├── .conda └── meta.yaml ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ ├── api_version_probe.py │ ├── joss_paper.yml │ ├── publish-pypi.yml │ ├── publish_doc_pages.yml │ ├── unit_test.yml │ └── update_api.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── doc ├── Makefile ├── advanced_socket.md ├── advanced_topics.md ├── api_changes.md ├── basic_usage.md ├── conf.py ├── contribute.md ├── examples.md ├── examples │ ├── external_mlff.md │ ├── geopt_compare.md │ ├── internal_mlff.md │ └── simple_dft.md ├── img │ ├── fig_sparc_api_overview.svg │ ├── scheme-SPARC-socke-modes.svg │ ├── scheme-SPARC-socket-modes.png │ ├── scheme_api_architecture.png │ ├── scheme_api_architecture.svg │ ├── scheme_socket_hetero.png │ ├── scheme_socket_hetero.svg │ ├── scheme_sparc_protocol.png │ ├── scheme_sparc_protocol.svg │ └── screenshots │ │ ├── api_update_pr_github.png │ │ ├── coverage_example.png │ │ ├── github_action_dispatch.png │ │ ├── github_pages_setting.png │ │ └── pypi_publisher_setup.png ├── index.md ├── installation.md ├── maintainers.md ├── maintainers │ ├── github.md │ ├── sparc-c-c++.md │ └── sparc-x-api.md ├── make.bat ├── package_components.md ├── setup_environment.md ├── test_coverage.md └── troubleshooting.md ├── examples ├── FileIO │ ├── md │ │ ├── ab-initio │ │ │ └── run.py │ │ └── mlff │ │ │ └── run.py │ └── relax │ │ ├── relax_cell │ │ └── ab-initio │ │ │ └── run.py │ │ └── relax_coords │ │ ├── ab-initio │ │ └── run.py │ │ └── mlff │ │ └── run.py ├── active_learning │ ├── example_finetuna_minimal.py │ └── ft_config_gemnet_gpu.yml ├── env.sh ├── simple_examples │ ├── ex0-eos.py │ └── ex1-ase-optimize.py └── socket │ ├── md │ ├── ab-initio │ │ ├── ase │ │ │ └── run.py │ │ └── plumed │ │ │ └── run.py │ └── mlff │ │ └── plumed │ │ └── run.py │ ├── relax │ ├── ab-initio │ │ ├── cell │ │ │ └── run.py │ │ └── coords │ │ │ └── run.py │ └── mlff │ │ └── coords │ │ └── run.py │ └── singlepoint │ ├── spin-paired │ └── run.py │ └── spin-polarized │ └── run.py ├── paper ├── README.md ├── fig │ ├── fig_socket_hetero.svg │ └── fig_sparc_api_overview.svg ├── paper.bib └── paper.md ├── pyproject.toml ├── setup.py ├── sparc ├── __init__.py ├── api.py ├── calculator.py ├── cli.py ├── client.py ├── common.py ├── docparser.py ├── download_data.py ├── io.py ├── psp │ └── README.md ├── quicktest.py ├── socketio.py ├── sparc_json_api │ └── parameters.json ├── sparc_parsers │ ├── __init__.py │ ├── aimd.py │ ├── atoms.py │ ├── geopt.py │ ├── inpt.py │ ├── ion.py │ ├── out.py │ ├── pseudopotential.py │ ├── static.py │ └── utils.py └── utils.py └── tests ├── archive ├── read_input.inpt ├── read_input.ion └── test.py ├── outputs ├── AlSi_primitive_quick_relax.sparc │ ├── AlSi_primitive_quick_relax.geopt │ ├── AlSi_primitive_quick_relax.inpt │ ├── AlSi_primitive_quick_relax.ion │ ├── AlSi_primitive_quick_relax.out │ └── output.sparc ├── Al_multi_geopt.sparc │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ ├── SPARC.geopt │ ├── SPARC.geopt_01 │ ├── SPARC.geopt_02 │ ├── SPARC.inpt │ ├── SPARC.ion │ ├── SPARC.out_01 │ ├── SPARC.out_02 │ └── SPARC.restart ├── Al_socket_bfgs.sparc │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ ├── SPARC.inpt │ ├── SPARC.ion │ ├── SPARC.out │ ├── SPARC.static │ ├── sparc-socket.traj │ └── sparc.log ├── Al_socket_volchange.sparc │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ ├── SPARC.inpt │ ├── SPARC.ion │ ├── SPARC.out │ ├── SPARC.static │ ├── single-points │ │ ├── sp_image00 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ │ ├── sp_image01 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ │ ├── sp_image02 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ │ ├── sp_image03 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ │ ├── sp_image04 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ │ ├── sp_image05 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ │ ├── sp_image06 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ │ ├── sp_image07 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ │ ├── sp_image08 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ │ └── sp_image09 │ │ │ ├── 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 │ │ │ ├── SPARC.inpt │ │ │ ├── SPARC.ion │ │ │ ├── SPARC.out │ │ │ ├── SPARC.static │ │ │ └── sparc.log │ └── sparc.log ├── Alloy_geopt_ppd_bc.sparc │ ├── SPARC.geopt │ ├── SPARC.inpt │ ├── SPARC.ion │ └── SPARC.out ├── Cu_FCC.sparc │ ├── Cu_FCC.inpt │ ├── Cu_FCC.ion │ ├── Cu_FCC.out │ └── Cu_FCC.static ├── Fe2_spin_scan_gamma.sparc │ ├── Fe2_spin_scan_gamma.inpt │ ├── Fe2_spin_scan_gamma.ion │ ├── Fe2_spin_scan_gamma.out │ └── Fe2_spin_scan_gamma.static ├── H2O_sheet_yz.sparc │ ├── H2O_sheet.inpt │ ├── H2O_sheet.ion │ ├── H2O_sheet.out │ ├── H2O_sheet.static │ └── output.sparc ├── H2O_socket_incomplete.sparc │ ├── 01_H_1_1.0_1.0_pbe_v1.0.psp8 │ ├── 08_O_6_1.2_1.4_pbe_n_v1.0.psp8 │ ├── SPARC.inpt │ ├── SPARC.ion │ ├── SPARC.out │ ├── SPARC.static │ └── sparc.log ├── H2O_wire_z.sparc │ ├── H2O_wire.inpt │ ├── H2O_wire.ion │ ├── H2O_wire.out │ ├── H2O_wire.static │ └── output.sparc ├── MoO3_hubbard.sparc │ ├── MoO3_hubbard.inpt │ ├── MoO3_hubbard.ion │ ├── MoO3_hubbard.out │ └── MoO3_hubbard.static ├── NH3_sort_lbfgs_opt.sparc │ ├── 01_H_1_1.0_1.0_pbe_v1.0.psp8 │ ├── 07_N_5_1.2_1.4_pbe_n_v1.0.psp8 │ ├── SPARC.geopt │ ├── SPARC.inpt │ ├── SPARC.ion │ ├── SPARC.out │ ├── SPARC.restart │ └── sparc.log ├── Si8_cell_geopt_relax2.sparc │ ├── Si8_cell_geopt.geopt │ ├── Si8_cell_geopt.inpt │ ├── Si8_cell_geopt.ion │ └── Si8_cell_geopt.out ├── SiH4_quick.sparc │ ├── SiH4_quick.inpt │ ├── SiH4_quick.ion │ ├── SiH4_quick.out │ └── SiH4_quick.static ├── TiO2_orthogonal_quick_md.sparc │ ├── TiO2_orthogonal_quick_md.aimd │ ├── TiO2_orthogonal_quick_md.inpt │ ├── TiO2_orthogonal_quick_md.ion │ └── TiO2_orthogonal_quick_md.out └── WSe2_helix_static.sparc │ ├── WSe2_cyclix.inpt │ ├── WSe2_cyclix.ion │ ├── WSe2_cyclix.out │ └── WSe2_cyclix.static ├── psps ├── 33_As_15_1.8_2.1_pbe_n_v1.0.psp8 ├── 47_Ag_19_1.9_2.5_pbe_n_v1.0.psp8 ├── Ag-LDA.pot ├── Ag-PBE.pot └── As-pbe-bad.psp8 ├── sparc-latex-doc-202302 ├── Electrostatics.tex ├── Introduction.tex ├── MD.tex ├── Manual.tex ├── Optimization.tex ├── Paral.tex ├── Print.tex ├── SCF.tex ├── Stress.tex ├── System.tex └── highT │ ├── Introduction.tex │ ├── Manual_highT.tex │ └── SQ.tex ├── sparc-latex-socket-202401 ├── BandStructure.tex ├── Electrostatics.tex ├── Introduction.tex ├── MD.tex ├── Manual.tex ├── Optimization.tex ├── Paral.tex ├── Print.tex ├── SCF.tex ├── Socket.tex ├── Stress.tex ├── System.tex ├── cyclix │ ├── FAQs.tex │ ├── Introduction.tex │ ├── Manual_cyclix.tex │ └── cyclix.tex └── highT │ ├── Introduction.tex │ ├── Manual_highT.tex │ └── SQ.tex ├── test_000_ase_io.py ├── test_aimd_parser.py ├── test_api_version.py ├── test_bundle_to_calc.py ├── test_calculator.py ├── test_docparser.py ├── test_downloader.py ├── test_geopt_parser.py ├── test_gui.py ├── test_hubbard.py ├── test_import.py ├── test_inpt_parser.py ├── test_ion_parser.py ├── test_output_parser.py ├── test_parse_atoms.py ├── test_parser_utils.py ├── test_psp.py ├── test_quicktest.py ├── test_read_all_examples.py ├── test_read_sparc.py ├── test_socket.py ├── test_sparc_bundle.py ├── test_sparc_input_api.py └── test_static_parser.py /.conda/meta.yaml: -------------------------------------------------------------------------------- 1 | {% set name = "SPARC-X-API" %} 2 | {% set version = "1.0.0" %} 3 | {% set file_ext = "tar.gz" %} 4 | {% set readme = load_file_regex(load_file="README.md", regex_pattern=".*")[0] %} 5 | 6 | package: 7 | name: '{{ name|lower }}' 8 | version: '{{ version }}' 9 | 10 | source: 11 | path: ../ 12 | 13 | build: 14 | noarch: python 15 | # Install and include the psp files 16 | script: "{{ PYTHON }} -m pip install . --no-deps -vv && cd .. && {{ PYTHON }} -m sparc.download_data" 17 | entry_points: 18 | - "sparc-ase = sparc.cli:main" 19 | 20 | 21 | requirements: 22 | host: 23 | - "python>=3.8" 24 | - pip 25 | run: 26 | - "python>=3.8" 27 | - "ase>=3.22" 28 | 29 | about: 30 | home: https://github.com/SPARC-X/{{ name }} 31 | license: GNU General Public License v3.0 32 | license_family: GPL3 33 | license_file: LICENSE 34 | summary: A Python API for the SPARC DFT Code 35 | description: {{ readme }} 36 | doc_url: https://github.com/SPARC-X/{{ name }}/blob/master/README.md 37 | dev_url: https://github.com/SPARC-X/{{ name }} 38 | 39 | extra: 40 | recipe-maintainers: Tian Tian (alchem0x2a@gmail.com) 41 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Bug report 3 | about: Create a report to help us improve 4 | title: '' 5 | labels: bug 6 | assignees: '' 7 | 8 | --- 9 | 10 | **Describe the bug** 11 | A concise description of the problem. 12 | 13 | **To Reproduce** 14 | Provide a minimal list of settings / codes to help us debug, such as 15 | - Python version 16 | - Version (git commit hash) of `SPARC-X-API` 17 | - `SPARC` C-code version (see the SPARC .out file header) 18 | - Your platform and architecture 19 | 20 | **Expected behavior** 21 | What is the code intended to achieve? 22 | 23 | **Actual output or error trace** 24 | Include the console output should be enough 25 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Feature request 3 | about: Suggest an idea for this project 4 | title: '' 5 | labels: enhancement 6 | assignees: '' 7 | 8 | --- 9 | 10 | **Is your feature request related to a problem? Please describe.** 11 | A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] 12 | 13 | **Describe the solution you'd like** 14 | A clear and concise description of what you want to happen. 15 | 16 | **Describe alternatives you've considered** 17 | A clear and concise description of any alternative solutions or features you've considered. 18 | 19 | **Additional context** 20 | Add any other context or screenshots about the feature request here. 21 | -------------------------------------------------------------------------------- /.github/workflows/api_version_probe.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | from packaging import version 4 | 5 | from sparc.api import SparcAPI # Replace with your actual module import 6 | 7 | 8 | def compare_versions(): 9 | default_version = SparcAPI().sparc_version 10 | new_version = SparcAPI(json_api="parameters.json").sparc_version 11 | print(f"Default api version: {default_version}, upstream version {new_version}") 12 | 13 | if version.parse(default_version) < version.parse(new_version): 14 | print(f"Version changed from {default_version} to {new_version}") 15 | sys.exit(1) 16 | else: 17 | print("No version change") 18 | sys.exit(0) 19 | 20 | 21 | if __name__ == "__main__": 22 | compare_versions() 23 | -------------------------------------------------------------------------------- /.github/workflows/joss_paper.yml: -------------------------------------------------------------------------------- 1 | name: Draft Paper for JOSS 2 | on: 3 | push: 4 | paths: 5 | - paper/** 6 | - .github/workflows/joss_paper.yml 7 | pull_request: 8 | paths: 9 | - paper/** 10 | - .github/workflows/joss_paper.yml 11 | workflow_dispatch: 12 | 13 | jobs: 14 | paper: 15 | runs-on: ubuntu-latest 16 | name: Paper Draft 17 | steps: 18 | - name: Checkout 19 | uses: actions/checkout@v4 20 | - name: Build draft PDF 21 | uses: openjournals/openjournals-draft-action@master 22 | with: 23 | journal: joss 24 | paper-path: paper/paper.md 25 | - name: Upload 26 | uses: actions/upload-artifact@v4 27 | with: 28 | name: paper 29 | path: paper/paper.pdf 30 | -------------------------------------------------------------------------------- /.github/workflows/publish-pypi.yml: -------------------------------------------------------------------------------- 1 | name: Publish PyPI package 2 | 3 | on: 4 | # The workflow runs on each push / PR but only allow upload 5 | # PyPI when tagged 6 | release: 7 | types: 8 | - created 9 | workflow_dispatch: 10 | 11 | jobs: 12 | publish-pypi: 13 | name: upload release to PyPI 14 | runs-on: ubuntu-latest 15 | # Specifying a GitHub environment is optional, but strongly encouraged 16 | environment: pypi 17 | permissions: 18 | # IMPORTANT: this permission is mandatory for trusted publishing 19 | id-token: write 20 | 21 | steps: 22 | - uses: actions/checkout@v4 23 | - uses: conda-incubator/setup-miniconda@v3 24 | with: 25 | python-version: "3.11" 26 | mamba-version: "*" 27 | channels: conda-forge,defaults 28 | channel-priority: true 29 | activate-environment: sparc-api-test 30 | - name: Install dependencies 31 | run: | 32 | pip install -U build 33 | - name: Download data 34 | run: | 35 | # Download the external psp data 36 | python -m sparc.download_data 37 | # Check if psp8 exists 38 | ls sparc/psp/*.psp8 39 | - name: Build wheel 40 | run: | 41 | # Wheels are inside dist/ folder 42 | python -m build 43 | # Check the contents, if psp exists 44 | TMP_DIR=$(mktemp -d) 45 | unzip dist/sparc_x_api-*.whl -d ${TMP_DIR} 46 | find $TMP_DIR/sparc/psp -name "*.psp8" 47 | 48 | - name: Publish package distributions to PyPI 49 | uses: pypa/gh-action-pypi-publish@release/v1 50 | with: 51 | packages-dir: dist/ 52 | if: github.event.release.draft == false 53 | -------------------------------------------------------------------------------- /.github/workflows/publish_doc_pages.yml: -------------------------------------------------------------------------------- 1 | name: Publish Document Pages for SPARC-X-API 2 | 3 | # SPARC source code components are also parsed at each submission 4 | on: 5 | push: 6 | branches: 7 | - master 8 | - badges 9 | paths: 10 | - 'doc/**' 11 | - 'sparc/**' 12 | - '.coverage' 13 | - '.github/workflows/publish_doc_pages.yml' 14 | pull_request: 15 | branches: 16 | - master 17 | - badges 18 | paths: 19 | - 'doc/**' 20 | - 'sparc/**' 21 | - '.coverage' 22 | - '.github/workflows/publish_doc_pages.yml' 23 | 24 | workflow_dispatch: 25 | 26 | jobs: 27 | sphinx-build: 28 | defaults: 29 | run: 30 | shell: bash -l {0} 31 | runs-on: ubuntu-latest 32 | 33 | steps: 34 | - uses: actions/checkout@v4 35 | - name: Checkout the latest .coverage file from badges branch 36 | uses: actions/checkout@v4 37 | with: 38 | ref: badges 39 | path: coverage 40 | - name: List current files 41 | run: | 42 | if [ -f coverage/.coverage ]; then 43 | cp coverage/.coverage . 44 | fi 45 | ls -al coverage/ 46 | ls -al . 47 | - uses: conda-incubator/setup-miniconda@v3 48 | with: 49 | python-version: "3.11" 50 | mamba-version: "*" 51 | channels: conda-forge,defaults 52 | channel-priority: true 53 | activate-environment: sparc-api-build-doc 54 | - name: Install doc-build dependencies 55 | run: | 56 | pip install -e ".[doc]" 57 | - name: Generate coverage files 58 | run: | 59 | mkdir -p doc/_static 60 | if [ -f .coverage ]; then 61 | coverage html --omit="tests/*.py" -d doc/_static/htmlcov 62 | fi 63 | ls -al . 64 | ls -al doc/_static 65 | - name: Build sphix doc 66 | run: | 67 | cd doc 68 | make clean && make html 69 | - name: Deploy to github pages 70 | uses: peaceiris/actions-gh-pages@v4 71 | if: github.ref == 'refs/heads/master' && (github.event_name != 'pull_request') 72 | with: 73 | github_token: ${{ secrets.GITHUB_TOKEN }} 74 | publish_branch: gh_pages 75 | publish_dir: doc/_build/html 76 | - name: Upload preview when creating pull request 77 | if: github.event_name == 'pull_request' 78 | uses: actions/upload-artifact@v4 79 | with: 80 | name: docs_build_preview 81 | path: doc/_build/html 82 | -------------------------------------------------------------------------------- /.github/workflows/update_api.yml: -------------------------------------------------------------------------------- 1 | name: Update JSON API (recurring job) 2 | 3 | on: 4 | push: 5 | branches: 6 | - master 7 | pull_request: 8 | branches: 9 | - master 10 | schedule: 11 | - cron: '0 0 * * *' # Runs every day at midnight 12 | workflow_dispatch: 13 | 14 | jobs: 15 | update-api: 16 | defaults: 17 | run: 18 | shell: bash -l {0} 19 | runs-on: ubuntu-latest 20 | # Only the upstream repo runs the automatic API update 21 | if: | 22 | !github.event.repository.fork || github.event_name == 'workflow_dispatch' 23 | 24 | steps: 25 | - uses: actions/checkout@v4 26 | - uses: conda-incubator/setup-miniconda@v2 27 | with: 28 | python-version: "3.11" 29 | mamba-version: "*" 30 | channels: conda-forge,alchem0x2a,defaults 31 | channel-priority: true 32 | activate-environment: sparc-api-test 33 | - name: Install package 34 | run: | 35 | pip install -e ".[test]" 36 | - name: Generate json api from github master 37 | run: | 38 | python -m sparc.docparser --git --include-subdirs 39 | - name: Env variable for api version 40 | run: | 41 | python -c "from sparc.api import SparcAPI; import os; ver=SparcAPI('parameters.json').sparc_version; os.system(f'echo API_VERSION={ver} >> $GITHUB_ENV')" 42 | - name: Test if json api is newer than current 43 | id: probe 44 | run: | 45 | # exit 0 --> no version change 46 | if python .github/workflows/api_version_probe.py; then 47 | echo "UPDATE_NEEDED=false" >> $GITHUB_ENV 48 | else 49 | echo "UPDATE_NEEDED=true" >> $GITHUB_ENV 50 | fi 51 | echo UPDATE_NEEDED is "${UPDATE_NEEDED}" 52 | echo API version is "${API_VERSION}" 53 | continue-on-error: true 54 | - name: Create or Update Pull Request 55 | # Manually disable to make sure it can rerun 56 | if: env.UPDATE_NEEDED == 'true' 57 | uses: peter-evans/create-pull-request@v7 58 | with: 59 | token: ${{ secrets.GITHUB_TOKEN }} 60 | commit-message: | 61 | Update JSON API to version ${{ env.API_VERSION }} 62 | 63 | The commit is created by a scheduled CI job. 64 | "" 65 | branch: update-api-${{ env.API_VERSION }} 66 | title: "[Automated] Update JSON API to version ${{ env.API_VERSION }}" 67 | body: | 68 | ## Automated JSON API Update 69 | 70 | Hello! This is an automatic pull request to merge the new JSON API to version **${{ env.API_VERSION }}**. 71 | 72 | ### Details 73 | - **Workflow Trigger:** Update JSON API (recurring job). 74 | - **Reason for Update:** A new JSON schema version was generated that differs from the existing one in the repository. 75 | 76 | ### Notes 77 | - If you notice any issues or have questions regarding this update, please reach out to the maintainers. 78 | 79 | # Eliminate unnecessary PRs if not closed 80 | delete-branch: true 81 | # Prevent PRs on forks 82 | base: master 83 | delete-branch: true 84 | base: master 85 | -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- 1 | # Pre-commit hooks for SPARC-X-API 2 | # Use pre-commit rn 3 | exclude: "^tests/outputs/|^tests/psps/|^tests/sparc-latex-.*/|^tests/archive/|^sparc/sparc_json_api/" 4 | repos: 5 | - repo: https://github.com/pre-commit/pre-commit-hooks 6 | rev: v2.3.0 7 | hooks: 8 | - id: check-yaml 9 | exclude: ".conda/meta.yaml" 10 | - id: end-of-file-fixer 11 | - id: trailing-whitespace 12 | 13 | - repo: https://github.com/pycqa/isort 14 | rev: 5.12.0 15 | hooks: 16 | - id: isort 17 | name: isort (python) 18 | args: ["--profile", "black"] 19 | 20 | - repo: https://github.com/psf/black 21 | rev: 22.10.0 22 | hooks: 23 | - id: black 24 | -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SPHINXDOC ?= sphinx-apidoc 9 | SOURCEDIR = . 10 | BUILDDIR = _build 11 | 12 | # Put it first so that "make" without argument is like "make help". 13 | help: 14 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 15 | 16 | # Build the api doc --> doc/api/modules.rst 17 | apidoc: 18 | @$(SPHINXDOC) -f -e -M -o "$(SOURCEDIR)"/api "$(SOURCEDIR)"/../sparc 19 | 20 | 21 | .PHONY: help Makefile apidoc coverage 22 | 23 | # Catch-all target: route all unknown targets to Sphinx using the new 24 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 25 | %: Makefile 26 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 27 | 28 | html: apidoc 29 | 30 | # Reuse the make clean rule from sphinx and remove api/ 31 | clean: 32 | @$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 33 | @$(SPHINXBUILD) -M clean "$(SOURCEDIR)" "$(SOURCEDIR)"/api $(SPHINXOPTS) $(O) 34 | -------------------------------------------------------------------------------- /doc/api_changes.md: -------------------------------------------------------------------------------- 1 | # Changes in API 2 | ## Major changes from [v1.0](https://github.com/SPARC-X/SPARC-X-API/tree/v1.0.0) 3 | 4 | - Support of socket communication layer 5 | - Migration to ASE 3.23 standard 6 | - Enhanced documents 7 | 8 | ## Major changes from [v0.1](https://github.com/SPARC-X/SPARC-X-API/tree/eac557f214b402122a506f88f38c7a8767283503) 9 | 10 | SPARC-X-API has been heavily refactored in v1.0. If you're using legacy Python codes 11 | that are written under v0.1 API, there are a few major changes that require your attention: 12 | 13 | 1. Support for single `.ion` file format is deprecated. Instead, v1.0 API treats the whole SPARC directory as a bundle format. Please use `read_sparc` and `write_sparc` methods for basic file I/O instead. 14 | Nevertheless, reading calculation results generated by a v0.1 API code will not be affected. 15 | 16 | 2. v1.0 API uses a different mapping scheme for the sorting of ASE atoms objects (similar to `Vasp`), add a comment section in `.ion` file similar to follows: 17 | ```python 18 | # ASE-SORT: 19 | # 3 2 1 0 20 | # END ASE-SORT 21 | ``` 22 | which maps atoms 3, 2, 1, 0 from the SPARC .ion file order to 23 | atoms 0, 1, 2, 3 in ASE order. This is useful for systems that are 24 | constructed by ASE's `add_adsorbate` method. 25 | 26 | 3. v1.0 API accepts all SPARC internal parameters 27 | (i.e. **CAPITALIZED**) in *atomic units* for consistency reason. 28 | However, we also keep a list of "special input params" that are 29 | conventionally used in other ASE calculators, that use Å / eV / GPa / 30 | fs unit system. 31 | 32 | 4. Defining `LATVEC`, `LATVEC_SCALE`, or `CELL` via the calculator 33 | parameters is no longer encouraged. Instead, all structure changes 34 | should be made to the `Atoms` object. 35 | 36 | Below are a list of v0.1 method of the `SPARC` calculator and their current status in v1.0 API. 37 | `calc` is an instance of `sparc.SPARC`. 38 | 39 | | old methods | status in v1.0 API | alternatives | 40 | |------------------------|--------------------|------------------------------------| 41 | | `interpret_grid_input` | deprecated | `calc.set(fd_grid=[20, 20, 20])` | 42 | | `interpret_kpoint_input` | deprecated | `calc.set(kpts=[3, 3, 3])` | 43 | | `interpret_downsampling_input` | deprecated | Manual setting not recommended | 44 | | `interpret_kpoint_shift` | deprecated | `calc.set(kpoint_shift=[0, 0, 0])` | 45 | | `get_pseudopotential_directory` | deprecated | `calc.psp_dir` | 46 | | `get_nstates` | maintained | | 47 | | `setup_parallel_env` | deprecated | Manual set | 48 | | `generate_command` | deprecated | `calc._make_command()` | 49 | | `estimate_memory` | maintained | | 50 | | `get_scf_steps` | maintained | | 51 | | `get_geometric_steps` | deprecated | `calc.get_number_of_ionic_steps()`| 52 | | `get_runtime` | maintained | | 53 | | `get_fermi_level` | maintained | | 54 | | `concatinate_output` | deprecated | Use `sparc.SparcBundle` instead | 55 | | `read_line` | deprecated | Use `sparc.SparcBundle` instead | 56 | | `parse_output` | deprecated | `calc.read_results()` | 57 | | `parse_relax` | deprecated | `calc.read_results()` | 58 | | `parse_md` | deprecated | `calc.read_results()` | 59 | | `parse_input_args` | deprecated | `calc.set(**kwargs)` | 60 | | `recover_index_order_from_ion_file` | deprecated | Use `calc.sort` and `calc.resort` | 61 | | `atoms_dict` | deprecated | Use third party library like `bson` | 62 | | `dict_atoms` | deprecated | Use third party library like `bson` | 63 | -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- 1 | # Configuration file for the Sphinx documentation builder. 2 | # 3 | # For the full list of built-in configuration values, see the documentation: 4 | # https://www.sphinx-doc.org/en/master/usage/configuration.html 5 | 6 | # -- Project information ----------------------------------------------------- 7 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information 8 | 9 | project = "SPARC-X-API" 10 | copyright = "2024, SPARC-X Developmers" 11 | author = "Tian Tian, Lucas R Timmerman, Ben Comer" 12 | 13 | 14 | # -- General configuration --------------------------------------------------- 15 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration 16 | 17 | extensions = [ 18 | "sphinx.ext.githubpages", 19 | "sphinx.ext.coverage", 20 | "sphinx.ext.autodoc", 21 | "sphinx.ext.napoleon", # For Google/NumPy style docstrings 22 | "sphinx.ext.autosummary", 23 | "sphinx.ext.viewcode", # Adds links to source code 24 | "myst_parser", 25 | ] 26 | 27 | source_suffix = { 28 | ".md": "markdown", 29 | ".txt": "markdown", 30 | ".rst": "restructuredtext", 31 | } 32 | 33 | templates_path = ["_templates"] 34 | exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] 35 | 36 | 37 | # -- Options for HTML output ------------------------------------------------- 38 | # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output 39 | 40 | html_theme = "sphinx_rtd_theme" 41 | html_static_path = ["_static"] 42 | html_context = { 43 | "display_github": True, # Integrate GitHub 44 | "github_user": "sparc-x", # Username 45 | "github_repo": "SPARC-X-API", # Repo name 46 | "github_version": "master", # Version 47 | "conf_py_path": "/doc/", # Path in the checkout to the docs root 48 | } 49 | 50 | myst_enable_extensions = [ 51 | "html_admonition", 52 | ] 53 | 54 | coverage_Show_missing_items = True 55 | autosummary_generate = True 56 | -------------------------------------------------------------------------------- /doc/examples.md: -------------------------------------------------------------------------------- 1 | # Examples 2 | 3 | For template scripts utilizing the API in socket mode and via FileIO mode, see the `examples/` directory in the [github repo](https://github.com/SPARC-X/SPARC-X-API/tree/master/examples). 4 | 5 | Please check the following topics for a brief overview of 6 | SPARC-X-API's capabilities and features. 