Merge branch 'main' into compathelper/new_version/2021-08-31-00-09-23…

…-462-00868494818

.github/workflows/CI.yml

@@ -2,10 +2,10 @@ name: CI
 on: 
   pull_request:
     branches:
-      - master
+      - main
   push:
     branches:
-      - master
+      - main
   workflow_dispatch:
 jobs:
   test:

.github/workflows/Documentation.yml

@@ -0,0 +1,27 @@
+
+name: Documentation
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: '1.6'
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        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/TagBot.yml

@@ -4,6 +4,8 @@ on:
     types:
       - created
   workflow_dispatch:
+  schedule:
+    - cron: 0 0 * * *
 jobs:
   TagBot:
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'

.gitignore

@@ -1,3 +1,4 @@
 legacy/
+docs/build/
 Manifest.toml
 __test__*

.vscode/settings.json

@@ -0,0 +1,188 @@
+{
+    "cSpell.words": [
+        "ADIIS",
+        "DIIS",
+        "EDIIS",
+        "Fconfig",
+        "Ffinal",
+        "Fmethods",
+        "Ftemp",
+        "abcd",
+        "accu",
+        "adii",
+        "admm",
+        "alloc",
+        "an",
+        "array",
+        "atemp",
+        "atms",
+        "b",
+        "basis",
+        "bf",
+        "body",
+        "bs",
+        "btemp",
+        "cart",
+        "cen",
+        "cens",
+        "cfrom",
+        "check",
+        "cint",
+        "cmethod",
+        "cmethods",
+        "cmpr",
+        "cnew",
+        "coeff",
+        "coeffs",
+        "config",
+        "coord",
+        "core",
+        "d",
+        "data",
+        "dcore",
+        "default",
+        "diffvals",
+        "dii",
+        "dmethod",
+        "dnew",
+        "dnuc",
+        "dtots",
+        "dᵀnew",
+        "e",
+        "edii",
+        "ee",
+        "elec",
+        "ending",
+        "enew",
+        "etarget",
+        "etot",
+        "etots",
+        "excdiffs",
+        "excs",
+        "eᵀcore",
+        "eᵀnew",
+        "f",
+        "fenegy",
+        "fenergy",
+        "fieldnames",
+        "finterrelated",
+        "fints",
+        "fmethod",
+        "fname",
+        "fnew",
+        "fockintermediate",
+        "ftype",
+        "ftypes",
+        "func",
+        "funcs",
+        "g",
+        "gcore",
+        "get",
+        "grad",
+        "guess",
+        "gwh",
+        "h",
+        "hartree",
+        "hijkl",
+        "icore",
+        "ijk",
+        "ijks",
+        "ints",
+        "key",
+        "kinetic",
+        "libcin",
+        "libcint",
+        "list",
+        "m",
+        "marker",
+        "mcontent",
+        "min",
+        "molden",
+        "new",
+        "nijk",
+        "nijkα",
+        "npars",
+        "nucs",
+        "occu",
+        "occup",
+        "occus",
+        "ocoeffs",
+        "orbital",
+        "orijks",
+        "ovlp",
+        "par",
+        "quiqbox's",
+        "s",
+        "sc",
+        "score",
+        "selector",
+        "size",
+        "skey",
+        "smethod",
+        "smethods",
+        "ssize",
+        "stext",
+        "strs",
+        "symms",
+        "tosymbol",
+        "two",
+        "unique",
+        "vals",
+        "vars",
+        "xcore",
+        "xinv",
+        "xmethods",
+        "xname",
+        "xpns",
+        "xtemp",
+        "yname",
+        "zname",
+        "ʃabcd"
+    ],
+    "cSpell.ignoreWords": [
+        "bsiz",
+        "codecov",
+        "deepcopy",
+        "deploydocs",
+        "eachcol",
+        "endswith",
+        "exclude",
+        "findall",
+        "findfirst",
+        "findlast",
+        "findnext",
+        "fsym",
+        "get",
+        "getfield",
+        "getindex",
+        "getproperty",
+        "ijkl",
+        "invokelatest",
+        "isdefined",
+        "isequal",
+        "iseven",
+        "isfile",
+        "last",
+        "lcov",
+        "libc",
+        "makedocs",
+        "nameof",
+        "natm",
+        "nbas",
+        "nlines",
+        "occursin",
+        "powerset",
+        "processcoverage",
+        "readlines",
+        "rstrip",
+        "shls",
+        "sigdigits",
+        "sitename",
+        "sortby",
+        "startswith",
+        "subbs",
+        "syms",
+        "tryparse",
+        "typemax"
+    ]
+}

Project.toml

@@ -1,10 +1,9 @@
 name = "Quiqbox"
 uuid = "7cb8c394-fae1-4ab9-92f2-30189d7746cd"
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
-COSMO = "1e616198-aa4e-51ec-90a2-23f7fbd31d8d"
-Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
+Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 PiecewiseQuadratics = "63c5698c-79a9-4248-aa10-bd2a91651b58"
 SeparableOptimization = "b66076ac-575f-47ff-93e2-9c43ffc8d39e"
@@ -14,8 +13,7 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 libcint_jll = "574b78ca-bebd-517c-801d-4735c93a9686"
 
 [compat]
-COSMO = "0.8"
-Convex = "0.14"
+Combinatorics = "1"
 PiecewiseQuadratics = "0.1"
 SeparableOptimization = "0.1"
 SymbolicUtils = "0.13, 0.15"

README.md

@@ -1,26 +1,92 @@
-# Quiqbox.jl
+<p align="center">
+  <img width="500" src="docs/src/assets/logo.png">
+</p>
 
+**Quiqbox** is a quantum chemistry and quantum computing software package that starts off around Gaussian basis set optimization of molecular electronic-structure problems. Quiqbox is written in pure [Julia](https://julialang.org/).
 
