Develop

.github/workflows/main.yml

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+name: AtomGPT github action
+on: [push, pull_request]
+
+jobs:
+  miniconda:
+    name: Miniconda ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: ["ubuntu-latest"]
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          environment-file: environment.yml
+          python-version: "3.9"
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda info
+          conda list
+      - name: Lint
+        shell: bash -l {0}
+        run: |
+            conda install flake8 pycodestyle pydocstyle
+            #flake8 --ignore E203,W503 --exclude=examples,tests,scripts --statistics --count --exit-zero intermat/calculators.py intermat/generate.py 
+            #pycodestyle --ignore E203,W503 --exclude=examples,tests,scripts intermat
+            #pydocstyle --match-dir=core --match-dir=io --match-dir=io --match-dir=ai --match-dir=analysis --match-dir=db --match-dir=tasks --count intermat
+
+      - name: Run pytest
+        shell: bash -l {0}
+        run: |
+            #source ~/.bashrc
+            find . -type f > before_test_files.txt
+            conda env create -f environment.yml
+            conda activate atomgpt 
+            pip install triton
+            #conda install alignn dgl=2.1.0 pytorch torchvision torchaudio pytorch-cuda transformers peft trl triton  -c pytorch -c nvidia -y
+            conda install pytest coverage codecov   -y
+            #conda install pytest coverage codecov pandas numpy matplotlib phonopy scikit-learn jarvis-tools --quiet
+            #export DGLBACKEND=pytorch
+            #export CUDA_VISIBLE_DEVICES="-1"
+            #pip install phonopy flake8 pytest pycodestyle pydocstyle codecov pytest-cov coverage
+
+            python setup.py develop
+            echo 'environment.yml'
+            conda env export
+            echo 'forward model'
+            echo 'ls'
+            ls 
+            echo 'ls atomgpt'
+            ls atomgpt
+            echo 'atomgpt/examples/'
+            ls atomgpt/examples/
+            echo 'atomgpt/examples/forward_model/'
+            ls atomgpt/examples/forward_model/ 
+            python atomgpt/forward_models/forward_models.py --config_name atomgpt/examples/forward_model/config.json
+
+            echo 'inverse model'
+            python atomgpt/examples/inverse_model/run.py            
+            coverage run -m pytest
+            coverage report -m -i
+            codecov
+            #codecov --token="85bd9c5d-9e55-4f6d-bd69-350ee5e3bb41"
+
+            #train_alignn.py -h 
+            #echo 'Pre-trained models'
+            #pretrained.py -h
+            #find . -type f > after_test_files.txt
+
+
+

README.md

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-# atomgpt
+# AtomGPT: atomistic generative pre-trained transformer for forward and inverse materials design
+
+## Forward model example
+
+python atomgpt/forward_models/forward_models.py --config_name atomgpt/examples/forward_model/config.json
+
+## Inverse model example
+
+python atomgpt/inverse_models/inverse_models.py --config_name atomgpt/examples/inverse_model/config.json
+
+#python atomgpt/examples/inverse_model/run.py

atomgpt/__init__.py

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-"""Initialize atomgpt."""
-# Code coming soon
+"""Version number."""
+__version__ = "2024.6.8"

atomgpt/config.py

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+from typing import Optional
+from pydantic_settings import BaseSettings
+class TrainingPropConfig(BaseSettings):
+    """Training config defaults and validation."""
+
+    benchmark_file: Optional[str] = None
+    # "AI-SinglePropertyPrediction-exfoliation_energy-dft_3d-test-mae"
+    id_prop_path: Optional[str] = None
+    prefix: str = "xyz"
+    model_name: str = "gpt2"
+    leaderboard_dir: str = (
+        "/wrk/knc6/AFFBench/jarvis_leaderboard/jarvis_leaderboard"
+    )
+    batch_size: int = 8
+    max_length: int = 512
+    num_epochs: int = 500
+    latent_dim: int = 1024
+    learning_rate: float = 1e-3
+    test_each_run: bool = True
+    include_struct: bool = False
+    pretrained_path: str = ""
+    seed_val: int = 42
+    n_train: Optional[int] = None
+    n_val: Optional[int] = None
+    n_test: Optional[int] = None
+    train_ratio: Optional[float] = None
+    val_ratio: float = 0.1
+    test_ratio: float = 0.1
+    keep_data_order: bool = False
+    output_dir: str = "temp"

atomgpt/data/__init__.py

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+"""Module for dataclass."""