7 | 8 | 9 | ```{toctree} 10 | :maxdepth: 2 11 | :caption: Topics 12 | examples/simple_dft.md 13 | examples/geopt_compare.md 14 | examples/internal_mlff.md 15 | examples/external_mlff.md 16 | ``` 17 | -------------------------------------------------------------------------------- /doc/examples/simple_dft.md: -------------------------------------------------------------------------------- 1 | # Simple DFT workflows with SPARC-X-API 2 | 3 | As documentation for [basic usage](../basic_usage.md) shows, replacing an 4 | existing DFT-based workflow using SPARC-X-API calculator interface can 5 | be as easy as simply swapping the calculator instance to `sparc.SPARC` 6 | from other codes like VASP, QE or GPAW. 7 | 8 | Here we show a simple example that calculates the equation of state 9 | (EOS) of bulk aluminum and determine its optimal lattice constant, 10 | adapted from GPAW's 11 | [tutorial](https://wiki.fysik.dtu.dk/gpaw/tutorialsexercises/structureoptimization/lattice_constants/lattice_constants.html). The full python script for this example can be downloaded [here](https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/refs/heads/master/examples/simple_examples/ex0-eos.py). 12 | 13 | In 14 | the GPAW tutorial, a GPAW calculator in Planewave (PW) mode is created 15 | like follows: 16 | 17 | ```{code} python 18 | from gpaw import GPAW, PW 19 | calc = GPAW(mode=PW(ecut), 20 | xc='PBE', 21 | kpts=(8, 8, 8), 22 | basis='dzp', 23 | txt=f'Al-{ecut}.txt') 24 | ``` 25 | 26 | We can create a SPARC-X-API calculator using similar parameters. Note 27 | that in real-space DFT, the parameter mesh spacing (`h`) controls the 28 | convergence. To avoid large "egg-box effect" due to large mesh 29 | spacing, we recommend to use a smaller `h` value. For demonstration 30 | purpose a rather rough mesh spacing `h=0.25` (in Angstrom) and a 3x3x3 31 | k-points are used. 32 | 33 | ```{code} python 34 | import numpy as np 35 | from ase.build import bulk 36 | from ase.eos import calculate_eos 37 | 38 | from sparc import SPARC 39 | 40 | 41 | def main(): 42 | # Al in conventional cell 43 | atoms = bulk("Al", cubic=True) 44 | calc = SPARC(h=0.25, kpts=(3, 3, 3), xc="pbe", directory="ex0-eos") 45 | vol = atoms.get_volume() 46 | atoms.calc = calc 47 | eos = calculate_eos(atoms, npoints=5, eps=0.05, trajectory="al-eos-sparc.traj") 48 | print("Original volume: Ang^3", vol) 49 | v, e, B = eos.fit() 50 | print("Fitted volume (Ang^3), energy (eV), modulus (eV/Ang^3)") 51 | print(v, e, B) 52 | a0 = v ** (1 / 3) 53 | print(f"Optimal cell length (cubic): {a0} Ang") 54 | atoms.set_cell([a0, a0, a0], scale_atoms=True) 55 | e0_sparc = atoms.get_potential_energy() 56 | print(f"Energy calculated by SPARC: {e0_sparc} eV") 57 | print(f"Energy diff {abs(e0_sparc - e)} eV") 58 | return 59 | 60 | 61 | if __name__ == "__main__": 62 | main() 63 | ``` 64 | 65 | The output from the above example may look like: 66 | ``` 67 | Fitted volume (Ang^3), energy (eV), modulus (eV/Ang^3) 68 | 65.97840834969949 -253.07755156337953 2.9095110471623173 69 | Optimal cell length (cubic): 4.040799280428726 Ang 70 | Energy calculated by SPARC: -253.0552324051582 eV 71 | Energy diff 0.02231915822133601 eV 72 | ``` 73 | 74 | ```{note} 75 | This example uses file I/O mode for demonstration purpose only. Consider choosing the [socket mode](../advanced_socket.md) if you need more flexibility. 76 | ``` 77 | -------------------------------------------------------------------------------- /doc/img/scheme-SPARC-socket-modes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/doc/img/scheme-SPARC-socket-modes.png -------------------------------------------------------------------------------- /doc/img/scheme_api_architecture.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/doc/img/scheme_api_architecture.png -------------------------------------------------------------------------------- /doc/img/scheme_socket_hetero.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/doc/img/scheme_socket_hetero.png -------------------------------------------------------------------------------- /doc/img/scheme_sparc_protocol.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/doc/img/scheme_sparc_protocol.png -------------------------------------------------------------------------------- /doc/img/screenshots/api_update_pr_github.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/doc/img/screenshots/api_update_pr_github.png -------------------------------------------------------------------------------- /doc/img/screenshots/coverage_example.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/doc/img/screenshots/coverage_example.png -------------------------------------------------------------------------------- /doc/img/screenshots/github_action_dispatch.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/doc/img/screenshots/github_action_dispatch.png -------------------------------------------------------------------------------- /doc/img/screenshots/github_pages_setting.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/doc/img/screenshots/github_pages_setting.png -------------------------------------------------------------------------------- /doc/img/screenshots/pypi_publisher_setup.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/doc/img/screenshots/pypi_publisher_setup.png -------------------------------------------------------------------------------- /doc/index.md: -------------------------------------------------------------------------------- 1 | ```{include} ../README.md 2 | :relative-docs: doc/ 3 | :relative-images: 4 | ``` 5 | 6 | 7 | 8 | 9 | ```{toctree} 10 | :maxdepth: 2 11 | :caption: Contents 12 | installation.md 13 | setup_environment.md 14 | basic_usage.md 15 | advanced_socket.md 16 | examples.md 17 | package_components.md 18 | advanced_topics.md 19 | api_changes.md 20 | contribute.md 21 | maintainers.md 22 | ``` 23 | -------------------------------------------------------------------------------- /doc/maintainers.md: -------------------------------------------------------------------------------- 1 | # Documentation for Maintainers 2 | 3 | This part contains maintenance guidelines for SPARC-X-API core 4 | developers. For general guidelines regarding how to contribute to this 5 | project please refer to the [how to contribute](contribute.md) page. 6 | 7 | Most of the tasks in this documentation require `maintain` or `admin` 8 | role for the repository. Please check the following topics for details: 9 | 10 | ```{toctree} 11 | :maxdepth: 2 12 | :caption: Topics 13 | maintainers/github.md 14 | maintainers/sparc-x-api.md 15 | maintainers/sparc-c-c++.md 16 | ``` 17 | -------------------------------------------------------------------------------- /doc/maintainers/github.md: -------------------------------------------------------------------------------- 1 | ## Github Settings 2 | ### Remote Branches 3 | 4 | There are multiple branches required for the CI/CD workflow in 5 | SPARC-X-API. Push / pull request to these branches should only be made by automatic github actions. 6 | 7 | - [`badges`](https://github.com/SPARC-X/SPARC-X-API/tree/badges): 8 | branch for maintaining the svg badges (package version, CI status, 9 | etc.) 10 | 11 | A list of svg badges can be found under `badges/` directory of this 12 | branch. See [the development guide](#doc-edit) for how to add / 13 | modify badges to be shown in the README. 14 | 15 | - [`gh_pages`](https://github.com/SPARC-X/SPARC-X-API/tree/gh_pages): 16 | branch to publish the documentation site. 17 | 18 | 19 | ### Github Pages 20 | 21 | To allow pushed to the `gh_pages` branches to be automatically 22 | deployed to the document pages, go to the [pages 23 | setting](https://github.com/SPARC-X/SPARC-X-API/settings/pages) and 24 | set the "Source" to "Deploy from a branch", as well as "Branch" to 25 | "gh_pages", as shown in the UI screenshot below: 26 | 27 | ![Github Pages Settings](../img/screenshots/github_pages_setting.png) 28 | 29 | 30 | ### Secrets 31 | 32 | Environment secrets (such as PyPI access key) can be configured in the 33 | [secrets 34 | setting](https://github.com/SPARC-X/SPARC-X-API/settings/secrets/actions) 35 | panel. Please check the [github 36 | documentation](https://docs.github.com/en/actions/security-for-github-actions/security-guides/using-secrets-in-github-actions) 37 | for more details. 38 | 39 | (cicd-sparc-x-api)= 40 | ## Managing CI/CD Pipelines 41 | 42 | CI/CD pipelines in the SPARC-X-API repo are managed by Github 43 | workflows, consisting of multiple "Actions". Workflow configuration 44 | YAML files are placed under `.github/workflows/` and the workflow 45 | status can be checked at the [Actions 46 | page](https://github.com/SPARC-X/SPARC-X-API/actions). Please take a 47 | look at the official [documentation for 48 | actions](https://docs.github.com/en/actions) to get familiar with the syntax. 49 | 50 | All workflows in the SPARC-X-API are designed to be able to run from 51 | manual dispatch (with the `workflow_dispatch` enabled in the YAML 52 | files) for debug purposes, from the "Run workflow" drop panel in the 53 | [actions 54 | page](https://github.com/SPARC-X/SPARC-X-API/actions/workflows), as 55 | shown in the screenshot below: 56 | 57 | ![Github Actions Manual Dispatch](../img/screenshots/github_action_dispatch.png) 58 | 59 | - [Unit-test 60 | workflow](https://github.com/SPARC-X/SPARC-X-API/blob/master/.github/workflows/unit_test.yml) 61 | includes several steps to run unit and coverage test. 62 | 63 | - The steps `Create badges` and ` Manually add git badges` defines how 64 | the status badges in `README.md` are created and pushed to the 65 | `badges` branch. 66 | - When adding unit test examples involving real SPARC calculations, 67 | do not use more than 4 MPI cores (may subject to changes) due to 68 | the [resource limitation](https://docs.github.com/en/actions/using-github-hosted-runners/using-github-hosted-runners/about-github-hosted-runners) 69 | of hosted runners. 70 | 71 | - [Publish doc pages 72 | workflow](https://github.com/SPARC-X/SPARC-X-API/blob/master/.github/workflows/publish_doc_pages.yml) 73 | uses Sphinx to convert `doc/` to doc html files. 74 | 75 | The rendered 76 | changes will only be pushed to the `gh_pages` branch with direct 77 | commit on the master branch or after one PR is merged. 78 | 79 | - [Update JSON schema 80 | workflow](https://github.com/SPARC-X/SPARC-X-API/blob/master/.github/workflows/update_api.yml) 81 | updates the JSON schema file after a new release in SPARC C/C++ 82 | source code. The workflow is run both nightly and after normal 83 | push. You can change the behavior as needed. 84 | 85 | An example pull request created by the update workflow can be seen 86 | in the following screenshot: 87 | 88 | ```{figure} ../img/screenshots/api_update_pr_github.png 89 | :alt: PR on github 90 | ``` 91 | 92 | Once the 93 | 94 | - [Publish PyPI 95 | workflow](https://github.com/SPARC-X/SPARC-X-API/blob/master/.github/workflows/publish-pypi.yml) 96 | package the source as `sparc-x-api` and publish on PyPI. Only 97 | activates on new releases. 98 | -------------------------------------------------------------------------------- /doc/maintainers/sparc-x-api.md: -------------------------------------------------------------------------------- 1 | # SPARC-X-API package releases 2 | ## On conda-forge 3 | 4 | SPARC-X-API is packaged as 5 | [`sparc-x-api`](https://anaconda.org/conda-forge/sparc-x-api) in the 6 | conda-forge channel. The source code (feedstock) for the package is 7 | managed at 8 | [`sparc-x-api-feedstock`](https://github.com/conda-forge/sparc-x-api-feedstock). 9 | Please note that this repository is under the conda-forge 10 | organization. If you wish to become a maintainer, please ping 11 | [@alchem0x2a](https://github.com/alchem0x2A). 12 | 13 | The feedstock is set to track new releases in SPARC-X-API, and usually 14 | no major maintenance is required. The bot system will create a PR for 15 | a version bump, see [one 16 | example](https://github.com/conda-forge/sparc-x-api-feedstock/pull/2) 17 | for the maintainers to modify and merge. Please also ensure: 18 | 19 | - Only the `recipe/meta.yaml` needs to be changed. 20 | - Follow the conda-forge's own [recipe standard](https://conda-forge.org/docs/maintainer/guidelines/) 21 | - Do not directly use the [`.conda/meta.yaml`](https://github.com/SPARC-X/SPARC-X-API/blob/master/.conda/meta.yaml) for conda-forge (it is designed for local packaging test) 22 | - Bump the `build.number` if you need to change the recipe YAML on the same SPARC-X-API release. 23 | 24 | (conda-forge-build-locally-api)= 25 | ### Debug the recipe using local build 26 | 27 | The build toolchain in conda-forge is slightly different from the 28 | standard `conda-build` command. If the build workflow fails after 29 | submitting the PR, you may run the recipe locally to debug. You need 30 | both the [docker engine](https://docs.docker.com/engine/) and a [conda distribution](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) on your local 31 | machine. Run the following command at the root of the local clone of `sparc-x-api-feedstock`: 32 | ```{code} bash 33 | python build-locally.py 34 | ``` 35 | 36 | ## Deploy on PyPI 37 | 38 | SPARC-X-API is deployed on PyPI under the name 39 | [`sparc-x-api`](https://pypi.org/project/sparc-x-api/). Please contact 40 | the current maintainer [@alchem0x2a](mailto:alchem0x2a@gmail.com) if 41 | you wish to become a co-contributor. 42 | 43 | Publishing on PyPI does not require setting an API token in the CI 44 | workflow. Instead, it uses the [OIDC 45 | protocol](https://docs.pypi.org/trusted-publishers/) for a trusted 46 | publisher. The current settings on PyPI are like follows: 47 | 48 | ![pypi-setting](../img/screenshots/pypi_publisher_setup.png) 49 | -------------------------------------------------------------------------------- /doc/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=. 11 | set BUILDDIR=_build 12 | 13 | %SPHINXBUILD% >NUL 2>NUL 14 | if errorlevel 9009 ( 15 | echo. 16 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 17 | echo.installed, then set the SPHINXBUILD environment variable to point 18 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 19 | echo.may add the Sphinx directory to PATH. 20 | echo. 21 | echo.If you don't have Sphinx installed, grab it from 22 | echo.https://www.sphinx-doc.org/ 23 | exit /b 1 24 | ) 25 | 26 | if "%1" == "" goto help 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /doc/package_components.md: -------------------------------------------------------------------------------- 1 | # SPARC-X-API Package Components 2 | 3 | 4 | ```{toctree} 5 | :maxdepth: 4 6 | 7 | api/modules.rst 8 | ``` 9 | -------------------------------------------------------------------------------- /doc/test_coverage.md: -------------------------------------------------------------------------------- 1 | # Test Coverage Report 2 | 3 | The following coverage test was generated by the [`coverage` package](https://coverage.readthedocs.io/en/7.6.7/other.html): 4 | 5 | ```{raw} html 6 | 10 | 23 | ``` 24 | -------------------------------------------------------------------------------- /doc/troubleshooting.md: -------------------------------------------------------------------------------- 1 | # Troubleshooting 2 | ### Known issues 3 | *This is a list of known bugs with the current SPARC-X-API, remove them when PRs are contributed* 4 | - [ ] `sparc-ase` command currently does not support multi-image yet 5 | - [ ] `SPARC` calculator may occasionally require more DFT steps than needed during optimization 6 | - [ ] Raw result parsing from SPARC files may need to be re-factored in a generator form 7 | -------------------------------------------------------------------------------- /examples/FileIO/md/ab-initio/run.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from ase import Atoms 3 | 4 | from sparc.calculator import SPARC 5 | 6 | Ag_cluster = Atoms( 7 | "Ag5", 8 | positions=[ 9 | (0.0, 2.6579, 0.9366), 10 | (0.0, -1.3587, -1.4045), 11 | (0.0, 0.0, 0.9358), 12 | (0.0, -2.6579, 0.9366), 13 | (0.0, 1.3587, -1.4045), 14 | ], 15 | pbc=(0, 0, 0), 16 | ) 17 | Ag_cluster.set_cell([20.0, 24.0, 24.0]) 18 | Ag_cluster.center() 19 | 20 | calc_params = { 21 | "EXCHANGE_CORRELATION": "GGA_PBE", 22 | "KPOINT_GRID": [1, 1, 1], 23 | "MESH_SPACING": 0.35, 24 | "TOL_SCF": 0.0001, 25 | "MAXIT_SCF": 100, 26 | "PRINT_RESTART_FQ": 10, 27 | "PRINT_ATOMS": 1, 28 | "PRINT_FORCES": 1, 29 | "SPIN_TYP": 0, 30 | "MD_FLAG": 1, 31 | "MD_METHOD": "NVK_G", 32 | "ION_TEMP": 10, 33 | "MD_NSTEP": 10, 34 | "MD_TIMESTEP": 2, 35 | } 36 | 37 | 38 | def main(): 39 | """Running a simple MD calculation using ab initio SPARC in FileIO mode""" 40 | Ag_cluster.calc = SPARC(label="Ag_cluster", **calc_params) 41 | energy = Ag_cluster.get_potential_energy() 42 | print("Energy: ", energy) 43 | forces = Ag_cluster.get_forces() 44 | print("Max Force: ", np.max(forces)) 45 | 46 | 47 | if __name__ == "__main__": 48 | main() 49 | -------------------------------------------------------------------------------- /examples/FileIO/md/mlff/run.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from ase import Atoms 3 | 4 | from sparc.calculator import SPARC 5 | 6 | Ag_cluster = Atoms( 7 | "Ag5", 8 | positions=[ 9 | (0.0, 2.6579, 0.9366), 10 | (0.0, -1.3587, -1.4045), 11 | (0.0, 0.0, 0.9358), 12 | (0.0, -2.6579, 0.9366), 13 | (0.0, 1.3587, -1.4045), 14 | ], 15 | pbc=(0, 0, 0), 16 | ) 17 | Ag_cluster.set_cell([20.0, 24.0, 24.0]) 18 | Ag_cluster.center() 19 | 20 | calc_params = { 21 | "EXCHANGE_CORRELATION": "GGA_PBE", 22 | "KPOINT_GRID": [1, 1, 1], 23 | "MESH_SPACING": 0.35, 24 | "TOL_SCF": 0.0001, 25 | "MAXIT_SCF": 100, 26 | "PRINT_RESTART_FQ": 10, 27 | "PRINT_ATOMS": 1, 28 | "PRINT_FORCES": 1, 29 | "SPIN_TYP": 0, 30 | "MD_FLAG": 1, 31 | "MD_METHOD": "NVK_G", 32 | "ION_TEMP": 10, 33 | "MD_NSTEP": 10, 34 | "MD_TIMESTEP": 2, 35 | "MLFF_FLAG": 1, 36 | "MLFF_INITIAL_STEPS_TRAIN": 3, 37 | } 38 | 39 | 40 | def main(): 41 | """Running a simple MD calculation using SPARC-MLFF in FileIO mode""" 42 | Ag_cluster.calc = SPARC(label="Ag_cluster", **calc_params) 43 | energy = Ag_cluster.get_potential_energy() 44 | print("Energy: ", energy) 45 | forces = Ag_cluster.get_forces() 46 | print("Max Force: ", np.max(forces)) 47 | 48 | 49 | if __name__ == "__main__": 50 | main() 51 | -------------------------------------------------------------------------------- /examples/FileIO/relax/relax_cell/ab-initio/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | from ase.build import bulk 3 | 4 | from sparc.calculator import SPARC 5 | 6 | calc_params = { 7 | "EXCHANGE_CORRELATION": "GGA_PBE", 8 | "KPOINT_GRID": [4, 4, 4], 9 | "MESH_SPACING": 0.35, 10 | "TOL_SCF": 0.0001, 11 | "MAXIT_SCF": 100, 12 | "CALC_STRESS": 1, 13 | "PRINT_RESTART_FQ": 10, 14 | "PRINT_ATOMS": 1, 15 | "PRINT_FORCES": 1, 16 | "SPIN_TYP": 0, 17 | "RELAX_FLAG": 2, 18 | } 19 | 20 | 21 | def main(): 22 | atoms = bulk("Rh", crystalstructure="fcc", a=3.81) 23 | atoms.calc = SPARC(**calc_params) 24 | # Trigger the calculation by calling a property that will be available after the calculation 25 | stress = atoms.get_stress() 26 | # Get the final energy and volume from a single point calculation 27 | del calc_params["RELAX_FLAG"] 28 | if type(atoms) == list: 29 | atoms = atoms[-1] 30 | atoms.calc = SPARC(**calc_params) 31 | energy = atoms.get_potential_energy() 32 | volume = atoms.get_volume() 33 | 34 | print( 35 | "***********************************************************************************************" 36 | ) 37 | print("v0 = {0} A^3\nE0 = {1} eV".format(volume, energy)) 38 | 39 | 40 | if __name__ == "__main__": 41 | main() 42 | -------------------------------------------------------------------------------- /examples/FileIO/relax/relax_coords/ab-initio/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | import numpy as np 3 | from ase.build import molecule 4 | 5 | from sparc.calculator import SPARC 6 | 7 | water = molecule("H2O", vacuum=7) 8 | water.pbc = [False, False, False] 9 | 10 | calc_params = { 11 | "EXCHANGE_CORRELATION": "GGA_PBE", 12 | "KPOINT_GRID": [1, 1, 1], 13 | "MESH_SPACING": 0.35, 14 | "TOL_SCF": 0.0001, 15 | "MAXIT_SCF": 100, 16 | "ELEC_TEMP_TYPE": "fermi-dirac", 17 | "ELEC_TEMP": 116, 18 | "PRINT_RESTART_FQ": 10, 19 | "PRINT_ATOMS": 1, 20 | "PRINT_FORCES": 1, 21 | "SPIN_TYP": 0, 22 | "RELAX_FLAG": 1, 23 | } 24 | 25 | 26 | def main(): 27 | """Geometric optimization of a water molecule using 28 | ab initio SPARC in FileIO mode 29 | """ 30 | water.calc = SPARC(**calc_params) 31 | energy = water.get_potential_energy() 32 | forces = water.get_forces() 33 | 34 | print("Energy:", energy) 35 | print("Max Force:", np.max(forces)) 36 | 37 | 38 | if __name__ == "__main__": 39 | main() 40 | -------------------------------------------------------------------------------- /examples/FileIO/relax/relax_coords/mlff/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | import numpy as np 3 | from ase.build import molecule 4 | 5 | from sparc.calculator import SPARC 6 | 7 | water = molecule("H2O", vacuum=7) 8 | water.pbc = [False, False, False] 9 | 10 | calc_params = { 11 | "EXCHANGE_CORRELATION": "GGA_PBE", 12 | "KPOINT_GRID": [1, 1, 1], 13 | "MESH_SPACING": 0.35, 14 | "TOL_SCF": 0.0001, 15 | "MAXIT_SCF": 100, 16 | "ELEC_TEMP_TYPE": "fermi-dirac", 17 | "ELEC_TEMP": 116, 18 | "PRINT_RESTART_FQ": 10, 19 | "PRINT_ATOMS": 1, 20 | "PRINT_FORCES": 1, 21 | "SPIN_TYP": 0, 22 | "RELAX_FLAG": 1, 23 | "MLFF_FLAG": 1, 24 | "MLFF_INITIAL_STEPS_TRAIN": 3, 25 | } 26 | 27 | 28 | def main(): 29 | """Geometric optimization of a water molecule using 30 | SPARC-MLFF in FileIO mode 31 | """ 32 | water.calc = SPARC(**calc_params) 33 | energy = water.get_potential_energy() 34 | forces = water.get_forces() 35 | 36 | print("Energy:", energy) 37 | print("Max Force:", np.max(forces)) 38 | 39 | 40 | if __name__ == "__main__": 41 | main() 42 | -------------------------------------------------------------------------------- /examples/active_learning/example_finetuna_minimal.py: -------------------------------------------------------------------------------- 1 | """A minimal example combining active learning library like Finetuna with SPARC 2 | 3 | usage 4 | First download the checkpoint from the url https://dl.fbaipublicfiles.com/opencatalystproject/models/2021_08/s2ef/gemnet_t_direct_h512_all.pt 5 | 6 | python example_finetuna_minimal.py 7 | """ 8 | import argparse 9 | import os 10 | from pathlib import Path 11 | 12 | import ase 13 | import torch 14 | import yaml 15 | from ase.build import molecule 16 | from ase.cluster.cubic import FaceCenteredCubic 17 | from ase.constraints import FixAtoms 18 | from ase.io.trajectory import Trajectory 19 | from ase.optimize import BFGS 20 | from finetuna.ml_potentials.finetuner_ensemble_calc import FinetunerEnsembleCalc 21 | from finetuna.online_learner.online_learner import OnlineLearner 22 | 23 | from sparc.calculator import SPARC 24 | 25 | cpu = not torch.cuda.is_available() 26 | curdir = Path(__file__).parent 27 | config_file = curdir / "ft_config_gemnet_gpu.yml" 28 | with open(config_file, "r") as fd: 29 | configs = yaml.load(fd, Loader=yaml.FullLoader) 30 | 31 | checkpoint = os.environ.get("CHECKPOINT_PATH", None) 32 | if checkpoint is None: 33 | # Use default (relative path) 34 | checkpoint = curdir / configs["ocp"]["checkpoint_path_list"][0] 35 | checkpoint = Path(checkpoint) 36 | 37 | if not checkpoint.is_file(): 38 | raise FileNotFoundError("Cannot found the model checkpoint file!") 39 | 40 | finetuner = configs["finetuner"] 41 | finetuner[0].update(cpu=cpu) 42 | learner = configs["learner"] 43 | 44 | ml_potential = FinetunerEnsembleCalc( 45 | checkpoint_paths=[checkpoint], 46 | mlp_params=finetuner, 47 | ) 48 | 49 | 50 | # init_molecule = molecule("H2O", pbc=False, cell=[8, 8, 8]) 51 | # init_molecule.center() 52 | # init_molecule.rattle() 53 | 54 | 55 | surfaces = [(1, 0, 0), (1, 1, 0), (1, 1, 1)] 56 | layers = [1, 2, 1] 57 | lc = 3.61000 58 | 59 | # init_atoms = molecule("CH4", pbc=True, cell=[8, 8, 8]) 60 | # init_atoms.constraints = [FixAtoms([0])] 61 | # init_atoms.center() 62 | # init_atoms.rattle(0.05) 63 | 64 | init_atoms = FaceCenteredCubic("Cu", surfaces, layers, latticeconstant=lc) 65 | init_atoms.cell = [12, 12, 12] 66 | init_atoms.center() 67 | init_atoms.pbc = False 68 | init_atoms.rattle(0.05) 69 | 70 | 71 | sparc_params = {"xc": "pbe", "h": 0.13} 72 | # with SPARC(directory="pure_BFGS", **sparc_params) as calc: 73 | # atoms = init_atoms.copy() 74 | # atoms.calc = calc 75 | # dyn = BFGS(atoms, maxstep=0.2, trajectory="pure_bfgs.traj") 76 | # dyn.run(fmax=0.03) 77 | 78 | 79 | with SPARC(directory="online_coldstart", **sparc_params) as parent_calc: 80 | atoms = init_atoms.copy() 81 | onlinecalc = OnlineLearner(learner, [], ml_potential, parent_calc) 82 | atoms.calc = onlinecalc 83 | dyn = BFGS(atoms, maxstep=0.2) 84 | dyn.run(fmax=0.03) 85 | -------------------------------------------------------------------------------- /examples/active_learning/ft_config_gemnet_gpu.yml: -------------------------------------------------------------------------------- 1 | finetuner: 2 | - cpu: false 3 | optim: 4 | batch_size: 1 5 | break_below_lr: 1.0e-07 6 | checkpoint_every: 100000 7 | eps: 1.0e-08 8 | eval_every: 1 9 | factor: 0.9 10 | force_coefficient: 100 11 | lr_initial: 0.0003 12 | max_epochs: 400 13 | num_workers: 0 14 | optimizer_params: 15 | eps: 1.0e-08 16 | weight_decay: 0 17 | patience: 3 18 | # print_loss_and_lr: true 19 | scheduler_loss: train 20 | weight_decay: 0 21 | task: 22 | primary_metric: loss 23 | tuner: 24 | num_threads: 8 25 | unfreeze_blocks: 26 | - out_blocks.3.seq_forces 27 | - out_blocks.3.scale_rbf_F 28 | - out_blocks.3.dense_rbf_F 29 | - out_blocks.3.out_forces 30 | - out_blocks.2.seq_forces 31 | - out_blocks.2.scale_rbf_F 32 | - out_blocks.2.dense_rbf_F 33 | - out_blocks.2.out_forces 34 | - out_blocks.1.seq_forces 35 | - out_blocks.1.scale_rbf_F 36 | - out_blocks.1.dense_rbf_F 37 | - out_blocks.1.out_forces 38 | learner: 39 | dyn_avg_steps: 15 40 | dyn_uncertain_tol: 1000000 # Dynamic uncertainty tolerance 41 | fmax_verify_threshold: 0.03 # Fmax threshold for calling VASP single point calculation 42 | initial_points_to_keep: [] 43 | # logger: 44 | # pca_quantify: true # Log PCA on wandb 45 | # uncertainty_quantify: false 46 | num_initial_points: 1 # Number of VASP calls at the beginning of the relaxation 47 | partial_fit: true 48 | query_every_n_steps: 30 # K-steps querying strategy: query every 100 steps 49 | stat_uncertain_tol: 1000000 # Static uncertainty tolerance 50 | tolerance_selection: min 51 | # valset_system_id: '1498818' 52 | # wandb_init: 53 | # entity: ulissi-group 54 | # project: project 55 | # group: group 56 | # name: name 57 | # notes: notes 58 | # wandb_log: false # Wandb disabled 59 | # optional_config: 60 | # links: 61 | # traj: /path/to/vasp/reference/traj 62 | ocp: 63 | model_class_list: 64 | - gemnet 65 | checkpoint_path_list: 66 | - "gemnet_t_direct_h512_all.pt" 67 | # relaxation: 68 | # # fmax: 0.03 69 | # max_parent_calls: null 70 | # maxstep: 0.2 71 | # replay_method: parent_only 72 | # steps: null 73 | # trajname: oal_relaxation.traj 74 | -------------------------------------------------------------------------------- /examples/env.