Merge pull request #115 from SotaYoshida/dev

Dev
SotaYoshida · Mar 4, 2024 · 0dfd2a1 · 0dfd2a1
2 parents 7035c0b + b8bcc38
commit 0dfd2a1
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -29,11 +29,9 @@ jobs:
           arch: x64
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
-        env:
-          JULIA_NUM_THREADS: 2
-        if: ${{ matrix.payload == 'serial' }}
-        continue-on-error: ${{ matrix.version == 'nightly' }}
+      - name: "Run tests"
+        run: |
+            julia --project -e 'import Pkg; Pkg.test()'
   build:
     runs-on: ubuntu-latest
     strategy:

diff --git a/.github/workflows/CI_pullrequest.yml b/.github/workflows/CI_pullrequest.yml
@@ -30,11 +30,13 @@ jobs:
           arch: x64
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
-        env:
-          JULIA_NUM_THREADS: 2
-        if: ${{ matrix.payload == 'serial' }}
-        continue-on-error: ${{ matrix.version == 'nightly' }}
+      - name: "Run tests"
+        run: |
+            julia --project -e 'import Pkg; Pkg.test()'
+        # env:
+        #   JULIA_NUM_THREADS: 2
+        # if: ${{ matrix.payload == 'serial' }}
+        # continue-on-error: ${{ matrix.version == 'nightly' }}
   build:
     runs-on: ubuntu-latest
     strategy:
@@ -63,35 +65,6 @@ jobs:
           export PATH=$PATH:/home/runner/.julia/bin
           mpiexecjl -n 4 julia --depwarn=yes --project=@. ./test/mpirun_test.jl	  
 
-  # build2:    
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       include:
-  #         - {version: '1.8',   os: ubuntu-latest}
-  #   name: Run sample_script.jl
-  #   steps:     
-  #     - uses: actions/checkout@v2
-  #       with:
-  #         fetch-depth: 0 
-  #     - uses: julia-actions/setup-julia@v1
-  #       with:
-  #         version: ${{ matrix.version }}
-  #         arch: x64
-  #     - uses: julia-actions/cache@v1
-  #     - uses: julia-actions/julia-buildpkg@v1 
-  #     - run: | 
-  #         git_hash=$(git rev-parse --short "$GITHUB_SHA")
-  #         echo git_hash $git_hash     
-  #         echo running on branch ${GITHUB_REF##*/}    
-  #         echo git_hash:[$git_hash]  > ./example/log_sample_script.txt
-  #         julia --project="@." -t 4 ./example/sample_script.jl >> ./example/log_sample_script.txt
-  #         git add example/log_sample_script.txt
-      # - name: commit changed logfile
-      #   uses: stefanzweifel/[email protected]
-      #   with:
-      #     commit_message: Update log_sample_script.txt  
   docs:
     name: Documentation
     runs-on: ubuntu-latest

diff --git a/.gitignore b/.gitignore
@@ -23,8 +23,8 @@ src/.DS_Store
 docs/.DS_Store
 
 # potential files and Omega generated through IMSRG flows
-*.snt
-*.snt.bin
+tbme*.snt
+tbme*.snt.bin
 /snts
 /flowOmega
 logfile.dat

diff --git a/.gitignore~ b/.gitignore~
@@ -0,0 +1,32 @@
+# Files generated by invoking Julia with --code-coverage
+*.jl.cov
+*.jl.*.cov
+
+# Files generated by invoking Julia with --track-allocation
+*.jl.mem
+
+# System-specific files and directories generated by the BinaryProvider and BinDeps packages
+# They contain absolute paths specific to the host computer, and so should not be committed
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# Build artifacts for creating documentation generated by the Documenter package
+docs/build/
+docs/site/
+
+# Mac
+.DS_Store
+src/.DS_Store
+docs/.DS_Store
+
+# potential files and Omega generated through IMSRG flows
+*.snt
+*.snt.bin
+/snts
+/flowOmega
+logfile.dat
+*/logfile.dat
+
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "NuclearToolkit"
 uuid = "89bb3bae-bcec-43ae-87b7-9dd181dc6334"
 authors = ["SotaYoshida <[email protected]> and contributors"]
-version = "0.4.0"
+version = "0.4.1"
 
