Merge pull request #67 from SotaYoshida/develop

Develop
SotaYoshida · Jan 13, 2023 · 706d1b8 · 706d1b8
2 parents eed67f8 + 3d4383d
commit 706d1b8
Show file tree

Hide file tree

Showing 23 changed files with 2,763 additions and 511 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -17,10 +17,10 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - {version: '1.7',   os: ubuntu-latest,  payload: serial}
-          - {version: '1.7',   os: macOS-latest,   payload: serial}
-          - {version: '1.7',   os: windows-2019,   payload: serial}
-          - {version: nightly,   os: ubuntu-latest,  payload: serial}
+          - {version: '1.8',   os: ubuntu-latest,  payload: serial}
+          - {version: '1.8',   os: macOS-latest,   payload: serial}
+          - {version: '1.8',   os: windows-2019,   payload: serial}
+          - {version: nightly, os: ubuntu-latest,  payload: serial}
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
@@ -35,12 +35,12 @@ jobs:
         if: ${{ matrix.payload == 'serial' }}
         continue-on-error: ${{ matrix.version == 'nightly' }}
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     strategy:
       fail-fast: false
       matrix:
         include:
-          - {version: '1.7',   os: ubuntu-latest,  payload: mpi}
+          - {version: '1.8',   os: 'ubuntu-18.04',  payload: mpi}
         mpi: [ 'openmpi' ]
     name: mpi test
     steps:
@@ -51,18 +51,23 @@ jobs:
           arch: x64
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
-      - name: Setup MPI
-        uses: mpi4py/setup-mpi@v1
-        with:
-          mpi: ${{ matrix.mpi }}
-      - run: mpiexec -n 4 julia --project="@." ./test/mpirun_test.jl
+      - name: "Run mpi tests"
+        run: |
+          export JULIA_PROJECT=@.
+          export JULIA_MPIEXEC=mpiexecjl
+          export JULIA_NUM_THREADS=1
+          julia --project -e 'ENV["JULIA_MPI_BINARY"]=""; using Pkg; Pkg.add("MPI"); Pkg.build("MPI"; verbose=true); using MPI; MPI.install_mpiexecjl()'
+          julia --project=@. -e "using InteractiveUtils; versioninfo(verbose=true)"
+          julia --project=@. -e "using Pkg; Pkg.instantiate(); Pkg.build()"
+          export PATH=$PATH:/home/runner/.julia/bin
+          mpiexecjl -n 4 julia --depwarn=yes --project=@. ./test/mpirun_test.jl	  
   build2:    
-    runs-on: ubuntu-latest
+    runs-on: 'ubuntu-18.04'
     strategy:
       fail-fast: false
       matrix:
         include:
-          - {version: '1.7',   os: ubuntu-latest}
+          - {version: '1.8',   os: 'ubuntu-18.04'}
     name: Run sample_script.jl
     steps:     
       - uses: actions/checkout@v2
@@ -81,12 +86,12 @@ jobs:
           commit_message: Update log_sample_script.txt  
   docs:
     name: Documentation
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.7'
+          version: '1.8'
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-docdeploy@v1
         env:

diff --git a/Manifest.toml b/Manifest.toml
@@ -1,10 +1,12 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.7.3"
+julia_version = "1.8.5"
 manifest_format = "2.0"
+project_hash = "2e06d70ed04492db9a8fbdf16aeace0744eb05b9"
 
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
+version = "1.1.1"
 
 [[deps.Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -31,18 +33,19 @@ version = "1.0.2"
 
 [[deps.Compat]]
 deps = ["Dates", "LinearAlgebra", "UUIDs"]
-git-tree-sha1 = "3ca828fe1b75fa84b021a7860bd039eaea84d2f2"
+git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.3.0"
+version = "4.5.0"
 
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
+version = "1.0.1+0"
 
 [[deps.DataAPI]]
-git-tree-sha1 = "e08915633fcb3ea83bf9d6126292e5bc5c739922"
+git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
-version = "1.13.0"
+version = "1.14.0"
 
 [[deps.DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -60,13 +63,14 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[deps.DocStringExtensions]]
 deps = ["LibGit2"]
-git-tree-sha1 = "c36550cb29cbe373e95b3f40486b9a4148f89ffd"
+git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-version = "0.9.2"
+version = "0.9.3"
 
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
 uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
+version = "1.6.0"
 
 [[deps.ExprTools]]
 git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d"
@@ -135,10 +139,12 @@ uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
 [[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
 uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
+version = "0.6.3"
 
 [[deps.LibCURL_jll]]
 deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
 uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
+version = "7.84.0+0"
 
 [[deps.LibGit2]]
 deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
@@ -147,6 +153,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 [[deps.LibSSH2_jll]]
 deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
 uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
+version = "1.10.2+0"
 