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # set path to any shared libraries such as mkl, blas, scalapack etc. 3 | ml intel-oneapi-compilers intel-oneapi-mkl intel-oneapi-mpi 4 | source ~/p-amedford6-0/venvs/joss-sparc-x-api/bin/activate 5 | 6 | cd ~ 7 | export HOME=$(pwd) 8 | cd - 9 | export SCRATCH=$HOME/scratch 10 | export DATA=$HOME/p-amedford6-0 11 | 12 | export PYTHONPATH=$DATA/active/JOSS-SPARC-X-API/SPARC-X-API:$PYTHONPATH 13 | 14 | # Check if Slurm is installed and running 15 | if command -v sinfo &> /dev/null; then 16 | export ASE_SPARC_COMMAND="srun ${DATA}/active/JOSS-SPARC-X-API/dev_SPARC/lib/sparc --export=ALL -K" 17 | else 18 | nprocs=$(nproc) 19 | export ASE_SPARC_COMMAND="mpirun -np $nprocs ${DATA}/SPARC/lib/sparc --export=ALL -K" 20 | fi 21 | # Set pseudopotential path is you did not download with python -m sparc.download_data 22 | export PLUMED_KERNEL=/storage/home/hcoda1/9/ltimmerman3/p-amedford6-0/active/JOSS-SPARC-X-API/plumed-2.9.2/src/lib/libplumedKernel.so 23 | -------------------------------------------------------------------------------- /examples/simple_examples/ex0-eos.py: -------------------------------------------------------------------------------- 1 | """A simple example using SPARC-X-API to calculate the equation of state of bulk Al. 2 | 3 | Example taken from GPAW's tutorial: 4 | https://wiki.fysik.dtu.dk/gpaw/tutorialsexercises/structureoptimization/lattice_constants/lattice_constants.html 5 | """ 6 | import numpy as np 7 | from ase.build import bulk 8 | from ase.eos import calculate_eos 9 | 10 | from sparc import SPARC 11 | 12 | 13 | def main(): 14 | # Al in conventional cell 15 | atoms = bulk("Al", cubic=True) 16 | calc = SPARC(h=0.25, kpts=(3, 3, 3), xc="pbe", directory="ex0-eos") 17 | vol = atoms.get_volume() 18 | atoms.calc = calc 19 | eos = calculate_eos(atoms, npoints=5, eps=0.05, trajectory="al-eos-sparc.traj") 20 | print("Original volume: Ang^3", vol) 21 | v, e, B = eos.fit() 22 | print("Fitted volume (Ang^3), energy (eV), modulus (eV/Ang^3)") 23 | print(v, e, B) 24 | a0 = v ** (1 / 3) 25 | print(f"Optimal cell length (cubic): {a0} Ang") 26 | atoms.set_cell([a0, a0, a0], scale_atoms=True) 27 | e0_sparc = atoms.get_potential_energy() 28 | print(f"Energy calculated by SPARC: {e0_sparc} eV") 29 | print(f"Energy diff {abs(e0_sparc - e)} eV") 30 | return 31 | 32 | 33 | if __name__ == "__main__": 34 | main() 35 | -------------------------------------------------------------------------------- /examples/simple_examples/ex1-ase-optimize.py: -------------------------------------------------------------------------------- 1 | """A simple example using SPARC to optimize a NH3 molecule using: 2 | 1) SPARC internal BFGS routine 3 | 2) SPARC single point + ASE BFGS 4 | 5 | 6 | """ 7 | import numpy as np 8 | from ase.build import molecule 9 | from ase.constraints import FixAtoms 10 | from ase.optimize.lbfgs import LBFGS 11 | 12 | from sparc import SPARC 13 | 14 | nh3 = molecule("NH3", cell=(8, 8, 8), pbc=False) 15 | nh3.center() 16 | # Fix the N center 17 | nh3.constraints = [FixAtoms([0])] 18 | nh3.rattle() 19 | 20 | 21 | def optimize_sparc_internal(): 22 | atoms = nh3.copy() 23 | calc = SPARC( 24 | h=0.18, 25 | kpts=(1, 1, 1), 26 | xc="pbe", 27 | convergence={"forces": 0.02}, 28 | relax_flag=True, 29 | print_relaxout=True, 30 | relax_method="LBFGS", 31 | directory="ex1-sparc", 32 | ) 33 | atoms.calc = calc 34 | e_fin = atoms.get_potential_energy() 35 | f_fin = atoms.get_forces() 36 | nsteps = len(calc.raw_results["geopt"]) 37 | print("SPARC internal LBFGS:") 38 | print(f"Final energy: {e_fin} eV") 39 | print(f"Final fmax: {np.max(np.abs(f_fin))} eV/Ang") 40 | print(f"N steps: {nsteps}") 41 | 42 | 43 | def optimize_ase_bfgs(): 44 | atoms = nh3.copy() 45 | calc = SPARC(h=0.18, kpts=(1, 1, 1), xc="pbe", directory="ex1-ase") 46 | atoms.calc = calc 47 | opt = LBFGS(atoms) 48 | opt.run(fmax=0.02) 49 | e_fin = atoms.get_potential_energy() 50 | f_fin = atoms.get_forces() 51 | nsteps = opt.nsteps 52 | print("ASE LBFGS (file I/O mode)") 53 | print(f"Final energy: {e_fin} eV") 54 | print(f"Final fmax: {np.max(np.abs(f_fin))} eV/Ang") 55 | print(f"N steps: {nsteps}") 56 | 57 | 58 | def optimize_ase_bfgs_socket(): 59 | atoms = nh3.copy() 60 | calc = SPARC( 61 | h=0.18, 62 | kpts=(1, 1, 1), 63 | xc="pbe", 64 | print_forces=True, 65 | directory="ex1-ase-socket", 66 | use_socket=True, 67 | ) 68 | atoms.calc = calc 69 | with calc: 70 | opt = LBFGS(atoms) 71 | opt.run(fmax=0.02) 72 | e_fin = atoms.get_potential_energy() 73 | f_fin = atoms.get_forces() 74 | nsteps = opt.nsteps 75 | print("ASE LBFGS (socket mode)") 76 | print(f"Final energy: {e_fin} eV") 77 | print(f"Final fmax: {np.max(np.abs(f_fin))} eV/Ang") 78 | print(f"N steps: {nsteps}") 79 | 80 | 81 | def main(): 82 | # Comment out specific ones if the examples run too long 83 | optimize_sparc_internal() 84 | optimize_ase_bfgs() 85 | optimize_ase_bfgs_socket() 86 | 87 | 88 | if __name__ == "__main__": 89 | main() 90 | -------------------------------------------------------------------------------- /examples/socket/md/ab-initio/ase/run.py: -------------------------------------------------------------------------------- 1 | from ase import Atoms 2 | from ase.constraints import FixedPlane 3 | from ase.md.nvtberendsen import NVTBerendsen 4 | from ase.md.verlet import VelocityVerlet 5 | from ase.units import fs 6 | 7 | from sparc.calculator import SPARC 8 | 9 | Ag_cluster = Atoms( 10 | "Ag5", 11 | positions=[ 12 | (0.0, 2.6579, 0.9366), 13 | (0.0, -1.3587, -1.4045), 14 | (0.0, 0.0, 0.9358), 15 | (0.0, -2.6579, 0.9366), 16 | (0.0, 1.3587, -1.4045), 17 | ], 18 | pbc=(0, 0, 0), 19 | ) 20 | Ag_cluster.set_cell([20.0, 24.0, 24.0]) 21 | Ag_cluster.center() 22 | cons = [FixedPlane(i, [1, 0, 0]) for i in range(5)] 23 | Ag_cluster.set_constraint(cons) 24 | 25 | calc_params = { 26 | "EXCHANGE_CORRELATION": "GGA_PBE", 27 | "KPOINT_GRID": [1, 1, 1], 28 | "MESH_SPACING": 0.35, 29 | "TOL_SCF": 0.0001, 30 | "MAXIT_SCF": 100, 31 | "PRINT_RESTART_FQ": 10, 32 | "PRINT_ATOMS": 1, 33 | "PRINT_FORCES": 1, 34 | "SPIN_TYP": 0, 35 | } 36 | 37 | taut = 50 * fs 38 | timestep = 2 * fs 39 | 40 | 41 | def main(): 42 | """MD simulation with implicit socket interface""" 43 | with SPARC(use_socket=True, **calc_params) as calc: 44 | Ag_cluster.calc = calc 45 | # dyn = NVTBerendsen(Ag_cluster, temperature_K=10, taut=taut, timestep=timestep, trajectory='Ag-cluster-md.traj') 46 | dyn = VelocityVerlet( 47 | Ag_cluster, 48 | dt=2.0 * fs, 49 | trajectory="Ag-cluster-verlet.traj", 50 | logfile="verlet-md.log", 51 | ) 52 | dyn.run(10) 53 | 54 | 55 | if __name__ == "__main__": 56 | main() 57 | -------------------------------------------------------------------------------- /examples/socket/md/ab-initio/plumed/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | from ase import Atoms, units 3 | from ase.calculators.plumed import Plumed 4 | from ase.md.nvtberendsen import NVTBerendsen 5 | 6 | from sparc.calculator import SPARC 7 | 8 | calc_params = { 9 | "EXCHANGE_CORRELATION": "GGA_PBE", 10 | "KPOINT_GRID": [1, 1, 1], 11 | "MESH_SPACING": 0.35, 12 | "TOL_SCF": 0.0001, 13 | "MAXIT_SCF": 100, 14 | "PRINT_RESTART_FQ": 10, 15 | "PRINT_ATOMS": 1, 16 | "PRINT_FORCES": 1, 17 | "SPIN_TYP": 0, 18 | } 19 | 20 | timestep = ( 21 | 2 * units.fs 22 | ) # the units module contains the conversion factor to go from units. to ASE units via multiplication 23 | ps = 1000 * units.fs 24 | 25 | # Units conversion: everything will be in ASE units, so a time step is in ASE unit and needs to be interpreted as some multiple of sensical units 26 | # Likewise, energy is in eV which is ~98.6 kJ/mol, so a single unit of energy is 98.6 kJ/mol which are the internal units of PLUMED 27 | setup = [ 28 | f"UNITS LENGTH=A TIME={1/ps} ENERGY={units.mol/units.kJ}", # Set units to match desired properties 29 | # Calculate the center of mass of atoms 1-5 30 | "com: COM ATOMS=1-5", 31 | # Define the coordination number (C) 32 | "c: COORDINATION GROUPA=1-5 SWITCH={RATIONAL R_0=3.0 NN=8 MM=16} NOPBC", 33 | # Define the radius of gyration (R) 34 | "r: GYRATION TYPE=RADIUS ATOMS=1-5 NOPBC", 35 | # Compute CV1 and CV2 as orthogonal linear combinations of C and R 36 | "cv1: COMBINE ARG=c,r COEFFICIENTS=0.99715,-0.07534 PERIODIC=NO", 37 | "cv2: COMBINE ARG=c,r COEFFICIENTS=0.07534,0.99715 PERIODIC=NO", 38 | # Apply lower wall on CV1 at 5.0 with harmonic constant 10 eV 39 | f"LOWER_WALLS ARG=cv1 AT=5.0 KAPPA=10.0", 40 | # Apply lower wall on CV2 at 3.0 with harmonic constant 50 eV 41 | f"UPPER_WALLS ARG=cv2 AT=3.0 KAPPA=50.0", 42 | # Perform well-tempered metadynamics on CV1 and CV2 43 | f"METAD ARG=cv1,cv2 HEIGHT=0.3 PACE=500 SIGMA=0.3,0.03 GRID_MIN=0.0,0.0 GRID_MAX=10.0,5.0 GRID_BIN=500,500 BIASFACTOR=100 FILE=HILLS", 44 | # Print out the collective variables for monitoring 45 | "PRINT ARG=cv1,cv2,c,r FILE=COLVAR STRIDE=1", 46 | ] 47 | 48 | Ag_cluster = Atoms( 49 | "Ag5", 50 | positions=[ 51 | (0.0, 2.6579, 0.9366), 52 | (0.0, -1.3587, -1.4045), 53 | (0.0, 0.0, 0.9358), 54 | (0.0, -2.6579, 0.9366), 55 | (0.0, 1.3587, -1.4045), 56 | ], 57 | pbc=(0, 0, 0), 58 | ) 59 | Ag_cluster.set_cell([20.0, 24.0, 24.0]) 60 | Ag_cluster.center() 61 | # cons = [FixedPlane(i, [1, 0, 0]) for i in range(5)] 62 | # Ag_cluster.set_constraint(cons) 63 | 64 | 65 | def main(): 66 | """Sampling via Plumed interface with SPARC's socket""" 67 | with SPARC(use_socket=True, **calc_params) as calc: 68 | Ag_cluster.calc = Plumed( 69 | calc=calc, input=setup, timestep=timestep, atoms=Ag_cluster, kT=0.00861733 70 | ) # 10 K in eV thermal energy units 71 | dyn = NVTBerendsen( 72 | Ag_cluster, 73 | timestep, 74 | temperature_K=0.00861733 / units.kB, 75 | taut=50 * units.fs, 76 | fixcm=False, 77 | trajectory="Ag-cluster-metadynamics.traj", 78 | ) 79 | dyn.run(10) 80 | 81 | """ 82 | # Restrain atoms 1-5 within 2.0 Å of the center of mass using upper walls 83 | "d1: DISTANCE ATOMS=1,com", 84 | "UPPER_WALLS ARG=d1 AT=2.0 KAPPA=100.0", 85 | "d2: DISTANCE ATOMS=2,com", 86 | "UPPER_WALLS ARG=d2 AT=2.0 KAPPA=100.0", 87 | "d3: DISTANCE ATOMS=3,com", 88 | "UPPER_WALLS ARG=d3 AT=2.0 KAPPA=100.0", 89 | "d4: DISTANCE ATOMS=4,com", 90 | "UPPER_WALLS ARG=d4 AT=2.0 KAPPA=100.0", 91 | "d5: DISTANCE ATOMS=5,com", 92 | "UPPER_WALLS ARG=d5 AT=2.0 KAPPA=100.0", 93 | 　　　""" 94 | 95 | 96 | if __name__ == "__main__": 97 | main() 98 | -------------------------------------------------------------------------------- /examples/socket/md/mlff/plumed/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | from ase import Atoms, units 3 | from ase.calculators.plumed import Plumed 4 | from ase.md.nvtberendsen import NVTBerendsen 5 | 6 | from sparc.calculator import SPARC 7 | 8 | calc_params = { 9 | "EXCHANGE_CORRELATION": "GGA_PBE", 10 | "KPOINT_GRID": [1, 1, 1], 11 | "MESH_SPACING": 0.35, 12 | "TOL_SCF": 0.0001, 13 | "MAXIT_SCF": 100, 14 | "PRINT_RESTART_FQ": 10, 15 | "PRINT_ATOMS": 1, 16 | "PRINT_FORCES": 1, 17 | "SPIN_TYP": 0, 18 | "MLFF_FLAG": 1, 19 | "MLFF_INITIAL_STEPS_TRAIN": 5, 20 | } 21 | 22 | timestep = ( 23 | 2 * units.fs 24 | ) # the units module contains the conversion factor to go from units. to ASE units via multiplication 25 | ps = 1000 * units.fs 26 | 27 | # Units conversion: everything will be in ASE units, so a time step is in ASE unit and needs to be interpreted as some multiple of sensical units 28 | # Likewise, energy is in eV which is ~98.6 kJ/mol, so a single unit of energy is 98.6 kJ/mol which are the internal units of PLUMED 29 | setup = [ 30 | f"UNITS LENGTH=A TIME={1/ps} ENERGY={units.mol/units.kJ}", # Set units to match desired properties 31 | # Calculate the center of mass of atoms 1-5 32 | "com: COM ATOMS=1-5", 33 | # Define the coordination number (C) 34 | "c: COORDINATION GROUPA=1-5 SWITCH={RATIONAL R_0=3.0 NN=8 MM=16} NOPBC", 35 | # Define the radius of gyration (R) 36 | "r: GYRATION TYPE=RADIUS ATOMS=1-5 NOPBC", 37 | # Compute CV1 and CV2 as orthogonal linear combinations of C and R 38 | "cv1: COMBINE ARG=c,r COEFFICIENTS=0.99715,-0.07534 PERIODIC=NO", 39 | "cv2: COMBINE ARG=c,r COEFFICIENTS=0.07534,0.99715 PERIODIC=NO", 40 | # Apply lower wall on CV1 at 5.0 with harmonic constant 10 eV 41 | f"LOWER_WALLS ARG=cv1 AT=5.0 KAPPA=10.0", 42 | # Apply lower wall on CV2 at 3.0 with harmonic constant 50 eV 43 | f"UPPER_WALLS ARG=cv2 AT=3.0 KAPPA=50.0", 44 | # Perform well-tempered metadynamics on CV1 and CV2 45 | f"METAD ARG=cv1,cv2 HEIGHT=0.3 PACE=500 SIGMA=0.3,0.03 GRID_MIN=0.0,0.0 GRID_MAX=10.0,5.0 GRID_BIN=500,500 BIASFACTOR=100 FILE=HILLS", 46 | # Print out the collective variables for monitoring 47 | "PRINT ARG=cv1,cv2,c,r FILE=COLVAR STRIDE=1", 48 | ] 49 | 50 | Ag_cluster = Atoms( 51 | "Ag5", 52 | positions=[ 53 | (0.0, 2.6579, 0.9366), 54 | (0.0, -1.3587, -1.4045), 55 | (0.0, 0.0, 0.9358), 56 | (0.0, -2.6579, 0.9366), 57 | (0.0, 1.3587, -1.4045), 58 | ], 59 | pbc=(0, 0, 0), 60 | ) 61 | Ag_cluster.set_cell([20.0, 24.0, 24.0]) 62 | Ag_cluster.center() 63 | # cons = [FixedPlane(i, [1, 0, 0]) for i in range(5)] 64 | # Ag_cluster.set_constraint(cons) 65 | 66 | 67 | def main(): 68 | with SPARC(use_socket=True, **calc_params) as calc: 69 | Ag_cluster.calc = Plumed( 70 | calc=calc, input=setup, timestep=timestep, atoms=Ag_cluster, kT=0.00861733 71 | ) # 10 K in eV thermal energy units 72 | dyn = NVTBerendsen( 73 | Ag_cluster, 74 | timestep, 75 | temperature_K=0.00861733 / units.kB, 76 | taut=50 * units.fs, 77 | fixcm=False, 78 | trajectory="Ag-cluster-metadynamics.traj", 79 | ) 80 | dyn.run(10) 81 | 82 | 83 | """ 84 | # Restrain atoms 1-5 within 2.0 Å of the center of mass using upper walls 85 | "d1: DISTANCE ATOMS=1,com", 86 | "UPPER_WALLS ARG=d1 AT=2.0 KAPPA=100.0", 87 | "d2: DISTANCE ATOMS=2,com", 88 | "UPPER_WALLS ARG=d2 AT=2.0 KAPPA=100.0", 89 | "d3: DISTANCE ATOMS=3,com", 90 | "UPPER_WALLS ARG=d3 AT=2.0 KAPPA=100.0", 91 | "d4: DISTANCE ATOMS=4,com", 92 | "UPPER_WALLS ARG=d4 AT=2.0 KAPPA=100.0", 93 | "d5: DISTANCE ATOMS=5,com", 94 | "UPPER_WALLS ARG=d5 AT=2.0 KAPPA=100.0", 95 | """ 96 | 97 | if __name__ == "__main__": 98 | main() 99 | -------------------------------------------------------------------------------- /examples/socket/relax/ab-initio/cell/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | from sparc.calculator import SPARC 3 | from ase.eos import EquationOfState 4 | from ase.build import bulk 5 | 6 | calc_params = { 7 | "EXCHANGE_CORRELATION": "GGA_PBE", 8 | "KPOINT_GRID": [4,4,4], 9 | "MESH_SPACING": 0.35, 10 | "TOL_SCF": 0.0001, 11 | "MAXIT_SCF": 100, 12 | "CALC_STRESS": 1, 13 | "PRINT_RESTART_FQ": 10, 14 | "PRINT_ATOMS": 1, 15 | "PRINT_FORCES": 1, 16 | "SPIN_TYP": 0, 17 | } 18 | 19 | LC = [3.7, 3.75, 3.8, 3.85, 3.9, 3.95, 4.0] 20 | energies = [] 21 | volumes = [] 22 | with SPARC(use_socket=True, **calc_params) as calc: 23 | for a in LC: 24 | atoms = bulk('Rh', crystalstructure='fcc', a = a) 25 | atoms.calc = calc 26 | volumes.append(atoms.get_volume()) 27 | energies.append(atoms.get_potential_energy()) 28 | 29 | eos = EquationOfState(volumes, energies) 30 | v0, e0, B = eos.fit() 31 | 32 | print('v0 = {0} A^3\nE0 = {1} eV\nB = {2} eV/A^3'.format(v0, e0, B)) 33 | 34 | eos.plot('Rh-fcc-eos.png') -------------------------------------------------------------------------------- /examples/socket/relax/ab-initio/coords/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | from sparc.calculator import SPARC 3 | from ase.optimize import BFGS 4 | from ase.build import molecule 5 | 6 | water = molecule('H2O', vacuum=7) 7 | water.pbc = [False,False,False] 8 | 9 | calc_params = { 10 | "EXCHANGE_CORRELATION": "GGA_PBE", 11 | "KPOINT_GRID": [1,1,1], 12 | "MESH_SPACING": 0.35, 13 | "TOL_SCF": 0.0001, 14 | "MAXIT_SCF": 100, 15 | "ELEC_TEMP_TYPE": "fermi-dirac", 16 | "ELEC_TEMP": 116, 17 | "PRINT_RESTART_FQ": 10, 18 | "PRINT_ATOMS": 1, 19 | "PRINT_FORCES": 1, 20 | "SPIN_TYP": 0, 21 | } 22 | 23 | with SPARC(use_socket=True, **calc_params) as calc: 24 | water.calc = calc 25 | dyn = BFGS(water, trajectory = 'water-bfgs-opt.traj', logfile= 'opt.log') 26 | dyn.run(fmax=0.05) -------------------------------------------------------------------------------- /examples/socket/relax/mlff/coords/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | from sparc.calculator import SPARC 3 | from ase.build import molecule 4 | import numpy as np 5 | from ase.optimize import BFGS 6 | 7 | water = molecule('H2O', vacuum=7) 8 | water.pbc = [False,False,False] 9 | 10 | calc_params = { 11 | "EXCHANGE_CORRELATION": "GGA_PBE", 12 | "KPOINT_GRID": [1,1,1], 13 | "MESH_SPACING": 0.35, 14 | "TOL_SCF": 0.0001, 15 | "MAXIT_SCF": 100, 16 | "ELEC_TEMP_TYPE": "fermi-dirac", 17 | "ELEC_TEMP": 116, 18 | "PRINT_RESTART_FQ": 10, 19 | "PRINT_ATOMS": 1, 20 | "PRINT_FORCES": 1, 21 | "SPIN_TYP": 0, 22 | "MLFF_FLAG": 1, 23 | "MLFF_INITIAL_STEPS_TRAIN": 3, 24 | } 25 | 26 | with SPARC(use_socket=True, **calc_params) as calc: 27 | water.calc = calc 28 | dyn = BFGS(water, trajectory = 'water-bfgs-opt.traj') 29 | dyn.run(fmax=0.05) -------------------------------------------------------------------------------- /examples/socket/singlepoint/spin-paired/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | from sparc.calculator import SPARC 3 | from ase.build import molecule 4 | import numpy as np 5 | 6 | water = molecule('H2O', vacuum=7) 7 | water.pbc = [False,False,False] 8 | 9 | calc_params = { 10 | "EXCHANGE_CORRELATION": "GGA_PBE", 11 | "KPOINT_GRID": [1,1,1], 12 | "MESH_SPACING": 0.35, 13 | "TOL_SCF": 0.0001, 14 | "MAXIT_SCF": 100, 15 | "ELEC_TEMP_TYPE": "fermi-dirac", 16 | "ELEC_TEMP": 116, 17 | "PRINT_RESTART_FQ": 10, 18 | "PRINT_ATOMS": 1, 19 | "PRINT_FORCES": 1, 20 | "SPIN_TYP": 0, 21 | } 22 | 23 | with SPARC(use_socket=True, **calc_params) as calc: 24 | water.calc = calc 25 | energy = water.get_potential_energy() 26 | forces = water.get_forces() 27 | print('***********************************************************************************************') 28 | print("Energy: {}\nMax Force: {}".format(energy, np.max(abs(forces)) ) ) -------------------------------------------------------------------------------- /examples/socket/singlepoint/spin-polarized/run.py: -------------------------------------------------------------------------------- 1 | # Using SPARC 2 | from sparc.calculator import SPARC 3 | from ase.build import molecule 4 | import numpy as np 5 | 6 | water = molecule('H2O', vacuum=7) 7 | water.pbc = [False,False,False] 8 | water.set_initial_magnetic_moments([0.1, 0.1, 0.1]) 9 | 10 | calc_params = { 11 | "EXCHANGE_CORRELATION": "GGA_PBE", 12 | "KPOINT_GRID": [1,1,1], 13 | "MESH_SPACING": 0.35, 14 | "TOL_SCF": 0.0001, 15 | "MAXIT_SCF": 100, 16 | "ELEC_TEMP_TYPE": "fermi-dirac", 17 | "ELEC_TEMP": 116, 18 | "PRINT_RESTART_FQ": 10, 19 | "PRINT_ATOMS": 1, 20 | "PRINT_FORCES": 1, 21 | "SPIN_TYP": 1, 22 | } 23 | 24 | with SPARC(use_socket=True, **calc_params) as calc: 25 | water.calc = calc 26 | print("Initial magnetic moments before calculation call:\n", water.get_initial_magnetic_moments()) 27 | # energy = water.get_potential_energy() 28 | # forces = water.get_forces() 29 | net_magmom = water.get_magnetic_moment() 30 | magmoms = water.get_magnetic_moments() 31 | # print('***********************************************************************************************') 32 | # print("Energy: {}\nMax Force: {}".format(energy, np.max(abs(forces)) ) ) 33 | print('*'*100) 34 | print("Net magnetic moment: ", net_magmom) 35 | print("Atomic magnetic moments:\n", magmoms) -------------------------------------------------------------------------------- /paper/README.md: -------------------------------------------------------------------------------- 1 | # Folder for JOSS submission 2 | 3 | This folder contains the `paper.md`, `paper.bib` and supporting 4 | figures for the JOSS submission of the SPARC-X-API. Please do not add 5 | SPARC doc in this directory. While most of the writings should be done 6 | in Markdown, please use either of the following methods for rendering 7 | the draft into pdf format. 8 | 9 | ## Building Locally 10 | 11 | Follow the instructions in the [JOSS 12 | manual](https://joss.readthedocs.io/en/latest/paper.html#docker), use 13 | docker (or equivalent) to build the paper locally: 14 | 15 | ```bash 16 | # At the paper/ subfolder of the SPARC-X-API repository 17 | docker run --rm \ 18 | --volume $PWD:/data \ 19 | --user $(id -u):$(id -g) \ 20 | --env JOURNAL=joss \ 21 | openjournals/inara 22 | ``` 23 | This command will create the `paper.pdf` under the `paper/` subfolder. 24 | 25 | ## Use Github Actions 26 | 27 | The draft pdf will be rendered after any changes are pushed the 28 | `paper/` under the `joss_paper` branch. Please check the [status 29 | page](https://github.com/SPARC-X/SPARC-X-API/actions/workflows/joss_paper.yml) 30 | for the latest build action. Once the compilation is finished, the zip 31 | archive containing the rendered `paper.pdf` can be downloaded via the 32 | link in the "Artifacts" section of the action status. 33 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | # A minimal pyproject.toml to make the pip installation 2 | # future-proof. The latest setuptools should be able to 3 | # suppress deprecation warnings for editable installation 4 | # https://github.com/pypa/pip/issues/11457 5 | # 6 | # Note: the actual installation is still handled by setup.py 7 | [build-system] 8 | requires = ["setuptools >= 64", "wheel", "setuptools-scm>=8"] 9 | build-backend = "setuptools.build_meta" 10 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | from distutils.core import setup 4 | from warnings import warn 5 | 6 | from setuptools import find_packages 7 | from setuptools.command.install import install 8 | from setuptools_scm import get_version 9 | 10 | print(f"Version from setuptools_scm is {get_version()}") 11 | 12 | test_requires = [ 13 | "pytest", 14 | "pyfakefs", 15 | "pytest-cov", 16 | "black", 17 | "isort", 18 | "flake8", 19 | "anybadge", 20 | "pre-commit", 21 | ] 22 | 23 | doc_requires = [ 24 | "sphinx_rtd_theme", 25 | "sphinx_tabs", 26 | "myst-parser", 27 | ] 28 | 29 | setup( 30 | name="sparc-x-api", 31 | # @TT 2025.06.07 we use setuptools_scm for future 32 | # releases before fully transition to pyproject.toml 33 | version=get_version(), 34 | python_requires=">=3.8", 35 | description="Python API for the SPARC DFT Code", 36 | long_description=open("README.md").read(), 37 | long_description_content_type="text/markdown", 38 | author="Tian Tian, Lucas R Timmerman, Ben Comer", 39 | author_email="alchem0x2a@gmail.com, ltimmerman3@gatech.edu, ben.comer@gatech.edu", 40 | url="https://github.com/SPARC-X/SPARC-X-API", 41 | packages=find_packages(), 42 | # ASE 3.22 dependency will be deprecated in 2.0+ release 43 | install_requires=["ase>=3.22.0", "numpy>=1.23", "packaging>=20.0", "psutil>=5.0.0"], 44 | entry_points={ 45 | # The ioformats are only compatible with ase>=3.23 46 | "ase.ioformats": [ 47 | "sparc = sparc.io:format_sparc", 48 | "sparc_ion = sparc.io:format_ion", 49 | "sparc_static = sparc.io:format_static", 50 | "sparc_geopt = sparc.io:format_geopt", 51 | "sparc_aimd = sparc.io:format_aimd", 52 | ], 53 | "console_scripts": ["sparc-ase=sparc.cli:main"], 54 | }, 55 | extras_require={ 56 | "test": test_requires, 57 | "doc": test_requires + doc_requires, 58 | }, 59 | package_data={"sparc": ["psp/*", "sparc_json_api/*.json"]}, 60 | include_package_data=True, 61 | ) 62 | -------------------------------------------------------------------------------- /sparc/__init__.py: -------------------------------------------------------------------------------- 1 | """Initialization of sparc-x-api 2 | 3 | For submodules like download_data and api, ase / numpy may be ignored, 4 | and run using standard python libaries. This may be useful for cases like 5 | conda build and CI where not all dependencies are present 6 | """ 7 | 8 | 9 | def _missing_deps_func(*args, **kwargs): 10 | raise ImportError("Importing fails for ase / numpy!") 11 | 12 | 13 | class SPARCMissingDeps: 14 | def __init__(self, *args, **kwargs): 15 | raise ImportError( 16 | "Cannot initialize sparc.SPARC because the required dependencies (ase and numpy) are not available." 17 | ) 18 | 19 | def __getattr__(self, name): 20 | raise ImportError( 21 | f"Cannot access '{name}' on sparc.SPARC because the required dependencies (ase and numpy) are not available." 22 | ) 23 | 24 | 25 | try: 26 | import ase 27 | import numpy 28 | 29 | _import_complete = True 30 | except ImportError: 31 | _import_complete = False 32 | 33 | if _import_complete: 34 | from packaging import version 35 | 36 | from .calculator import SPARC 37 | from .io import read_sparc, register_ase_io_sparc, write_sparc 38 | 39 | # If ase version less than 3.23, use manual register function 40 | # Otherwise use the new entry point 41 | if version.parse(ase.