Merge pull request #47 from alchem0x2A/master

Compatibility with ase 3.23
SPARC-X · Sep 5, 2024 · 9136ce8 · 9136ce8
2 parents c419ce2 + 6e53fb3
commit 9136ce8
Show file tree

Hide file tree

Showing 27 changed files with 591 additions and 311 deletions.
diff --git a/.conda/meta.yaml b/.conda/meta.yaml
@@ -16,7 +16,7 @@ build:
   script: "{{ PYTHON }} -m pip install . --no-deps -vv && cd .. && {{ PYTHON }} -m sparc.download_data"
   entry_points:
     - "sparc-ase = sparc.cli:main"
-    
+
 
 requirements:
   host:

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -16,7 +16,7 @@ Provide a minimal list of settings / codes to help us debug, such as
 - Version (git commit hash) of `SPARC-X-API`
 - `SPARC` C-code version (see the SPARC .out file header)
 - Your platform and architecture
- 
+
 **Expected behavior**
 What is the code intended to achieve?
 

diff --git a/.github/workflows/installation_test.yml b/.github/workflows/installation_test.yml
@@ -39,8 +39,12 @@ jobs:
         python -m sparc.download_data
     - name: Download SPARC output files to SPARC-master
       run: |
-        wget https://github.com/SPARC-X/SPARC/archive/refs/heads/master.zip
-        unzip master.zip
+        # Pin the current version of SPARC to versions before MLFF
+        # wget https://github.com/SPARC-X/SPARC/archive/refs/heads/master.zip
+        # unzip master.zip
+        wget -O SPARC-master.zip https://codeload.github.com/SPARC-X/SPARC/zip/3371b4401e4ebca0921fb77a02587f578f3bf3f7
+        unzip SPARC-master.zip
+        mv SPARC-33* SPARC-master
     - name: Test with pytest
       run: |
         # python -m pytest -svv tests/ --cov=sparc --cov-report=json --cov-report=html
@@ -53,7 +57,7 @@ jobs:
         COVERAGE=`cat coverage.json | jq .totals.percent_covered | xargs printf '%.*f' 0`
         echo "Current coverage is $COVERAGE"
         echo "COVPERCENT=$COVERAGE" >> $GITHUB_ENV
-        
+
     - name: Lint with flake8
       run: |
         echo $CONDA_PREFIX
@@ -88,7 +92,7 @@ jobs:
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         RID: ${{ github.run_id }}
-        
+
   test-socket:
     defaults:
       run:
@@ -139,7 +143,67 @@ jobs:
         COVERAGE=`cat coverage.json | jq .totals.percent_covered | xargs printf '%.*f' 0`
         echo "Current coverage is $COVERAGE"
         echo "COVPERCENT=$COVERAGE" >> $GITHUB_ENV
-        
+
+    - name: Lint with flake8
+      run: |
+        echo $CONDA_PREFIX
+        conda info
+        flake8 sparc/ --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 sparc/ --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+  # To be deleted once 1.0 release is done
+  build-linux-ase-3-22:
+    defaults:
+      run:
+        shell: bash -l {0}
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v3
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        python-version: "3.10"
+        mamba-version: "*"
+        channels: conda-forge,alchem0x2a,defaults
+        channel-priority: true
+        activate-environment: sparc-api-test
+    - name: Install dependencies
+      run: |
+        # mamba install -c conda-forge ase>=3.22 pymatgen flake8 pytest
+        mamba install -c conda-forge make compilers openmpi fftw scalapack openblas
+    - name: Install package
+      run: |
+        pip install -e ".[test]" ase==3.22 numpy==1.24 scipy==1.10
+        # Manually downgrade
+        # Download the external psp data
+        python -m sparc.download_data
+    - name: Download SPARC output files to SPARC-master
+      run: |
+        # TODO: merge to master
+        wget -O SPARC-socket.zip https://codeload.github.com/alchem0x2A/SPARC/zip/refs/heads/socket
+        unzip SPARC-socket.zip
+    - name: Compile SPARC with socket
+      run: |
+        cd SPARC-socket/src
+        make clean
+        make -j2 USE_SOCKET=1 USE_MKL=0 USE_SCALAPACK=1 DEBUG_MODE=1
+        ls ../lib
+    - name: Test with pytest
+      run: |
+        ls ./SPARC-socket/lib/sparc
+        PWD=$(pwd)
+        export SPARC_TESTS_DIR="${PWD}/SPARC-socket/tests"
+        export ASE_SPARC_COMMAND="mpirun -n 1 ${PWD}/SPARC-socket/lib/sparc"
+        export SPARC_DOC_PATH="${PWD}/SPARC-socket/doc/.LaTeX"
+        coverage run -a -m pytest -svv tests/
+        coverage json --omit="tests/*.py"
+        coverage html --omit="tests/*.py"
+        COVERAGE=`cat coverage.json | jq .totals.percent_covered | xargs printf '%.*f' 0`
+        echo "Current coverage is $COVERAGE"
+        echo "COVPERCENT=$COVERAGE" >> $GITHUB_ENV
+
     - name: Lint with flake8
       run: |
         echo $CONDA_PREFIX