 [[deps.Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
@@ -157,18 +164,18 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[deps.LogExpFunctions]]
 deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "94d9c52ca447e23eac0c0f074effbcd38830deb5"
+git-tree-sha1 = "946607f84feb96220f480e0422d3484c49c00239"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.18"
+version = "0.3.19"
 
 [[deps.Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[deps.MPI]]
 deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "Requires", "Serialization", "Sockets"]
-git-tree-sha1 = "649b1c447a6c737d3bec80d0b72ccb7aba82310d"
+git-tree-sha1 = "3bb087eb4322bd73db110722f97624f3f2edb047"
 uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195"
-version = "0.20.4"
+version = "0.20.7"
 
 [[deps.MPICH_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "Pkg", "TOML"]
@@ -178,9 +185,9 @@ version = "4.0.2+5"
 
 [[deps.MPIPreferences]]
 deps = ["Libdl", "Preferences"]
-git-tree-sha1 = "34892fb69751a76bcf8b7add84ec77015208a1ec"
+git-tree-sha1 = "71f937129731a29eabe6969db2c90368a4408933"
 uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
-version = "0.1.6"
+version = "0.1.7"
 
 [[deps.MPItrampoline_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "Pkg", "TOML"]
@@ -195,6 +202,7 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 [[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
+version = "2.28.0+0"
 
 [[deps.MicrosoftMPI_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -204,23 +212,27 @@ version = "10.1.3+2"
 
 [[deps.Missings]]
 deps = ["DataAPI"]
-git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f"
+git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272"
 uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
-version = "1.0.2"
+version = "1.1.0"
 
 [[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
+version = "2022.2.1"
 
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
+version = "1.2.0"
 
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
+version = "0.3.20+0"
 
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
+version = "0.8.1+0"
 
 [[deps.OpenMPI_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "Pkg", "TOML"]
@@ -242,6 +254,7 @@ version = "1.4.1"
 [[deps.Pkg]]
 deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+version = "1.8.0"
 
 [[deps.Preferences]]
 deps = ["TOML"]
@@ -280,6 +293,7 @@ version = "1.3.0"
 
 [[deps.SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
+version = "0.7.0"
 
 [[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
@@ -289,9 +303,9 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
 [[deps.SortingAlgorithms]]
 deps = ["DataStructures"]
-git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508"
+git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00"
 uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
-version = "1.0.1"
+version = "1.1.0"
 
 [[deps.SparseArrays]]
 deps = ["LinearAlgebra", "Random"]
@@ -328,10 +342,12 @@ version = "0.33.21"
 [[deps.TOML]]
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+version = "1.0.0"
 
 [[deps.Tar]]
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
+version = "1.10.1"
 
 [[deps.Test]]
 deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
@@ -359,15 +375,19 @@ version = "2.0.0"
 [[deps.Zlib_jll]]
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
+version = "1.2.12+3"
 
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
+version = "5.1.1+0"
 
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
+version = "1.48.0+0"
 
 [[deps.p7zip_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
+version = "17.4.0+0"
diff --git a/Project.toml b/Project.toml
@@ -28,4 +28,4 @@ SpecialFunctions = "1.8, 2"
 StatsBase = "0.33"
 TimerOutputs = "0.5"
 WignerSymbols = "1.1, 2"
-julia = "1.7"
+julia = "1.8"
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -17,10 +17,11 @@ You can try the package in the following ways:
 
     `$ julia -t 8 example/sample_script.jl`
 
-    This performs:
-      - calculation of NN potential from Chiral EFT
-      - HFMBPT(3) and IMSRG/VS-IMSRG(2) calculation with it
-      - shell-model calculations with the effective interaction derived by VS-IMSRG
+    This performs:  
+    - calculation of NN potential from Chiral EFT
+    - HFMBPT(3) and IMSRG/VS-IMSRG(2) calculation with it
+    - shell-model calculations with the effective interaction derived by VS-IMSRG
+
     An expected results using the latest dev branch can be found [here](https://github.com/SotaYoshida/NuclearToolkit.jl/blob/develop/example/log_sample_script.txt).
 * Try sample codes in [HowToUse](howtouse) page.
 

diff --git a/example/log_sample_script.txt b/example/log_sample_script.txt
@@ -1,13 +1,13 @@
-@emax 4 hitCG 29351 dWS <  11.31 MB   9j(1430) <   2.51 MB   HOB (5179) <   0.31 MB
+@emax 4 hitCG 29351 dWS <   9.52 MB   9j(1430) <   2.51 MB   HOB (5179) <   0.31 MB
 target: O16 Ref. => Z=8 N=8 E:    -132.9506  = E1b    363.70  + E2b   -496.65   (    -55.16  -367.32   -74.18)
 EMP2    -23.70628 1b    -0.000 pp    -1.437 pn   -20.815 nn    -1.454
 EMP3      0.37645 pp    -0.111 hh    -1.895 ph     2.383
 E_HF   -132.95058  E_MBPT(3) =    -156.2804  Eexp:     -127.619
 