__version__) < version.parse("3.23"): 42 | register_ase_io_sparc() 43 | else: 44 | # register calculator class 45 | from ase.calculators.calculator import register_calculator_class 46 | 47 | register_calculator_class("sparc", SPARC) 48 | else: 49 | # If importing is not complete, any code trying to directly import 50 | # the following attributes will raise ImportError 51 | read_sparc = _missing_deps_func 52 | write_sparc = _missing_deps_func 53 | SPARC = SPARCMissingDeps 54 | -------------------------------------------------------------------------------- /sparc/cli.py: -------------------------------------------------------------------------------- 1 | # Temporary fix to recognize .sparc from commandline 2 | from .io import __register_new_filetype 3 | 4 | __register_new_filetype() 5 | 6 | 7 | # The cli part should be considered deprecated now. 8 | def main( 9 | prog="sparc-ase", 10 | description="ASE command line tool with SPARC support", 11 | hook=None, 12 | args=None, 13 | ): 14 | import sys 15 | 16 | from ase.cli.main import main as ase_main 17 | 18 | ase_main(prog=prog, description=description, hook=hook, args=args) 19 | 20 | 21 | if __name__ == "__main__": 22 | main() 23 | -------------------------------------------------------------------------------- /sparc/client.py: -------------------------------------------------------------------------------- 1 | import argparse 2 | from pathlib import Path 3 | 4 | from ase.io import read 5 | 6 | import sparc 7 | 8 | from .calculator import SPARC 9 | from .io import read_sparc 10 | 11 | 12 | def split_socket_name(name): 13 | """Split the host:address 14 | 15 | Returns: 16 | (host, port, unixsocket) tuple 17 | """ 18 | name = name.strip() 19 | assert ":" in name, "Socket name must be in the format of host:port" 20 | host, port = name.split(":") 21 | if port.lower() == "unix": 22 | unixsocket = host 23 | port = -1 24 | host = "" 25 | assert len(unixsocket) > 0, "Unix socket length must be non-zero!" 26 | else: 27 | port = int(port) 28 | unixsocket = None 29 | host = host if len(host) > 0 else "localhost" 30 | 31 | return host, port, unixsocket 32 | 33 | 34 | def main(): 35 | """Running SPARC-X-API as a socket client from command line 36 | 37 | The client wraps a socket communication layer on top of the SPARC 38 | binary. The implementation is both compatible with 39 | `SocketIOCalculator` in ase (using standard i-PI protocol), or 40 | with SPARC-X-API in socket server mode (using SPARC's extended 41 | i-PI protocol). 42 | 43 | Usage: 44 | 1. Start the socket client and outputs to current directory: 45 | python -m sparc.client -s host:port --workdir . 46 | 47 | If the workdir is a SPARC calculation bundle, the initial atoms and parameters will be reloaded. 48 | 49 | 2. Start the socket client with initial atoms read from file 50 | python -m sparc.client -s host:port --atoms-from-file input.xyz 51 | 52 | If the client is communicating with the standard i-PI server, an 53 | initial atoms object is required (either read from SPARC input 54 | files or via --atoms-from-file). However, if the server uses the 55 | SPARC protocol, the client can be started without initial atoms. 56 | """ 57 | parser = argparse.ArgumentParser( 58 | usage=main.__doc__, 59 | formatter_class=argparse.RawDescriptionHelpFormatter, 60 | ) 61 | parser.add_argument( 62 | "-s", 63 | "--socket", 64 | help=( 65 | "Address of the socket server " 66 | "in the format of host:port. If host is not defined, localhost will be used." 67 | ), 68 | ) 69 | parser.add_argument( 70 | "-w", 71 | "--workdir", 72 | help=("Workdir for performing the SPARC calculations"), 73 | default=".", 74 | ) 75 | parser.add_argument( 76 | "--atoms-from-file", 77 | help=("File or directory to read the input atoms information"), 78 | default=None, 79 | ) 80 | parser.add_argument( 81 | "--atoms-format", 82 | help="File format to read from external file.", 83 | default=None, 84 | ) 85 | args = parser.parse_args() 86 | host, port, unixsocket = split_socket_name(args.socket) 87 | workdir = Path(args.workdir) 88 | # TODO: implement unixsocket 89 | # TODO: reuse init params 90 | try: 91 | init_atoms = read_sparc(workdir) 92 | except: 93 | init_atoms = None 94 | if (init_atoms is None) and args.atoms_from_file: 95 | atoms_file = Path(args.atoms_from_file) 96 | atoms_format = args.atoms_format 97 | init_atoms = read(atoms_file, format=atoms_format) 98 | 99 | client_calc = SPARC( 100 | directory=workdir, 101 | use_socket=True, 102 | socket_params=dict(host=host, port=port, server_only=False), 103 | ) 104 | # We should always enable use_stress, since the 105 | # SPARC implementation ensures it will also be present 106 | client_calc.run_client(atoms=init_atoms, use_stress=True) 107 | 108 | 109 | if __name__ == "__main__": 110 | main() 111 | -------------------------------------------------------------------------------- /sparc/common.py: -------------------------------------------------------------------------------- 1 | import importlib.resources 2 | 3 | repo_dir = importlib.resources.files("sparc") 4 | psp_dir = repo_dir / "psp" 5 | -------------------------------------------------------------------------------- /sparc/download_data.py: -------------------------------------------------------------------------------- 1 | """Download the pseudopotential and other related files after sparc-x-api is installed 2 | 3 | Run: 4 | 5 | python -m sparc.download_data 6 | """ 7 | 8 | import hashlib 9 | import shutil 10 | import tempfile 11 | import zipfile 12 | from io import BytesIO 13 | from pathlib import Path 14 | 15 | # import urllib.request 16 | from urllib.request import urlopen 17 | 18 | from .common import psp_dir 19 | 20 | sparc_tag = "b702c1061400a2d23c0e223e32182609d7958156" 21 | sparc_source_url = "https://github.com/SPARC-X/SPARC/archive/{sparc_tag}.zip" 22 | # This is a all_psp8_checksum 23 | all_psp8_checksum = "5ef42c4a81733a90b0e080b771c5a73a" 24 | 25 | 26 | def download_psp(sparc_tag=sparc_tag, psp_dir=psp_dir): 27 | """Download the external PSPs into the sparc/psp folder 28 | 29 | Arguments: 30 | sparc_tag (str): Commit hash or git tag for the psp files 31 | psp_dir (str or PosixPath): Directory to download the psp files 32 | """ 33 | if is_psp_download_complete(): 34 | print("PSPs have been successfully downloaded!") 35 | return 36 | download_url = sparc_source_url.format(sparc_tag=sparc_tag) 37 | print(f"Download link: {download_url}") 38 | with tempfile.TemporaryDirectory() as tmpdir: 39 | tmpdir = Path(tmpdir) 40 | with urlopen(download_url) as zipresp: 41 | with zipfile.ZipFile(BytesIO(zipresp.read())) as zfile: 42 | zfile.extractall(tmpdir) 43 | # print(list(os.walk(tmpdir))) 44 | source_dir = next(tmpdir.glob("SPARC-*/psps")) 45 | print(f"Found source_dir at {source_dir}") 46 | if not source_dir.is_dir(): 47 | raise FileNotFoundError("Error downloading or extracting zip") 48 | print(f"Moving psp files to {psp_dir}") 49 | for ext in ("*.psp8", "*.psp", "*.pot"): 50 | for pspf in source_dir.glob(ext): 51 | print(f"Found {pspf} --> {psp_dir}") 52 | shutil.copy(pspf, psp_dir) 53 | if not is_psp_download_complete(psp_dir): 54 | raise RuntimeError(f"Files downloaded to {psp_dir} have different checksums!") 55 | return 56 | 57 | 58 | def checksum_all(psp_dir=psp_dir, extension="*.psp8"): 59 | """Checksum all the files under the psp_dir to make sure the psp8 files 60 | are the same as intended 61 | 62 | Arguments: 63 | psp_dir (str or PosixPath): Directory for the psp files 64 | extension (str): Search pattern for the psp files, either '.psp', '.psp8' or '.pot' 65 | 66 | Returns: 67 | str: Checksum for all the files concatenated 68 | """ 69 | checker = hashlib.md5() 70 | psp_dir = Path(psp_dir) 71 | # Use sorted to make sure file order is correct 72 | for filename in sorted(psp_dir.glob(extension)): 73 | # Open the file in binary mode and update the group checksum 74 | print(f"Checking {filename}") 75 | with open(filename, "r") as f: 76 | f_checker = hashlib.md5() 77 | content = f.read().encode("utf8") 78 | f_checker.update(content) 79 | checker.update(f_checker.hexdigest().encode("ascii")) 80 | final_checksum = checker.hexdigest() 81 | print(f"Final checksum is {final_checksum}") 82 | return final_checksum 83 | 84 | 85 | def is_psp_download_complete(psp_dir=psp_dir): 86 | return checksum_all(psp_dir) == all_psp8_checksum 87 | 88 | 89 | if __name__ == "__main__": 90 | print("Running command-line psp downloader") 91 | download_psp() 92 | -------------------------------------------------------------------------------- /sparc/psp/README.md: -------------------------------------------------------------------------------- 1 | This is the folder for storing the pseudo potential files with SPARC-X-API. 2 | During installation, this folder will be intentially kept empty. 3 | 4 | User `python -m sparc.download_data` to download the default pseudo potential files after installation. 5 | -------------------------------------------------------------------------------- /sparc/sparc_parsers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/sparc/sparc_parsers/__init__.py -------------------------------------------------------------------------------- /sparc/sparc_parsers/inpt.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | from ase.units import Bohr 3 | 4 | # Safe wrappers for both string and fd 5 | from ase.utils import reader, writer 6 | 7 | from ..api import SparcAPI 8 | from .utils import read_block_input, strip_comments 9 | 10 | defaultAPI = SparcAPI() 11 | 12 | 13 | @reader 14 | def _read_inpt(fileobj, validator=defaultAPI): 15 | contents = fileobj.read() 16 | # label = get_label(fileobj, ".ion") 17 | data, comments = strip_comments(contents) 18 | # We do not read the cell at this time! 19 | 20 | # find the index for all atom type lines. They should be at the 21 | # top of their block 22 | inpt_blocks = read_block_input(data, validator=validator) 23 | return {"inpt": {"params": inpt_blocks, "comments": comments}} 24 | 25 | 26 | @writer 27 | def _write_inpt(fileobj, data_dict, validator=defaultAPI): 28 | if "inpt" not in data_dict: 29 | raise ValueError("Your dict does not contain inpt section!") 30 | 31 | inpt_dict = data_dict["inpt"] 32 | 33 | if "params" not in inpt_dict: 34 | raise ValueError("Input dict for inpt file does not have `params` field!") 35 | 36 | comments = inpt_dict.get("comments", []) 37 | banner = "Input File Generated By SPARC ASE Calculator" 38 | if len(comments) == 0: 39 | comments = [banner] 40 | elif "ASE" not in comments[0]: 41 | comments = [banner] + comments 42 | for line in comments: 43 | fileobj.write(f"# {line}\n") 44 | fileobj.write("\n") 45 | params = inpt_dict["params"] 46 | for key, val in params.items(): 47 | # TODO: can we add a multiline argument? 48 | val_string = validator.convert_value_to_string(key, val) 49 | if (val_string.count("\n") > 0) or ( 50 | key 51 | in [ 52 | "LATVEC", 53 | ] 54 | ): 55 | output = f"{key}:\n{val_string}\n" 56 | else: 57 | output = f"{key}: {val_string}\n" 58 | fileobj.write(output) 59 | return 60 | 61 | 62 | def _inpt_cell_to_ase_cell(data_dict): 63 | """Convert the inpt cell convention to a real cell (in ASE Angstrom unit) 64 | 65 | Arguments: 66 | inpt_blocks: an already validated inpt file blocks dict 67 | (i.e. parsed by _read_inpt) 68 | 69 | Returns: 70 | cell in ASE-unit 71 | """ 72 | inpt_blocks = data_dict["inpt"]["params"] 73 | if ("CELL" in inpt_blocks) and ("LATVEC_SCALE" in inpt_blocks): 74 | # TODO: customize the exception class 75 | # TODO: how do we convert the rule from doc? 76 | raise ValueError("LATVEC_SCALE and CELL cannot be specified simultaneously!") 77 | 78 | # if "CELL" in inpt_blocks: 79 | # cell = np.eye(inpt_blocks["CELL"]) * Bohr 80 | if "LATVEC" not in inpt_blocks: 81 | if ("CELL" in inpt_blocks) or ("LATVEC_SCALE" in inpt_blocks): 82 | lat_array = np.eye(3) * Bohr 83 | else: 84 | raise KeyError( 85 | "LATVEC is missing in inpt file and no CELL / LATVEC_SCALE provided!" 86 | ) 87 | else: 88 | lat_array = np.array(inpt_blocks["LATVEC"]) * Bohr 89 | 90 | # LATVEC_SCALE: just multiplies 91 | if "LATVEC_SCALE" in inpt_blocks: 92 | scale = np.array(inpt_blocks["LATVEC_SCALE"]) 93 | cell = (lat_array.T * scale).T 94 | 95 | # CELL: the lengths are in the LATVEC directions 96 | # TODO: the documentation about CELL is a bit messy. Is CELL always orthogonal? 97 | # Anyway the lat_array when CELL is none should be ok 98 | elif "CELL" in inpt_blocks: 99 | scale = np.array(inpt_blocks["CELL"]) 100 | unit_lat_array = ( 101 | lat_array / np.linalg.norm(lat_array, axis=1, keepdims=True) * Bohr 102 | ) 103 | cell = (unit_lat_array.T * scale).T 104 | else: 105 | cell = lat_array 106 | return cell 107 | -------------------------------------------------------------------------------- /sparc/sparc_parsers/utils.py: -------------------------------------------------------------------------------- 1 | from warnings import warn 2 | 3 | 4 | def get_label(fileobj, ext): 5 | """Return the label of file by stripping the extension (e.g. .ion)""" 6 | return fileobj.name.rsplit(ext, 1)[0] 7 | 8 | 9 | def strip_comments(rawtext, symbol="#"): 10 | """Strip comments from the text, including trailing comments""" 11 | stripped = [] 12 | comments = [] 13 | for line in rawtext.splitlines(): 14 | data, comment = bisect_and_strip(line, symbol) 15 | if data: 16 | stripped.append(data) 17 | if comment: 18 | comments.append(comment) 19 | return stripped, comments 20 | 21 | 22 | def bisect_and_strip(text, delimiter): 23 | """split string in 2 at first occurence of a character and remove whitespace 24 | useful for separating comments from data, keys from values, etc. 25 | """ 26 | # wrap around to len(text) if not found (-1) 27 | index = text.find(delimiter) % (len(text) + 1) 28 | return text[:index].strip(), text[index + len(delimiter) :].strip() 29 | 30 | 31 | def read_block_input(block, validator=None): 32 | """Read blocks of inputs from ion or inpt file and convert with validator 33 | 34 | the following inputs are accepted: 35 | 1) single line input: KEY: VALUE 36 | 2) multiline input: KEY: VALUE1 \n VALUE2 --> (concanate the values) 37 | 3) multiline input w/ blank first line: KEY: \n VALUE1 \n VALUE2 --> (append the values) 38 | """ 39 | # print(block) 40 | block_dict = {} 41 | multiline_key = "" 42 | concat = False 43 | use_validator = True if validator else False 44 | for line in block: 45 | if ":" not in line: 46 | # no key, assume multiline value. 47 | # be careful not to add blank lines 48 | if multiline_key: 49 | if concat: 50 | block_dict[multiline_key] = ( 51 | block_dict[multiline_key] + f" {line.strip()}" 52 | ) 53 | else: 54 | block_dict[multiline_key].append(line.strip()) 55 | continue 56 | key, value = bisect_and_strip(line, ":") 57 | key = key.upper() 58 | 59 | if key and value: 60 | block_dict[key] = value 61 | multiline_key = key 62 | concat = True 63 | elif key: 64 | # no value, assume that this key has a list of values 65 | # in the following lines 66 | block_dict[key] = [] 67 | multiline_key = key 68 | concat = False 69 | for key, val in block_dict.items(): 70 | _use_validator_this_key = use_validator 71 | if _use_validator_this_key: 72 | if key not in validator.parameters.keys(): 73 | warn( 74 | f"Key {key} not in validator's parameter list, ignore value conversion!" 75 | ) 76 | _use_validator_this_key = False 77 | if _use_validator_this_key: 78 | val = validator.convert_string_to_value(key, val) 79 | block_dict[key] = val 80 | return block_dict 81 | 82 | 83 | def make_reverse_mapping(mapping): 84 | """Given a list of mapping, get its reverse mapping 85 | 86 | For example: 87 | mapping = [0, 2, 3, 1, 5, 4] 88 | reverse = [0, 3, 1, 2, 5, 4] 89 | """ 90 | reverse = [0] * len(mapping) 91 | for i, j in enumerate(mapping): 92 | reverse[j] = i 93 | return reverse 94 | -------------------------------------------------------------------------------- /tests/archive/read_input.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator # 2 | FD_GRID: 30 30 30 3 | CELL: 11.338356755021570 11.338356755021570 11.338356755021570 4 | LATVEC: 5 | 1.000000000000000 0.000000000000000 0.000000000000000 6 | 0.000000000000000 1.000000000000000 0.000000000000000 7 | 0.000000000000000 0.000000000000000 1.000000000000000 8 | BC: P P P 9 | KPOINT_GRID: 1 1 1 10 | EXCHANGE_CORRELATION: LDA_PZ 11 | PRINT_FORCES: 1 12 | PRINT_ATOMS: 1 13 | TOL_SCF: 0.0001 14 | MD_FLAG: 1 15 | ION_TEMP: 500 16 | MD_NSTEP: 50 17 | -------------------------------------------------------------------------------- /tests/archive/read_input.ion: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator # 2 | #CELL: 11.338356755021570 11.338356755021570 11.338356755021570 3 | #LATVEC 4 | # 1.000000000000000 0.000000000000000 0.000000000000000 5 | # 0.000000000000000 1.000000000000000 0.000000000000000 6 | # 0.000000000000000 0.000000000000000 1.000000000000000 7 | #PBC: True True True 8 | # 9 | 10 | 11 | ATOM_TYPE: N 12 | N_TYPE_ATOM: 2 13 | PSEUDO_POT: N.pot 14 | ATOMIC_MASS: 14.007 15 | COORD_FRAC: 16 | 0.000000000000000 0.000000000000000 0.094165000000000 # index 0 17 | 0.000000000000000 0.000000000000000 -0.094165000000000 # index 1 18 | RELAX: 19 | 1 1 1 20 | 1 1 1 21 | 22 | 23 | -------------------------------------------------------------------------------- /tests/archive/test.py: -------------------------------------------------------------------------------- 1 | import os 2 | from copy import deepcopy as dc 3 | 4 | import numpy as np 5 | from ase.build import bulk, molecule 6 | from ase.calculators.calculator import CalculatorSetupError, compare_atoms 7 | from ase.constraints import FixAtoms, FixedLine, FixedPlane 8 | from ase.visualize import view 9 | 10 | from sparc.ion import read_ion, write_ion 11 | from sparc.sparc_core import SPARC 12 | 13 | atoms = bulk("NaCl", crystalstructure="rocksalt", a=5) * (2, 1, 1) 14 | atoms.set_initial_magnetic_moments([1.1] * len(atoms)) 15 | l = SPARC(atoms=atoms, h=0.1, label="in1", xc="GGA", spin_typ=1, pseudo_dir=".") 16 | l.write_input(atoms=atoms, h=0.1, spin_typ=1, pseudo_dir=".", SPIN_TYP=1) 17 | 18 | print("input writing functional") 19 | # check reading and writing .ion files 20 | atoms.set_constraint([FixAtoms([0]), FixedLine(1, [0, 1, 0]), FixedPlane(2, [1, 0, 0])]) 21 | write_ion(open("in1.ion", "w"), atoms, pseudo_dir=".") 22 | recovered_atoms = read_ion(open("in1.ion", "r")) 23 | assert compare_atoms(atoms, recovered_atoms) == [] 24 | 25 | calc = SPARC(atoms=atoms, pseudo_dir=".", SPIN_TYP=1) 26 | try: # check that `h` is required 27 | calc.write_input() 28 | raise Exception("test failed") 29 | except CalculatorSetupError: 30 | pass 31 | 32 | print(".ion reading test passed") 33 | 34 | calc = SPARC.read("read_input") 35 | 36 | print("reading test passed") 37 | 38 | d = calc.todict() 39 | print("to dict test passed") 40 | -------------------------------------------------------------------------------- /tests/outputs/AlSi_primitive_quick_relax.sparc/AlSi_primitive_quick_relax.geopt: -------------------------------------------------------------------------------- 1 | :RELAXSTEP: 1 2 | :E(Ha): -5.774163825437492E+00 3 | :R(Bohr): 4 | 0.000000000000000 0.000000000000000 0.000000000000000 5 | 3.657724819665000 3.622889345192000 3.657724819665000 6 | :F(Ha/Bohr): 7 | 0.113139770628281 0.087368929971100 0.113139763970798 8 | -0.113139770628281 -0.087368929971100 -0.113139763970798 9 | :CELL: 4.9264800451E+00 4.9264800451E+00 4.9264800451E+00 10 | :VOLUME: 8.4546412886E+01 11 | :LATVEC: 12 | 0.0000000000E+00 5.0000000000E-01 5.0000000000E-01 13 | 5.0000000000E-01 0.0000000000E+00 5.0000000000E-01 14 | 5.0000000000E-01 5.0000000000E-01 0.0000000000E+00 15 | :STRESS: 16 | -6.5373541539E+02 1.5358155364E+00 5.1364935602E+00 17 | 1.5358155364E+00 -6.4458329707E+02 1.5364037537E+00 18 | 5.1364935602E+00 1.5364037537E+00 -6.5373541688E+02 19 | :RELAXSTEP: 2 20 | :E(Ha): -5.775437935275552E+00 21 | :R(Bohr): 22 | 0.002194196103526 0.001694404758356 0.002194195974413 23 | 3.655530623561474 3.621194940433644 3.655530623690587 24 | :F(Ha/Bohr): 25 | 0.110411027039840 0.085419023529961 0.110411024664740 26 | -0.110411027039840 -0.085419023529961 -0.110411024664740 27 | :CELL: 4.9264800451E+00 4.9264800451E+00 4.9264800451E+00 28 | :VOLUME: 8.4546412886E+01 29 | :LATVEC: 30 | 0.0000000000E+00 5.0000000000E-01 5.0000000000E-01 31 | 5.0000000000E-01 0.0000000000E+00 5.0000000000E-01 32 | 5.0000000000E-01 5.0000000000E-01 0.0000000000E+00 33 | :STRESS: 34 | -6.5313614259E+02 9.0682890659E-01 4.3139086021E+00 35 | 9.0682890659E-01 -6.4446221862E+02 9.0731929019E-01 36 | 4.3139086021E+00 9.0731929019E-01 -6.5313614220E+02 37 | :RELAXSTEP: 3 38 | :E(Ha): -5.794556768421822E+00 39 | :R(Bohr): 40 | 0.047359563668326 0.036636400120512 0.047359562567641 41 | 3.610365255996675 3.586252945071489 3.610365257097359 42 | :F(Ha/Bohr): 43 | 0.052498938225036 0.042849311571086 0.052498939943199 44 | -0.052498938225036 -0.042849311571086 -0.052498939943199 45 | :CELL: 4.9264800451E+00 4.9264800451E+00 4.9264800451E+00 46 | :VOLUME: 8.4546412886E+01 47 | :LATVEC: 48 | 0.0000000000E+00 5.0000000000E-01 5.0000000000E-01 49 | 5.0000000000E-01 0.0000000000E+00 5.0000000000E-01 50 | 5.0000000000E-01 5.0000000000E-01 0.0000000000E+00 51 | :STRESS: 52 | -6.4415620548E+02 -8.6396949567E+00 -8.0141975097E+00 53 | -8.6396949567E+00 -6.4250622311E+02 -8.6415211701E+00 54 | -8.0141975097E+00 -8.6415211701E+00 -6.4415620598E+02 55 | :RELAXSTEP: 4 56 | :E(Ha): -5.800046313085624E+00 57 | :R(Bohr): 58 | 0.088817234444247 0.070409417644916 0.088817234618174 59 | 3.568907585220755 3.552479927547084 3.568907585046826 60 | :F(Ha/Bohr): 61 | -0.002316182978578 -0.000896147882701 -0.002316181899298 62 | 0.002316182978578 0.000896147882701 0.002316181899298 63 | :CELL: 4.9264800451E+00 4.9264800451E+00 4.9264800451E+00 64 | :VOLUME: 8.4546412886E+01 65 | :LATVEC: 66 | 0.0000000000E+00 5.0000000000E-01 5.0000000000E-01 67 | 5.0000000000E-01 0.0000000000E+00 5.0000000000E-01 68 | 5.0000000000E-01 5.0000000000E-01 0.0000000000E+00 69 | :STRESS: 70 | -6.4167808183E+02 -1.1488628417E+01 -1.1484645019E+01 71 | -1.1488628417E+01 -6.4166849406E+02 -1.1490464116E+01 72 | -1.1484645019E+01 -1.1490464116E+01 -6.4167808184E+02 73 | :RELAXSTEP: 5 74 | :E(Ha): -5.800057594119798E+00 75 | :R(Bohr): 76 | 0.087177352609414 0.069437155473653 0.087177353155337 77 | 3.570547467055587 3.553452189718348 3.570547466509663 78 | :F(Ha/Bohr): 79 | -0.000124428376470 0.000340548405068 -0.000124428470943 80 | 0.000124428376470 -0.000340548405068 0.000124428470943 81 | :CELL: 4.9264800451E+00 4.9264800451E+00 4.9264800451E+00 82 | :VOLUME: 8.4546412886E+01 83 | :LATVEC: 84 | 0.0000000000E+00 5.0000000000E-01 5.0000000000E-01 85 | 5.0000000000E-01 0.0000000000E+00 5.0000000000E-01 86 | 5.0000000000E-01 5.0000000000E-01 0.0000000000E+00 87 | :STRESS: 88 | -6.4167181594E+02 -1.1491312956E+01 -1.1491173282E+01 89 | -1.1491312956E+01 -6.4167099339E+02 -1.1493172604E+01 90 | -1.1491173282E+01 -1.1493172604E+01 -6.4167181583E+02 91 | -------------------------------------------------------------------------------- /tests/outputs/AlSi_primitive_quick_relax.sparc/AlSi_primitive_quick_relax.inpt: -------------------------------------------------------------------------------- 1 | # nprocs: 8 2 | 3 | # Test: CuSi7 # 4 | LATVEC_SCALE: 6.9670948946E+00 6.9670948946E+00 6.9670948946E+00 5 | LATVEC: 6 | 0.0 0.5 0.5 7 | 0.5 0.0 0.5 8 | 0.5 0.5 0.0 9 | MESH_SPACING: 0.3 10 | FD_ORDER: 12 11 | BC: P P P 12 | EXCHANGE_CORRELATION: GGA_PBE 13 | TOL_SCF: 1e-6 14 | 15 | KPOINT_GRID: 2 2 2 16 | 17 | PRINT_FORCES: 1 18 | PRINT_ATOMS: 1 19 | CALC_STRESS: 1 20 | 21 | RELAX_FLAG: 1 22 | RELAX_METHOD: LBFGS 23 | 24 | PRINT_RELAXOUT: 1 25 | RESTART_FLAG: 0 -------------------------------------------------------------------------------- /tests/outputs/AlSi_primitive_quick_relax.sparc/AlSi_primitive_quick_relax.ion: -------------------------------------------------------------------------------- 1 | #========================= 2 | # format of ion file 3 | #========================= 4 | # ATOM_TYPE: 5 | # PSEUDO_POT: 6 | # N_TYPE_ATOM: 7 | # ATOMIC_MASS: #(optional, for MD only) 8 | # COORD: 9 | # 10 | # ... 11 | # RELAX: #(optional) 12 | # 13 | # ... 