From 913e7c3034061427435d1cbfbbf0f952e8b1654f Mon Sep 17 00:00:00 2001 From: Joroks <32484985+Joroks@users.noreply.github.com> Date: Thu, 27 Jun 2024 23:52:20 +0200 Subject: [PATCH] Dependency-Bump (#53) Co-authored-by: Valentin Churavy --- Project.toml | 4 +-- res/Manifest.toml | 89 ++++++++++++++++++++++++++--------------------- src/LAMMPS.jl | 6 ++-- src/api.jl | 37 +++++++++++--------- 4 files changed, 75 insertions(+), 61 deletions(-) diff --git a/Project.toml b/Project.toml index 4eba013..31ab158 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "LAMMPS" uuid = "ee2e13b9-eee9-4449-aafa-cfa6a2dbe14d" authors = ["Valentin Churavy "] -version = "0.4.1" +version = "0.4.2" [deps] CEnum = "fa961155-64e5-5f13-b03f-caf6b980ea82" @@ -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" diff --git a/res/Manifest.toml b/res/Manifest.toml index 5b3d977..9b6aab3 100644 --- a/res/Manifest.toml +++ b/res/Manifest.toml @@ -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"] @@ -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"] @@ -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" @@ -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"] @@ -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"] @@ -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]] @@ -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" diff --git a/src/LAMMPS.jl b/src/LAMMPS.jl index 7f73af4..ffdc91f 100644 --- a/src/LAMMPS.jl +++ b/src/LAMMPS.jl @@ -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 diff --git a/src/api.jl b/src/api.jl index d40d62c..d9571e6 100644 --- a/src/api.jl +++ b/src/api.jl @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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