Copied from old repo

README.md

@@ -1,3 +1,38 @@
 ---
 license: mit
 ---
+
+# WannierDatasets
+
+Datasets for playing with Wannier functions.
+
+Specifically, this repo
+
+- provides input data files for running the examples inside
+  [`Wannier.jl`](https://github.com/qiaojunfeng/Wannier.jl) documentation
+- provides a set of cheap and small datasets for testing
+  [`Wannier.jl`](https://github.com/qiaojunfeng/Wannier.jl)
+  and [`WannierIO.jl`](https://github.com/qiaojunfeng/WannierIO.jl)
+- allow users to quickly load typical systems when developing algorithms for
+  Wannier functions. Fully focus on Wannier algorithms, without the need of
+  running density functional theory (DFT) calculations
+
+On technical side, we use [Julia Artifacts](https://pkgdocs.julialang.org/v1/artifacts/)
+to manage the datasets. This allows us to
+
+- keep the `Wannier.jl` and `WannierIO.jl` repositories small and clean
+- safely rewrite the datasets without the risk of rebasing the history of
+  `Wannier.jl` and `WannierIO.jl` repositories
+- still providing a convenient way to load the datasets in Julia scripts/REPL.
+
+## Structure of the repo
+
+- [`datasets/`](./datasets/) each subfolder contains a dataset for a specific system
+- [`pseudo/`](./pseudo/) pseudopotentials used when generating the datasets
+- [`src/`](./src/) a fake folder just to make `Project.toml` happy
+- [`util/`](./util/) Several small scripts that help with running the examples
+
+## Contributing
+
+If you feel your dataset is useful for the community, please feel free to contribute.
+Please have a look at the [contributing guidelines](./docs/CONTRIBUTING.md).

datasets/.gitignore

@@ -0,0 +1,37 @@
+# pseudo
+*.upf
+*.UPF
+
+# QE outputs
+out/
+*.out
+bands.dat
+*.projwfc_up
+*.pdos_atm#*
+*.pdos_tot
+
+# W90 inputs
+# I should git add these files
+# *.amn
+# *.mmn
+# *.eig
+# *.spn
+# UNK*
+
+# W90 outputs
+*.nnkp
+*.wout
+*.cube
+*.xsf
+*_band.gnu
+*_band.dat
+*_band.labelinfo.dat
+*_band.kpt
+*.chk
+*.chk.fmt
+*.werr
+
+# misc
+*.log
+CRASH
+.ipynb_checkpoints

datasets/README.md

@@ -0,0 +1,33 @@
+# Datasets
+
+## List of datasets
+
+- `Si2_valence`: Silicon valence band only
+- `Si2`: Silicon valence and conduction bands
+- `Cu`: copper, metal
+- `CrI3`: chromium triiodide, magnetic calculation
+
+## Dataset generation
+
+These files are generated by the respective `creator/run.sh` script in each subdirectory.
+The `creator` subdirectory contains all the script and input files for DFT codes
+to generate the Wannier input `amn/mmn/eig/...` files.
+
+The Fortran binary (also called unformatted) files are written by QE binaries
+which are compiled with
+
+```bash
+GNU Fortran (Ubuntu 11.2.0-19ubuntu1) 11.2.0
+```
+
+To add a new dataset:
+
+- Create a new subdirectory, e.g. `Si2`
+- Put all the input files for the DFT code in the subdirectory `Si2/creator/`
+- Create a `run.sh` script in `creator/` which runs the DFT code and generates the `amn/mmn/eig/...` files
+- Move the `amn/mmn/eig/...` files to `Si2/`
+- (Optional) Create a `README.md` file in `Si2/` which describes the dataset
+- (Optional) Add reference results in a subdirectory `Si2/reference/`
+
+Out goal is that the `run.sh` script should be able to reproduce the `amn/mmn/eig/...` files,
+on any machine. So we can easily regenerate the dataset if we need to.