14 | 15 | # this is a comment 16 | 17 | ATOM_TYPE: Al # atom type 18 | N_TYPE_ATOM: 1 # number of atoms of this type 19 | PSEUDO_POT: ../../../psps/13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 # pseudopotential 20 | COORD_FRAC: # coordinates follows 21 | 0.00 0.00 0.00 22 | 23 | ATOM_TYPE: Si # atom type 24 | N_TYPE_ATOM: 1 # number of atoms of this type 25 | PSEUDO_POT: ../../../psps/14_Si_4_1.9_1.9_pbe_n_v1.0.psp8 # pseudopotential 26 | COORD_FRAC: # coordinates follows 27 | 0.52 0.53 0.52 28 | 29 | 30 | -------------------------------------------------------------------------------- /tests/outputs/AlSi_primitive_quick_relax.sparc/output.sparc: -------------------------------------------------------------------------------- 1 | --------------------------------------- 2 | Begin PBS Prologue Wed Oct 27 17:50:31 EDT 2021 3 | Job ID: 7040477.sched-hive.pace.gatech.edu 4 | User ID: skumar416 5 | Job name: testing_suite 6 | Queue: hive-interact 7 | End PBS Prologue Wed Oct 27 17:50:31 EDT 2021 8 | --------------------------------------- 9 | /storage/hive/scratch/5/skumar416/00merge_dev_sparc_10272021/sparc_public/tests_LHQ/CuSi7/temp_run 10 | --------------------------------------- 11 | Begin PBS Epilogue Wed Oct 27 17:50:36 EDT 2021 12 | Job ID: 7040477.sched-hive.pace.gatech.edu 13 | User ID: skumar416 14 | Job name: testing_suite 15 | Resources: nodes=1:ppn=24,pmem=7gb,walltime=01:00:00,neednodes=1:ppn=24 16 | Rsrc Used: cput=00:00:36,vmem=0kb,walltime=00:00:05,mem=0kb,energy_used=0 17 | Queue: hive-interact 18 | Nodes: 19 | atl1-1-01-017-3-r.pace.gatech.edu 20 | End PBS Epilogue Wed Oct 27 17:50:36 EDT 2021 21 | --------------------------------------- 22 | -------------------------------------------------------------------------------- /tests/outputs/Al_multi_geopt.sparc/SPARC.geopt: -------------------------------------------------------------------------------- 1 | :RELAXSTEP: 1 2 | :E(Ha): -9.052841822385940E+00 3 | :R(Bohr): 4 | 0.095865400000000 7.627261800000000 0.122395000000000 5 | 0.297811000000000 3.782450000000000 3.782450000000000 6 | 4.425120000000000 0.145024000000000 3.737980000000000 7 | 3.829220000000000 3.739120000000000 7.565379800000000 8 | :F(Ha/Bohr): 9 | 0.005147731065701 -0.001066890163457 -0.007141055737244 10 | 0.001478478247868 0.003140582165144 0.002025907597284 11 | -0.008903664572768 -0.006257553671765 0.004496591545909 12 | 0.002277455259199 0.004183861670078 0.000618556594051 13 | :RELAXSTEP: 2 14 | :E(Ha): -9.052891986175165E+00 15 | :R(Bohr): 16 | 0.097472462231678 7.626928729203341 0.120165644809692 17 | 0.298272563846709 3.783430453508287 3.783082464972026 18 | 4.422340378672506 0.143070463958540 3.739383783988029 19 | 3.829930995249107 3.740426153329833 7.565572906230253 20 | :F(Ha/Bohr): 21 | 0.004893268802518 -0.000861145998705 -0.006815426088504 22 | 0.001397638928025 0.002915857592138 0.001855709710195 23 | -0.008698885740238 -0.006035904506556 0.004187002987289 24 | 0.002407978009696 0.003981192913123 0.000772713391019 25 | :RELAXSTEP: 3 26 | :E(Ha): -9.053618936214750E+00 27 | :R(Bohr): 28 | 0.116904714853397 7.623508927989395 0.093100080496463 29 | 0.303822897135031 3.795009968884639 3.790451898644367 30 | 4.387795179531842 0.119100552248066 3.756011298858055 31 | 3.839493608479729 3.756236350877901 7.568641522001116 32 | :F(Ha/Bohr): 33 | 0.004260092312641 -0.000712966798020 -0.005322202416789 34 | 0.000818378748039 0.002374335637220 0.001439878885502 35 | -0.007812970482679 -0.005162285387695 0.003149513792273 36 | 0.002734499421999 0.003500916548495 0.000732809739014 37 | :RELAXSTEP: 4 38 | :E(Ha): -9.056169343609362E+00 39 | :R(Bohr): 40 | 0.181636647712387 7.612675425916400 0.012229426946717 41 | 0.316258129586240 3.831087904237633 3.812330800907779 42 | 4.269077404517124 0.040659831580192 3.803868035374048 43 | 3.881044218184246 3.809432638265775 7.579776536771456 44 | :F(Ha/Bohr): 45 | 0.001410750394171 0.000932746009291 -0.000815829712265 46 | -0.001476399127699 -0.000231680774296 -0.000497847129708 47 | -0.003895909831698 -0.001249819605180 -0.000160023078570 48 | 0.003961558565226 0.000548754370185 0.001473699920542 49 | -------------------------------------------------------------------------------- /tests/outputs/Al_multi_geopt.sparc/SPARC.geopt_01: -------------------------------------------------------------------------------- 1 | :RELAXSTEP: 5 2 | :E(Ha): -9.056794565845324E+00 3 | :R(Bohr): 4 | 0.199289707274814 7.623689779165953 0.002230082069005 5 | 0.299391321476416 3.828405438300385 3.806897548787078 6 | 4.222993483627602 0.026280958941829 3.802603984345621 7 | 3.926341887621165 3.815479623591832 7.596473184798296 8 | :F(Ha/Bohr): 9 | 0.001348740747191 0.000519944983722 -0.000471254413325 10 | -0.001339080655298 0.000001510075108 -0.000427672494722 11 | -0.003379884185292 -0.000952168732683 -0.000199968816160 12 | 0.003370224093399 0.000430713673853 0.001098895724208 13 | :RELAXSTEP: 6 14 | :E(Ha): -9.057481297802305E+00 15 | :R(Bohr): 16 | 0.249030897156113 7.642865207962792 7.638240348191730 17 | 0.250006393142157 3.828461129457374 3.791125104148432 18 | 4.098344279258630 7.644555236494754 3.795229189096287 19 | 4.050634830443096 3.831364226085080 7.637000158563550 20 | :F(Ha/Bohr): 21 | -0.000102999211261 0.000449955498366 -0.000681311994338 22 | -0.000140822699749 -0.000359475275413 0.000657805345506 23 | -0.000490766483801 0.000369770497067 0.000636729632394 24 | 0.000734588394812 -0.000460250720020 -0.000613222983562 25 | :RELAXSTEP: 7 26 | :E(Ha): -9.057488887961474E+00 27 | :R(Bohr): 28 | 0.246907349432143 7.652141997199744 7.624193652909588 29 | 0.247103033787519 3.821049782384152 3.804687159888064 30 | 4.088226084789823 7.652178841450763 3.808356724201617 31 | 4.065779931990512 3.821875178965341 7.624357263000731 32 | :F(Ha/Bohr): 33 | -0.000009785880810 -0.000026214467282 0.000037130080207 34 | -0.000054257971358 0.000063956736419 -0.000013318129566 35 | -0.000295301734852 -0.000052365396741 -0.000057828154613 36 | 0.000359345587020 0.000014623127604 0.000034016203972 37 | -------------------------------------------------------------------------------- /tests/outputs/Al_multi_geopt.sparc/SPARC.geopt_02: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/tests/outputs/Al_multi_geopt.sparc/SPARC.geopt_02 -------------------------------------------------------------------------------- /tests/outputs/Al_multi_geopt.sparc/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.65339 0 0 5 | 0 7.65339 0 6 | 0 0 7.65339 7 | LATVEC_SCALE: 1 1 1 8 | EXCHANGE_CORRELATION: GGA_PBE 9 | FD_GRID: 17 17 17 10 | KPOINT_GRID: 1 1 1 11 | RELAX_FLAG: 1 12 | RESTART_FLAG: 1 13 | RELAX_NITER: 4 14 | 15 | -------------------------------------------------------------------------------- /tests/outputs/Al_multi_geopt.sparc/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.0958654 -0.0261282 0.122395 12 | 0.297811 3.78245 3.78245 13 | 4.42512 0.145024 3.73798 14 | 3.82922 3.73912 -0.0880102 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_bfgs.sparc/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.65339080963956 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.65339080963956 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.65339080963956 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 1 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_bfgs.sparc/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.18773074240366 -0.05225633243875 0.24479079037080 12 | 0.57562186201678 3.73819825488627 3.73820445990562 13 | 4.42355134796394 0.29004829151097 3.64925980231727 14 | 4.03175338265970 3.65154890056322 -0.17602033658026 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_bfgs.sparc/sparc-socket.traj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/tests/outputs/Al_socket_bfgs.sparc/sparc-socket.traj -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.65339080963956 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.65339080963956 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.65339080963956 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.33335758055190 0.07561875310935 0.18495467389136 12 | 0.42346744237413 4.17961271736997 3.64201665063928 13 | 4.00623609526510 -0.02860236708539 3.80718986872846 14 | 3.90428727645402 3.85391569478794 0.27481786402204 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image00/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.65339080963956 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.65339080963956 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.65339080963956 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image00/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.33335758055190 0.07561875310935 0.18495467389136 12 | 0.42346744237413 4.17961271736997 3.64201665063928 13 | 4.00623609526510 -0.02860236708539 3.80718986872846 14 | 3.90428727645402 3.85391569478794 0.27481786402204 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image00/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.0435568480 0.0098804249 0.0241663700 6 | 0.0553306963 0.5461125430 0.4758696820 7 | 0.5234589733 0.9962627850 0.4974513864 8 | 0.5101382346 0.5035566314 0.0359079878 9 | Total free energy (Ha): -9.041897494954158E+00 10 | Atomic forces (Ha/Bohr): 11 | -6.3263660275E-03 4.1224438525E-03 -9.7573141360E-03 12 | -1.1198940824E-02 -9.4391851505E-03 1.3724648201E-02 13 | 7.1551844744E-03 6.8108725330E-03 8.1322757442E-03 14 | 1.0370122377E-02 -1.4941312349E-03 -1.2099609809E-02 15 | Stress (GPa): 16 | -1.2943266428E+01 -7.3004908329E-01 1.0042725753E+00 17 | -7.3004908329E-01 -1.3976465331E+01 5.9432478434E-01 18 | 1.0042725753E+00 5.9432478434E-01 -8.2525496306E+00 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image01/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.72992471773595 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.72992471773595 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.72992471773595 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image01/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.31002635498075 -0.11676125982981 -0.10080809587731 12 | -0.20478930058667 4.03013608293795 3.42568530055092 13 | 4.19798121279424 -0.14528572934667 3.92585490688121 14 | 3.81736694579949 4.14402369917815 -0.39320327388543 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image01/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.0401072929 0.9848949034 0.9869587222 6 | 0.9735069476 0.5213680896 0.4431718840 7 | 0.5430817720 0.9812047679 0.5078775085 8 | 0.4938427068 0.5361014305 0.9491323282 9 | Total free energy (Ha): -9.043784594535243E+00 10 | Atomic forces (Ha/Bohr): 11 | -4.6545659010E-03 1.0910500836E-02 -2.1484091463E-03 12 | 7.9034706129E-03 -1.0332272794E-02 4.6320681206E-03 13 | -5.5312544787E-03 1.4037844226E-02 -9.0032967529E-03 14 | 2.2823497668E-03 -1.4616072269E-02 6.5196377787E-03 15 | Stress (GPa): 16 | -7.3370513709E+00 1.8635028645E+00 -7.2876683300E-01 17 | 1.8635028645E+00 -2.2951430546E+01 1.6496611617E+00 18 | -7.2876683300E-01 1.6496611617E+00 -9.4337661633E-01 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image02/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.80645862583235 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.80645862583235 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.80645862583235 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image02/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | -0.08033093562375 -0.01084554712961 -0.41175620833334 12 | 0.31616558520924 3.55754090072064 3.74098077011621 13 | 4.00016074444072 -0.24003185000843 3.69930683823330 14 | 3.72801621818795 4.00952321866431 0.44182782750226 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image02/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.9897096828 0.9986106956 0.9472544174 6 | 0.0405005138 0.4557176399 0.4792161144 7 | 0.5124168251 0.9692521460 0.4738777230 8 | 0.4775553675 0.5136161492 0.0565977287 9 | Total free energy (Ha): -9.049946219980990E+00 10 | Atomic forces (Ha/Bohr): 11 | 3.4983196881E-03 -2.5771700762E-03 -3.8304353125E-03 12 | -1.3648434921E-02 4.3201426170E-03 5.5532264248E-03 13 | 2.2414549146E-03 5.1274299183E-03 4.2342097525E-03 14 | 7.9086603180E-03 -6.8704024590E-03 -5.9570008648E-03 15 | Stress (GPa): 16 | 5.3310222375E+00 5.5148480239E-01 1.4621470847E+00 17 | 5.5148480239E-01 8.2658443311E-01 -8.1726042162E-01 18 | 1.4621470847E+00 -8.1726042162E-01 -3.3490689483E+01 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image03/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.88299253392875 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.88299253392875 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.88299253392875 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image03/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.34814184943268 0.08496305907586 0.01878244000876 12 | -0.36271355722600 3.88750493043546 3.87244534387989 13 | 3.92539131682184 -0.12204053467088 3.93296742007826 14 | 3.84860969485622 3.68576327828906 0.17218448446480 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image03/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.0441636660 0.0107780210 0.0023826535 6 | 0.9539878345 0.4931509086 0.4912405190 7 | 0.4979570005 0.9845185018 0.4989180699 8 | 0.4882168388 0.4675588950 0.0218425279 9 | Total free energy (Ha): -9.055230019263519E+00 10 | Atomic forces (Ha/Bohr): 11 | 4.1781641350E-03 -3.8149257152E-03 -1.6645408146E-04 12 | -5.9870939391E-03 4.9750737355E-04 2.3869055006E-03 13 | 2.6554691309E-03 -1.5437864999E-03 3.2513858154E-03 14 | -8.4653932684E-04 4.8612048415E-03 -5.4718372345E-03 15 | Stress (GPa): 16 | -2.8951496890E+01 -4.1737032390E-01 -2.6525391877E-01 17 | -4.1737032390E-01 -1.2291874451E+00 1.7633488643E-01 18 | -2.6525391877E-01 1.7633488643E-01 1.5339643691E+01 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image04/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.95952644202514 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.95952644202514 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.95952644202514 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 16 16 16 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image04/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.00993696901131 0.09825619399092 -0.19572749311097 12 | 0.13631396708380 3.89755378868187 3.66834385305440 13 | 3.85246842744257 0.11763888703045 4.04506082397363 14 | 3.75424789751787 4.10135131357279 -0.01729220451054 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image04/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.0012484372 0.0123444774 0.9754096560 6 | 0.0171258891 0.4896715674 0.4608746362 7 | 0.4840072403 0.0147796339 0.5082037045 8 | 0.4716672436 0.5152757948 0.9978274833 9 | Total free energy (Ha): -9.057145588265648E+00 10 | Atomic forces (Ha/Bohr): 11 | -4.2339372674E-03 -5.6593650263E-04 -1.2339977349E-03 12 | -3.6671313053E-03 2.3923983267E-03 -1.1977998972E-03 13 | 4.1355210899E-03 -1.8214502291E-03 1.8206741576E-03 14 | 3.7655474828E-03 -5.0115948835E-06 6.1112347455E-04 15 | Stress (GPa): 16 | -5.5026184590E+00 3.5780834926E-01 4.4240743901E-01 17 | 3.5780834926E-01 9.2471907584E+00 -2.1332362749E-01 18 | 4.4240743901E-01 -2.1332362749E-01 -1.1075645456E+01 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image05/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.65339080963956 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.65339080963956 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.65339080963956 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image05/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.08337991094040 -0.06252539702939 0.45934918180202 12 | -0.04763850834288 3.84740866294769 4.12574099587526 13 | 3.65487538182834 -0.11180312494937 3.86214727653533 14 | 3.76435901708534 3.60129555981306 -0.03871604946277 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image05/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.0108945058 0.9918303666 0.0600190417 6 | 0.9937755030 0.5027064158 0.5390736078 7 | 0.4775498172 0.9853916875 0.5046321784 8 | 0.4918550628 0.4705490219 0.9949413207 9 | Total free energy (Ha): -9.044014572035739E+00 10 | Atomic forces (Ha/Bohr): 11 | -6.4383507156E-03 -1.7503934315E-03 -3.5140925546E-03 12 | -2.2271019282E-03 -5.5990101886E-03 4.4954429082E-04 13 | 5.9977955350E-03 1.9666995689E-03 2.2135453683E-03 14 | 2.6676571088E-03 5.3827040511E-03 8.5100289551E-04 15 | Stress (GPa): 16 | -1.3874286734E+01 -2.0542245214E-01 -6.5598722945E-01 17 | -2.0542245214E-01 1.0199279100E+01 -9.1615449397E-02 18 | -6.5598722945E-01 -9.1615449397E-02 -2.9918239595E+01 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image06/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.57685690154316 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.57685690154316 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.57685690154316 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image06/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | -0.05832938958648 0.13638415826853 0.04075054176378 12 | -0.16820468848862 3.32319434847749 3.95928218142642 13 | 3.99928278584834 -0.28326093157844 4.09511175831219 14 | 3.70800271465139 4.28069601250493 0.11259064365630 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image06/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.9923016377 0.0180000969 0.0053782911 6 | 0.9778002026 0.4385980086 0.5225494203 7 | 0.5278287340 0.9626149820 0.5404763230 8 | 0.4893853431 0.5649698903 0.0148598086 9 | Total free energy (Ha): -9.035924426688817E+00 10 | Atomic forces (Ha/Bohr): 11 | 5.5845432699E-03 2.7105682219E-03 1.0197450819E-02 12 | 8.5972146543E-03 5.2504361549E-03 -3.2509737736E-03 13 | -1.5552104596E-02 1.5480318661E-03 -1.3859174812E-02 14 | 1.3703466717E-03 -9.5090362429E-03 6.9126977664E-03 15 | Stress (GPa): 16 | 1.7759555830E+01 -4.6546546866E-01 -6.3891690648E-01 17 | -4.6546546866E-01 -4.4874740031E+01 1.8066076363E+00 18 | -6.3891690648E-01 1.8066076363E+00 -2.5353486003E+01 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image07/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.50032299344677 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.50032299344677 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.50032299344677 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image07/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.31307379770930 -0.08628841416725 0.00607806983425 12 | 0.07546922833488 3.60405834779348 3.75054402669773 13 | 3.74999660335244 -0.32496293980352 3.93862479892939 14 | 3.86136971466121 3.63433632847127 -0.03176956464030 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image07/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.0417413754 0.9884953736 0.0008103744 6 | 0.0100621304 0.4805204190 0.5000510018 7 | 0.4999780152 0.9566734739 0.5251273582 8 | 0.5148271238 0.4845573093 0.9957642405 9 | Total free energy (Ha): -9.034213680048802E+00 10 | Atomic forces (Ha/Bohr): 11 | -1.0180268410E-02 -1.3545411899E-03 3.7172707548E-03 12 | -8.8847081615E-04 -2.3416680362E-03 -4.5091589004E-04 13 | 7.7536505809E-03 7.7803685287E-03 -8.4374529685E-03 14 | 3.3150886455E-03 -4.0841593026E-03 5.1710981038E-03 15 | Stress (GPa): 16 | -1.7027746650E+01 -2.2828391408E-01 5.4052045902E-01 17 | -2.2828391408E-01 -1.5863178018E+01 5.1374020884E-01 18 | 5.4052045902E-01 5.1374020884E-01 -1.6615330738E+01 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image08/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.42378908535037 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.42378908535037 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.42378908535037 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 15 15 15 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image08/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.01671813777221 0.20003587269869 -0.35688634394130 12 | -0.25412263026917 3.29093975049837 4.15362544634555 13 | 4.02861284612154 0.40410273785996 3.85758917856974 14 | 3.89087588287684 3.49496828243622 0.35127603099891 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image08/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.0022519683 0.0269452527 0.9519266590 6 | 0.9657691474 0.4432965043 0.5595020816 7 | 0.5426626214 0.0544334885 0.5196253738 8 | 0.5241091629 0.4707795766 0.0473176200 9 | Total free energy (Ha): -8.984190762502326E+00 10 | Atomic forces (Ha/Bohr): 11 | 1.3917785591E-02 -4.4169443843E-02 3.8341549666E-02 12 | 4.3295731608E-02 6.6870036035E-02 -2.6412225841E-02 13 | -4.4462499659E-02 -4.9668713085E-02 -9.5925769433E-03 14 | -1.2751017540E-02 2.6968120893E-02 -2.3367468818E-03 15 | Stress (GPa): 16 | 3.7152930067E+00 -5.3592154346E+00 -1.9862739090E+00 17 | -5.3592154346E+00 -4.5853884151E+01 7.4079969226E+00 18 | -1.9862739090E+00 7.4079969226E+00 -4.9712135261E+01 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image09/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 7.34725517725398 0.00000000000000 0.00000000000000 5 | 0.00000000000000 7.34725517725398 0.00000000000000 6 | 0.00000000000000 0.00000000000000 7.34725517725398 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 14 14 14 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 0 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image09/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 0 1 2 3 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: Al 8 | N_TYPE_ATOM: 4 9 | PSEUDO_POT: 13_Al_3_1.9_1.9_pbe_n_v1.0.psp8 10 | COORD: 11 | 0.00020110702095 -0.05252726325535 -0.20246972650244 12 | -0.00233710867155 3.60498763241032 3.58634303835891 13 | 3.39836291309574 -0.08905090630618 3.62996483241790 14 | 3.55608103722695 3.78898694742978 0.31568113284656 15 | 16 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/single-points/sp_image09/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Al: 5 | 0.0000273717 0.9928507637 0.9724428073 6 | 0.9996819072 0.4906577416 0.4881201145 7 | 0.4625350326 0.9878797042 0.4940572697 8 | 0.4840012973 0.5157010143 0.0429658594 9 | Total free energy (Ha): -9.012237977721181E+00 10 | Atomic forces (Ha/Bohr): 11 | -1.0381291894E-02 4.3429562926E-03 5.0100029696E-03 12 | -1.1850630022E-02 4.5099581043E-04 6.7121333898E-03 13 | 1.5313668564E-02 7.5517479856E-03 5.0398871647E-03 14 | 6.9182533525E-03 -1.2345700089E-02 -1.6762023524E-02 15 | Stress (GPa): 16 | -1.4265348869E+01 2.2353336466E-01 1.1804155850E+00 17 | 2.2353336466E-01 -1.5050365360E+01 -9.7665280730E-01 18 | 1.1804155850E+00 -9.7665280730E-01 -4.6322393542E+01 19 | -------------------------------------------------------------------------------- /tests/outputs/Al_socket_volchange.sparc/sparc.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/tests/outputs/Al_socket_volchange.sparc/sparc.log -------------------------------------------------------------------------------- /tests/outputs/Alloy_geopt_ppd_bc.sparc/SPARC.geopt: -------------------------------------------------------------------------------- 1 | :RELAXSTEP: 1 2 | :CELL: 1.4934716981E+01 1.2194150943E+01 4.3212600000E+01 3 | :VOLUME: 7.8697142088E+03 4 | :LATVEC: 5 | 1.5830800000E+01 0.0000000000E+00 0.0000000000E+00 6 | 0.0000000000E+00 1.2925800000E+01 0.0000000000E+00 7 | 0.0000000000E+00 0.0000000000E+00 4.3212600000E+01 8 | :STRESS: 9 | -3.5037591424E-02 -1.1032579647E-04 10 | -1.1032579647E-04 -2.1767437682E-02 11 | :RELAXSTEP: 2 12 | :CELL: 1.6780648000E+01 1.3701348000E+01 4.3212600000E+01 13 | :VOLUME: 9.9353328703E+03 14 | :LATVEC: 15 | 1.5830800000E+01 0.0000000000E+00 0.0000000000E+00 16 | 0.0000000000E+00 1.2925800000E+01 0.0000000000E+00 17 | 0.0000000000E+00 0.0000000000E+00 4.3212600000E+01 18 | :STRESS: 19 | 6.9350778815E-03 -2.3878906427E-04 20 | -2.3878906427E-04 1.1825868115E-02 21 | :RELAXSTEP: 3 22 | :CELL: 1.6341823477E+01 1.3343049113E+01 4.3212600000E+01 23 | :VOLUME: 9.4224967678E+03 24 | :LATVEC: 25 | 1.5830800000E+01 0.0000000000E+00 0.0000000000E+00 26 | 0.0000000000E+00 1.2925800000E+01 0.0000000000E+00 27 | 0.0000000000E+00 0.0000000000E+00 4.3212600000E+01 28 | :STRESS: 29 | 2.3038837271E-03 -2.3552520596E-04 30 | -2.3552520596E-04 8.2044246296E-03 31 | :RELAXSTEP: 4 32 | :CELL: 1.5856755490E+01 1.2946992579E+01 4.3212600000E+01 33 | :VOLUME: 8.8714299185E+03 34 | :LATVEC: 35 | 1.5830800000E+01 0.0000000000E+00 0.0000000000E+00 36 | 0.0000000000E+00 1.2925800000E+01 0.0000000000E+00 37 | 0.0000000000E+00 0.0000000000E+00 4.3212600000E+01 38 | :STRESS: 39 | -5.8391744555E-03 -1.9199532298E-04 40 | -1.9199532298E-04 1.6852012741E-03 41 | :RELAXSTEP: 5 42 | :CELL: 1.5995673610E+01 1.3060418800E+01 4.3212600000E+01 43 | :VOLUME: 9.0275527502E+03 44 | :LATVEC: 45 | 1.5830800000E+01 0.0000000000E+00 0.0000000000E+00 46 | 0.0000000000E+00 1.2925800000E+01 0.0000000000E+00 47 | 0.0000000000E+00 0.0000000000E+00 4.3212600000E+01 48 | :STRESS: 49 | -3.0766423916E-03 -2.0678413497E-04 50 | -2.0678413497E-04 3.8969679010E-03 51 | :RELAXSTEP: 6 52 | :CELL: 1.5972847428E+01 1.3041781293E+01 4.3212600000E+01 53 | :VOLUME: 9.0018060974E+03 54 | :LATVEC: 55 | 1.5830800000E+01 0.0000000000E+00 0.0000000000E+00 56 | 0.0000000000E+00 1.2925800000E+01 0.0000000000E+00 57 | 0.0000000000E+00 0.0000000000E+00 4.3212600000E+01 58 | :STRESS: 59 | -3.5463716456E-03 -2.1944699830E-04 60 | -2.1944699830E-04 3.5360081998E-03 61 | :RELAXSTEP: 7 62 | :CELL: 1.5973132402E+01 1.3042013973E+01 4.3212600000E+01 63 | :VOLUME: 9.0021273055E+03 64 | :LATVEC: 65 | 1.5830800000E+01 0.0000000000E+00 0.0000000000E+00 66 | 0.0000000000E+00 1.2925800000E+01 0.0000000000E+00 67 | 0.0000000000E+00 0.0000000000E+00 4.3212600000E+01 68 | :STRESS: 69 | -3.5276721460E-03 -2.1266090360E-04 70 | -2.1266090360E-04 3.5218752746E-03 71 | -------------------------------------------------------------------------------- /tests/outputs/Alloy_geopt_ppd_bc.sparc/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 15.8308 0 0 5 | 0 12.9258 0 6 | 0 0 43.2126 7 | LATVEC_SCALE: 1 1 1 8 | KPOINT_GRID: 1 1 1 9 | MESH_SPACING: 0.3 10 | BC: P P D 11 | EXCHANGE_CORRELATION: GGA_PBE 12 | D3_FLAG: 1 13 | TOL_SCF: 0.0001 14 | CALC_STRESS: 0 15 | MAXIT_SCF: 150 16 | RESTART_FLAG: 0 17 | MD_FLAG: 0 18 | SPIN_TYP: 0 19 | RELAX_FLAG: 2 20 | TOL_RELAX_CELL: 0.01 21 | ELEC_TEMP: 500 22 | -------------------------------------------------------------------------------- /tests/outputs/Alloy_geopt_ppd_bc.sparc/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 6 7 32 30 26 17 16 9 28 33 3 4 10 11 5 24 18 25 2 1 27 13 0 29 23 35 12 31 22 21 5 | # 20 8 19 34 14 15 6 | # END ASE-SORT 7 | 8 | ATOM_TYPE: Ag 9 | N_TYPE_ATOM: 6 10 | PSEUDO_POT: Ag.pot 11 | COORD: 12 | 6.62298 10.8319 23.9625 13 | 9.24421 6.47877 22.5729 14 | 4.02062 6.55283 22.4382 15 | 6.59615 6.46288 17.798 16 | 11.8731 6.46288 17.798 17 | 14.5115 10.7715 19.3213 18 | RELAX: 19 | 1 1 1 20 | 1 1 1 21 | 1 1 1 22 | 0 0 0 23 | 0 0 0 24 | 0 0 0 25 | 26 | ATOM_TYPE: Au 27 | N_TYPE_ATOM: 6 28 | PSEUDO_POT: Au.pot 29 | COORD: 30 | 3.95769 6.46288 13.2281 31 | 9.23461 6.46288 13.2281 32 | 9.2714 10.5307 28.6615 33 | 9.23461 2.15429 16.2747 34 | 3.95769 10.7715 19.3213 35 | 9.23461 10.7715 19.3213 36 | RELAX: 37 | 0 0 0 38 | 0 0 0 39 | 1 1 1 40 | 0 0 0 41 | 0 0 0 42 | 0 0 0 43 | 44 | ATOM_TYPE: Ir 45 | N_TYPE_ATOM: 6 46 | PSEUDO_POT: Ir.pot 47 | COORD: 48 | 14.4226 2.05199 25.1452 49 | 1.22066 10.8112 23.9916 50 | 6.74081 1.97517 29.0663 51 | 11.8827 1.92864 29.2973 52 | 3.95769 2.15429 16.2747 53 | 11.8731 10.7715 14.7514 54 | RELAX: 55 | 1 1 1 56 | 1 1 1 57 | 1 1 1 58 | 1 1 1 59 | 0 0 0 60 | 0 0 0 61 | 62 | ATOM_TYPE: Pd 63 | N_TYPE_ATOM: 6 64 | PSEUDO_POT: Pd.pot 65 | COORD: 66 | 6.59615 2.15429 20.8447 67 | 14.6108 10.7083 28.307 68 | 3.87347 10.8007 28.3182 69 | 11.9389 6.37768 27.1754 70 | 6.49618 6.45233 27.3903 71 | 3.87485 2.21716 25.1879 72 | RELAX: 73 | 0 0 0 74 | 1 1 1 75 | 1 1 1 76 | 1 1 1 77 | 1 1 1 78 | 1 1 1 79 | 80 | ATOM_TYPE: Pt 81 | N_TYPE_ATOM: 6 82 | PSEUDO_POT: Pt.pot 83 | COORD: 84 | 1.31923 2.15429 20.8447 85 | 11.8731 2.15429 20.8447 86 | 6.59615 10.7715 14.7514 87 | 14.6105 6.40821 22.4748 88 | 14.5115 2.15429 16.2747 89 | 11.9304 10.7623 23.7826 90 | RELAX: 91 | 0 0 0 92 | 0 0 0 93 | 0 0 0 94 | 1 1 1 95 | 0 0 0 96 | 1 1 1 97 | 98 | ATOM_TYPE: Rh 99 | N_TYPE_ATOM: 6 100 | PSEUDO_POT: Rh.pot 101 | COORD: 102 | 1.31923 10.7715 14.7514 103 | 1.30085 6.43695 26.8384 104 | 14.5115 6.46288 13.2281 105 | 1.31923 6.46288 17.798 106 | 1.22472 2.09656 29.1675 107 | 9.52773 2.07456 25.2209 108 | RELAX: 109 | 0 0 0 110 | 1 1 1 111 | 0 0 0 112 | 0 0 0 113 | 1 1 1 114 | 1 1 1 115 | 116 | -------------------------------------------------------------------------------- /tests/outputs/Cu_FCC.sparc/Cu_FCC.inpt: -------------------------------------------------------------------------------- 1 | 2 | LATVEC_SCALE: 5.416914 5.416914 5.416914 3 | LATVEC: 4 | 1.00 0.00 0.00 5 | 0.00 1.00 0.00 6 | 0.00 0.00 1.00 7 | BC: P P P 8 | 9 | 10 | EXCHANGE_CORRELATION: GGA_PBE 11 | 12 | 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300 15 | 16 | 17 | MESH_SPACING: 0.22 18 | 19 | KPOINT_GRID: 1 1 1 20 | 21 | 22 | 23 | PRECOND_KERKER_THRESH: 0.0 24 | MIXING_PARAMETER: 1.0 25 | TOL_SCF: 1e-4 26 | 27 | 28 | 29 | CALC_STRESS: 0 30 | PRINT_ATOMS: 1 31 | PRINT_VELS: 0 32 | PRINT_FORCES: 0 33 | PRINT_EIGEN: 0 34 | PRINT_DENSITY: 0 35 | -------------------------------------------------------------------------------- /tests/outputs/Cu_FCC.sparc/Cu_FCC.ion: -------------------------------------------------------------------------------- 1 | #========================= 2 | # format of ion file 3 | #========================= 4 | # ATOM_TYPE: 5 | # N_TYPE_ATOM: 6 | # COORD: 7 | # 8 | # ... 