Added test files. Using relative paths from project root to read data and newtonet related files.

Author: kumaranu

tests/geodesic_ts_with_hessian/test_using_mace.py

@@ -0,0 +1,36 @@
+import pytest
+import logging
+from ase.io import read
+from pathlib import Path
+from quacc import get_settings
+from ts_workflow_examples.geodesic_ts_with_hessian.using_mace import geodesic_ts_hess_irc_mace
+
+
+# Define the paths relative to the project root
+project_root = Path(__file__).resolve().parents[2]
+
+
+@pytest.fixture()
+def setup_test_environment(tmp_path):
+    reactant = read(project_root / "tests" / '000_R.xyz')
+    product = read(project_root / "tests" / '000_P.xyz')
+
+    return reactant, product
+
+
+def test_geodesic_ts_hess_irc_mace(setup_test_environment):
+    reactant, product = setup_test_environment
+    # Create mock jobs
+    calc_kwargs = {}
+
+    # Setup logging
+    logging.basicConfig(level=logging.INFO)
+    logger = logging.getLogger(__name__)
+
+    settings = get_settings()
+    settings.CHECK_CONVERGENCE = False
+
+    jobs = geodesic_ts_hess_irc_mace(reactant, product, calc_kwargs, logger)
+
+    # Assertions
+    assert len(jobs) == 4

tests/geodesic_ts_with_hessian/test_using_newtonnet.py

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+import os
+import pytest
+import logging
+from ase.io import read
+from pathlib import Path
+from quacc import get_settings
+from ts_workflow_examples.geodesic_ts_with_hessian.using_newtonnet import geodesic_ts_hess_irc_newtonnet
+
+
+# Define the paths relative to the project root
+project_root = Path(__file__).resolve().parents[2]
+
+
+@pytest.fixture()
+def setup_test_environment(tmp_path):
+    reactant = read(project_root / "tests" / '000_R.xyz')
+    product = read(project_root / "tests" / '000_P.xyz')
+
+    return reactant, product
+
+
+def test_geodesic_ts_hess_irc_newtonnet(setup_test_environment):
+    reactant, product = setup_test_environment
+
+    # Calculation and optimization keyword arguments
+    calc_kwargs1 = {
+        'hess_method': None,
+    }
+    calc_kwargs2 = {
+        'hess_method': 'autograd',
+    }
+
+    settings = get_settings()
+    settings.NEWTONNET_MODEL_PATH = project_root / "tests" / "best_model_state.tar"
+    settings.NEWTONNET_CONFIG_PATH = project_root / "tests" / "config0.yml"
+    settings.CHECK_CONVERGENCE = False
+
+    # Setup logging
+    logging.basicConfig(level=logging.INFO)
+    logger = logging.getLogger(__name__)
+
+    jobs = geodesic_ts_hess_irc_newtonnet(reactant, product, calc_kwargs1, calc_kwargs2, logger)
+
+    # Assertions
+    assert len(jobs) == 4

tests/geodesic_ts_without_hessian/test_using_mace.py

@@ -0,0 +1,35 @@
+import pytest
+import logging
+from ase.io import read
+from quacc import get_settings
+from pathlib import Path
+from ts_workflow_examples.geodesic_ts_without_hessian.using_mace import geodesic_ts_no_hess_irc_mace
+
+
+# Define the paths relative to the project root
+project_root = Path(__file__).resolve().parents[2]
+
+
+@pytest.fixture()
+def setup_test_environment(tmp_path):
+    reactant = read(project_root / "tests" / '000_R.xyz')
+    product = read(project_root / "tests" / '000_P.xyz')
+
+    return reactant, product
+
+
+def test_geodesic_ts_hess_irc_mace(setup_test_environment):
+    reactant, product = setup_test_environment
+    calc_kwargs = {}
+
+    # Setup logging
+    logging.basicConfig(level=logging.INFO)
+    logger = logging.getLogger(__name__)
+
+    settings = get_settings()
+    settings.CHECK_CONVERGENCE = False
+
+    jobs = geodesic_ts_no_hess_irc_mace(reactant, product, calc_kwargs, logger)
+
+    # Assertions
+    assert len(jobs) == 4

tests/geodesic_ts_without_hessian/test_using_newtonnet.py

@@ -0,0 +1,42 @@
+import os
+import pytest
+import logging
+from ase.io import read
+from quacc import get_settings
+from pathlib import Path
+from ts_workflow_examples.geodesic_ts_without_hessian.using_newtonnet import geodesic_ts_no_hess_irc_newtonnet
+
+
+# Define the paths relative to the project root
+project_root = Path(__file__).resolve().parents[2]
+
+
+@pytest.fixture()
+def setup_test_environment(tmp_path):
+    reactant = read(project_root / "tests" / '000_R.xyz')
+    product = read(project_root / "tests" / '000_P.xyz')
+
+    return reactant, product
+
+
+def test_geodesic_ts_hess_irc_newtonnet(setup_test_environment):
+    reactant, product = setup_test_environment
+
+    # Calculation and optimization keyword arguments
+    calc_kwargs1 = {
+        'hess_method': None,
+    }
+
+    settings = get_settings()
+    settings.NEWTONNET_MODEL_PATH = project_root / "tests" / "best_model_state.tar"
+    settings.NEWTONNET_CONFIG_PATH = project_root / "tests" / "config0.yml"
+    settings.CHECK_CONVERGENCE = False
+
+    # Setup logging
+    logging.basicConfig(level=logging.INFO)
+    logger = logging.getLogger(__name__)
+
+    jobs = geodesic_ts_no_hess_irc_newtonnet(reactant, product, calc_kwargs1, logger)
+
+    # Assertions
+    assert len(jobs) == 4