docs/CONTRIBUTING.md

@@ -0,0 +1,30 @@
+# Contributing guidelines
+
+Thanks for taking the time to contribute! :+1:
+
+In general, we would like to
+
+- keep the repository as small as possible but still produce (more or less)
+    physically meaningful results (e.g., roughly correct band structures).
+    Of course, for testing datasets, no such requirement is needed.
+- keep the original DFT input files and scripts for generating the datasets,
+    to ensure reproducibility. This also allows us to regenerate the datasets
+    if needed.
+
+## All Code Changes Happen Through Pull Requests
+
+Pull requests are the best way to propose changes to the codebase.
+We actively welcome your pull requests:
+
+1. Fork the repo and create your branch from `main`.
+2. Add dataset(s), ideally small (in terms of file size) but still gives
+    physical results. The `prefix` of the files (i.e. `prefix.amn`/`prefix.mmn`)
+    should be the same as the folder name, to allow easy loading of the dataset
+    by `Wannier.jl` (the function `Wannier.Datasets.load_dataset`)
+3. Make sure the original input files are committed in a `generator` subfolder,
+    so we can always reproduce the results on different machines.
+4. (Optional) put useful reference files in a `reference` subfolder
+5. Always `git rebase` your branch on top of the latest `main` branch, so that
+    we can merge your PR without ugly :worried: merge commits.
+    Otherwise, we will rebase explicitly your branch when merging.
+6. Create that pull request!

docs/GitHub_actions.md

@@ -0,0 +1,30 @@
+# Notes on GitHub Actions
+
+## Release process
+
+The current process of bumping version is:
+
+- create a branch, since the `main` branch is protected.
+  The branch name can be `bumpversion`.
+- use `bump2version (major|minor|patch)` to update
+  `.bumpversion.cfg` and `Project.toml`, and it will create a git commit
+- create a PR
+- the release workflow will run, it will
+  - build the artifact tarballs
+  - commit `Artifacts.toml`
+  - create a draft release, with tarballs attached
+  - check if the version in `Project.toml` is consistent with that suggested
+    by the `release-drafter` workflow, and if not, add a comment to the PR
+- once the PR is merged, publish the draft release, and it will create
+  a git tag pointing to main (thus including the just merged PR)
+
+In the end, we have:
+
+- a new version git tagged
+- an `Artifacts.toml` with updated tarball SHA
+- a GitHub release with tarballs attached
+- the version in `Project.toml` is consistent with the git tag
+
+## Debugging
+
+- to debug github workflows, set `ACTIONS_STEP_DEBUG` to `true` in secrets

docs/large_files.md

@@ -0,0 +1,31 @@
+# Notes on large files
+
+## `util/GitHub-ForceLargeFiles`
+
+GitHub has a limit of 100MB per file, to bypass this limit, there is a
+python script `util/GitHub-ForceLargeFiles/src/main.py` that will auto
+compress large files and split them into chunks.
+
+To use it
+
+```shell
+python util/GitHub-ForceLargeFiles/src/main.py DIR_TO_CHECK
+```
+
+where `DIR_TO_CHECK` is the directory to check for large files.
+
+To decompress the files, use
+
+```shell
+python util/GitHub-ForceLargeFiles/src/reverse.py DIR_TO_CHECK
+```
+
+For more information, see the two scripts.
+
+## Adding large dataset files
+
+Therefore, in general we should avoid adding large files. However, if e.g.
+without enough kpoint sampling the band structure is really poor, then we
+can use `main.py` script to compress the files and git commit the 7z files.
+In the GitHub workflow, the `reverse.py` script will be run to decompress
+the files and pack them into artifact tarballs.