9 | # RELAX: 10 | # 11 | # ... 12 | # ASE-SORT: 13 | # 3 2 14 | # 1 0 15 | # END ASE-SORT 16 | 17 | ATOM_TYPE: Cu # atom type 18 | ATOMIC_MASS: 63.546 # atomic mass (amu) 19 | PSEUDO_POT: ../../../psps/29_Cu_19_1.7_1.9_pbe_n_v1.0.psp8 # pseudopotential file 20 | N_TYPE_ATOM: 4 # number of atoms of this type 21 | # COORD: # Cartesian coordinates (au) 22 | COORD_FRAC: # fractional coordinates (in lattice vector basis) 23 | 0.0 0.0 0.0 24 | 0.0 0.5 0.5 25 | 0.5 0.0 0.5 26 | 0.5 0.5 0.0 27 | RELAX: 28 | 0 0 0 29 | 1 1 1 30 | 1 1 1 31 | 1 1 1 -------------------------------------------------------------------------------- /tests/outputs/Cu_FCC.sparc/Cu_FCC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Cu: 5 | 0.0000000000 0.0000000000 0.0000000000 6 | 0.0000000000 0.5000000000 0.5000000000 7 | 0.5000000000 0.0000000000 0.5000000000 8 | 0.5000000000 0.5000000000 0.0000000000 9 | Total free energy (Ha): -7.287745795466985E+02 10 | -------------------------------------------------------------------------------- /tests/outputs/Fe2_spin_scan_gamma.sparc/Fe2_spin_scan_gamma.inpt: -------------------------------------------------------------------------------- 1 | # nprocs: 24 2 | 3 | SPIN_TYP: 1 4 | LATVEC: 5 | 1.00 0.10 0.00 6 | 0.10 1.00 0.00 7 | 0.00 0.00 1.00 8 | LATVEC_SCALE: 2.840052 2.840052 2.840052 9 | 10 | MESH_SPACING: 0.10 11 | FD_ORDER: 12 12 | BC: P P P 13 | EXCHANGE_CORRELATION: SCAN 14 | ELEC_TEMP_TYPE: fermi-dirac 15 | ELEC_TEMP: 315.775131 16 | TOL_SCF: 1e-5 17 | TOL_POISSON: 1e-8 18 | TOL_PSEUDOCHARGE: 1e-8 19 | # NSTATES: 10 20 | KPOINT_GRID: 1 1 1 21 | # KPOINT_SHIFT: 0 0 0.5 22 | MIXING_VARIABLE: potential 23 | MIXING_PRECOND: kerker 24 | PRINT_FORCES: 1 25 | PRINT_ATOMS: 1 26 | CALC_STRESS: 1 27 | -------------------------------------------------------------------------------- /tests/outputs/Fe2_spin_scan_gamma.sparc/Fe2_spin_scan_gamma.ion: -------------------------------------------------------------------------------- 1 | #========================= 2 | # format of ion file 3 | #========================= 4 | # ATOM_TYPE: 5 | # N_TYPE_ATOM: 6 | # COORD: 7 | # 8 | # ... 9 | # RELAX: 10 | # 11 | # ... 12 | 13 | 14 | # Reminder: when changing number of atoms, change the RELAX flags accordingly 15 | # as well. 16 | 17 | ATOM_TYPE: Fe # atom type followed with valence charge 18 | N_TYPE_ATOM: 2 # number of atoms of this type 19 | PSEUDO_POT: ../Fe_LDA.psp8 20 | #ATOMIC_MASS: 21 | COORD_FRAC: # coordinates follows 22 | 0.000000 0.000000 0.000000 23 | 0.520000 0.510000 0.490000 24 | SPIN: 25 | 1.0 26 | 1.0 27 | -------------------------------------------------------------------------------- /tests/outputs/Fe2_spin_scan_gamma.sparc/Fe2_spin_scan_gamma.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Fe: 5 | 0.0000000000 0.0000000000 0.0000000000 6 | 0.5200000000 0.5100000000 0.4900000000 7 | Total free energy (Ha): -2.283157353113279E+02 8 | Atomic forces (Ha/Bohr): 9 | 8.0738249305E-01 3.7399117306E-01 -3.5796157735E-01 10 | -8.0738249305E-01 -3.7399117306E-01 3.5796157735E-01 11 | Stress (GPa): 12 | -2.1918863425E+04 1.3932450782E+03 -5.1023512490E+01 13 | 1.3932450782E+03 -2.1975897437E+04 -1.2676410947E+02 14 | -5.1023512490E+01 -1.2676410947E+02 -2.2380745784E+04 15 | -------------------------------------------------------------------------------- /tests/outputs/H2O_sheet_yz.sparc/H2O_sheet.inpt: -------------------------------------------------------------------------------- 1 | # nprocs: 1 2 | # Test: H2O sheet in x,y plane # 3 | LATVEC_SCALE: 24 5.67 5.67 4 | LATVEC: 5 | 1 0 0 6 | 0 1 0 7 | 0 0 1 8 | MESH_SPACING: 0.2 9 | FD_ORDER: 12 10 | BC: D P P 11 | EXCHANGE_CORRELATION: GGA_PBE 12 | ELEC_TEMP_TYPE: fd 13 | SMEARING: 0.003674932 14 | TOL_SCF: 1e-6 15 | MIXING_VARIABLE: potential 16 | MIXING_PRECOND: none 17 | NSTATES: 8 18 | PRINT_FORCES: 1 19 | PRINT_ATOMS: 1 20 | 21 | CALC_STRESS: 1 22 | -------------------------------------------------------------------------------- /tests/outputs/H2O_sheet_yz.sparc/H2O_sheet.ion: -------------------------------------------------------------------------------- 1 | #========================= 2 | # format of ion file 3 | #========================= 4 | # ATOM_TYPE: 5 | # PSEUDO_POT: 6 | # N_TYPE_ATOM: 7 | # COORD: 8 | # 9 | # ... 10 | # RELAX: 11 | # 12 | # ... 13 | 14 | # Reminder: when changing number of atoms, change the RELAX flags accordingly 15 | # as well. 16 | 17 | ATOM_TYPE: H # atom type 18 | PSEUDO_POT: ../../../psps/01_H_1_1.0_1.0_pbe_v1.0.psp8 19 | N_TYPE_ATOM: 2 # number of atoms of this type 20 | COORD: # coordinates follows 21 | 12.556010134214192 4.265111864110533 2.834589187490385 22 | 12.556010134214192 1.404066510870237 2.834589187490385 23 | 24 | ATOM_TYPE: O # atom type 25 | PSEUDO_POT: ../../../psps/08_O_6_1.2_1.4_pbe_n_v1.0.psp8 26 | N_TYPE_ATOM: 1 # number of atoms of this type 27 | COORD: # coordinates follows 28 | 11.448630624967949 2.834589187490385 2.834589187490385 29 | 30 | -------------------------------------------------------------------------------- /tests/outputs/H2O_sheet_yz.sparc/H2O_sheet.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of H: 5 | 0.5231670889 0.7522243147 0.4999275463 6 | 0.5231670889 0.2476307779 0.4999275463 7 | Fractional coordinates of O: 8 | 0.4770262760 0.4999275463 0.4999275463 9 | Total free energy (Ha): -1.762271099378250E+01 10 | Atomic forces (Ha/Bohr): 11 | -7.0091512819E-03 -2.8155137475E-02 4.7625587321E-08 12 | -7.0083540340E-03 2.8155728229E-02 4.1091979535E-08 13 | 1.4017505316E-02 -5.9075452258E-07 -8.8717566856E-08 14 | Stress (Ha/Bohr**2): 15 | -5.9325459799E-03 3.7871815297E-11 16 | 3.7871815297E-11 -5.4929931315E-03 17 | Stress equiv. to all periodic (GPa): 18 | -7.2725636831E+00 4.6426136346E-08 19 | 4.6426136346E-08 -6.7337265476E+00 20 | -------------------------------------------------------------------------------- /tests/outputs/H2O_sheet_yz.sparc/output.sparc: -------------------------------------------------------------------------------- 1 | --------------------------------------- 2 | Begin PBS Prologue Wed Oct 27 17:53:39 EDT 2021 3 | Job ID: 7040483.sched-hive.pace.gatech.edu 4 | User ID: skumar416 5 | Job name: testing_suite 6 | Queue: hive-interact 7 | End PBS Prologue Wed Oct 27 17:53:39 EDT 2021 8 | --------------------------------------- 9 | /storage/hive/scratch/5/skumar416/00merge_dev_sparc_10272021/sparc_public/tests_LHQ/H2O_sheet/temp_run3 10 | --------------------------------------- 11 | Begin PBS Epilogue Wed Oct 27 17:54:05 EDT 2021 12 | Job ID: 7040483.sched-hive.pace.gatech.edu 13 | User ID: skumar416 14 | Job name: testing_suite 15 | Resources: nodes=1:ppn=1,mem=10gb,walltime=01:00:00,neednodes=1:ppn=1 16 | Rsrc Used: cput=00:00:26,vmem=0kb,walltime=00:00:26,mem=0kb,energy_used=0 17 | Queue: hive-interact 18 | Nodes: 19 | atl1-1-01-017-3-l.pace.gatech.edu 20 | End PBS Epilogue Wed Oct 27 17:54:05 EDT 2021 21 | --------------------------------------- 22 | -------------------------------------------------------------------------------- /tests/outputs/H2O_socket_incomplete.sparc/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 22.67671351004314 0.00000000000000 0.00000000000000 5 | 0.00000000000000 25.56133886715844 0.00000000000000 6 | 0.00000000000000 0.00000000000000 23.80357420641483 7 | LATVEC_SCALE: 1.00000000000000 1.00000000000000 1.00000000000000 8 | BC: P P P 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | FD_GRID: 43 49 45 11 | KPOINT_GRID: 1 1 1 12 | PRECOND_KERKER_THRESH: 0.00000000000000 13 | ELEC_TEMP_TYPE: Fermi-Dirac 14 | ELEC_TEMP: 300.00000000000000 15 | MIXING_PARAMETER: 1.00000000000000 16 | TOL_SCF: 0.00100000000000 17 | RELAX_FLAG: 1 18 | CALC_STRESS: 1 19 | PRINT_ATOMS: 1 20 | PRINT_FORCES: 1 21 | -------------------------------------------------------------------------------- /tests/outputs/H2O_socket_incomplete.sparc/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # 3 | # ASE-SORT: 4 | # 2 0 1 5 | # END ASE-SORT 6 | 7 | ATOM_TYPE: H 8 | N_TYPE_ATOM: 2 9 | PSEUDO_POT: 01_H_1_1.0_1.0_pbe_v1.0.psp8 10 | COORD: 11 | 11.33835675502157 14.22298211213687 11.33835675502157 12 | 11.33835675502157 11.33835675502157 11.33835675502157 13 | 14 | ATOM_TYPE: O 15 | N_TYPE_ATOM: 1 16 | PSEUDO_POT: 08_O_6_1.2_1.4_pbe_n_v1.0.psp8 17 | COORD: 18 | 11.33835675502157 12.78066943357922 12.46521745139326 19 | 20 | -------------------------------------------------------------------------------- /tests/outputs/H2O_socket_incomplete.sparc/SPARC.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions (socket step 1) 3 | *************************************************************************** 4 | Fractional coordinates of H: 5 | 0.5000000000 0.5000000000 0.5236699894 6 | 0.5000000000 0.5564255529 0.4763300106 7 | Fractional coordinates of O: 8 | 0.5000000000 0.4435744471 0.4763300106 9 | Lattice (Bohr): 10 | 2.2676713510E+01 0.0000000000E+00 0.0000000000E+00 11 | 0.0000000000E+00 2.5561338867E+01 0.0000000000E+00 12 | 0.0000000000E+00 0.0000000000E+00 2.3803574206E+01 13 | Total free energy (Ha): -1.809197416636433E+01 14 | Atomic forces (Ha/Bohr): 15 | -8.6777704136E-07 1.1527629608E-02 -3.5795923825E-02 16 | -6.5073941539E-07 -6.2354126553E-03 -7.6030620070E-02 17 | 1.5185164568E-06 -5.2922169523E-03 1.1182654390E-01 18 | Stress (GPa): 19 | 5.1281197310E+00 -7.1825837052E-06 -5.5671926432E-07 20 | -7.1825837052E-06 1.3873103987E+00 7.7353336700E-02 21 | -5.5671926432E-07 7.7353336700E-02 4.0607092494E+00 22 | *************************************************************************** 23 | Atom positions (socket step 2) 24 | *************************************************************************** 25 | Fractional coordinates of H: 26 | 0.4999999563 0.5005155679 0.5219508112 27 | 0.4999999672 0.5561466769 0.4726784726 28 | Fractional coordinates of O: 29 | 0.5000000766 0.4433377551 0.4817007268 30 | Lattice (Bohr): 31 | 2.2676713510E+01 0.0000000000E+00 0.0000000000E+00 32 | 0.0000000000E+00 2.5561338867E+01 0.0000000000E+00 33 | 0.0000000000E+00 0.0000000000E+00 2.3803574206E+01 34 | Total free energy (Ha): -1.802814507208867E+01 35 | Atomic forces (Ha/Bohr): 36 | 5.1674838864E-06 -9.8544275964E-03 1.7809432997E-01 37 | 3.6498044305E-06 -3.9491135111E-03 6.2624074397E-02 38 | -8.8172883169E-06 1.3803541107E-02 -2.4071840436E-01 39 | Stress (GPa): 40 | 5.5346139689E+00 -5.0783418699E-06 -2.1047346943E-05 41 | -5.0783418699E-06 1.5865756909E+00 7.2529353262E-02 42 | -2.1047346943E-05 7.2529353262E-02 2.2277236868E+00 43 | *************************************************************************** 44 | Atom positions (socket step 3) 45 | *************************************************************************** 46 | Fractional coordinates of H: 47 | 0.5000000399 0.5004259418 0.5246645375 48 | 0.5000000261 0.5560536750 0.4732744366 49 | Fractional coordinates of O: 50 | 0.4999999340 0.4435203833 0.4783910366 51 | Lattice (Bohr): 52 | 2.2676713510E+01 0.0000000000E+00 0.0000000000E+00 53 | 0.0000000000E+00 2.5561338867E+01 0.0000000000E+00 54 | 0.0000000000E+00 0.0000000000E+00 2.3803574206E+01 55 | Total free energy (Ha): -1.807552915316842E+01 56 | Atomic forces (Ha/Bohr): 57 | -2.5268751391E-06 2.2707737699E-02 7.2727514813E-02 58 | -3.6382858541E-06 -8.3257331752E-03 1.9519856383E-02 59 | 6.1651609931E-06 -1.4382004524E-02 -9.2247371196E-02 60 | Stress (GPa): 61 | 5.0251692445E+00 3.2211893630E-06 1.6859330449E-07 62 | 3.2211893630E-06 1.3920726609E+00 2.0740747762E-02 63 | 1.6859330449E-07 2.0740747762E-02 4.3580851448E+00 64 | *************************************************************************** 65 | Atom positions (socket step 4) 66 | *************************************************************************** 67 | Fractional coordinates of H: 68 | 0.4999997345 0.5023022347 0.5271021340 69 | 0.4999996579 0.5554741671 0.4732689984 70 | Fractional coordinates of O: 71 | 0.5000006076 0.4422235982 0.4759588783 72 | Lattice (Bohr): 73 | 2.2676713510E+01 0.0000000000E+00 0.0000000000E+00 74 | 0.0000000000E+00 2.5561338867E+01 0.0000000000E+00 75 | 0.0000000000E+00 0.0000000000E+00 2.3803574206E+01 76 | -------------------------------------------------------------------------------- /tests/outputs/H2O_socket_incomplete.sparc/sparc.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SPARC-X/SPARC-X-API/12422228c142965d7decf5b64db57d07e98a6a8c/tests/outputs/H2O_socket_incomplete.sparc/sparc.log -------------------------------------------------------------------------------- /tests/outputs/H2O_wire_z.sparc/H2O_wire.inpt: -------------------------------------------------------------------------------- 1 | # nprocs: 1 2 | # Test: H2O wire in z direction # 3 | LATVEC_SCALE: 14.00 14.00 6.00 4 | LATVEC: 5 | 1 0 0 6 | 0 1 0 7 | 0 0 1 8 | MESH_SPACING: 0.1 9 | FD_ORDER: 12 10 | BC: D D P 11 | #BOUNDARY_CONDITION: 4 12 | EXCHANGE_CORRELATION: GGA_PBE 13 | ELEC_TEMP_TYPE: fd 14 | SMEARING: 0.003674932 15 | TOL_SCF: 1e-6 16 | 17 | #MIXING_VARIABLE: density 18 | PRINT_FORCES: 1 19 | PRINT_ATOMS: 1 20 | CALC_STRESS: 1 21 | 22 | -------------------------------------------------------------------------------- /tests/outputs/H2O_wire_z.sparc/H2O_wire.ion: -------------------------------------------------------------------------------- 1 | #========================= 2 | # format of ion file 3 | #========================= 4 | # ATOM_TYPE: 5 | # PSEUDO_POT: 6 | # N_TYPE_ATOM: 7 | # COORD: 8 | # 9 | # ... 10 | # RELAX: 11 | # 12 | # ... 13 | 14 | # Reminder: when changing number of atoms, change the RELAX flags accordingly 15 | # as well. 16 | 17 | ATOM_TYPE: H # atom type 18 | PSEUDO_POT: ../../../psps/01_H_1_1.0_1.0_pbe_v1.0.psp8 19 | N_TYPE_ATOM: 2 # number of atoms of this type 20 | COORD: # coordinates follows 21 | 7.369126503082081 7.000000000000000 4.430522676620148 22 | 7.369126503082081 7.000000000000000 1.569477323379852 23 | 24 | ATOM_TYPE: O # atom type 25 | PSEUDO_POT: ../../../psps/08_O_6_1.2_1.4_pbe_n_v1.0.psp8 26 | N_TYPE_ATOM: 1 # number of atoms of this type 27 | COORD: # coordinates follows 28 | 6.261746993835837 7.000000000000000 3.000000000000000 29 | 30 | -------------------------------------------------------------------------------- /tests/outputs/H2O_wire_z.sparc/H2O_wire.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of H: 5 | 0.5263661788 0.5000000000 0.7384204461 6 | 0.5263661788 0.5000000000 0.2615795539 7 | Fractional coordinates of O: 8 | 0.4472676424 0.5000000000 0.5000000000 9 | Total free energy (Ha): -1.768512003719815E+01 10 | Atomic forces (Ha/Bohr): 11 | -6.0667427045E-03 3.2520689190E-08 -2.2838126515E-02 12 | -6.0667226226E-03 4.7399932144E-08 2.2838125847E-02 13 | 1.2133465327E-02 -7.9920621334E-08 6.6746163366E-10 14 | Stress (Ha/Bohr): 15 | -1.9995447051E-02 16 | Stress equiv. to all periodic (GPa): 17 | -3.0014610284E+00 18 | -------------------------------------------------------------------------------- /tests/outputs/H2O_wire_z.sparc/output.sparc: -------------------------------------------------------------------------------- 1 | --------------------------------------- 2 | Begin PBS Prologue Wed Oct 27 17:54:10 EDT 2021 3 | Job ID: 7040484.sched-hive.pace.gatech.edu 4 | User ID: skumar416 5 | Job name: testing_suite 6 | Queue: hive-interact 7 | End PBS Prologue Wed Oct 27 17:54:10 EDT 2021 8 | --------------------------------------- 9 | /storage/hive/scratch/5/skumar416/00merge_dev_sparc_10272021/sparc_public/tests_LHQ/H2O_wire/temp_run1 10 | --------------------------------------- 11 | Begin PBS Epilogue Wed Oct 27 17:55:00 EDT 2021 12 | Job ID: 7040484.sched-hive.pace.gatech.edu 13 | User ID: skumar416 14 | Job name: testing_suite 15 | Resources: nodes=1:ppn=1,mem=10gb,walltime=01:00:00,neednodes=1:ppn=1 16 | Rsrc Used: cput=00:00:50,vmem=645340kb,walltime=00:00:50,mem=98232kb,energy_used=0 17 | Queue: hive-interact 18 | Nodes: 19 | atl1-1-01-017-3-l.pace.gatech.edu 20 | End PBS Epilogue Wed Oct 27 17:55:00 EDT 2021 21 | --------------------------------------- 22 | -------------------------------------------------------------------------------- /tests/outputs/MoO3_hubbard.sparc/MoO3_hubbard.inpt: -------------------------------------------------------------------------------- 1 | # nprocs: 1 2 | # Test: MoO3 # 3 | LATVEC: 4 | 6.954192 0 0 5 | 0 7.407726 0 6 | 0 0 26.890803 7 | LATVEC_SCALE: 1 1 1 8 | MESH_SPACING: 0.2 9 | KPOINT_GRID: 1 1 1 10 | BC: P P P 11 | EXCHANGE_CORRELATION: GGA_PBE 12 | HUBBARD_FLAG: 1 13 | TOL_SCF: 1e-6 14 | PRINT_FORCES: 1 15 | PRINT_ATOMS: 1 16 | CALC_STRESS: 1 -------------------------------------------------------------------------------- /tests/outputs/MoO3_hubbard.sparc/MoO3_hubbard.ion: -------------------------------------------------------------------------------- 1 | 2 | #========================= 3 | # format of ion file 4 | #========================= 5 | # ATOM_TYPE: 6 | # PSEUDO_POT: 7 | # N_TYPE_ATOM: 8 | # COORD: 9 | # 10 | # ... 11 | # RELAX: 12 | # 13 | # ... 14 | 15 | # Reminder: when changing number of atoms, change the RELAX flags accordingly 16 | # as well. 17 | 18 | ATOM_TYPE: Mo # atom type 19 | PSEUDO_POT: ../../../psps/42_Mo_14_2.0_2.6_pbe_n_v1.0.psp8 20 | N_TYPE_ATOM: 1 # number of atoms of this type 21 | COORD_FRAC: # coordinates follows 22 | 0.25 0.42301 0.602057 23 | 24 | 25 | ATOM_TYPE: O # atom type 26 | PSEUDO_POT: ../../../psps/08_O_6_1.2_1.4_pbe_n_v1.0.psp8 27 | N_TYPE_ATOM: 3 # number of atoms of this type 28 | COORD_FRAC: # coordinates follows 29 | 0.25 0.466327 0.718344 30 | 0.25 0.498536 0.435585 31 | 0.25 0.982682 0.587091 32 | 33 | HUBBARD: 34 | U_ATOM_TYPE: Mo 35 | U_VAL: 0 0 0.05 0 # U values in hartrees for s p d f orbitals (valence only) 36 | -------------------------------------------------------------------------------- /tests/outputs/MoO3_hubbard.sparc/MoO3_hubbard.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Mo: 5 | 0.2500000000 0.4230100000 0.6020570000 6 | Fractional coordinates of O: 7 | 0.2500000000 0.4663270000 0.7183440000 8 | 0.2500000000 0.4985360000 0.4355850000 9 | 0.2500000000 0.9826820000 0.5870910000 10 | Total free energy (Ha): -1.193017119895254E+02 11 | Atomic forces (Ha/Bohr): 12 | -3.0115166041E-05 -1.0388563139E-01 6.4656600822E-02 13 | 6.5627841409E-06 1.6887899866E-02 -1.8666310086E-02 14 | 4.0006244503E-05 4.7528526782E-03 3.8420463088E-02 15 | -1.6453862604E-05 8.2244878848E-02 -8.4410753824E-02 16 | Stress (GPa): 17 | 5.8170874325E-01 4.8668100165E-04 -7.7274428237E-04 18 | 4.8668100165E-04 -7.5937303823E+00 3.1138748238E-02 19 | -7.7274428237E-04 3.1138748238E-02 4.1635623448E+00 20 | -------------------------------------------------------------------------------- /tests/outputs/NH3_sort_lbfgs_opt.sparc/SPARC.inpt: -------------------------------------------------------------------------------- 1 | # Input File Generated By SPARC ASE Calculator 2 | 3 | LATVEC: 4 | 11.3384 0 0 5 | 0 11.3384 0 6 | 0 0 11.3384 7 | LATVEC_SCALE: 1 1 1 8 | EXCHANGE_CORRELATION: GGA_PBE 9 | FD_GRID: 24 24 24 10 | KPOINT_GRID: 1 1 1 11 | TOL_RELAX: 0.000388938 12 | RELAX_FLAG: 1 13 | PRINT_RELAXOUT: 1 14 | RELAX_METHOD: LBFGS 15 | -------------------------------------------------------------------------------- /tests/outputs/NH3_sort_lbfgs_opt.sparc/SPARC.ion: -------------------------------------------------------------------------------- 1 | # Ion File Generated by SPARC ASE Calculator 2 | # This example is a real calculation by sparc-dft-api interface 3 | # Things to test are the sorting / constraints / result parsing 4 | # 5 | # ASE-SORT: 6 | # 3 0 1 2 7 | # END ASE-SORT 8 | 9 | ATOM_TYPE: H 10 | N_TYPE_ATOM: 3 11 | PSEUDO_POT: 01_H_1_1.0_1.0_pbe_v1.0.psp8 12 | COORD: 13 | 0.00287811 1.77539 -0.514085 14 | 1.5409 -0.886466 -0.51453 15 | -1.53689 -0.888792 -0.514523 16 | RELAX: 17 | 1 1 1 18 | 1 1 1 19 | 1 1 1 20 | 21 | ATOM_TYPE: N 22 | N_TYPE_ATOM: 1 23 | PSEUDO_POT: 07_N_5_1.2_1.4_pbe_n_v1.0.psp8 24 | COORD: 25 | 0 0 0.220132 26 | RELAX: 27 | 0 0 0 28 | 29 | -------------------------------------------------------------------------------- /tests/outputs/NH3_sort_lbfgs_opt.sparc/sparc.log: -------------------------------------------------------------------------------- 1 | 2 | ******************************************************************************** 3 | SPARC program started by sparc-python-api at 2023-05-22T17:15:36.477200 4 | command: /home/pink/miniforge3/envs/sparc/bin/mpirun -n 1 /home/pink/miniforge3/envs/sparc/bin/sparc -name SPARC 5 | 6 | 7 | fchrg = 4.00000000 > 0.0 (icmod != 0) 8 | This pseudopotential contains non-linear core correction. 9 | 10 | fchrg = 4.000000, READING MODEL CORE CHARGE! 11 | 12 | WARNING: The density after mixing has negative components! 13 | WARNING: The density after mixing has negative components! 14 | WARNING: The density after mixing has negative components! 15 | WARNING: The density after mixing has negative components! 16 | WARNING: The density after mixing has negative components! 17 | WARNING: The density after mixing has negative components! 18 | WARNING: The density after mixing has negative components! 19 | WARNING: The density after mixing has negative components! 20 | WARNING: The density after mixing has negative components! 21 | WARNING: The density after mixing has negative components! 22 | WARNING: The density after mixing has negative components! 23 | WARNING: The density after mixing has negative components! 24 | WARNING: The density after mixing has negative components! 25 | WARNING: The density after mixing has negative components! 26 | WARNING: The density after mixing has negative components! 27 | WARNING: The density after mixing has negative components! 28 | WARNING: The density after mixing has negative components! 29 | WARNING: The density after mixing has negative components! 30 | WARNING: The density after mixing has negative components! 31 | WARNING: The density after mixing has negative components! 32 | WARNING: The density after mixing has negative components! 33 | WARNING: The density after mixing has negative components! 34 | WARNING: The density after mixing has negative components! 35 | WARNING: The density after mixing has negative components! 36 | WARNING: The density after mixing has negative components! 37 | WARNING: The density after mixing has negative components! 38 | WARNING: The density after mixing has negative components! 39 | WARNING: The density after mixing has negative components! 40 | WARNING: The density after mixing has negative components! 41 | WARNING: The density after mixing has negative components! 42 | WARNING: The density after mixing has negative components! 43 | WARNING: The density after mixing has negative components! 44 | WARNING: The density after mixing has negative components! 45 | WARNING: The density after mixing has negative components! 46 | WARNING: The density after mixing has negative components! 47 | WARNING: The density after mixing has negative components! 48 | WARNING: The density after mixing has negative components! 49 | WARNING: The density after mixing has negative components! 50 | The program took 10.071 s. 51 | -------------------------------------------------------------------------------- /tests/outputs/Si8_cell_geopt_relax2.sparc/Si8_cell_geopt.geopt: -------------------------------------------------------------------------------- 1 | :RELAXSTEP: 1 2 | :CELL: 9.3272727273E+00 9.3272727273E+00 9.3272727273E+00 3 | :VOLUME: 8.1145422690E+02 4 | :LATVEC: 5 | 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 6 | 0.0000000000E+00 1.0000000000E+00 0.0000000000E+00 7 | 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 8 | :STRESS: 9 | -5.6292942161E+01 8.8196137948E-04 -3.6637837366E-04 10 | 8.8196137948E-04 -5.6292757276E+01 3.2138320412E-04 11 | -3.6637837366E-04 3.2138320412E-04 -5.6292624801E+01 12 | :RELAXSTEP: 2 13 | :CELL: 1.1286000000E+01 1.1286000000E+01 1.1286000000E+01 14 | :VOLUME: 1.4375406617E+03 15 | :LATVEC: 16 | 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 17 | 0.0000000000E+00 1.0000000000E+00 0.0000000000E+00 18 | 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 19 | :STRESS: 20 | 1.0020626895E+01 -5.9541735443E-10 4.2704367421E-09 21 | -5.9541735443E-10 1.0020626902E+01 -5.7918792773E-10 22 | 4.2704367421E-09 -5.7918792773E-10 1.0020626897E+01 23 | :RELAXSTEP: 3 24 | :CELL: 1.1032774586E+01 1.1032774586E+01 1.1032774586E+01 25 | :VOLUME: 1.3429326576E+03 26 | :LATVEC: 27 | 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 28 | 0.0000000000E+00 1.0000000000E+00 0.0000000000E+00 29 | 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 30 | :STRESS: 31 | 7.1033863815E+00 -1.5545092313E-11 -6.8196461183E-10 32 | -1.5545092313E-11 7.1033863823E+00 -2.8989733148E-11 33 | -6.8196461183E-10 -2.8989733148E-11 7.1033863808E+00 34 | :RELAXSTEP: 4 35 | :CELL: 1.0441480472E+01 1.0441480472E+01 1.0441480472E+01 36 | :VOLUME: 1.1383773384E+03 37 | :LATVEC: 38 | 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 39 | 0.0000000000E+00 1.0000000000E+00 0.0000000000E+00 40 | 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 41 | :STRESS: 42 | -5.1546636018E+00 4.1523866475E-13 -4.1382550152E-11 43 | 4.1523866475E-13 -5.1546636025E+00 6.6904849258E-12 44 | -4.1382550152E-11 6.6904849258E-12 -5.1546636022E+00 45 | :RELAXSTEP: 5 46 | :CELL: 1.0698114243E+01 1.0698114243E+01 1.0698114243E+01 47 | :VOLUME: 1.2243954131E+03 48 | :LATVEC: 49 | 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 50 | 0.0000000000E+00 1.0000000000E+00 0.0000000000E+00 51 | 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 52 | :STRESS: 53 | 1.3144091941E+00 -8.5788897523E-10 1.3579211628E-08 54 | -8.5788897523E-10 1.3144092015E+00 -5.5324285731E-10 55 | 1.3579211628E-08 -5.5324285731E-10 1.3144091977E+00 56 | :RELAXSTEP: 6 57 | :CELL: 1.0646967198E+01 1.0646967198E+01 1.0646967198E+01 58 | :VOLUME: 1.2069179550E+03 59 | :LATVEC: 60 | 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 61 | 0.0000000000E+00 1.0000000000E+00 0.0000000000E+00 62 | 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 63 | :STRESS: 64 | 1.8255733527E-01 1.1690610590E-10 -1.8251209346E-09 65 | 1.1690610590E-10 1.8255733453E-01 7.5006354546E-11 66 | -1.8251209346E-09 7.5006354546E-11 1.8255733497E-01 67 | :RELAXSTEP: 7 68 | :CELL: 1.0638955458E+01 1.0638955458E+01 1.0638955458E+01 69 | :VOLUME: 1.2041954223E+03 70 | :LATVEC: 71 | 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 72 | 0.0000000000E+00 1.0000000000E+00 0.0000000000E+00 73 | 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 74 | :STRESS: 75 | -1.4216711673E-03 1.0292458134E-10 -1.8760770611E-09 76 | 1.0292458134E-10 -1.4216727292E-03 7.2696789785E-11 77 | -1.8760770611E-09 7.2696789785E-11 -1.4216721414E-03 78 | :RELAXSTEP: 8 79 | :CELL: 1.0639017414E+01 1.0639017414E+01 1.0639017414E+01 80 | :VOLUME: 1.2042164603E+03 81 | :LATVEC: 82 | 1.0000000000E+00 0.0000000000E+00 0.0000000000E+00 83 | 0.0000000000E+00 1.0000000000E+00 0.0000000000E+00 84 | 0.0000000000E+00 0.0000000000E+00 1.0000000000E+00 85 | :STRESS: 86 | -5.6848955674E-06 4.1602791230E-12 -2.9734568924E-11 87 | 4.1602791230E-12 -5.6848342716E-06 1.2355227433E-12 88 | -2.9734568924E-11 1.2355227433E-12 -5.6848234006E-06 89 | -------------------------------------------------------------------------------- /tests/outputs/Si8_cell_geopt_relax2.sparc/Si8_cell_geopt.inpt: -------------------------------------------------------------------------------- 1 | # nprocs: 24 2 | # Test: Si8 # 3 | LATVEC: 4 | 1 0 0 5 | 0 1 0 6 | 0 0 1 7 | LATVEC_SCALE: 10.26 10.26 10.26 8 | FD_GRID: 26 26 26 # FD grid 9 | FD_ORDER: 12 10 | BC: P P P 11 | EXCHANGE_CORRELATION: GGA_PBE 12 | TOL_SCF: 1e-6 13 | TOL_POISSON: 1e-8 14 | TOL_PSEUDOCHARGE: 1e-8 15 | ELEC_TEMP: 315.775131 16 | ELEC_TEMP_TYPE: fd 17 | 18 | RELAX_FLAG: 2 19 | RELAX_NITER: 50 20 | 21 | RELAX_MAXDILAT: 1.1 22 | TOL_RELAX_CELL: 1e-4 23 | CALC_STRESS: 1 24 | MAXIT_SCF: 30 -------------------------------------------------------------------------------- /tests/outputs/Si8_cell_geopt_relax2.sparc/Si8_cell_geopt.ion: -------------------------------------------------------------------------------- 1 | #========================= 2 | # format of ion file 3 | #========================= 4 | # ATOM_TYPE: 5 | # N_TYPE_ATOM: 6 | # COORD: 7 | # 8 | # ... 