm !== nothing
Expand Down
37 changes: 21 additions & 16 deletions src/api.jl
View file
Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
module API

using CEnum
using CEnum: CEnum, @cenum

import LAMMPS_jll
import LAMMPS_jll: liblammps
import MPI: MPI_Comm

@cenum _LMP_DATATYPE_CONST::UInt32 begin
@cenum _LMP_DATATYPE_CONST::Int32 begin
LAMMPS_NONE = -1
LAMMPS_INT = 0
LAMMPS_INT_2D = 1
LAMMPS_DOUBLE = 2
Expand Down Expand Up @@ -62,22 +63,22 @@ function lammps_close(handle)
ccall((:lammps_close, liblammps), Cvoid, (Ptr{Cvoid},), handle)
end

# no prototype is found for this function at library.h:128:6, please use with caution
# no prototype is found for this function at library.h:129:6, please use with caution
function lammps_mpi_init()
ccall((:lammps_mpi_init, liblammps), Cvoid, ())
end

# no prototype is found for this function at library.h:129:6, please use with caution
# no prototype is found for this function at library.h:130:6, please use with caution
function lammps_mpi_finalize()
ccall((:lammps_mpi_finalize, liblammps), Cvoid, ())
end

# no prototype is found for this function at library.h:130:6, please use with caution
# no prototype is found for this function at library.h:131:6, please use with caution
function lammps_kokkos_finalize()
ccall((:lammps_kokkos_finalize, liblammps), Cvoid, ())
end

# no prototype is found for this function at library.h:131:6, please use with caution
# no prototype is found for this function at library.h:132:6, please use with caution
function lammps_python_finalize()
ccall((:lammps_python_finalize, liblammps), Cvoid, ())
end
Expand Down Expand Up @@ -110,6 +111,10 @@ function lammps_get_thermo(handle, keyword)
ccall((:lammps_get_thermo, liblammps), Cdouble, (Ptr{Cvoid}, Ptr{Cchar}), handle, keyword)
end

function lammps_last_thermo(handle, what, index)
ccall((:lammps_last_thermo, liblammps), Ptr{Cvoid}, (Ptr{Cvoid}, Ptr{Cchar}, Cint), handle, what, index)
end

function lammps_extract_box(handle, boxlo, boxhi, xy, yz, xz, pflags, boxflag)
ccall((:lammps_extract_box, liblammps), Cvoid, (Ptr{Cvoid}, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cdouble}, Ptr{Cint}, Ptr{Cint}), handle, boxlo, boxhi, xy, yz, xz, pflags, boxflag)
end
Expand Down Expand Up @@ -254,32 +259,32 @@ function lammps_get_os_info(buffer, buf_size)
ccall((:lammps_get_os_info, liblammps), Cvoid, (Ptr{Cchar}, Cint), buffer, buf_size)
end

# no prototype is found for this function at library.h:231:5, please use with caution
# no prototype is found for this function at library.h:233:5, please use with caution
function lammps_config_has_mpi_support()
ccall((:lammps_config_has_mpi_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:232:5, please use with caution
# no prototype is found for this function at library.h:234:5, please use with caution
function lammps_config_has_gzip_support()
ccall((:lammps_config_has_gzip_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:233:5, please use with caution
# no prototype is found for this function at library.h:235:5, please use with caution
function lammps_config_has_png_support()
ccall((:lammps_config_has_png_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:234:5, please use with caution
# no prototype is found for this function at library.h:236:5, please use with caution
function lammps_config_has_jpeg_support()
ccall((:lammps_config_has_jpeg_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:235:5, please use with caution
# no prototype is found for this function at library.h:237:5, please use with caution
function lammps_config_has_ffmpeg_support()
ccall((:lammps_config_has_ffmpeg_support, liblammps), Cint, ())
end

# no prototype is found for this function at library.h:236:5, please use with caution
# no prototype is found for this function at library.h:238:5, please use with caution
function lammps_config_has_exceptions()
ccall((:lammps_config_has_exceptions, liblammps), Cint, ())
end
Expand All @@ -288,7 +293,7 @@ function lammps_config_has_package(arg1)
ccall((:lammps_config_has_package, liblammps), Cint, (Ptr{Cchar},), arg1)
end

# no prototype is found for this function at library.h:239:5, please use with caution
# no prototype is found for this function at library.h:241:5, please use with caution
function lammps_config_package_count()
ccall((:lammps_config_package_count, liblammps), Cint, ())
end
Expand All @@ -301,7 +306,7 @@ function lammps_config_accelerator(arg1, arg2, arg3)
ccall((:lammps_config_accelerator, liblammps), Cint, (Ptr{Cchar}, Ptr{Cchar}, Ptr{Cchar}), arg1, arg2, arg3)
end

# no prototype is found for this function at library.h:243:5, please use with caution
# no prototype is found for this function at library.h:245:5, please use with caution
function lammps_has_gpu_device()
ccall((:lammps_has_gpu_device, liblammps), Cint, ())
end
Expand Down Expand Up @@ -334,7 +339,7 @@ function lammps_id_name(arg1, arg2, arg3, arg4, arg5)
ccall((:lammps_id_name, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}, Cint, Ptr{Cchar}, Cint), arg1, arg2, arg3, arg4, arg5)
end

# no prototype is found for this function at library.h:254:5, please use with caution
# no prototype is found for this function at library.h:256:5, please use with caution
function lammps_plugin_count()
ccall((:lammps_plugin_count, liblammps), Cint, ())
end
Expand Down Expand Up @@ -410,7 +415,7 @@ function lammps_get_last_error_message(handle, buffer, buf_size)
ccall((:lammps_get_last_error_message, liblammps), Cint, (Ptr{Cvoid}, Ptr{Cchar}, Cint), handle, buffer, buf_size)
end

# no prototype is found for this function at library.h:297:5, please use with caution
# no prototype is found for this function at library.h:299:5, please use with caution
function lammps_python_api_version()
ccall((:lammps_python_api_version, liblammps), Cint, ())
end
Expand Down

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Registration pull request created: JuliaRegistries/General/109967

Tip: Release Notes

Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.

@JuliaRegistrator register

Release notes:

## Breaking changes

- blah

To add them here just re-invoke and the PR will be updated.

Tagging

After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.

This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via:

git tag -a v0.4.2 -m "<description of version>" 913e7c3034061427435d1cbfbbf0f952e8b1654f
git push origin v0.4.2

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