 [deps]
 Arpack = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97"
@@ -32,9 +32,9 @@ WignerSymbols = "9f57e263-0b3d-5e2e-b1be-24f2bb48858b"
 [compat]
 Arpack = "0.5"
 AssociatedLegendrePolynomials = "1"
-CodecZlib="0.7"
+CodecZlib = "0.7"
 Combinatorics = "1"
-DocStringExtensions="0.9"
+DocStringExtensions = "0.9"
 FLoops = "0.2"
 Glob = "1"
 HDF5 = "0.16, 0.17"
@@ -44,8 +44,8 @@ LatinHypercubeSampling = "1.8"
 MKL = "0.6"
 MPI = "0.19, 0.20"
 Measures = "0.3"
-Plots = "1"
 Parsers = "2.8"
+Plots = "1"
 SpecialFunctions = "2"
 Statistics = "1"
 StatsBase = "0.33, 0.34"

diff --git a/example/log_sample_script.txt b/example/log_sample_script.txt
@@ -1,3 +1,4 @@
+option in optional_parameters.jl will be used.
 --- chiEFTparameters used ---
 n_mesh = 50
 pmax_fm = 5.0
@@ -31,6 +32,7 @@ size of dWS (jmax 9 lmax 40 e2max 8 Nnmax 20):
 # of sp states 15
 # of channels 2bstate 55 #TBME = 34320
 E(2H): bare = -2.224578 srg = -2.224578 Diff.1.484e-10
+option in optional_parameters.jl will be used.
 size of dWS (jmax 9 lmax 40 e2max 8 Nnmax 20):
      dtri    4.46 MB    dcgm0    1.11 MB  d6j_int    1.11 MB   d6j_lj    0.28 MB
   d9j_lsj    1.76 MB  dictHOB    0.44 MB

diff --git a/src/IMSRG.jl/emulator_imsrg.jl b/src/IMSRG.jl/emulator_imsrg.jl
@@ -341,13 +341,13 @@ function check_stationarity(z, z_k, z_pred,  Atilde, itnum=1000)
 end
 
 """
-function extrapolate_DMD(x_start, U_r, Atilde, s_pred, fn_exact, s_end, ds, nuc, inttype, emax, oupdir)
+function extrapolate_DMD(x_start, U_r, Atilde, s_pred, fn_exact, s_end, ds, nuc, inttype, emax, oupdir; verbose=false)
 
 Function to perform the DMD extrapolation.
 The time evolution (IMSRG flow) of original data `x` is approximated by the time evolution of 
 `z` in the latent space, and then the approximated data `x'` is written to a HDF5 file.
 """
-function extrapolate_DMD(x_start, U_r, Atilde, s_pred, fn_exact, s_end, ds, nuc, inttype, emax, oupdir)
+function extrapolate_DMD(x_start, U_r, Atilde, s_pred, fn_exact, s_end, ds, nuc, inttype, emax, oupdir; verbose=false)
     @assert length(s_pred) == length(fn_exact) "s_pred and fn_exact must have the same length"
     if length(s_pred) > 0
         r = size(U_r)[2]
@@ -377,7 +377,9 @@ function extrapolate_DMD(x_start, U_r, Atilde, s_pred, fn_exact, s_end, ds, nuc,
             end
             write_dmdvec_hdf5(x_pred,s,E_imsrg,nuc,inttype,emax,oupdir)
         end
-        check_stationarity(z1_r, z_k, z_new, Atilde)
+        if verbose
+            check_stationarity(z1_r, z_k, z_new, Atilde)
+        end
     end
     return nothing
 end
@@ -387,7 +389,7 @@ function write_dmdvec_hdf5(vec_in,s,E_imsrg,nuc,inttype,emax,oupdir)
     vec[1] = s
     vec[2] = E_imsrg
     vec[3:end] .= vec_in
-    fname = oupdir*"omega_dmdvec_$(inttype)_e$(emax)_$(nuc)_s"*strip(@sprintf("%6.2f",s))*".h5"
+    fname = oupdir*"omega_dmdvec"*ifelse(inttype=="","","_"*inttype)*"_e$(emax)_$(nuc)_s"*strip(@sprintf("%6.2f",s))*".h5"
     io = h5open(fname,"w")
     write(io,"vec",vec)
     close(io)