make_artifacts.jl

@@ -0,0 +1,108 @@
+#!/usr/bin/env -S julia --project
+# Script to generate `Artifacts.toml` and `artifacts/*.tar.gz`.
+#
+# For the 1st time running this script, you need to run
+#   using Pkg; Pkg.instantiate()
+# to install the dependencies.
+#
+# Artifacts docs:
+# https://pkgdocs.julialang.org/v1/artifacts/
+#
+using Tar, Inflate, SHA, TOML
+
+# let Artifacts.toml point to local tarballs, otherwise point to GitHub releases
+LOCAL = false
+# if on local machine, I assume all the 7z files are already decompressed
+DECOMPRESS_7Z = true
+
+# check if we are running in github actions
+if isnothing(get(ENV, "GITHUB_ACTIONS", nothing))
+    LOCAL = true
+    DECOMPRESS_7Z = false
+else
+    LOCAL = false
+    DECOMPRESS_7Z = true
+end
+
+if DECOMPRESS_7Z
+    PY_SCRIPT = joinpath(@__DIR__, "util/GitHub-ForceLargeFiles/src/reverse.py")
+    run(
+        Cmd([
+            "python",
+            PY_SCRIPT,
+            # reverse.py will delete the 7z files by default
+            "--delete_partitions",
+            # workaround for python argparse: only empty string "" -> false
+            "",
+            "--root_dir",
+            joinpath(@__DIR__, "datasets"),
+        ]),
+    )
+end
+
+artifacts = Dict()
+
+const datasets_dir = joinpath(@__DIR__, "datasets")
+const artifacts_dir = joinpath(@__DIR__, "artifacts")
+# exclude the generator folder which contains the inputs for generating the datasets
+const tar_excludes = ["generator", ".gitignore", "README.md", "*.7z.*"]
+
+# gzip compression level, highest
+const GZIP = "-9"
+# By default, use gzip
+compress_prog = "gzip $GZIP"
+# Try to use pigz for parallel compression.
+# However, it is not available in github workflow (ubuntu-latest)
+try
+    run(`which pigz`)
+    # -k: keep original files
+    global compress_prog = "pigz $GZIP -k"
+catch
+    # pigz is not available
+end
+
+TAR_CMD = [
+    "tar",
+    "--exclude-vcs",
+    "--exclude-vcs-ignores",
+    "--use-compress-program=$compress_prog",
+]
+append!(TAR_CMD, ["--exclude=" * f for f in tar_excludes])
+
+mkpath(artifacts_dir)
+
+for data in readdir(datasets_dir)
+    startswith(data, "_") && continue
+    fullpath = joinpath(datasets_dir, data)
+    isdir(fullpath) || continue
+
+    tar_name = "$(data).tar.gz"
+    outpath = joinpath(artifacts_dir, tar_name)
+    cd(fullpath) do
+        files = readdir()
+        run(Cmd(vcat(TAR_CMD, ["-cvf", outpath], files)))
+    end
+
+    if LOCAL
+        # if you want to test locally
+        url = "file://$(outpath)"
+    else
+        # use github release to host the artifacts
+        # https://docs.github.com/en/repositories/releasing-projects-on-github/linking-to-releases
+        # 2GB limit per file, no limit on total size, no bandwidth limit
+        # https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases
+        url = "https://github.com/qiaojunfeng/WannierDatasets/releases/latest/download/$(tar_name)"
+    end
+
+    artifact_name = data
+    artifacts[artifact_name] = Dict(
+        "git-tree-sha1" => Tar.tree_hash(IOBuffer(inflate_gzip(outpath))),
+        "lazy" => true,
+        "download" =>
+            [Dict("url" => url, "sha256" => bytes2hex(open(sha256, outpath)))],
+    )
+end
+
+open("Artifacts.toml", "w") do io
+    TOML.print(io, artifacts)
+end

pseudo/.gitignore

@@ -0,0 +1,8 @@
+SSSP_1.1.2_PBEsol_efficiency.tar.gz
+archive.tar.gz
+#metadata.json
+
+nc-fr-04_pbe_standard_upf.tgz
+
+*.UPF
+*.upf