+| Documentation | License | Code Status |
+| :--- | :---: | ---: |
+| [![][Doc-s-img]][Doc-stable] <br /> [![][Doc-l-img]][Doc-latest] | [![License: MIT][License-img]][License-url] | [![CI][GA-CI-img]][GA-CI-url] <br /> [![codecov][codecov-img]][codecov-url] |
 
-[![CI][GA-CI-img]][GA-CI-url]
-[![codecov][codecov-img]][codecov-url]
-[![License: MIT][License-img]][License-url]
-
-A Julia software package that aims for floating Gaussian-type orbital (GTO) optimization in electronic structure problems.
+<br />
 
 # Features
 
-* Floating or fixed-basis GTO configuration.
-* Symbolic representation of basis functions.
-* Restricted closed-shell Hartree–Fock method (RHF).
-* Unrestricted open-shell Hartree–Fock method (UHF).
-* Molecular orbital data output in [Molden](https://www3.cmbi.umcn.nl/molden/) file format.
+* Floating and fixed-basis Gaussian-type orbital (GTO) configurations.
+* Symbolic representation and analysis of basis function parameters.
 * Standalone 1-electron and 2-electron integral functions (powered by [libcint_jll](https://github.com/JuliaBinaryWrappers/libcint_jll.jl)).
-* Variational orbital geometry optimization based on Automatic differentiation (AD).
+* Restricted (closed-shell) and unrestricted (open-shell) Hartree–Fock methods (RHF & UHF).
+* Molecular orbital data output in [Molden](https://www3.cmbi.umcn.nl/molden/) file format.
+* Variational optimization of orbital geometry based on automatic differentiation (AD).
+
+# Setup
+
+## Supported system platforms (64-bit)
+* Linux
+* Mac OS
+* [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/about)
+
+## Julia Environment
+* [1.5+](https://github.com/frankwswang/Quiqbox.jl/actions/workflows/CI.yml)
+
+## Installation in Julia [REPL](https://docs.julialang.org/en/v1/manual/getting-started/)
+
+Type `]` to enter the [`Pkg` mode](https://docs.julialang.org/en/v1/stdlib/REPL/#Pkg-mode):
+
+```julia
+(@v1.x) pkg>
+```
+
+Type `add Quiqbox` and hit *Enter* key to install Quiqbox:
+
+```julia
+(@v1.x) pkg> add Quiqbox
+```
+
+After the installation completes, hit *Backspace* key to go back to Julia REPL and use [`using`](https://docs.julialang.org/en/v1/base/base/#using) to load Quiqbox:
+
+```julia
+julia> using Quiqbox
+```
+
+# Use cases
+
+## Apply existed basis set
+```julia
+coords = [[-0.7,0,0], [0.7,0,0]]
+
+bsH₂ = genBasisFunc.(coords, "STO-3G") |> flatten
+```
+
+## Build your own basis set
+```julia
+bs = genBasisFunc.(coords, fill(GaussFunc(1, 0.75), 2))
+```
+
+## Run Hartree-Fock method
+```julia
+nuc = ["H", "H"]
+
+runHF(bs, nuc, coords)
+```
+
+## Optimize a basis set
+```
+pars = uniqueParams!(bs, filterMapping=true)
+
+optimizeParams!(bs, pars[1:4], nuc, coords)
+```
+
+For more basic usage of the programming language behind Quiqbox, Julia, please refer to [the official documentation](https://docs.julialang.org/) or [one official tutorial](https://juliaacademy.com/p/intro-to-julia).
+
 
+[Doc-stable]:  https://frankwswang.github.io/Quiqbox.jl/stable
+[Doc-latest]:  https://frankwswang.github.io/Quiqbox.jl/dev
+[Doc-s-img]:   https://img.shields.io/badge/docs-stable-blue.svg
+[Doc-l-img]:   https://img.shields.io/badge/docs-latest-blue.svg
 [GA-CI-img]:   https://github.com/frankwswang/Quiqbox.jl/actions/workflows/CI.yml/badge.svg?branch=main
 [GA-CI-url]:   https://github.com/frankwswang/Quiqbox.jl/actions/workflows/CI.yml
 [codecov-img]: https://codecov.io/gh/frankwswang/Quiqbox.jl/branch/main/graph/badge.svg?token=Z1XOA39DV2
 [codecov-url]: https://codecov.io/gh/frankwswang/Quiqbox.jl
-[License-img]: https://img.shields.io/badge/License-MIT-blue.svg
+[License-img]: https://img.shields.io/badge/License-MIT-blueviolet.svg
 [License-url]: https://opensource.org/licenses/MIT

docs/Project.toml

@@ -0,0 +1,5 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "^0.27"