diff --git a/src/IMSRG.jl/imsrg_util.jl b/src/IMSRG.jl/imsrg_util.jl
@@ -21,7 +21,7 @@
 - `restart_from_files`: files to be read for restart 1st one is for IMSRG and 2nd one is for VSIMSRG
 """
 function imsrg_main(binfo::basedat,Chan1b::chan1b,Chan2bD::chan2bD,HFobj::HamiltonianNormalOrdered,dictsnt,dWS,valencespace,Operators,MatOp,to;
-                    delete_Ops=false,core_generator_type="atan",valence_generator_type="shell-model-atan",fn_params="optional_parameters.jl",debugmode=0,Hsample=false,restart_from_files=String[])
+                    delete_Ops=false,core_generator_type="atan",valence_generator_type="shell-model-atan",fn_params="optional_parameters.jl",debugmode=0,Hsample=0,restart_from_files=String[])
     if binfo.nuc.corenuc == "" && vsIMSRG; println("core (hole) for VS-IMSRG is not specified."); return nothing;end 
     dictMono = deepcopy(dictsnt.dictMonopole)
     vsIMSRG = ifelse(valencespace!=[]&&valencespace!="",true,false)
@@ -36,6 +36,8 @@ function imsrg_main(binfo::basedat,Chan1b::chan1b,Chan2bD::chan2bD,HFobj::Hamilt
     if length(restart_from_files) >= 1; IMSRGobj.smax = IMSRGobj.dsmax;end
     d6j_defbyrun = Dict{UInt64,Float64}()
     IMSRGflow(binfo,HFobj,IMSRGobj,PandyaObj,Chan1b,Chan2bD,dictMono,d6j_defbyrun,core_generator_type,valence_generator_type,to;debugmode=debugmode,Hsample=Hsample,restart_from_files=restart_from_files)
+    IMSRGobj.ExpectationValues["E0"] = IMSRGobj.H.zerobody[1]
+
     if vsIMSRG && length(restart_from_files) == 0
         IMSRGflow(binfo,HFobj,IMSRGobj,PandyaObj,Chan1b,Chan2bD,dictMono,d6j_defbyrun,core_generator_type,valence_generator_type,to;valenceflow=true,Hsample=Hsample)
         effOps = flow_Operators(binfo,HFobj,IMSRGobj,PandyaObj,Chan1b,Chan2bD,dWS,d6j_defbyrun,dictMono,Operators,MatOp,restart_from_files,to)
@@ -54,7 +56,7 @@ function imsrg_main(binfo::basedat,Chan1b::chan1b,Chan2bD::chan2bD,HFobj::Hamilt
     else        
         flow_Operators(binfo,HFobj,IMSRGobj,PandyaObj,Chan1b,Chan2bD,dWS,d6j_defbyrun,dictMono,Operators,MatOp,restart_from_files,to)
     end
-
+    
     if length(restart_from_files) >= 1
         if binfo.nuc.cZ != binfo.nuc.Z || binfo.nuc.cN != binfo.nuc.N
             println("normal ordering...")
@@ -72,7 +74,7 @@ function imsrg_main(binfo::basedat,Chan1b::chan1b,Chan2bD::chan2bD,HFobj::Hamilt
         end
         #write_vs_snt(binfo,HFobj,IMSRGobj,Operators,Chan1b,Chan2bD,valencespace)
     end
-    if !delete_Ops
+    if delete_Ops
         pid = getpid()
         for f in glob("flowOmega/Omega_$(pid)*.bin")
             rm(f)
@@ -650,7 +652,7 @@ function sort_d6j_lj(d6j)
 end
 