pseudo/download.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+# pseudos are downloaded from SSSP
+# https://www.materialscloud.org/discover/sssp/table/efficiency
+
+# auto download with either aiida-pseudo, or wget
+# aiida-pseudo install sssp -x PBEsol --download-only
+
+F='SSSP_1.1.2_PBEsol_efficiency.tar.gz'
+wget "https://archive.materialscloud.org/record/file?filename=${F}&parent_id=19" -O $F
+tar xvf $F
+
+F='nc-fr-04_pbe_standard_upf.tgz'
+wget "http://www.pseudo-dojo.org/pseudos/${F}" -O $F
+tar xvf $F

pseudo/metadata.json

@@ -0,0 +1,597 @@
+{
+    "Ag": {
+        "filename": "Ag_ONCV_PBEsol-1.0.upf",
+        "md5": "be0296cafe7c2d67c3292db0cbbac4d1",
+        "pseudopotential": "SG15",
+        "cutoff_wfc": 50.0,
+        "cutoff_rho": 200.0
+    },
+    "Al": {
+        "filename": "Al.pbesol-n-kjpaw_psl.1.0.0.UPF",
+        "md5": "3401bcfaaf5f9b08e46a00870a1ef39d",
+        "pseudopotential": "100PAW",
+        "cutoff_wfc": 30.0,
+        "cutoff_rho": 240.0
+    },
+    "Ar": {
+        "filename": "Ar_ONCV_PBEsol-1.1.upf",
+        "md5": "c01a123fbe80b3fe80f6f94f1eb776dd",
+        "pseudopotential": "SG15-1.1",
+        "cutoff_wfc": 60.0,
+        "cutoff_rho": 240.0
+    },
+    "As": {
+        "filename": "As.pbesol-n-rrkjus_psl.0.2.UPF",
+        "md5": "1aa86e6aa4f77befd3aa87cac6788838",
+        "pseudopotential": "031US",
+        "cutoff_wfc": 35.0,
+        "cutoff_rho": 280.0
+    },
+    "Au": {
+        "filename": "Au_ONCV_PBEsol-1.0.upf",
+        "md5": "107326c382cdbc7cf544f5ac04d81467",
+        "pseudopotential": "SG15",
+        "cutoff_wfc": 45.0,
+        "cutoff_rho": 180.0
+    },
+    "B": {
+        "filename": "b_pbesol_v1.4.uspp.F.UPF",
+        "md5": "369b69bef2c3aeed4453bd8b804fd6a8",
+        "pseudopotential": "GBRV-1.4",
+        "cutoff_wfc": 35.0,
+        "cutoff_rho": 280.0
+    },
+    "Ba": {
+        "filename": "Ba.pbesol-spn-kjpaw_psl.1.0.0.UPF",
+        "md5": "f28c4a63d325c1a0d00fd3a4f19b8d73",
+        "pseudopotential": "100PAW",
+        "cutoff_wfc": 30.0,
+        "cutoff_rho": 240.0
+    },
+    "Be": {
+        "filename": "be_pbesol_v1.4.uspp.F.UPF",
+        "md5": "09f0a726f30643f9a0ebddd893618f5c",
+        "pseudopotential": "GBRV-1.4",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "Bi": {
+        "filename": "bi_pbesol_v1.uspp.F.UPF",
+        "md5": "588b87649a5c12ad5a0392deab1dcc00",
+        "pseudopotential": "GBRV-1.2",
+        "cutoff_wfc": 45.0,
+        "cutoff_rho": 360.0
+    },
+    "Br": {
+        "filename": "br_pbesol_v1.4.uspp.F.UPF",
+        "md5": "7bf6084e715f6bfd1944787c04c43e72",
+        "pseudopotential": "GBRV-1.4",
+        "cutoff_wfc": 30.0,
+        "cutoff_rho": 240.0
+    },
+    "C": {
+        "filename": "C.pbesol-n-kjpaw_psl.1.0.0.UPF",