diff --git a/.github/workflows/update_api.yml b/.github/workflows/update_api.yml
@@ -59,4 +59,3 @@ jobs:
         gh pr create --base master --title "[PR Bot] New JSON API version ${API_VERSION}"  --body "Merge new JSON API version ${API_VERSION} into master" -R ${{ github.repository_owner }}/SPARC-X-API
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,23 @@
+# Pre-commit hooks for SPARC-X-API
+# Use pre-commit rn
+exclude: "^tests/outputs/|^tests/psps/|^tests/sparc-latex-.*/|^tests/archive/|^sparc/sparc_json_api/"
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: check-yaml
+        exclude: ".conda/meta.yaml"
+    -   id: end-of-file-fixer
+    -   id: trailing-whitespace
+
+- repo: https://github.com/pycqa/isort
+  rev: 5.12.0
+  hooks:
+  - id: isort
+    name: isort (python)
+    args: ["--profile", "black"]
+
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black
diff --git a/README.md b/README.md
@@ -322,7 +322,7 @@ The reasoning and details about unit conversion can be found in the [Rules for I
 
 
 In order for `SPARC-X-API` to be compatible with other ASE-based DFT calculators,
-there is a list of special parameters consistent with the ASE convention and uses Å / eV / GPa / fs 
+there is a list of special parameters consistent with the ASE convention and uses Å / eV / GPa / fs
 unit system:
 
 | parameter name | meaning                         | example        | equivalent `SPARC` input |
@@ -394,7 +394,7 @@ bottleneck. The underlying software architecture is shown in [Fig. 3](#fig-3-spa
 ![scheme-sparc-socket](doc/img/scheme_socket_hetero.png)
 
 
- 
+
 
 **Requirements**: the SPARC binary must be manually compiled from the source
 code with [socket
@@ -425,10 +425,10 @@ Based on the scenarios, the socket communication layer can be accessed via the f
 
 
 1. **SPARC binary only** ([Fig. 5](#fig-5-different-ways-of-using-sparcs-socket-mode) **a**)
-   
+
    SPARC binary with socket support can be readily coupled with any i-PI compatible socker server, such as
    `ase.calculators.socketio.SocketIOCalculator`, for example
-   
+
    ```python
    from ase.calculators.socketio import SocketIOCalculator
    from subprocess import Popen
@@ -439,17 +439,17 @@ Based on the scenarios, the socket communication layer can be accessed via the f
 	   # Single point calculations
 	   process.kill()
    ```
-   
+
    The end user is responsible for generating the input files and
    making sure the same atoms structures are used by
    `SocketIOCalculator` and the SPARC binary. The mode is also limited
-   to be run on a single computer system. 
+   to be run on a single computer system.
 
 
 2. **Local-only Mode** ([Fig. 5](#fig-5-different-ways-of-using-sparcs-socket-mode) **b**)
-   
+
    Ideal for standalone calculations, this mode simulates a conventional calculator while benefiting from socket-based efficiency.
-   
+
    ```python
    with SPARC(use_socket=True, **normal_parameters) as calc:
        # Execute single-point calculations
@@ -464,15 +464,15 @@ Based on the scenarios, the socket communication layer can be accessed via the f
    message to a local SPARC binary and send results back through the
    socket pipe. The server side can either be a normal i-PI compatible
    server (such as `SocketIOCalculator`) or server-mode `sparc.SPARC` (see 4).
-   
+
    Start the client by:
    ```python
    client = SPARC(use_socket=True,
 	              socket_params=dict(host="host.address.com", port=31415))
    with client:
        client.run()
    ```
-   
+
    Or via Command-Line:
    ```bash
    python -m sparc.client -s host:port
@@ -483,33 +483,33 @@ Based on the scenarios, the socket communication layer can be accessed via the f
    new atoms positions and parameters arrive, the client will
    automatically determine if it is necessary to restart the SPARC
    subprocess.
-   
+
 4. **Server Mode** ([Fig. 5](#fig-5-different-ways-of-using-sparcs-socket-mode) **d**)
 
