Merge pull request #2 from fkfest/auto/from-devel-repo

Merge changes from development repository

.github/workflows/clean_docs.yml

@@ -0,0 +1,28 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+            if [ -d "previews/PR$PRNUM" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "previews/PR$PRNUM"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+            fi
+        env:
+            PRNUM: ${{ github.event.number }}

.github/workflows/documentation.yml

@@ -0,0 +1,36 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main # update to match your development branch (master, main, dev, trunk, ...)
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    permissions:
+      contents: write
+      statuses: write
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        julia-version: ['1.9']
+        julia-arch: [x64]
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.julia-arch }}
+      #- name: Install dependencies
+        #run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      #- name: Build and deploy
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-docdeploy@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          #DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        #run: julia --project=docs/ docs/make.jl

.github/workflows/push-to-stable.yml

@@ -11,32 +11,33 @@ on:
 # (this job does not run unless build_and_test is successful)
 env:
   BOT_TOKEN: ${{ secrets.PRIVATE_TO_PUBLIC_PAT }} # PAT for jph-bot
-  TARGET_REPO: e-cojl
+  ORGA_NAME: fkfest
+  TARGET_REPO: ElemCo.jl
   TARGET_BRANCH: main
-  SOURCE_REPO: e-cojl-devel
+  SOURCE_REPO: ElemCo.jl-devel
   SOURCE_BRANCH: stable
 
 jobs:
   push-changes:
     runs-on: ubuntu-latest
     steps:
       - name: checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
-          ref: stable # unfortunately, cannot use env here, must change manually as well
+          ref: ${{ env.SOURCE_BRANCH }}
           fetch-depth: 0
 
       - name: clone $SOURCE_BRANCH repo
         run: |
-          git clone https://fkfest:[email protected]/fkfest/$TARGET_REPO.git
+          git clone https://$ORGA_NAME:[email protected]/$ORGA_NAME/$TARGET_REPO.git
           cd $TARGET_REPO
           git checkout -b auto/from-devel-repo
           git config user.name "actions-user"
           git config user.email "[email protected]"
       - name: pull changes into local copy of public repo from private repo
         run: |
           cd $TARGET_REPO
-          git remote add source https://fkfest:[email protected]/fkfest/$SOURCE_REPO
+          git remote add source https://$ORGA_NAME:[email protected]/$ORGA_NAME/$SOURCE_REPO
           git fetch source $SOURCE_BRANCH
       - name: merge changes in public repo
         run: |
@@ -53,7 +54,7 @@ jobs:
           PR_BODY="This pull request merges changes from the private development repository and was automatically generated by GitHub Actions."
           PR_HEAD="auto/from-devel-repo" # branch with changes
           PR_BASE="$TARGET_BRANCH"
-          PR_API_URL=$(curl --silent --request POST --url https://api.github.com/repos/fkfest/$TARGET_REPO/pulls \
+          PR_API_URL=$(curl --silent --request POST --url https://api.github.com/repos/$ORGA_NAME/$TARGET_REPO/pulls \
             --header "authorization: Bearer $BOT_TOKEN" \
             --header "content-type: application/json" \
             --data "{\"title\":\"$PR_TITLE\",\"body\":\"$PR_BODY\",\"head\":\"$PR_HEAD\",\"base\":\"$PR_BASE\"}" \

.github/workflows/test.yml

@@ -0,0 +1,29 @@
+name: Run tests
+
+on: 
+  #push:
+  #branches:
+      #- main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        julia-version: ['1.9']
+        julia-arch: [x64]
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: ${{ matrix.julia-arch }}
+      - uses: julia-actions/julia-buildpkg@latest
+      - uses: julia-actions/julia-runtest@latest
+        with:
+          annotate: true

.gitignore

@@ -0,0 +1,9 @@
+Manifest.toml
+docs/build
+examples/*.out
+examples/ElemCo.jl-devel
+docs/equations/*.bbl
+docs/equations/*.blg
+docs/equations/*.log
+docs/equations/*.out
+docs/equations/*.toc

Project.toml

@@ -0,0 +1,28 @@
+name = "ElemCo"
+uuid = "094d408e-8508-40f4-9646-a254980d91ac"
+authors = ["Daniel Kats <[email protected]> and contributors"]
+version = "1.0.0-DEV"
+
+[deps]
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+GaussianBasis = "9bb1a3dc-0d1c-467e-84f5-0c4ef701360a"
+IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
+Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
+NPZ = "15e1cf62-19b3-5cfa-8e77-841668bca605"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+TensorOperations = "6aa20fa7-93e2-5fca-9bc0-fbd0db3c71a2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+TensorOperations = ">=3.2.5"
+julia = "1.8.5"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