+        "md5": "5f3a56537b2bcef3348431d8311bb923",
+        "pseudopotential": "100PAW",
+        "cutoff_wfc": 45.0,
+        "cutoff_rho": 360.0
+    },
+    "Ca": {
+        "filename": "ca_pbesol_v1.uspp.F.UPF",
+        "md5": "0533207b58cddeaa036efa5b63902087",
+        "pseudopotential": "GBRV-1.2",
+        "cutoff_wfc": 30.0,
+        "cutoff_rho": 240.0
+    },
+    "Cd": {
+        "filename": "Cd.pbesol-dn-rrkjus_psl.0.3.1.UPF",
+        "md5": "1f02951eb1ebb2be2329879281757063",
+        "pseudopotential": "031US",
+        "cutoff_wfc": 60.0,
+        "cutoff_rho": 480.0
+    },
+    "Ce": {
+        "filename": "Ce.GGA-PBESOL-paw.UPF",
+        "md5": "23607d9236a12d616006a21dc3c8e039",
+        "pseudopotential": "Wentzcovitch",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "Cl": {
+        "filename": "cl_pbesol_v1.4.uspp.F.UPF",
+        "md5": "ed6bbcf06f19043c0df9f6394706ff8f",
+        "pseudopotential": "GBRV-1.4",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "Co": {
+        "filename": "co_pbesol_v1.2.uspp.F.UPF",
+        "md5": "3b4cd4e7cc7df4da9fdede0fd33e2193",
+        "pseudopotential": "GBRV-1.2",
+        "cutoff_wfc": 45.0,
+        "cutoff_rho": 360.0
+    },
+    "Cr": {
+        "filename": "cr_pbesol_v1.5.uspp.F.UPF",
+        "md5": "a621641e0be27168676a837af8893d0f",
+        "pseudopotential": "GBRV-1.5",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "Cs": {
+        "filename": "cs_pbesol_v1.uspp.F.UPF",
+        "md5": "ae4559e5c840913b791237f814e2d884",
+        "pseudopotential": "GBRV-1.2",
+        "cutoff_wfc": 30.0,
+        "cutoff_rho": 240.0
+    },
+    "Cu": {
+        "filename": "cu_pbesol_v1.2.uspp.F.UPF",
+        "md5": "9756a2ec9488b52ead7a8e4006543bdf",
+        "pseudopotential": "GBRV-1.2",
+        "cutoff_wfc": 55.0,
+        "cutoff_rho": 440.0
+    },
+    "Dy": {
+        "filename": "Dy.GGA-PBESOL-paw.UPF",
+        "md5": "87300e485cfe89bd0b23a3ce6d7c616b",
+        "pseudopotential": "Wentzcovitch",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "Er": {
+        "filename": "Er.GGA-PBESOL-paw.UPF",
+        "md5": "d8b3a218689ff1ecfc4479e98c14c765",
+        "pseudopotential": "Wentzcovitch",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "Eu": {
+        "filename": "Eu.GGA-PBESOL-paw.UPF",
+        "md5": "f3820d3063e0c66ddd8b5316f2038eb4",
+        "pseudopotential": "Wentzcovitch",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "F": {
+        "filename": "f_pbesol_v1.4.uspp.F.UPF",
+        "md5": "d2815ecb49b17b99c5724ffd2f9bbd8d",
+        "pseudopotential": "GBRV-1.4",
+        "cutoff_wfc": 45.0,
+        "cutoff_rho": 360.0
+    },
+    "Fe": {
+        "filename": "Fe.pbesol-spn-kjpaw_psl.0.2.1.UPF",
+        "md5": "4d7ec5aa2156491519a4322664fbbf52",
+        "pseudopotential": "031PAW",