 parameters in optional_parameters.jl will be used.
  step:        s             E0   ||Omega_1||   ||Omega_2||     ||Eta_1||     ||Eta_2||    Ncomm.  nwritten
-     0    0.000  -132.95057781  0.000000e+00  0.000000e+00  7.576852e-17  1.410292e+00         0         0
-     1    0.500  -150.64837608  3.788426e-17  7.051459e-01  4.457285e-02  6.465559e-01         8         0
+     0    0.000  -132.95057781  0.000000e+00  0.000000e+00  8.338154e-17  1.410292e+00         0         0
+     1    0.500  -150.64837608  4.169077e-17  7.051459e-01  4.457285e-02  6.465559e-01         8         0
      2    1.000  -154.78704837  2.228643e-02  3.232779e-01  5.387093e-02  3.441643e-01        15         1
      3    1.500  -156.02709506  2.693546e-02  1.720822e-01  5.200791e-02  1.968159e-01        21         2
      4    2.000  -156.46234613  5.291574e-02  2.697514e-01  4.609815e-02  1.192463e-01        28         2
@@ -282,6 +282,6 @@ Starting VS-IMSRG flow
 Operator:Rp2
    HF point proton radius     2.045093 charge radius     2.206924 => HF+PT     2.219037
 IMSRG point proton radius     2.091495 charge radius     2.249990
-  Mg24    Z,N=(12,12)     c(8,8)     v(4,4)  mdim:        28503 (  4.45 ) J [0.0, 2.0, 2.0, 3.0, 4.0, 4.0, 5.0, 1.0, -1.0, -1.0]
+  Mg24    Z,N=(12,12)     c(8,8)     v(4,4)  mdim:        28503 (  4.45 ) J [0.0, 2.0, 2.0, 3.0, 4.0, 4.0, 5.0, 1.0, 6.0, 2.0]
 En.  -109.065  -107.717  -106.056  -104.800  -104.748  -103.238  -101.177  -100.704  -100.138  -100.119 
 Ex.     0.000     1.348     3.010     4.265     4.317     5.828     7.889     8.361     8.928     8.946 
diff --git a/sample_3nf.jl b/sample_3nf.jl
@@ -0,0 +1,6 @@
+include("src/genuine3NF.jl")
+using .genuine3NF
+
+#make_chiEFTint(;is_show=true)
+
+test3NF()
diff --git a/src/IMSRG.jl/imsrg_util.jl b/src/IMSRG.jl/imsrg_util.jl
@@ -559,14 +559,6 @@ function DoPandyaTransformation(O,Obar_ph,tbc_cc,Chan2bD,HFobj,numbers_ch,dict6j
     return nothing
 end
 
-function get_nkey_from_key6j(tkey;ofst_unit=1000)
-    nkey = tkey[1] + tkey[2] * ofst_unit + tkey[3] * ofst_unit^2 + tkey[4] * ofst_unit^3 +  tkey[5] * ofst_unit^4
-    return nkey
-end
-function get_nkey_from_key6j(ji,jj,jk,jl,Jp;ofst_unit=1000)
-    return ji + jj*ofst_unit + jk * ofst_unit^2+ jl* ofst_unit^3 + Jp * ofst_unit^4
-end
-
 function IMSRGflow(binfo::basedat,HFobj::HamiltonianNormalOrdered,IMSRGobj::IMSRGobject,PandyaObj::PandyaObject,Chan1b::chan1b,Chan2bD,dictMono,dict6j,
                    core_generator,valence_generator,to;valenceflow=false,debugmode=0,maxstep=2000,magnusmethod="split") 
     Chan2b = Chan2bD.Chan2b

diff --git a/src/NuclearToolkit.jl b/src/NuclearToolkit.jl
@@ -27,6 +27,8 @@ include("chiEFTint/calibration.jl")
 include("chiEFTint/valence.jl")
 include("chiEFTint/renorm.jl")
 include("chiEFTint/threebodyforce.jl")
+include("chiEFTint/threebody_Jacobi.jl")
+include("chiEFTint/threebody_JacobiHO.jl")
 include("chiEFTint/matter.jl")
 include("chiEFTint/nn_sampling.jl")
 export make_chiEFTint

diff --git a/src/ShellModel/lanczos_methods.jl b/src/ShellModel/lanczos_methods.jl
@@ -218,8 +218,7 @@ function diagonalize_T!(k::Int64,num_ev::Int64,
                         en::Array{Array{Float64,1}},
                         num_history::Int64,
                         TF::Array{Bool,1},
-                        tol::Float64) where{FA<:Array{Float64,1},
-                                            FA2<:Array{Float64,2}}
+                        tol::Float64) 
     for ith = num_history:-1:2
         en[ith] .= en[ith-1]
     end