Dependency-Bump (cesmix-mit#53)

Co-authored-by: Valentin Churavy <[email protected]>
Joroks · Jun 27, 2024 · 913e7c3 · 913e7c3
1 parent cdad665
commit 913e7c3
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Showing 4 changed files with 75 additions and 61 deletions.
diff --git a/Project.toml b/Project.toml
@@ -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"
@@ -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
@@ -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
@@ -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
@@ -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