 function IMSRGflow(binfo::basedat,HFobj::HamiltonianNormalOrdered,IMSRGobj::IMSRGobject,PandyaObj::PandyaObject,Chan1b::chan1b,Chan2bD,dictMono,d6j_lj,
-                   core_generator,valence_generator,to;valenceflow=false,debugmode=0,maxstep=2000,Hsample=false,num_Hsample=50,modsample=4,
+                   core_generator,valence_generator,to;valenceflow=false,debugmode=0,maxstep=2000,Hsample=0,
                    restart_from_files=String[])     
     Chan2b = Chan2bD.Chan2b
     ncomm = IMSRGobj.Ncomm
@@ -730,10 +732,13 @@ function IMSRGflow(binfo::basedat,HFobj::HamiltonianNormalOrdered,IMSRGobj::IMSR
         func_Eta(HFobj,IMSRGobj,Chan2b,dictMono,norms)
 
         # remnant for IMSRG-Net sampling
-        #if Hsample && ( ( 15.0 <= s <= 20.00  || s == 30.0  || s == 50.0 ) || valenceflow) #(istep <=10 && valenceflow)
-        if Hsample && ( ( s <= 20.00  || s == 30.0  || s == 50.0 ) || valenceflow) #(istep <=10 && valenceflow)
-            Nested = deepcopy(IMSRGobj.Omega)
-            gather_omega_sofar_write(Hsample,istep, s, fvec, Omega, nOmega, tmpOp, binfo, Chan1b, Chan2bD, HFobj, IMSRGobj, dictMono, d6j_lj, PandyaObj,to,dict_idx_op_to_flatvec, dict_idx_flatvec_to_op,dict_if_idx_for_hdf5)
+        if Hsample > 0 
+            cond_1 = Hsample == 1 && ( (s <= 20.00  || s == 30.0  || s == 50.0 ) || valenceflow) # for DMD
+            cond_2 = Hsample == 2 && ( (15.0 <= s <= 20.00  || s == 30.0  || s == 50.0 ) || valenceflow) # for IMSRG-Net
+            if cond_1 || cond_2
+                Nested = deepcopy(IMSRGobj.Omega)
+                gather_omega_sofar_write(Hsample,istep, s, fvec, Omega, nOmega, tmpOp, binfo, Chan1b, Chan2bD, HFobj, IMSRGobj, dictMono, d6j_lj, PandyaObj,to,dict_idx_op_to_flatvec, dict_idx_flatvec_to_op,dict_if_idx_for_hdf5)
+            end
         end
 
         print_flowstatus(istep,s,ncomm,norms,IMSRGobj,Chan2b)
@@ -797,12 +802,11 @@ function normHs(Hs::Operator)
     return sqrt(norm(Hs.onebody[1],2)^2 + norm(Hs.onebody[2],2)^2 + norm2b^2)
 end
 