tests/neb_ts_with_hessian/test_using_mace.py

@@ -0,0 +1,35 @@
+import pytest
+import logging
+from ase.io import read
+from quacc import get_settings
+from pathlib import Path
+from ts_workflow_examples.neb_ts_with_hessian.using_mace import neb_ts_hess_irc_mace
+
+
+# Define the paths relative to the project root
+project_root = Path(__file__).resolve().parents[2]
+
+
+@pytest.fixture()
+def setup_test_environment(tmp_path):
+    reactant = read(project_root / "tests" / '000_R.xyz')
+    product = read(project_root / "tests" / '000_P.xyz')
+
+    return reactant, product
+
+
+def test_neb_ts_hess_irc_mace(setup_test_environment):
+    reactant, product = setup_test_environment
+    calc_kwargs = {}
+
+    # Setup logging
+    logging.basicConfig(level=logging.INFO)
+    logger = logging.getLogger(__name__)
+
+    settings = get_settings()
+    settings.CHECK_CONVERGENCE = False
+
+    jobs = neb_ts_hess_irc_mace(reactant, product, calc_kwargs, logger)
+
+    # Assertions
+    assert len(jobs) == 4

tests/neb_ts_with_hessian/test_using_newtonnet.py

@@ -0,0 +1,44 @@
+import pytest
+import logging
+from ase.io import read
+from pathlib import Path
+from quacc import get_settings
+from ts_workflow_examples.neb_ts_with_hessian.using_newtonnet import neb_ts_hess_irc_newtonnet
+
+
+# Define the paths relative to the project root
+project_root = Path(__file__).resolve().parents[2]
+
+
+@pytest.fixture()
+def setup_test_environment(tmp_path):
+    reactant = read(project_root / "tests" / '000_R.xyz')
+    product = read(project_root / "tests" / '000_P.xyz')
+
+    return reactant, product
+
+
+def test_neb_ts_hess_irc_newtonnet(setup_test_environment):
+    reactant, product = setup_test_environment
+
+    # Calculation and optimization keyword arguments
+    calc_kwargs1 = {
+        'hess_method': None,
+    }
+    calc_kwargs2 = {
+        'hess_method': 'autograd',
+    }
+
+    settings = get_settings()
+    settings.NEWTONNET_MODEL_PATH = project_root / "tests" / "best_model_state.tar"
+    settings.NEWTONNET_CONFIG_PATH = project_root / "tests" / "config0.yml"
+    settings.CHECK_CONVERGENCE = False
+
+    # Setup logging
+    logging.basicConfig(level=logging.INFO)
+    logger = logging.getLogger(__name__)
+
+    jobs = neb_ts_hess_irc_newtonnet(reactant, product, calc_kwargs1, calc_kwargs2, logger)
+
+    # Assertions
+    assert len(jobs) == 4

tests/neb_ts_without_hessian/test_using_mace.py

@@ -0,0 +1,36 @@
+import pytest
+import logging
+from ase.io import read
+from pathlib import Path
+from quacc import get_settings
+from ts_workflow_examples.neb_ts_without_hessian.using_mace import neb_ts_no_hess_irc_mace
+
+
+# Define the paths relative to the project root
+project_root = Path(__file__).resolve().parents[2]
+
+
+@pytest.fixture()
+def setup_test_environment(tmp_path):
+    reactant = read(project_root / "tests" / '000_R.xyz')
+    product = read(project_root / "tests" / '000_P.xyz')
+
+    return reactant, product
+
+
+def test_neb_ts_no_hess_irc_mace(setup_test_environment):
+    reactant, product = setup_test_environment
+
+    calc_kwargs = {}
+
+    # Setup logging
+    logging.basicConfig(level=logging.INFO)
+    logger = logging.getLogger(__name__)
+
+    settings = get_settings()
+    settings.CHECK_CONVERGENCE = False
+
+    jobs = neb_ts_no_hess_irc_mace(reactant, product, calc_kwargs, logger)
+
+    # Assertions
+    assert len(jobs) == 4

tests/neb_ts_without_hessian/test_using_newtonnet.py

@@ -0,0 +1,41 @@
+import pytest
+import logging
+from ase.io import read
+from pathlib import Path
+from quacc import get_settings
+from ts_workflow_examples.neb_ts_without_hessian.using_newtonnet import neb_ts_no_hess_irc_newtonnet
+
+
+# Define the paths relative to the project root
+project_root = Path(__file__).resolve().parents[2]
+
+
+@pytest.fixture()
+def setup_test_environment(tmp_path):
+    reactant = read(project_root / "tests" / '000_R.xyz')
+    product = read(project_root / "tests" / '000_P.xyz')
+
+    return reactant, product
+
+
+def test_neb_ts_no_hess_irc_newtonnet(setup_test_environment):
+    reactant, product = setup_test_environment
+
+    # Calculation and optimization keyword arguments
+    calc_kwargs1 = {
+        'hess_method': None,
+    }
+
+    settings = get_settings()
+    settings.NEWTONNET_MODEL_PATH = project_root / "tests" / "best_model_state.tar"
+    settings.NEWTONNET_CONFIG_PATH = project_root / "tests" / "config0.yml"
+    settings.CHECK_CONVERGENCE = False
+
+    # Setup logging
+    logging.basicConfig(level=logging.INFO)
+    logger = logging.getLogger(__name__)
+
+    jobs = neb_ts_no_hess_irc_newtonnet(reactant, product, calc_kwargs1, logger)
+
+    # Assertions
+    assert len(jobs) == 4