    Paired with the client mode in (3), SPARC-X-API can be run as a
    socket server, isolated from the node that performs the
    computation. This can be useful for highly-distributed
    computational workflows.
-   
+
    On the server node, run:
    ```python
    server_calc = SPARC(use_socket=True, socket_params=dict(port=31415, server_only=True), **normal_parameters)
    with server_calc:
        # Execute single point calculations for atoms_1
 	   # Execute single point calculations for atoms_2
    ```
-   
+
    In this case, the server will opens `0.0.0.0:31415` for
    connection. Make sure your server is directly accessible from the
    clients and the port is not occupied. The socker server is capable
    of receiving `raw_results` directly from the clients, making it
    possible to access `server_calc.raw_results` without access to the
    file systems on the client side.
-   
+
 
 ### (In-progress) Controlling SPARC routines from socket interface
 
-As shown in [Fig. 4](#fig-4-overview-of-the-sparc-protocol-as-an-extension-to-the-standard-i-pi-protocol), 
+As shown in [Fig. 4](#fig-4-overview-of-the-sparc-protocol-as-an-extension-to-the-standard-i-pi-protocol),
 the SPARC socket protocol designs allows bidirectional control of
 internal SPARC routines. Local- or server-mode `sparc.SPARC`
 calculators can communicate with the SPARC binary via functions like

diff --git a/doc/advanced_topics.md b/doc/advanced_topics.md
@@ -4,11 +4,11 @@ The design of `SPARC-X-API` is schematically shown in the following figure
 
 ### Behind the bundle file format
 
-Instead of parsing individual `.ion` and `.inpt` files, 
-the bundle format (recognized by ASE by `format="sparc"`) will 
+Instead of parsing individual `.ion` and `.inpt` files,
+the bundle format (recognized by ASE by `format="sparc"`) will
 gather information from all files and check if atomic information
-and calculation results can be retrieved. 
-The central piece for handling the bundle format is 
+and calculation results can be retrieved.
+The central piece for handling the bundle format is
 `sparc.io.SpardBundle` class. You can use it to parse an existing bundle
 
 ```python
@@ -28,15 +28,15 @@ bundle = SparcBundle("path/to/your-calc.sparc", mode="w")
 bundle._write_ion_and_inpt(atoms, label="SPARC")
 ```
 
-For each individual SPARC file (e.g. `.ion`, `.inpt`, `.static`, `.geopt`, `.aimd`), 
-file-specific parsers are in `sparc.sparc_parsers.<format>` files. 
+For each individual SPARC file (e.g. `.ion`, `.inpt`, `.static`, `.geopt`, `.aimd`),
+file-specific parsers are in `sparc.sparc_parsers.<format>` files.
 Each `_read_<format>` method will return the structured raw-data dictionary of the files.
 Similarly, `_write_<format>` takes the structured dictionary as input and write the file
 using only relevant data.
 
 ### Behind the JSON API
 
-The JSON API are directly parsed from the `SPARC` documentation [LaTeX files](https://github.com/SPARC-X/SPARC/tree/master/doc/.LaTeX). 
+The JSON API are directly parsed from the `SPARC` documentation [LaTeX files](https://github.com/SPARC-X/SPARC/tree/master/doc/.LaTeX).
 The JSON API file (`sparc/sparc_json_api/parameters.json`) distributed by `SPARC-X-API` is generated by:
 
 ```bash
@@ -77,9 +77,9 @@ sis = SparcAPI()
 
 ### Retriving parameters from old SPARC calculations
 
-`sparc.SPARC` calculator supports the `restart` mode which will reconstruct all 
-parameters, psp files and atomic information from an existing SPARC calculation and 
-rerun them. 
+`sparc.SPARC` calculator supports the `restart` mode which will reconstruct all
+parameters, psp files and atomic information from an existing SPARC calculation and
+rerun them.
 