-function gather_omega_sofar_write(Hsample::Bool, istep, s, fvec, oOmega, nOmega, tmpOp, binfo, Chan1b, Chan2bD,
+function gather_omega_sofar_write(Hsample, istep, s, fvec, oOmega, nOmega, tmpOp, binfo, Chan1b, Chan2bD,
                                   HFobj, IMSRGobj, dictMono, d6j_lj, PandyaObj,to,
                                   dict_idx_op_to_flatvec, dict_idx_flatvec_to_op,dict_if_idx_for_hdf5;debug_mode=true)
-    if !Hsample; return nothing;end
+    if Hsample==0; return nothing;end
     magnusmethod = IMSRGobj.magnusmethod
-    #splitting = ifelse((magnusmethod!="" && magnusmethod!="split"),true,false)
     splitting = ifelse((magnusmethod!="" && magnusmethod!="split"),false,true)
     fvec .*= 0.0
     ncom = zeros(Int64,3)
@@ -828,8 +832,10 @@ function gather_omega_sofar_write(Hsample::Bool, istep, s, fvec, oOmega, nOmega,
     end
     get_fvec_from_Op!(s, fvec, tildeO, dict_idx_op_to_flatvec, dict_idx_flatvec_to_op)
     write_fvec_hdf5(binfo,fvec,dict_if_idx_for_hdf5,s,IMSRGobj.H.zerobody[1];label="omega")  
-    get_fvec_from_Op!(s, fvec, IMSRGobj.eta, dict_idx_op_to_flatvec, dict_idx_flatvec_to_op)
-    write_fvec_hdf5(binfo,fvec,dict_if_idx_for_hdf5,s,IMSRGobj.H.zerobody[1];label="eta")
+    if Hsample == 2
+        get_fvec_from_Op!(s, fvec, IMSRGobj.eta, dict_idx_op_to_flatvec, dict_idx_flatvec_to_op)
+        write_fvec_hdf5(binfo,fvec,dict_if_idx_for_hdf5,s,IMSRGobj.H.zerobody[1];label="eta")
+    end
     return nothing 
 end
 
@@ -1049,7 +1055,7 @@ Constructor for IMSRGobject
 - `n_written_omega::Int` # of written Omega by splitting to solve IMSRGflow
 - `Ncomm::Vector{Int}` # of commutator evaluated during IMSRG flow
 """
-function init_IMSRGobject(HFobj,filename;smax=500.0,dsmax=1.0,maxnormOmega=0.25,eta_criterion=1.e-6,denominatorDelta=0.0)
+function init_IMSRGobject(HFobj,filename;smax=500.0,dsmax=0.5,maxnormOmega=0.25,eta_criterion=1.e-6,denominatorDelta=0.0)
     tf = isfile(filename)
     ds = min(dsmax,1.0)
     s = [0.0,ds] 
@@ -1064,7 +1070,8 @@ function init_IMSRGobject(HFobj,filename;smax=500.0,dsmax=1.0,maxnormOmega=0.25,
     n_written_omega = [0]
     Ncomm =[0] 
     magnusmethod = ""
-    IMSRGobj = IMSRGobject(H0,Hs,s,smax,dsmax,maxnormOmega,magnusmethod,eta,Omega,eta_criterion,denominatorDelta,n_written_omega,Ncomm)
+    ExpectationValues = Dict{String,Float64}()
+    IMSRGobj = IMSRGobject(H0,Hs,s,smax,dsmax,maxnormOmega,magnusmethod,eta,Omega,eta_criterion,denominatorDelta,n_written_omega,Ncomm,ExpectationValues)
     if !tf
         println("Since $filename is not found, the default parameters will be used.")
         return IMSRGobj

diff --git a/src/NuclearToolkit.jl b/src/NuclearToolkit.jl
@@ -46,7 +46,7 @@ include("chiEFTint/nn_sampling.jl")
 include("chiEFTint/read_me3j.jl")
 export make_chiEFTint
 export nn_IMSRG_sampling
-export test_me3j
+export test3NF
 
 ### NuclData.jl
 include("NuclData.jl/amedata.jl")

diff --git a/src/ShellModel/betadecay.jl b/src/ShellModel/betadecay.jl
@@ -402,7 +402,7 @@ function eval_bFF_files(fns,qfactors::quenching_factors,parent,daughter,Qvals;ve
             fFF = f_0 + f_1 + f_2
             thalf = K/fFF
             logft = log10(fis[2]*thalf) 
-            if false #verbose                
+            if verbose                
                 println("Energy $tkey Ex.",@sprintf("%8.3f",tkey-daughter.Egs)," J2",@sprintf("%4i",J2),ffobj.prty)
                 println("M0s,M0t,M0s'", @sprintf("%12.4e", ffobj.M0rs),@sprintf("%12.4e", ffobj.M0sp),@sprintf("%12.4e", ffobj.M0rsd))
                 println("x, u, xi'y  ", @sprintf("%12.4e", x),@sprintf("%12.4e", u),@sprintf("%12.4e", xidy))