9 | # RELAX: 10 | # 11 | # ... 12 | 13 | 14 | # Reminder: when changing number of atoms, change the RELAX flags accordingly 15 | # as well. 16 | 17 | ATOM_TYPE: Si # atom type followed with valence charge 18 | N_TYPE_ATOM: 8 # number of atoms of this type 19 | PSEUDO_POT: ../../../psps/14_Si_4_1.9_1.9_pbe_n_v1.0.psp8 20 | ATOMIC_MASS: 28.0855 21 | COORD_FRAC: # coordinates follows 22 | 0 0 0 23 | 0.250000000000000 0.250000000000000 0.250000000000000 24 | 0 0.500000000000000 0.500000000000000 25 | 0.250000000000000 0.750000000000000 0.750000000000000 26 | 0.500000000000000 0 0.500000000000000 27 | 0.750000000000000 0.250000000000000 0.750000000000000 28 | 0.500000000000000 0.500000000000000 0 29 | 0.750000000000000 0.750000000000000 0.250000000000000 30 | 31 | #COORD: # coordinates follows 32 | # 0 0 0 33 | # 2.565000000000000 2.565000000000000 2.565000000000000 34 | # 0 5.130000000000000 5.130000000000000 35 | # 2.565000000000000 7.695000000000000 7.695000000000000 36 | # 5.130000000000000 0 5.130000000000000 37 | # 7.695000000000000 2.565000000000000 7.695000000000000 38 | # 5.130000000000000 5.130000000000000 0 39 | # 7.695000000000000 7.695000000000000 2.565000000000000 40 | -------------------------------------------------------------------------------- /tests/outputs/SiH4_quick.sparc/SiH4_quick.inpt: -------------------------------------------------------------------------------- 1 | # nprocs: 1 2 | # Test: SiH4 # 3 | LATVEC: 4 | 1 0 0 5 | 0 1 0 6 | 0 0 1 7 | LATVEC_SCALE: 13 13 13 8 | FD_GRID: 26 26 26 9 | BOUNDARY_CONDITION: 1 10 | RHO_TRIGGER: 4 11 | EXCHANGE_CORRELATION: GGA_PBE 12 | MAXIT_SCF: 30 13 | TOL_SCF: 1e-5 14 | TOL_PSEUDOCHARGE: 1e-5 15 | NSTATES: 10 16 | PRINT_FORCES: 1 17 | PRINT_ATOMS: 1 18 | 19 | 20 | -------------------------------------------------------------------------------- /tests/outputs/SiH4_quick.sparc/SiH4_quick.ion: -------------------------------------------------------------------------------- 1 | #========================= 2 | # format of ion file 3 | #========================= 4 | # ATOM_TYPE: 5 | # N_TYPE_ATOM: 6 | # COORD: 7 | # 8 | # ... 9 | # RELAX: 10 | # 11 | # ... 12 | 13 | 14 | # Reminder: when changing number of atoms, change the RELAX flags accordingly 15 | # as well. 16 | 17 | ATOM_TYPE: Si # atom type followed with valence charge 18 | PSEUDO_POT: ../../../psps/14_Si_4_1.9_1.9_pbe_n_v1.0.psp8 19 | N_TYPE_ATOM: 1 # number of atoms of this type 20 | COORD: # coordinates follows 21 | 6.5 6.5 6.5 22 | 23 | 24 | ATOM_TYPE: H # atom type followed with valence charge 25 | PSEUDO_POT: ../../../psps/01_H_1_1.0_1.0_pbe_v1.0.psp8 # pseudopotential 26 | N_TYPE_ATOM: 4 # number of atoms of this type 27 | COORD: # coordinates follows 28 | 8.127432021000001 8.127432021000001 8.127432021000001 29 | 4.872567978999999 4.872567978999999 8.127432021000001 30 | 4.872567978999999 8.127432021000001 4.872567978999999 31 | 8.127432021000001 4.872567978999999 4.872567978999999 32 | 33 | -------------------------------------------------------------------------------- /tests/outputs/SiH4_quick.sparc/SiH4_quick.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of Si: 5 | 0.5000000000 0.5000000000 0.5000000000 6 | Fractional coordinates of H: 7 | 0.6251870785 0.6251870785 0.6251870785 8 | 0.3748129215 0.3748129215 0.6251870785 9 | 0.3748129215 0.6251870785 0.3748129215 10 | 0.6251870785 0.3748129215 0.3748129215 11 | Total free energy (Ha): -6.551906787524707E+00 12 | Atomic forces (Ha/Bohr): 13 | 2.7841214148E-07 2.4232519093E-07 8.2437137313E-08 14 | -4.2951392225E-03 -4.2950974246E-03 -4.2950641764E-03 15 | 4.2949302306E-03 4.2949736382E-03 -4.2950197241E-03 16 | 4.2950028584E-03 -4.2950525571E-03 4.2950108370E-03 17 | -4.2950722786E-03 4.2949340183E-03 4.2949906265E-03 18 | -------------------------------------------------------------------------------- /tests/outputs/TiO2_orthogonal_quick_md.sparc/TiO2_orthogonal_quick_md.inpt: -------------------------------------------------------------------------------- 1 | # nprocs: 8 2 | 3 | # Test: CuSi7 # 4 | LATVEC_SCALE: 8.79468 8.79468 8.79468 5 | LATVEC: 6 | 1 0 0 7 | 0 1 0 8 | 0 0 1 9 | MESH_SPACING: 0.35 10 | FD_ORDER: 12 11 | BC: P P P 12 | EXCHANGE_CORRELATION: GGA_PBE 13 | TOL_SCF: 1e-6 14 | 15 | 16 | PRINT_FORCES: 1 17 | PRINT_ATOMS: 1 18 | CALC_STRESS: 1 19 | 20 | MD_FLAG: 1 # 1= MD, 0= no MD (default) 21 | ION_TEMP: 800 22 | MD_METHOD: NVE 23 | MD_TIMESTEP: 0.6 24 | MD_NSTEP: 5 25 | -------------------------------------------------------------------------------- /tests/outputs/TiO2_orthogonal_quick_md.sparc/TiO2_orthogonal_quick_md.ion: -------------------------------------------------------------------------------- 1 | #========================= 2 | # format of ion file 3 | #========================= 4 | # ATOM_TYPE: 5 | # PSEUDO_POT: 6 | # N_TYPE_ATOM: 7 | # ATOMIC_MASS: #(optional, for MD only) 8 | # COORD: 9 | # 10 | # ... 11 | # RELAX: #(optional) 12 | # 13 | # ... 14 | 15 | # this is a comment 16 | 17 | ATOM_TYPE: Ti # atom type 18 | N_TYPE_ATOM: 2 # number of atoms of this type 19 | PSEUDO_POT: ../../../psps/22_Ti_12_2.0_2.8_pbe_n_v1.0.psp8 # pseudopotential 20 | COORD_FRAC: # coordinates follows 21 | 0.5000000000000000 0.5000000000000000 0.5000000000000000 22 | 0.0000000000000000 0.0000000000000000 0.0000000000000000 23 | 24 | ATOM_TYPE: O # atom type 25 | N_TYPE_ATOM: 4 # number of atoms of this type 26 | PSEUDO_POT: ../../../psps/08_O_6_1.2_1.4_pbe_n_v1.0.psp8 # pseudopotential 27 | COORD_FRAC: # coordinates follows 28 | 0.1954200000000000 0.8045800000000000 0.5000000000000000 29 | 0.8045800000000000 0.1954200000000000 0.5000000000000000 30 | 0.3045800000000001 0.3045800000000000 0.0000000000000000 31 | 0.6954200000000000 0.6954200000000000 0.0000000000000000 32 | 33 | -------------------------------------------------------------------------------- /tests/outputs/WSe2_helix_static.sparc/WSe2_cyclix.inpt: -------------------------------------------------------------------------------- 1 | # nprocs: 24 2 | CELL: 30.349896582200003 0.299199300341885 3.135906672400000 3 | TWIST_ANGLE: 0.047705389796071 4 | FD_GRID: 120 42 25 5 | KPOINT_GRID: 1 3 4 6 | KPOINT_SHIFT: 0 0 0 7 | CHEB_DEGREE: 100 8 | BC: D C H 9 | EXCHANGE_CORRELATION: GGA_PBE 10 | TOL_SCF: 1e-6 11 | SMEARING: 0.001 12 | ELEC_TEMP_TYPE: fd 13 | CALC_STRESS: 1 14 | PRINT_FORCES: 1 15 | MIXING_VARIABLE: potential 16 | MIXING_PRECOND: none -------------------------------------------------------------------------------- /tests/outputs/WSe2_helix_static.sparc/WSe2_cyclix.ion: -------------------------------------------------------------------------------- 1 | ATOM_TYPE: W 2 | N_TYPE_ATOM: 1 3 | PSEUDO_POT: ../../../psps/74_W_14_2.3_2.5_pbe_n_v1.0.psp8 4 | COORD: 5 | 35.932050040279556 5.415857727989695 3.135799543546264 6 | ATOM_TYPE: Se 7 | N_TYPE_ATOM: 2 8 | PSEUDO_POT: ../../../psps/34_Se_16_1.9_2.1_pbe_n_v1.0.psp8 9 | COORD: 10 | 32.959304779880675 3.357462537482735 0.000032907355847 11 | 39.278965212349100 3.880850013508314 0.000074221497889 -------------------------------------------------------------------------------- /tests/outputs/WSe2_helix_static.sparc/WSe2_cyclix.static: -------------------------------------------------------------------------------- 1 | *************************************************************************** 2 | Atom positions 3 | *************************************************************************** 4 | Fractional coordinates of W: 5 | 1.1972993167 0.0000145889 0.9999658380 6 | Fractional coordinates of Se: 7 | 1.0915974792 0.3392894457 0.0000104937 8 | 1.3005058466 0.3291420709 0.0000236683 9 | Total free energy (Ha): -3.055065628300148E+02 10 | Atomic forces (Ha/Bohr): 11 | -1.9631231365E-04 2.0197957296E-03 -9.3342235956E-04 12 | -1.4864255791E-03 -8.3883915724E-04 5.1817786556E-04 13 | -1.5069571202E-02 -2.7428580192E-03 4.1524449400E-04 14 | Stress (Ha/Bohr): 15 | 5.9636521405E-01 16 | Stress equiv. to all periodic (GPa): 17 | 2.5346951054E+00 18 | -------------------------------------------------------------------------------- /tests/sparc-latex-doc-202302/Manual.tex: -------------------------------------------------------------------------------- 1 | \documentclass[xcolor=dvipsnames,t]{beamer} 2 | % \usepackage[utf8]{inputenc} 3 | \usepackage{verbatim} % for comment 4 | \usetheme{Madrid} 5 | \usecolortheme{seahorse} 6 | \usepackage{beamerouterthemesplit} 7 | \usepackage{array} 8 | \usepackage{algorithm} 9 | \usepackage{algpseudocode} 10 | \usepackage[T1]{fontenc} 11 | 12 | 13 | \setbeamerfont{institute}{size=\normalsize} 14 | 15 | \title[] {SPARC \\ {\normalsize Simulation Package for Ab-initio Real-space Calculations} \\ {\small User guide}} 16 | %\author{} 17 | %\author{Qimen Xu, Abhiraj Sharma, Phanish Suryanarayana, } 18 | 19 | \institute[] 20 | { 21 | Material Physics \& Mechanics Group \\ 22 | PI: Phanish Suryanarayana \\ 23 | Main Developers: Qimen Xu, Abhiraj Sharma \\ 24 | Collaborators: J.E. Pask (LLNL), A.J. Medford (GT), E. Chow (GT) \\ 25 | Georgia Institute of Technology 26 | } 27 | 28 | \date{} 29 | \setbeamertemplate{frametitle continuation}{} 30 | \setbeamertemplate{navigation symbols}{} 31 | \setbeamercolor{block title}{bg=Apricot!50,fg=black} 32 | %\addtobeamertemplate{block begin}{\vskip -\smallskipamount}{} 33 | %\addtobeamertemplate{block end}{}{\vskip -\smallskipamount} 34 | \addtobeamertemplate{block begin}{\vspace*{-0.6pt}}{} 35 | \addtobeamertemplate{block end}{}{\vspace*{-0.6pt}} 36 | \hypersetup{colorlinks, 37 | citecolor=violet, 38 | linkcolor=blue, 39 | menucolor=white, 40 | anchorcolor=yellow 41 | filecolor=pink, 42 | } 43 | 44 | 45 | \setbeamertemplate{footline}{ 46 | \hbox{% 47 | \begin{beamercolorbox}[wd=\paperwidth,ht=1ex,dp=1.5ex,leftskip=2ex,rightskip=2ex]{page footer}% 48 | \usebeamerfont{title in head/foot}% 49 | \insertshorttitle \hfill 50 | \insertsection \hfill 51 | \insertframenumber{} / \inserttotalframenumber 52 | \end{beamercolorbox}}% 53 | } 54 | 55 | % \setbeamertemplate{headline} [split theme] 56 | % {% 57 | % \begin{beamercolorbox}{section in head/foot} 58 | % \vskip2pt\insertnavigation{\paperwidth}\vskip2pt 59 | % \end{beamercolorbox}% 60 | % } 61 | 62 | % \defbeamertemplate*{footline}{split theme} 63 | % {% 64 | % \leavevmode% 65 | % \hbox{\begin{beamercolorbox}[wd=.5\paperwidth,ht=2.5ex,dp=1.125ex,leftskip=.3cm plus1fill,rightskip=.3cm]{section in head/foot}% 66 | % \usebeamerfont{author in head/foot}\insertshortauthor 67 | % \end{beamercolorbox}% 68 | % \begin{beamercolorbox}[wd=.5\paperwidth,ht=2.5ex,dp=1.125ex,leftskip=.3cm,rightskip=.3cm plus1fil]{title in head/foot}% 69 | % \usebeamerfont{title in head/foot}\insertshorttitle 70 | % \end{beamercolorbox}}% 71 | % \vskip0pt% 72 | % } 73 | 74 | 75 | 76 | \let\otp\titlepage 77 | \renewcommand{\titlepage}{\otp\addtocounter{framenumber}{-1}} 78 | 79 | 80 | %\includeonly{Introduction,Stress,MD,Optimization,Print} 81 | %\includeonly{Introduction} 82 | 83 | \begin{document} 84 | 85 | %\frame{\titlepage} 86 | 87 | \begin{frame}[plain] 88 | \titlepage 89 | \end{frame} 90 | 91 | \include{Introduction} 92 | \include{System} 93 | \include{SCF} 94 | \include{Electrostatics} 95 | \include{Stress} 96 | \include{MD} 97 | \include{Optimization} 98 | \include{Print} 99 | \include{Paral} 100 | \include{SQ} 101 | 102 | \end{document} 103 | -------------------------------------------------------------------------------- /tests/sparc-latex-doc-202302/Stress.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | 3 | 4 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 5 | \begin{frame}[allowframebreaks,c]{} \label{Stress calculation} 6 | 7 | \begin{center} 8 | \Huge \textbf{Stress calculation} 9 | \end{center} 10 | 11 | \end{frame} 12 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 13 | 14 | 15 | 16 | 17 | 18 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 19 | \begin{frame}[allowframebreaks]{\texttt{CALC\_STRESS}} \label{CALC_STRESS} 20 | \vspace*{-12pt} 21 | \begin{columns} 22 | \column{0.4\linewidth} 23 | \begin{block}{Type} 24 | Integer 25 | \end{block} 26 | 27 | \begin{block}{Default} 28 | 0 29 | \end{block} 30 | 31 | \column{0.4\linewidth} 32 | \begin{block}{Unit} 33 | No unit 34 | \end{block} 35 | 36 | \begin{block}{Example} 37 | \texttt{CALC\_STRESS}: 1 38 | \end{block} 39 | \end{columns} 40 | 41 | \begin{block}{Description} 42 | Flag for calculation of the Hellmann-Feynman stress tensor (in cartesian coordinates). 43 | \end{block} 44 | 45 | %\begin{block}{Remark} 46 | %\end{block} 47 | 48 | \end{frame} 49 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 50 | 51 | 52 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 53 | \begin{frame}[allowframebreaks]{\texttt{CALC\_PRES}} \label{CALC_PRES} 54 | \vspace*{-12pt} 55 | \begin{columns} 56 | \column{0.4\linewidth} 57 | \begin{block}{Type} 58 | Integer 59 | \end{block} 60 | 61 | \begin{block}{Default} 62 | 0 63 | \end{block} 64 | 65 | \column{0.4\linewidth} 66 | \begin{block}{Unit} 67 | No unit 68 | \end{block} 69 | 70 | \begin{block}{Example} 71 | \texttt{CALC\_PRES}: 1 72 | \end{block} 73 | \end{columns} 74 | 75 | \begin{block}{Description} 76 | Flag for calculation of the pressure. 77 | \end{block} 78 | 79 | \begin{block}{Remark} 80 | Pressure is directly calculated, without calculation of the stress tensor. 81 | \end{block} 82 | 83 | \end{frame} 84 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 85 | -------------------------------------------------------------------------------- /tests/sparc-latex-doc-202302/highT/Introduction.tex: -------------------------------------------------------------------------------- 1 | 2 | \begin{frame}[allowframebreaks]{\textbf{Comments}} \label{Introduction} 3 | The code will fail with the following options and the related input options are listed. 4 | \begin{itemize} 5 | \item Polarized calculation: \texttt{SPIN\_TYP}. 6 | \item K-point calculation: \texttt{KPOINT\_GRID}, \texttt{KPOINT\_SHIFT}. 7 | \item Dirichlet boundary condition in any direction: \texttt{BC} 8 | \item Define number of states/orbitals: \texttt{NSTATES} 9 | \item Hybrid functionals: \texttt{EXCHANGE\_CORRELATION} 10 | \item Print eigenvalues into file: \texttt{PRINT\_EIGEN} 11 | \end{itemize} 12 | 13 | \end{frame} 14 | 15 | \begin{frame}[allowframebreaks]{\textbf{Input file options}} \label{Index} 16 | \vspace{-2mm} 17 | \begin{block}{Spectral Quadrature} 18 | \hyperlink{SQ_FLAG}{\texttt{SQ\_FLAG}} $\vert$ 19 | \hyperlink{SQ_RCUT}{\texttt{SQ\_RCUT}} $\vert$ 20 | \hyperlink{SQ_NPL_G}{\texttt{SQ\_NPL\_G}} $\vert$ 21 | \hyperlink{SQ_GAUSS_MEM}{\texttt{SQ\_GAUSS\_MEM}} $\vert$ 22 | \hyperlink{SQ_TOL_OCC}{\texttt{SQ\_TOL\_OCC}} $\vert$ 23 | \hyperlink{NP_DOMAIN_SQ_PARAL}{\texttt{NP\_DOMAIN\_SQ\_PARAL}} 24 | \end{block} 25 | 26 | \end{frame} 27 | -------------------------------------------------------------------------------- /tests/sparc-latex-doc-202302/highT/Manual_highT.tex: -------------------------------------------------------------------------------- 1 | \documentclass[xcolor=dvipsnames,t]{beamer} 2 | %\usepackage[utf8]{inputenc} 3 | \usepackage{verbatim} % for comment 4 | \usetheme{Madrid} 5 | \usecolortheme{seahorse} 6 | \usepackage{beamerouterthemesplit} 7 | \usepackage[T1]{fontenc} 8 | 9 | \setbeamerfont{institute}{size=\normalsize} 10 | 11 | \title[] {SPARC - SQ \\ {\normalsize Spectral Quadrature method} \\ {\small User guide}} 12 | %\author{} 13 | %\author{Qimen Xu, Abhiraj Sharma, Phanish Suryanarayana, } 14 | 15 | \institute[] 16 | { 17 | Material Physics \& Mechanics Group \\ 18 | PI: Phanish Suryanarayana \\ 19 | Main Developers: Xin Jing, Abhiraj Sharma, Phanisri P. Pratapa\\ 20 | Collaborators: J.E. Pask (LLNL)\\ 21 | Georgia Institute of Technology 22 | } 23 | 24 | \date{} 25 | \setbeamertemplate{frametitle continuation}{} 26 | \setbeamertemplate{navigation symbols}{} 27 | \setbeamercolor{block title}{bg=Apricot!50,fg=black} 28 | %\addtobeamertemplate{block begin}{\vskip -\smallskipamount}{} 29 | %\addtobeamertemplate{block end}{}{\vskip -\smallskipamount} 30 | \addtobeamertemplate{block begin}{\vspace*{-0.6pt}}{} 31 | \addtobeamertemplate{block end}{}{\vspace*{-0.6pt}} 32 | \hypersetup{colorlinks, 33 | citecolor=violet, 34 | linkcolor=blue, 35 | menucolor=white, 36 | anchorcolor=yellow 37 | filecolor=pink, 38 | } 39 | 40 | 41 | \setbeamertemplate{footline}{ 42 | \hbox{% 43 | \begin{beamercolorbox}[wd=\paperwidth,ht=1ex,dp=1.5ex,leftskip=2ex,rightskip=2ex]{page footer}% 44 | \usebeamerfont{title in head/foot}% 45 | \insertshorttitle \hfill 46 | \insertsection \hfill 47 | \insertframenumber{} / \inserttotalframenumber 48 | \end{beamercolorbox}}% 49 | } 50 | 51 | \let\otp\titlepage 52 | \renewcommand{\titlepage}{\otp\addtocounter{framenumber}{-1}} 53 | 54 | 55 | %\includeonly{Introduction,Stress,MD,Optimization,Print} 56 | %\includeonly{Introduction} 57 | 58 | \begin{document} 59 | 60 | %\frame{\titlepage} 61 | 62 | \begin{frame}[plain] 63 | \titlepage 64 | \end{frame} 65 | 66 | \include{Introduction} 67 | \include{SQ} 68 | 69 | 70 | \end{document} 71 | -------------------------------------------------------------------------------- /tests/sparc-latex-socket-202401/Manual.tex: -------------------------------------------------------------------------------- 1 | \documentclass[xcolor=dvipsnames,t]{beamer} 2 | % \usepackage[utf8]{inputenc} 3 | \usepackage{verbatim} % for comment 4 | \usetheme{Madrid} 5 | \usecolortheme{seahorse} 6 | \usepackage{beamerouterthemesplit} 7 | \usepackage{array} 8 | \usepackage{algorithm} 9 | \usepackage{algpseudocode} 10 | \usepackage[T1]{fontenc} 11 | 12 | 13 | \setbeamerfont{institute}{size=\normalsize} 14 | 15 | \title[] {SPARC \\ {\normalsize Simulation Package for Ab-initio Real-space Calculations} \\ {\small User guide}} 16 | %\author{} 17 | %\author{Qimen Xu, Abhiraj Sharma, Phanish Suryanarayana, } 18 | 19 | \institute[] 20 | { 21 | Material Physics \& Mechanics Group, Georgia Tech \\ 22 | PI: Phanish Suryanarayana \\ 23 | \hyperlink{Contributors}{\texttt{Contributors}} \\ 24 | \hyperlink{Citation}{\texttt{Citation}}\\ 25 | \hyperlink{Acknowledgments}{\texttt{Acknowledgements}}\\ 26 | %Collaborators: J.E. Pask (LLNL), A.J. Medford (GT), E. Chow (GT) \\ 27 | %Georgia Institute of Technology 28 | } 29 | 30 | \date{} 31 | \setbeamertemplate{frametitle continuation}{} 32 | \setbeamertemplate{navigation symbols}{} 33 | \setbeamercolor{block title}{bg=Apricot!50,fg=black} 34 | %\addtobeamertemplate{block begin}{\vskip -\smallskipamount}{} 35 | %\addtobeamertemplate{block end}{}{\vskip -\smallskipamount} 36 | \addtobeamertemplate{block begin}{\vspace*{-0.6pt}}{} 37 | \addtobeamertemplate{block end}{}{\vspace*{-0.6pt}} 38 | \hypersetup{colorlinks, 39 | citecolor=violet, 40 | linkcolor=blue, 41 | menucolor=white, 42 | anchorcolor=yellow 43 | filecolor=pink, 44 | } 45 | 46 | 47 | \setbeamertemplate{footline}{ 48 | \hbox{% 49 | \begin{beamercolorbox}[wd=\paperwidth,ht=1ex,dp=1.5ex,leftskip=2ex,rightskip=2ex]{page footer}% 50 | \usebeamerfont{title in head/foot}% 51 | \insertshorttitle \hfill 52 | \insertsection \hfill 53 | \insertframenumber{} / \inserttotalframenumber 54 | \end{beamercolorbox}}% 55 | } 56 | 57 | % \setbeamertemplate{headline} [split theme] 58 | % {% 59 | % \begin{beamercolorbox}{section in head/foot} 60 | % \vskip2pt\insertnavigation{\paperwidth}\vskip2pt 61 | % \end{beamercolorbox}% 62 | % } 63 | 64 | % \defbeamertemplate*{footline}{split theme} 65 | % {% 66 | % \leavevmode% 67 | % \hbox{\begin{beamercolorbox}[wd=.5\paperwidth,ht=2.5ex,dp=1.125ex,leftskip=.3cm plus1fill,rightskip=.3cm]{section in head/foot}% 68 | % \usebeamerfont{author in head/foot}\insertshortauthor 69 | % \end{beamercolorbox}% 70 | % \begin{beamercolorbox}[wd=.5\paperwidth,ht=2.5ex,dp=1.125ex,leftskip=.3cm,rightskip=.3cm plus1fil]{title in head/foot}% 71 | % \usebeamerfont{title in head/foot}\insertshorttitle 72 | % \end{beamercolorbox}}% 73 | % \vskip0pt% 74 | % } 75 | 76 | 77 | 78 | \let\otp\titlepage 79 | \renewcommand{\titlepage}{\otp\addtocounter{framenumber}{-1}} 80 | 81 | 82 | %\includeonly{Introduction,Stress,MD,Optimization,Print} 83 | %\includeonly{Introduction} 84 | 85 | \begin{document} 86 | 87 | %\frame{\titlepage} 88 | 89 | \begin{frame}[plain] 90 | \titlepage 91 | \end{frame} 92 | 93 | \include{Introduction} 94 | \include{System} 95 | \include{SCF} 96 | \include{Electrostatics} 97 | \include{Stress} 98 | \include{MD} 99 | \include{Optimization} 100 | \include{BandStructure} 101 | \include{Print} 102 | \include{Paral} 103 | \include{SQ} 104 | \include{Socket} 105 | 106 | \end{document} 107 | -------------------------------------------------------------------------------- /tests/sparc-latex-socket-202401/Stress.tex: -------------------------------------------------------------------------------- 1 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 2 | 3 | 4 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 5 | \begin{frame}[allowframebreaks,c]{} \label{Stress calculation} 6 | 7 | \begin{center} 8 | \Huge \textbf{Stress calculation} 9 | \end{center} 10 | 11 | \end{frame} 12 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 13 | 14 | 15 | 16 | 17 | 18 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 19 | \begin{frame}[allowframebreaks]{\texttt{CALC\_STRESS}} \label{CALC_STRESS} 20 | \vspace*{-12pt} 21 | \begin{columns} 22 | \column{0.4\linewidth} 23 | \begin{block}{Type} 24 | Integer 25 | \end{block} 26 | 27 | \begin{block}{Default} 28 | 0 29 | \end{block} 30 | 31 | \column{0.4\linewidth} 32 | \begin{block}{Unit} 33 | No unit 34 | \end{block} 35 | 36 | \begin{block}{Example} 37 | \texttt{CALC\_STRESS}: 1 38 | \end{block} 39 | \end{columns} 40 | 41 | \begin{block}{Description} 42 | Flag for calculation of the Hellmann-Feynman stress tensor (in cartesian coordinates). 43 | \end{block} 44 | 45 | %\begin{block}{Remark} 46 | %\end{block} 47 | 48 | \end{frame} 49 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 50 | 51 | 52 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 53 | \begin{frame}[allowframebreaks]{\texttt{CALC\_PRES}} \label{CALC_PRES} 54 | \vspace*{-12pt} 55 | \begin{columns} 56 | \column{0.4\linewidth} 57 | \begin{block}{Type} 58 | Integer 59 | \end{block} 60 | 61 | \begin{block}{Default} 62 | 0 63 | \end{block} 64 | 65 | \column{0.4\linewidth} 66 | \begin{block}{Unit} 67 | No unit 68 | \end{block} 69 | 70 | \begin{block}{Example} 71 | \texttt{CALC\_PRES}: 1 72 | \end{block} 73 | \end{columns} 74 | 75 | \begin{block}{Description} 76 | Flag for calculation of the pressure. 77 | \end{block} 78 | 79 | \begin{block}{Remark} 80 | Pressure is directly calculated, without calculation of the stress tensor. 81 | \end{block} 82 | 83 | \end{frame} 84 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 85 | -------------------------------------------------------------------------------- /tests/sparc-latex-socket-202401/cyclix/FAQs.tex: -------------------------------------------------------------------------------- 1 | \begin{frame}[allowframebreaks]{\textbf{FAQs}} \label{FAQs} 2 | %\begin{itemize} 3 | % \item Q : U.S. National Science Foundation: 1553212 4 | %\end{itemize} 5 | 6 | \noindent 7 | {\bf Q:} How can SCF convergence be made better in SPARC-cyclix calculations? 8 | \\ 9 | {\color{blue} {\bf A:} In cases of smaller radius and finer mesh, we need to use higher Chebyshev Degree. Increasing the option CHEB\_DEGREE should help with the SCF convergence. }\\ 10 | 11 | \vspace{3mm} 12 | 13 | 14 | {\bf Q:} Are pseudopotentials with non-linear core corrections and relativistic effect supported by SPARC-cyclix? 15 | \\ 16 | {\color{blue} {\bf A:} Yes.}\\ 17 | 18 | \vspace{3mm} 19 | 20 | {\bf Q:} Is non-collinear spin calculation supported by SPARC-cyclix? 21 | \\ 22 | {\color{blue} {\bf A:} No, currently we only have the collinear spin calculations available in SPARC-cyclix.}\\ 23 | 24 | 25 | \end{frame} 26 | -------------------------------------------------------------------------------- /tests/sparc-latex-socket-202401/cyclix/Introduction.tex: -------------------------------------------------------------------------------- 1 | 2 | %\begin{frame}[allowframebreaks]{\textbf{Comments}} \label{Introduction} 3 | %The code will fail with the following options and the related input options are listed. 4 | %\begin{itemize} 5 | % \item Polarized calculation: \texttt{SPIN\_TYP}. 6 | % \item K-point calculation: \texttt{KPOINT\_GRID}, \texttt{KPOINT\_SHIFT}. 