+        "cutoff_wfc": 90.0,
+        "cutoff_rho": 1080.0
+    },
+    "Ga": {
+        "filename": "Ga.pbesol-dn-kjpaw_psl.1.0.0.UPF",
+        "md5": "2a7819223b42fad6ccd7f29fc9cbee49",
+        "pseudopotential": "100PAW",
+        "cutoff_wfc": 70.0,
+        "cutoff_rho": 560.0
+    },
+    "Gd": {
+        "filename": "Gd.GGA-PBESOL-paw.UPF",
+        "md5": "d9fdc7360015cd9620bad644bcc14b0d",
+        "pseudopotential": "Wentzcovitch",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "Ge": {
+        "filename": "ge_pbesol_v1.4.uspp.F.UPF",
+        "md5": "7bed0412183f5e553a4d27ec7023354d",
+        "pseudopotential": "GBRV-1.4",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "H": {
+        "filename": "H.pbesol-rrkjus_psl.1.0.0.UPF",
+        "md5": "0324ed591cc0147dc3d88cad0d33f665",
+        "pseudopotential": "100US",
+        "cutoff_wfc": 60.0,
+        "cutoff_rho": 480.0
+    },
+    "He": {
+        "filename": "He_ONCV_PBEsol-1.0.upf",
+        "md5": "3a98d7dc8e9b0e8c7e1be02b8995cc9d",
+        "pseudopotential": "SG15",
+        "cutoff_wfc": 50.0,
+        "cutoff_rho": 200.0
+    },
+    "Hf": {
+        "filename": "Hf-sp.oncvpsp.upf",
+        "md5": "3619c98de2ee908b1d969add25be4863",
+        "pseudopotential": "Dojo",
+        "cutoff_wfc": 50.0,
+        "cutoff_rho": 200.0
+    },
+    "Hg": {
+        "filename": "Hg_ONCV_PBEsol-1.0.upf",
+        "md5": "9b18bbaf32e5d8994dbbbf1f0a8e2d63",
+        "pseudopotential": "SG15",
+        "cutoff_wfc": 50.0,
+        "cutoff_rho": 200.0
+    },
+    "Ho": {
+        "filename": "Ho.GGA-PBESOL-paw.UPF",
+        "md5": "e4331f82ae8f480097e745152a969825",
+        "pseudopotential": "Wentzcovitch",
+        "cutoff_wfc": 40.0,
+        "cutoff_rho": 320.0
+    },
+    "I": {
+        "filename": "I.pbesol-n-kjpaw_psl.0.2.UPF",
+        "md5": "cecf1a22a184a0b1ae701638a037a48d",
+        "pseudopotential": "031PAW",
+        "cutoff_wfc": 35.0,
+        "cutoff_rho": 280.0
+    },
+    "In": {
+        "filename": "In.pbesol-dn-rrkjus_psl.0.2.2.UPF",
+        "md5": "2a3399a31491503da6b8c7d8e01e9843",
+        "pseudopotential": "031US",
+        "cutoff_wfc": 50.0,
+        "cutoff_rho": 400.0
+    },
+    "Ir": {
+        "filename": "ir_pbesol_v1.2.uspp.F.UPF",
+        "md5": "965d8bb5733ec2587acb56a50491f36d",
+        "pseudopotential": "GBRV-1.2",
+        "cutoff_wfc": 55.0,
+        "cutoff_rho": 440.0
+    },
+    "K": {
+        "filename": "K.pbesol-spn-kjpaw_psl.1.0.0.UPF",
+        "md5": "b302bede38c4f5fe00638ceae66f121b",
+        "pseudopotential": "100PAW",
+        "cutoff_wfc": 60.0,
+        "cutoff_rho": 480.0
+    },
+    "Kr": {
+        "filename": "Kr_ONCV_PBEsol-1.0.upf",
+        "md5": "5ac180be35b0c9edbb375e438c4855d9",
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