 ```python
 from sparc import SPARC
@@ -96,14 +96,14 @@ old_atoms.get_potential_energy()
 
 ### Rules for input parameters in `sparc.SPARC` calculator
 
-When constructing the `sparc.SPARC` calculator using the syntax 
+When constructing the `sparc.SPARC` calculator using the syntax
 ```python
 calc = SPARC(directory="", **kwargs)
 ```
 the parameters are handled in the following priority:
 1) Parameters available to `.inpt` files (i.e. **CAPITALIZED**) have highest priority and overwrite all special inputs. They should be set directly using the atomic unit values (i.e the same value as they appear in the `.inpt` files).
-2) Special inputs (i.e, `h`, `kpts`, `gpts`, `xc`, `convergence`) have second highest priority and overwrite default values. They are using the ASE unit system (i.e. Å, eV, GPa, fs). 
-3) If none of the parameters are provided, `SPARC` uses its default parameter set, currently 
+2) Special inputs (i.e, `h`, `kpts`, `gpts`, `xc`, `convergence`) have second highest priority and overwrite default values. They are using the ASE unit system (i.e. Å, eV, GPa, fs).
+3) If none of the parameters are provided, `SPARC` uses its default parameter set, currently
 ```python
 {"xc": "pbe", "h": 0.25, "kpts": (1, 1, 1)}
 ```
@@ -114,11 +114,11 @@ Additionally, boolean inputs (i.e. `PRINT_FORCES`) can be written in both intege
 
 ### Multiple occurance of output files
 
-In a typical SPARC calculation, there may be multiple result files in the SPARC bundle, with different suffixes (e.g. `.out`, `.out_01`, `.out_02` etc.). 
+In a typical SPARC calculation, there may be multiple result files in the SPARC bundle, with different suffixes (e.g. `.out`, `.out_01`, `.out_02` etc.).
 These files can be a result of restarted geometry optimization / AIMD or written by an ASE optimizer.
 
 When using `read_sparc` to access the files, you can add `include_all_files=True` option to parse
-trajectories from all files. 
+trajectories from all files.
 
 ```python
 from sparc.io import read_sparc

diff --git a/doc/changes_v0.1.md b/doc/changes_v0.1.md
@@ -14,14 +14,14 @@ Nevertheless, reading calculation results generated by a v0.1 API code will not
 ```
 which maps atoms 3, 2, 1, 0 from the SPARC .ion file order to atoms 0, 1, 2, 3 in ASE order. This is useful for systems that are constructed by ASE's `add_adsorbate` method.
 
-3. v1.0 API accepts all SPARC internal parameters (i.e. **CAPITALIZED**) in *atomic units* for consistency reason. 
+3. v1.0 API accepts all SPARC internal parameters (i.e. **CAPITALIZED**) in *atomic units* for consistency reason.
 However, we also keep a list of "special input params" that are conventionally used in other ASE calculators, that use Å / eV / GPa / fs unit system.
 
 4. Defining `LATVEC`, `LATVEC_SCALE`, or `CELL` via the calculator parameters is no longer encouraged. Instead, all structure changes should be made to the `Atoms` object.
 
 For more discussion please see [Advanced Topic] section.
 
-Below are a list of v0.1 method of the `SPARC` calculator and their current status in v0.2 API. 
+Below are a list of v0.1 method of the `SPARC` calculator and their current status in v0.2 API.
 `calc` is an instance of `sparc.SPARC`.
 
 |  old methods           | status in v1.0 API |     alternatives                   |
Original file line number	Diff line number	Diff line change
Expand Up		@@ -59,4 +59,3 @@ jobs:
		gh pr create --base master --title "[PR Bot] New JSON API version ${API_VERSION}" --body "Merge new JSON API version ${API_VERSION} into master" -R ${{ github.repository_owner }}/SPARC-X-API
		env:
		GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}