7 | % \item Dirichlet boundary condition in any direction: \texttt{BC} 8 | % \item Define number of states/orbitals: \texttt{NSTATES} 9 | % \item Hybrid functionals: \texttt{EXCHANGE\_CORRELATION} 10 | % \item Print eigenvalues into file: \texttt{PRINT\_EIGEN} 11 | %\end{itemize} 12 | % 13 | %\end{frame} 14 | 15 | 16 | \begin{frame}[allowframebreaks]{\textbf{Contributors}} \label{Contributors} 17 | %\begin{itemize} 18 | %\item U.S. Department of Energy, Office of Science: DE-SC0019410 19 | %\item U.S. National Science Foundation: 1333500 and 1553212 20 | %\end{itemize} 21 | 22 | \begin{itemize} 23 | \item \textbf{Phanish Suryanarayana} (PI) 24 | \begin{itemize} 25 | \item \textbf{Abhiraj Sharma}: Code infrastructure, CheFSI, PBE, Energy, Force, Stress, atomic \& cell relaxation \\ 26 | \item \textbf{Qimen Xu}: Code infrastructure \\ 27 | \item \textbf{Xin Jing}: Code infrastructure, Spin, SOC \\ 28 | \item \textbf{Arpit Bhardwaj}: Spin, SOC \\ 29 | % \item \textbf{Boqin Zhang}: vdW-DF, DFT-D3, meta-GGA (SCAN) \\ 30 | % \item \textbf{Shashikant Kumar}: Testing framework, NLCC \\ 31 | % \item \textbf{Mostafa Faghih Shojaei}: SPMS table of pseudopotentials \\ 32 | \end{itemize} 33 | % \item \textbf{John E. Pask} (co-PI) 34 | % \item \textbf{Edmond Chow} (co-PI) 35 | % \begin{itemize} 36 | % \item \textbf{Hua Huang}: Subspace eigensolver, DP 37 | % \item \textbf{Lucas Erlandson}: Subspace eigensolver, DP 38 | % \end{itemize} 39 | % \item \textbf{Andrew J. Medford} (co-PI) 40 | % \begin{itemize} 41 | % \item \textbf{Benjamin Comer}: Code testing, Initial testing framework 42 | % \item \textbf{Sushree Jagriti Sahoo}: Code testing 43 | % \end{itemize} 44 | \end{itemize} 45 | 46 | \end{frame} 47 | 48 | 49 | \begin{frame}[allowframebreaks]{\textbf{Citation}} \label{Citation} 50 | If you publish work using/regarding SPARC-cyclix, please cite the following article, in addition to SPARC citations: 51 | \begin{itemize} 52 | \item \url{https://doi.org/10.1103/PhysRevB.103.035101} 53 | \item Additional references for initial developments: \url{https://doi.org/10.1016/j.jmps.2016.08.007}, \url{https://doi.org/10.1103/PhysRevB.100.125143} 54 | % \item Non-orthogonal systems: \url{https://doi.org/10.1016/j.cplett.2018.04.018} 55 | % \item Linear solvers: \url{https://doi.org/10.1016/j.cpc.2018.07.007}, \url{https://doi.org/10.1016/j.jcp.2015.11.018} 56 | % \item Stress tensor/pressure: \url{https://doi.org/10.1063/1.5057355} 57 | % \item Atomic forces: \url{https://doi.org/10.1016/j.cpc.2016.09.020}, \url{https://doi.org/10.1016/j.cpc.2017.02.019} 58 | % \item Mixing: \url{https://doi.org/10.1016/j.cplett.2016.01.033}, \url{https://doi.org/10.1016/j.cplett.2015.06.029}, \url{https://doi.org/10.1016/j.cplett.2019.136983} 59 | % \item SPMS pseudopotentials: \url{https://doi.org/10.1016/j.cpc.2022.108594} 60 | \end{itemize} 61 | \end{frame} 62 | 63 | 64 | \begin{frame}[allowframebreaks]{\textbf{Acknowledgements}} \label{Acknowledgements} 65 | \begin{itemize} 66 | \item \textbf{U.S. National Science Foundation (NSF): 1553212 67 | } \\ 68 | \end{itemize} 69 | \end{frame} 70 | 71 | 72 | \begin{frame}[allowframebreaks]{\textbf{Input file options}} \label{Index} 73 | \vspace{-2mm} 74 | Input file options for SPARC-cyclix, in addition to SPARC: 75 | \begin{block}{Cyclix} 76 | \hyperlink{TWIST_ANGLE}{\texttt{TWIST\_ANGLE}} $\vert$ 77 | \hyperlink{BC}{\texttt{BC}} $\vert$ 78 | \hyperlink{CELL}{\texttt{CELL}} $\vert$ 79 | \hyperlink{COORD}{\texttt{COORD}} $\vert$ 80 | \hyperlink{COORD_FRAC}{\texttt{COORD\_FRAC}} $\vert$ 81 | \hyperlink{EXCHANGE_CORRELATION}{\texttt{EXCHANGE\_CORRELATION}} $\vert$ 82 | \hyperlink{KPOINT_GRID}{\texttt{KPOINT\_GRID}} $\vert$ 83 | 84 | %\hyperlink{SPIN_TYP}{\texttt{SPIN\_TYP}} $\vert$ 85 | %\hyperlink{SPIN}{\texttt{SPIN}} $\vert$ 86 | \end{block} 87 | \end{frame} 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | -------------------------------------------------------------------------------- /tests/sparc-latex-socket-202401/cyclix/Manual_cyclix.tex: -------------------------------------------------------------------------------- 1 | \documentclass[xcolor=dvipsnames,t]{beamer} 2 | %\usepackage[utf8]{inputenc} 3 | \usepackage{verbatim} % for comment 4 | \usetheme{Madrid} 5 | \usecolortheme{seahorse} 6 | \usepackage{beamerouterthemesplit} 7 | \usepackage[T1]{fontenc} 8 | 9 | \setbeamerfont{institute}{size=\normalsize} 10 | 11 | \title[] {SPARC-cyclix \\ {\small User guide}} 12 | %\author{} 13 | %\author{Qimen Xu, Abhiraj Sharma, Phanish Suryanarayana, } 14 | 15 | \institute[] 16 | { 17 | Material Physics \& Mechanics Group, Georgia Tech \\ 18 | PI: Phanish Suryanarayana \\ 19 | %Main Developers: Abhiraj Sharma, Qimen Xu, Xin Jing \\ 20 | %Collaborators: J.E. Pask (LLNL)\\ 21 | \hyperlink{Contributors}{Contributors}\\ 22 | \hyperlink{Citation}{Citation} \\ 23 | \hyperlink{Acknowledgements}{Acknowledgements} 24 | 25 | } 26 | 27 | \date{} 28 | \setbeamertemplate{frametitle continuation}{} 29 | \setbeamertemplate{navigation symbols}{} 30 | \setbeamercolor{block title}{bg=Apricot!50,fg=black} 31 | %\addtobeamertemplate{block begin}{\vskip -\smallskipamount}{} 32 | %\addtobeamertemplate{block end}{}{\vskip -\smallskipamount} 33 | \addtobeamertemplate{block begin}{\vspace*{-0.6pt}}{} 34 | \addtobeamertemplate{block end}{}{\vspace*{-0.6pt}} 35 | \hypersetup{colorlinks, 36 | citecolor=violet, 37 | linkcolor=blue, 38 | menucolor=white, 39 | anchorcolor=yellow 40 | filecolor=pink, 41 | } 42 | 43 | 44 | \setbeamertemplate{footline}{ 45 | \hbox{% 46 | \begin{beamercolorbox}[wd=\paperwidth,ht=1ex,dp=1.5ex,leftskip=2ex,rightskip=2ex]{page footer}% 47 | \usebeamerfont{title in head/foot}% 48 | \insertshorttitle \hfill 49 | \insertsection \hfill 50 | \insertframenumber{} / \inserttotalframenumber 51 | \end{beamercolorbox}}% 52 | } 53 | 54 | \let\otp\titlepage 55 | \renewcommand{\titlepage}{\otp\addtocounter{framenumber}{-1}} 56 | 57 | 58 | %\includeonly{Introduction,Stress,MD,Optimization,Print} 59 | %\includeonly{Introduction} 60 | 61 | \begin{document} 62 | 63 | %\frame{\titlepage} 64 | 65 | \begin{frame}[plain] 66 | \titlepage 67 | \end{frame} 68 | 69 | \include{Introduction} 70 | \include{cyclix} 71 | \include{FAQs} 72 | 73 | 74 | \end{document} 75 | 76 | -------------------------------------------------------------------------------- /tests/sparc-latex-socket-202401/highT/Introduction.tex: -------------------------------------------------------------------------------- 1 | \begin{frame}[allowframebreaks]{\textbf{Contributors}} \label{Contributors} 2 | %\begin{itemize} 3 | %\item U.S. Department of Energy, Office of Science: DE-SC0019410 4 | %\item U.S. National Science Foundation: 1333500 and 1553212 5 | %\end{itemize} 6 | 7 | \begin{itemize} 8 | \item \textbf{Phanish Suryanarayana} (PI) 9 | \begin{itemize} 10 | \item \textbf{Xin Jing}: Code infrastructure \\ 11 | \item \textbf{Abhiraj Sharma}: Initial development \\ 12 | \item \textbf{Phanisri P. Pratapa}: Initial development \\ 13 | % \item \textbf{Boqin Zhang}: vdW-DF, DFT-D3, meta-GGA (SCAN) \\ 14 | % \item \textbf{Shashikant Kumar}: Testing framework, NLCC \\ 15 | % \item \textbf{Mostafa Faghih Shojaei}: SPMS table of pseudopotentials \\ 16 | \end{itemize} 17 | \item \textbf{John E. Pask} (co-PI) 18 | % \item \textbf{Edmond Chow} (co-PI) 19 | % \begin{itemize} 20 | % \item \textbf{Hua Huang}: Subspace eigensolver, DP 21 | % \item \textbf{Lucas Erlandson}: Subspace eigensolver, DP 22 | % \end{itemize} 23 | % \item \textbf{Andrew J. Medford} (co-PI) 24 | % \begin{itemize} 25 | % \item \textbf{Benjamin Comer}: Code testing, Initial testing framework 26 | % \item \textbf{Sushree Jagriti Sahoo}: Code testing 27 | % \end{itemize} 28 | \end{itemize} 29 | 30 | \end{frame} 31 | 32 | 33 | \begin{frame}[allowframebreaks]{\textbf{Citation}} \label{Citation} 34 | If you publish work using/regarding SPARC-SQ, please cite the following articles, in addition to SPARC citations: 35 | \begin{itemize} 36 | \item \url{https://doi.org/10.1016/j.cpc.2015.11.005}, 37 | \url{https://doi.org/10.1016/j.cplett.2013.08.035}, 38 | \url{https://doi.org/10.1007/978-3-031-22340-2_12} 39 | % \item Non-orthogonal systems: \url{https://doi.org/10.1016/j.cplett.2018.04.018} 40 | % \item Linear solvers: \url{https://doi.org/10.1016/j.cpc.2018.07.007}, \url{https://doi.org/10.1016/j.jcp.2015.11.018} 41 | % \item Stress tensor/pressure: \url{https://doi.org/10.1063/1.5057355} 42 | % \item Atomic forces: \url{https://doi.org/10.1016/j.cpc.2016.09.020}, \url{https://doi.org/10.1016/j.cpc.2017.02.019} 43 | % \item Mixing: \url{https://doi.org/10.1016/j.cplett.2016.01.033}, \url{https://doi.org/10.1016/j.cplett.2015.06.029}, \url{https://doi.org/10.1016/j.cplett.2019.136983} 44 | % \item SPMS pseudopotentials: \url{https://doi.org/10.1016/j.cpc.2022.108594} 45 | \end{itemize} 46 | \end{frame} 47 | 48 | \begin{frame}[allowframebreaks]{\textbf{Acknowledgements}} \label{Acknowledgements} 49 | \begin{itemize} 50 | \item \textbf{U.S. Department of Energy (DOE), National Nuclear Security Administration (NNSA): DE-NA0004128 51 | } \\ 52 | \end{itemize} 53 | \end{frame} 54 | 55 | 56 | \begin{frame}[allowframebreaks]{\textbf{Comments}} \label{Introduction} 57 | The code will fail with the following options and the related input options are listed. 58 | \begin{itemize} 59 | \item Polarized calculation: \texttt{SPIN\_TYP}. 60 | \item K-point calculation: \texttt{KPOINT\_GRID}, \texttt{KPOINT\_SHIFT}. 61 | \item Dirichlet boundary condition in any direction: \texttt{BC} 62 | \item Define number of states/orbitals: \texttt{NSTATES} 63 | \item Hybrid functionals: \texttt{EXCHANGE\_CORRELATION} 64 | \item Print eigenvalues into file: \texttt{PRINT\_EIGEN} 65 | \end{itemize} 66 | 67 | \end{frame} 68 | 69 | \begin{frame}[allowframebreaks]{\textbf{Input file options}} \label{Index} 70 | \vspace{-2mm} 71 | \begin{block}{Spectral Quadrature} 72 | \hyperlink{SQ_FLAG}{\texttt{SQ\_FLAG}} $\vert$ 73 | \hyperlink{SQ_RCUT}{\texttt{SQ\_RCUT}} $\vert$ 74 | \hyperlink{SQ_NPL_G}{\texttt{SQ\_NPL\_G}} $\vert$ 75 | \hyperlink{SQ_GAUSS_MEM}{\texttt{SQ\_GAUSS\_MEM}} $\vert$ 76 | \hyperlink{SQ_TOL_OCC}{\texttt{SQ\_TOL\_OCC}} $\vert$ 77 | \hyperlink{NP_DOMAIN_SQ_PARAL}{\texttt{NP\_DOMAIN\_SQ\_PARAL}} 78 | \end{block} 79 | 80 | \end{frame} 81 | 82 | -------------------------------------------------------------------------------- /tests/sparc-latex-socket-202401/highT/Manual_highT.tex: -------------------------------------------------------------------------------- 1 | \documentclass[xcolor=dvipsnames,t]{beamer} 2 | % \usepackage[utf8]{inputenc} 3 | \usepackage{verbatim} % for comment 4 | \usetheme{Madrid} 5 | \usecolortheme{seahorse} 6 | \usepackage{beamerouterthemesplit} 7 | \usepackage{array} 8 | \usepackage{algorithm} 9 | \usepackage{algpseudocode} 10 | \usepackage[T1]{fontenc} 11 | 12 | 13 | \setbeamerfont{institute}{size=\normalsize} 14 | 15 | \title[] {SPARC - SQ \\ {\normalsize Spectral Quadrature method} \\ {\small User guide}} 16 | %\author{} 17 | %\author{Qimen Xu, Abhiraj Sharma, Phanish Suryanarayana, } 18 | 19 | \institute[] 20 | { 21 | Material Physics \& Mechanics Group, Georgia Tech \\ 22 | PI: Phanish Suryanarayana \\ 23 | \hyperlink{Contributors}{\texttt{Contributors}} \\ 24 | \hyperlink{Citation}{\texttt{Citation}}\\ 25 | \hyperlink{Acknowledgments}{\texttt{Acknowledgements}}\\ 26 | %Collaborators: J.E. Pask (LLNL), A.J. Medford (GT), E. Chow (GT) \\ 27 | %Georgia Institute of Technology 28 | } 29 | 30 | \date{} 31 | \setbeamertemplate{frametitle continuation}{} 32 | \setbeamertemplate{navigation symbols}{} 33 | \setbeamercolor{block title}{bg=Apricot!50,fg=black} 34 | %\addtobeamertemplate{block begin}{\vskip -\smallskipamount}{} 35 | %\addtobeamertemplate{block end}{}{\vskip -\smallskipamount} 36 | \addtobeamertemplate{block begin}{\vspace*{-0.6pt}}{} 37 | \addtobeamertemplate{block end}{}{\vspace*{-0.6pt}} 38 | \hypersetup{colorlinks, 39 | citecolor=violet, 40 | linkcolor=blue, 41 | menucolor=white, 42 | anchorcolor=yellow 43 | filecolor=pink, 44 | } 45 | 46 | 47 | \setbeamertemplate{footline}{ 48 | \hbox{% 49 | \begin{beamercolorbox}[wd=\paperwidth,ht=1ex,dp=1.5ex,leftskip=2ex,rightskip=2ex]{page footer}% 50 | \usebeamerfont{title in head/foot}% 51 | \insertshorttitle \hfill 52 | \insertsection \hfill 53 | \insertframenumber{} / \inserttotalframenumber 54 | \end{beamercolorbox}}% 55 | } 56 | 57 | % \setbeamertemplate{headline} [split theme] 58 | % {% 59 | % \begin{beamercolorbox}{section in head/foot} 60 | % \vskip2pt\insertnavigation{\paperwidth}\vskip2pt 61 | % \end{beamercolorbox}% 62 | % } 63 | 64 | % \defbeamertemplate*{footline}{split theme} 65 | % {% 66 | % \leavevmode% 67 | % \hbox{\begin{beamercolorbox}[wd=.5\paperwidth,ht=2.5ex,dp=1.125ex,leftskip=.3cm plus1fill,rightskip=.3cm]{section in head/foot}% 68 | % \usebeamerfont{author in head/foot}\insertshortauthor 69 | % \end{beamercolorbox}% 70 | % \begin{beamercolorbox}[wd=.5\paperwidth,ht=2.5ex,dp=1.125ex,leftskip=.3cm,rightskip=.3cm plus1fil]{title in head/foot}% 71 | % \usebeamerfont{title in head/foot}\insertshorttitle 72 | % \end{beamercolorbox}}% 73 | % \vskip0pt% 74 | % } 75 | 76 | 77 | 78 | \let\otp\titlepage 79 | \renewcommand{\titlepage}{\otp\addtocounter{framenumber}{-1}} 80 | 81 | 82 | \begin{document} 83 | 84 | %\frame{\titlepage} 85 | 86 | \begin{frame}[plain] 87 | \titlepage 88 | \end{frame} 89 | 90 | \include{Introduction} 91 | \include{SQ} 92 | 93 | 94 | \end{document} 95 | 96 | -------------------------------------------------------------------------------- /tests/test_aimd_parser.py: -------------------------------------------------------------------------------- 1 | import os 2 | from pathlib import Path 3 | 4 | import numpy as np 5 | import pytest 6 | from ase.units import Bohr, Hartree, eV, kB 7 | 8 | curdir = Path(__file__).parent 9 | test_output_dir = curdir / "outputs" 10 | 11 | 12 | def test_aimd_parser(): 13 | from sparc.common import repo_dir 14 | from sparc.sparc_parsers.aimd import _read_aimd 15 | 16 | data_dict = _read_aimd( 17 | test_output_dir 18 | / "TiO2_orthogonal_quick_md.sparc" 19 | / "TiO2_orthogonal_quick_md.aimd" 20 | ) 21 | assert "aimd" in data_dict 22 | md_steps = data_dict["aimd"] 23 | assert len(md_steps) == 5 24 | for i, step in enumerate(md_steps): 25 | assert i == step.get("step", -1) 26 | for key in [ 27 | "positions", 28 | "velocities", 29 | "forces", 30 | "electron temp", 31 | "ion temp", 32 | "total energy per atom", 33 | "kinetic energy per atom", 34 | "kinetic energy (ideal gas) per atom", 35 | "free energy per atom", 36 | "stress", 37 | "pressure", 38 | ]: 39 | assert key in step 40 | assert step["positions"].shape == (6, 3) 41 | assert step["forces"].shape == (6, 3) 42 | assert step["velocities"].shape == (6, 3) 43 | # TODO: may subject to changes 44 | assert step["stress"].shape == (3, 3) 45 | 46 | # A simple test to see if we're using the correct types 47 | T0 = md_steps[0]["electron temp"] 48 | ek_ig0 = md_steps[0]["kinetic energy (ideal gas) per atom"] 49 | assert np.isclose(T0, 800) 50 | assert np.isclose(T0, ek_ig0 * eV / kB / (1.5), 1.0e-2) 51 | -------------------------------------------------------------------------------- /tests/test_api_version.py: -------------------------------------------------------------------------------- 1 | import os 2 | from pathlib import Path 3 | 4 | import pytest 5 | from packaging import version 6 | 7 | curdir = Path(__file__).parent 8 | 9 | 10 | def test_sparc_api(monkeypatch): 11 | from sparc.api import SparcAPI 12 | from sparc.utils import locate_api 13 | 14 | monkeypatch.delenv("SPARC_DOC_PATH", raising=False) 15 | default_ver = SparcAPI().sparc_version 16 | # No location provided, use default version 17 | assert default_ver == locate_api().sparc_version 18 | # Directly load from another doc. 19 | # Version not detected since src not presented 20 | older_ver = locate_api(doc_path=curdir / "sparc-latex-doc-202302").sparc_version 21 | assert older_ver is None 22 | # Specify SPARC_DOC_PATH 23 | monkeypatch.setenv( 24 | "SPARC_DOC_PATH", (curdir / "sparc-latex-doc-202302").resolve().as_posix() 25 | ) 26 | older_version = locate_api().sparc_version 27 | assert older_version is None 28 | 29 | 30 | def test_sparc_params(): 31 | if "SPARC_DOC_PATH" not in os.environ: 32 | pytest.skip("No $SPARC_DOC_PATH set. Skip") 33 | 34 | from sparc.utils import locate_api 35 | 36 | # Use the default api with SPARC_DOC_PATH 37 | api = locate_api() 38 | if api.sparc_version is None: 39 | pytest.skip("SPARC version not known. skip") 40 | 41 | if version.parse(api.sparc_version) > version.parse("2023.09.01"): 42 | assert "NPT_SCALE_VECS" in api.parameters 43 | assert "NPT_SCALE_CONSTRAINTS" in api.parameters 44 | assert "TWIST_ANGLE" in api.parameters 45 | -------------------------------------------------------------------------------- /tests/test_bundle_to_calc.py: -------------------------------------------------------------------------------- 1 | import os 2 | import re 3 | import tempfile 4 | from pathlib import Path 5 | 6 | import numpy as np 7 | import pytest 8 | from ase.units import Hartree 9 | 10 | curdir = Path(__file__).parent 11 | test_psp_dir = curdir / "psps" 12 | test_output_dir = curdir / "outputs" 13 | 14 | 15 | def test_files_glob(): 16 | """Only match the re part""" 17 | pattern = r"^\.out(?:_\d+)?$" 18 | assert re.fullmatch(pattern, ".out") 19 | assert re.fullmatch(pattern, ".out_0") 20 | assert re.fullmatch(pattern, ".out_01") 21 | assert re.fullmatch(pattern, ".out_009") 22 | assert re.fullmatch(pattern, ".out_") is None 23 | assert re.fullmatch(pattern, ".out_00_") is None 24 | assert re.fullmatch(pattern, ".out#") is None 25 | assert re.fullmatch(pattern, ".out~") is None 26 | assert re.fullmatch(pattern, ".out_01~") is None 27 | 28 | 29 | def test_bundle_convert(): 30 | from sparc.io import SparcBundle 31 | 32 | for bundle in test_output_dir.glob("*.sparc"): 33 | if bundle.name not in ("Al_multi_geopt.sparc",): 34 | sp = SparcBundle(directory=bundle) 35 | sp.convert_to_ase() 36 | else: 37 | sp = SparcBundle(directory=bundle) 38 | sp.convert_to_ase(include_all_files=True) 39 | 40 | return 41 | 42 | 43 | def test_bundle_read(): 44 | from sparc.io import read_sparc 45 | 46 | for bundle in test_output_dir.glob("*.sparc"): 47 | if bundle.name not in ("Al_multi_geopt.sparc",): 48 | print(bundle) 49 | images = read_sparc(bundle) 50 | else: 51 | images = read_sparc(bundle, include_all_files=True) 52 | return 53 | 54 | 55 | def test_multi_file_geopt_read(): 56 | from sparc.io import read_sparc 57 | 58 | bundle = test_output_dir / "Al_multi_geopt.sparc" 59 | 60 | # Last image is empty, must use include_all_files=True 61 | with pytest.raises(Exception): 62 | images = read_sparc(bundle, include_all_files=False) 63 | 64 | # default 65 | with pytest.raises(Exception): 66 | images = read_sparc(bundle, include_all_files) 67 | 68 | images = read_sparc(bundle, index=":", include_all_files=True) 69 | assert len(images) == 7 70 | 71 | last = read_sparc(bundle, index=-1, include_all_files=True) 72 | assert np.isclose(last.get_potential_energy(), -9.057488887961474 * Hartree, 1e-4) 73 | return 74 | -------------------------------------------------------------------------------- /tests/test_downloader.py: -------------------------------------------------------------------------------- 1 | import pytest 2 | 3 | 4 | def test_download(fs, monkeypatch): 5 | from sparc import download_data 6 | from sparc.download_data import download_psp 7 | 8 | fs.create_dir("fake") 9 | download_psp(psp_dir="fake") 10 | -------------------------------------------------------------------------------- /tests/test_geopt_parser.py: -------------------------------------------------------------------------------- 1 | import os 2 | from pathlib import Path 3 | 4 | import numpy as np 5 | import pytest 6 | from ase.units import Bohr, Hartree 7 | 8 | curdir = Path(__file__).parent 9 | test_output_dir = curdir / "outputs" 10 | 11 | 12 | def test_geopt_parser(): 13 | from sparc.common import repo_dir 14 | from sparc.sparc_parsers.geopt import _read_geopt 15 | 16 | data_dict = _read_geopt( 17 | test_output_dir 18 | / "AlSi_primitive_quick_relax.sparc" 19 | / "AlSi_primitive_quick_relax.geopt" 20 | ) 21 | assert "geopt" in data_dict 22 | geopt_steps = data_dict["geopt"] 23 | for i, step in enumerate(geopt_steps): 24 | assert i == step.get("step", -1) 25 | assert "positions" in step 26 | assert "forces" in step 27 | assert "energy" in step 28 | assert "cell" in step 29 | assert "volume" in step 30 | assert "latvec" in step 31 | assert "stress" in step 32 | assert "ase_cell" in step 33 | 34 | # Value assertions 35 | ase_cell = step["ase_cell"] 36 | vol_ase = np.linalg.det(ase_cell) 37 | assert np.isclose(vol_ase, step["volume"]) 38 | 39 | max_final_f = np.max(np.abs(step["forces"])) 40 | assert max_final_f < 1.0e-3 * Hartree / Bohr 41 | 42 | 43 | def test_geopt_parser_relax2(): 44 | from sparc.common import repo_dir 45 | from sparc.sparc_parsers.geopt import _read_geopt 46 | 47 | data_dict = _read_geopt( 48 | test_output_dir / "Si8_cell_geopt_relax2.sparc" / "Si8_cell_geopt.geopt" 49 | ) 50 | geopt_steps = data_dict["geopt"] 51 | for i, step in enumerate(geopt_steps): 52 | assert i == step.get("step", -1) 53 | # RELAX=2 no position information 54 | assert "positions" not in step 55 | assert "stress" in step 56 | assert "cell" in step 57 | assert "latvec" in step 58 | 59 | 60 | def test_geopt_low_dim_stress(): 61 | from sparc.sparc_parsers.geopt import _read_geopt 62 | 63 | data_dict = _read_geopt( 64 | test_output_dir / "Alloy_geopt_ppd_bc.sparc" / "SPARC.geopt" 65 | ) 66 | geopt_steps = data_dict["geopt"] 67 | for i, step in enumerate(geopt_steps): 68 | assert i == step.get("step", -1) 69 | assert "stress_2d" in step 70 | assert "stress" not in step 71 | assert "cell" in step 72 | -------------------------------------------------------------------------------- /tests/test_gui.py: -------------------------------------------------------------------------------- 1 | import os 2 | from pathlib import Path 3 | from subprocess import run 4 | 5 | import numpy as np 6 | import pytest 7 | from ase.units import Bohr, Hartree, eV, kB 8 | 9 | curdir = Path(__file__).parent 10 | test_output_dir = curdir / "outputs" 11 | 12 | 13 | def test_cli(): 14 | """Simply call the sparc-ase methods""" 15 | proc = run(["sparc-ase"]) 16 | assert proc.returncode == 0 17 | 18 | 19 | def test_info(): 20 | """Call the sparc-ase info on sparc file. Be aware of the API changes in 3.22->3.23""" 21 | import ase 22 | from packaging import version 23 | 24 | bundle = test_output_dir / "Cu_FCC.sparc" 25 | if version.parse(ase.__version__) < version.parse("3.23"): 26 | proc = run(["sparc-ase", "info", f"{bundle}"], capture_output=True) 27 | else: 28 | proc = run(["sparc-ase", "info", "--files", f"{bundle}"], capture_output=True) 29 | assert proc.returncode == 0 30 | assert "SPARC" in proc.stdout.decode("utf8") 31 | 32 | 33 | def test_gui_single(): 34 | """Call the sparc-ase gui on a static calculation""" 35 | bundle = test_output_dir / "Cu_FCC.sparc" 36 | proc = run(["sparc-ase", "gui", "-t", f"{bundle}"], capture_output=True) 37 | assert proc.returncode == 0 38 | 39 | 40 | def test_gui_geopt(): 41 | """Call the sparc-ase info on a geopt calculation""" 42 | bundle = test_output_dir / "AlSi_primitive_quick_relax.sparc" 43 | proc = run(["sparc-ase", "gui", "-t", f"{bundle}"], capture_output=True) 44 | assert proc.returncode == 0 45 | 46 | 47 | def test_gui_md(): 48 | """Call the sparc-ase info on an AIMD calculation""" 49 | bundle = test_output_dir / "TiO2_orthogonal_quick_md.sparc" 50 | proc = run(["sparc-ase", "gui", "-t", f"{bundle}"], capture_output=True) 51 | assert proc.returncode == 0 52 | -------------------------------------------------------------------------------- /tests/test_import.py: -------------------------------------------------------------------------------- 1 | """Unit test for order of importing. 2 | Submodules like `docparser` `api` and `download_data` should be independent of ase / numpy, 3 | should such modules are not yet available during processes like conda-forge build 4 | """ 5 | import sys 6 | 7 | import ase 8 | import pytest 9 | 10 | 11 | def test_download_data(monkeypatch): 12 | monkeypatch.setitem(sys.modules, "ase", None) 13 | with pytest.raises(ImportError): 14 | import ase 15 | from sparc.download_data import download_psp 16 | 17 | 18 | def test_api(monkeypatch): 19 | monkeypatch.setitem(sys.modules, "ase", None) 20 | with pytest.raises(ImportError): 21 | import ase 22 | from sparc.api import SparcAPI 23 | 24 | 25 | def test_docparser(monkeypatch): 26 | monkeypatch.setitem(sys.modules, "ase", None) 27 | with pytest.raises(ImportError): 28 | import ase 29 | from sparc.docparser import SparcDocParser 30 | -------------------------------------------------------------------------------- /tests/test_quicktest.py: -------------------------------------------------------------------------------- 1 | import os 2 | from pathlib import Path 3 | 4 | import pytest 5 | 6 | 7 | def test_run_quicktest(): 8 | """Just import and run quicktest""" 9 | from sparc.quicktest import main 10 | 11 | main() 12 | -------------------------------------------------------------------------------- /tests/test_read_sparc.py: -------------------------------------------------------------------------------- 1 | import os 2 | from pathlib import Path 3 | 4 | import numpy as np 5 | import pytest 6 | 7 | curdir = Path(__file__).parent 8 | test_output_dir = curdir / "outputs" 9 | 10 | 11 | def test_read_sparc_all(): 12 | from sparc.common import repo_dir 13 | from sparc.io import read_sparc 14 | 15 | for bundle in test_output_dir.glob("*.sparc/"): 16 | if bundle.name not in ("Al_multi_geopt.sparc",): 17 | results = read_sparc(bundle) 18 | else: 19 | results = read_sparc(bundle, include_all_files=True) 20 | 21 | 22 | def test_atoms_read_pbc(): 23 | from sparc.io import read_sparc 24 | from sparc.sparc_parsers.atoms import atoms_to_dict 25 | 26 | # Case 1: H2O sheet 27 | water_sheet = read_sparc(test_output_dir / "H2O_sheet_yz.sparc") 28 | assert all(water_sheet.pbc == [False, True, True]) 29 | 30 | # Case 2: H2O wire 31 | water_wire = read_sparc(test_output_dir / "H2O_wire_z.sparc") 32 | assert all(water_wire.pbc == [False, False, True]) 33 | --------------------------------------------------------------------------------