README.md

@@ -1,30 +1,86 @@
-# e-Co.jl <img style="float: right;" src="e-coil.png"> <br/><br/>
+# ElemCo.jl <img align="right" src="files/coil.png" height=74> <br/><br/>
+
+Julia implementation of various electron-correlation methods (main focus on coupled cluster methods).
+The integrals are obtained from a FCIDUMP file or calculated using the `GaussianBasis` package.
+
+## Capabilities
+
+|          | Canonical          | DF               | Only closed-shell      |
+|:----------|:--------------------:|:------------------:|:-----------------------:|
+| RHF      |    :x:             |:heavy_check_mark:|:heavy_exclamation_mark:|
+| UHF      |    :x:             |:heavy_check_mark:|                        |
+| BO-HF    |:heavy_check_mark:  |                  |                        |
+| MCSCF    |   :x:              |:wrench:          |                        |
+| MP2      |:heavy_check_mark:  |                  |                        |
+| CCSD     | :heavy_check_mark: |                  |:heavy_check_mark:      |
+| RCCSD    | :heavy_check_mark: |                  |                        |
+| UCCSD    | :heavy_check_mark: |                  |                        |
+| ΛCCSD    | :heavy_check_mark: |                  |:heavy_exclamation_mark:|
+| CCSD(T)  | :heavy_check_mark: |                  |:heavy_exclamation_mark:|
+| ΛCCSD(T) | :heavy_check_mark: |                  |:heavy_exclamation_mark:|
+| FR-CCSD  | :heavy_check_mark: |                  |                        |
+| 2D-CCSD  | :heavy_check_mark: |                  |                        |
+| DCSD     | :heavy_check_mark: |                  |:heavy_check_mark:      |
+| RDCSD    | :heavy_check_mark: |                  |                        |
+| UDCSD    | :heavy_check_mark: |                  |                        |
+| ΛDCSD    | :heavy_check_mark: |                  |:heavy_exclamation_mark:|
+| FR-DCSD  | :heavy_check_mark: |                  |                        |
+| 2D-DCSD  | :heavy_check_mark: |                  |                        |
+| SVD-DCSD | :heavy_check_mark: |:heavy_check_mark:|:heavy_exclamation_mark:|
+| SVD-DC-CCSDT|:heavy_check_mark:|:heavy_check_mark:|:heavy_exclamation_mark:|
 
-Julia implementation of various electron-correlation methods (main focus on coupled cluster) 
-using fcidump/npy interface.  
 
 ## Getting started
 
 Requirements: julia (>1.8)
 
-Packages: LinearAlgebra, NPZ, Mmap, TensorOperations, Printf, ArgParse, Parameters, MKL(optional)
+Packages: LinearAlgebra, NPZ, Mmap, TensorOperations, Printf, IterativeSolvers, GaussianBasis, DocStringExtensions, MKL(optional)
 
 ## Usage
-
+For a development version of `ElemCo.jl`, clone the repository and create a symbolic link in the working directory to the `ElemCo.jl-devel` directory:
 ```
 cd <working dir>
-ln -s <path_to_e-cojl>/e-co.sh .
+ln -s <path_to_ElemCo.jl-devel> .
 ```
 
-`julia` has to be in the PATH (or modify `e-co.sh`).
+Default scratch directory path on Windows is the first environment variable found in the ordered list `TMP`, `TEMP`, `USERPROFILE`. 
+On all other operating systems `TMPDIR`, `TMP`, `TEMP`, and `TEMPDIR`. If none of these are found, the path `/tmp` is used. 
+Default scratch folder name is `elemcojlscr`. 
 
-Various options are available (use `-h` option for a list of `e-co.jl` options):
+Variable names `fcidump`, `geometry` and `basis` are reserved for the file name of FCIDUMP, geometry specification and basis sets, respectively.
 
+### Example
+#### DCSD calculation using integrals from a FCIDUMP file
+The ground state energy can be calculated using the DCSD method with the following script:
+```julia
+include("ElemCo.jl-devel/src/ElemCo.jl")
+using .ElemCo
+
+fcidump = "../test/H2O.FCIDUMP"
+@cc dcsd
 ```
-./e-co.sh [@j "<options to send to julia>"] [-s <scratch dir>] [-m <method name>] [<fcidump file>]
+#### DCSD calculation of the water molecule using density-fitted integrals
+In order to calculate the ground state energy of the water molecule using the DCSD method, the following script can be used:
+```julia
+include("ElemCo.jl-devel/src/ElemCo.jl")
+using .ElemCo
+geometry="bohr
+     O      0.000000000    0.000000000   -0.130186067
+     H1     0.000000000    1.489124508    1.033245507
+     H2     0.000000000   -1.489124508    1.033245507"
+
+basis = Dict("ao"=>"cc-pVDZ",
+             "jkfit"=>"cc-pvtz-jkfit",
+             "mp2fit"=>"cc-pvdz-rifit")
+@dfhf
+@cc dcsd
 ```
+The `@dfhf` macro calculates the density-fitted Hartree-Fock energy and orbitals 
+and then DCSD calculation is performed using density-fitted integrals.
+
+Further example scripts are provided in the `examples` directory.
 
-Default scratch dir is `./ecojlscr` and default fcidump file is `FCIDUMP`.
+Documentation is available at https://elem.co.il.
 
 ```
 Electron coil

docs/Project.toml

@@ -0,0 +1,8 @@
+[deps]
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+ElemCo = "094d408e-8508-40f4-9646-a254980d91ac"
+MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
+
+[compat]
+Documenter = "1.1"