Merge pull request #47 from coltonbh/feature-terachem-opt

.pre-commit-config.yaml

@@ -27,6 +27,10 @@ repos:
       - id: mypy
         additional_dependencies:
           [pydantic>=2.0.0, types-paramiko, qcio>=0.11.8, types-toml]
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.24.5
+    hooks:
+      - id: typos
   - repo: local
     hooks:
       - id: tests

CHANGELOG.md

@@ -6,6 +6,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [unreleased]
 
+### Added
+
+- `CalcType.optimization` support for TeraChem.
+- `typos` pre-commit check.
+
 ## [0.9.0] - 2024-09-11
 
 ### Changed

docs/examples/optimization.md

@@ -1,3 +1,11 @@
+## geomeTRIC
+
 ```python
 {!examples/geometric.py!}
-```
+```
+
+## TeraChem
+
+```python
+{!examples/terachem_opt.py!}
+```

docs/programs/terachem.md

@@ -1 +1,5 @@
-::: qcop.adapters.terachem.TeraChemAdapter
+::: qcop.adapters.terachem.TeraChemAdapter
+
+::: qcop.adapters.terachem_fe.TeraChemFEAdapter
+
+::: qcop.adapters.terachem_pbs.TeraChemPBSAdapter

examples/terachem_opt.py

@@ -0,0 +1,50 @@
+"""Example of how to run an optimization calculation with TeraChem using qcop."""
+
+from qcio import ProgramInput, Structure
+
+from qcop import compute, exceptions
+
+# Create the structure
+# Can also open a structure from a file
+# structure = Structure.open("path/to/h2o.xyz")
+structure = Structure(
+    symbols=["O", "H", "H"],
+    geometry=[  # type: ignore
+        [0.0, 0.0, 0.0],
+        [0.52421003, 1.68733646, 0.48074633],
+        [1.14668581, -0.45032174, -1.35474466],
+    ],
+)
+
+# Define the program input
+prog_input = ProgramInput(
+    structure=structure,
+    # Can be "energy", "gradient", "hessian", "optimization", "transition_state"
+    calctype="optimization",  # type: ignore
+    model={"method": "hf", "basis": "sto-3g"},  # type: ignore
+    keywords={"purify": "no", "new_minimizer": "yes"},  # new_minimizer yes is required
+)
+
+# Run the calculation
+try:
+    # prog_output is instance of ProgramOutput
+    prog_output = compute("terachem", prog_input, collect_files=True)
+except exceptions.QCOPBaseError as e:
+    prog_output = e.program_output
+    print(prog_output.stdout)  # or output.pstdout for short
+    print(f"Success: {prog_output.success}")  # False
+    print(prog_output.input_data)  # Input data used to generate the calculation
+    print(prog_output.provenance)  # Provenance of generated calculation
+    print(prog_output.traceback)  # or output.ptraceback for short
+    raise
+
+else:
+    # Check results
+    print(prog_output.stdout)  # or output.pstdout for short
+    print(f"Success: {prog_output.success}")  # True
+    print("output.results: ", prog_output.results)
+    print("output.results.energies:", prog_output.results.energies)
+    print("output.results.structures:", prog_output.results.structures)
+    print("output.results.final_structure:", prog_output.results.final_structure)
+    print(prog_output.input_data)  # Input data used to generate the calculation
+    print(prog_output.provenance)  # Provenance of generated calculation

mkdocs.yml

@@ -93,7 +93,8 @@ markdown_extensions:
   - markdown_include.include
 
 watch:
-  - qcop # Adjust this
+  - qcop
+  - examples
 
 nav:
   - Getting Started:

pyproject.toml

@@ -20,7 +20,7 @@ xtb = { version = "^22.1", optional = true }
 tcpb = { version = "^0.14.1", optional = true }
 tomli-w = "^1.0.0"
 qcio = "^0.11.8"
-qcparse = "^0.6.2"
+qcparse = "^0.6.3"
 
 [tool.poetry.extras]
 qcengine = ["qcelemental", "qcengine"]
@@ -82,3 +82,7 @@ markers = [
     "integration: marks tests as integration (deselect with '-m \"not integration\"')",
 ]
 filterwarnings = ["ignore::DeprecationWarning:qcengine.*"]
+
+[tool.typos]
+# Exclude specific files or directories
+files.extend-exclude = [".vscode/**"]

qcop/adapters/terachem.py

@@ -4,7 +4,7 @@
 import qcparse
 from qcio import CalcType, ProgramInput, ProgramOutput, SinglePointResults
 from qcparse.encoders.terachem import XYZ_FILENAME
-from qcparse.parsers.terachem import parse_version_string
+from qcparse.parsers.terachem import parse_optimization_dir, parse_version_string
 
 from qcop.exceptions import AdapterError, AdapterInputError
 
@@ -15,7 +15,12 @@
 class TeraChemAdapter(ProgramAdapter[ProgramInput, SinglePointResults]):
     """Adapter for TeraChem."""
 
-    supported_calctypes = [CalcType.energy, CalcType.gradient, CalcType.hessian]
+    supported_calctypes = [
+        CalcType.energy,
+        CalcType.gradient,
+        CalcType.hessian,
+        CalcType.optimization,
+    ]
     program = "terachem"
 
     def program_version(self, stdout: Optional[str] = None) -> str:
@@ -53,18 +58,28 @@ def compute_results(
         Returns:
             A tuple of SinglePointResults and the stdout str.
         """
+        # Construct and write input file and xyz file to disk
         input_filename = "tc.in"
         try:
             native_input = qcparse.encode(inp_obj, self.program)
-        except qcparse.exceptions.EncoderError as e:
-            raise AdapterInputError(self.program, "Invalid input for TeraChem") from e
+        except qcparse.exceptions.EncoderError:
+            raise AdapterInputError(self.program, "Invalid input for TeraChem")
         Path(input_filename).write_text(native_input.input_file)
         Path(native_input.geometry_filename).write_text(native_input.geometry_file)
 
+        # Execute TeraChem
         stdout = execute_subprocess(
             self.program, [input_filename], update_func, update_interval
         )
-        parsed_output = qcparse.parse(stdout, self.program, "stdout")
+
+        # Parse output
+        if inp_obj.calctype == CalcType.optimization:
+            parsed_output = parse_optimization_dir(
+                f"scr.{XYZ_FILENAME.split('.')[0]}", stdout, inp_obj=inp_obj
+            )
+        else:
+            parsed_output = qcparse.parse(stdout, self.program, "stdout")
+
         return parsed_output, stdout
 
     def collect_wfn(self) -> dict[str, Union[str, bytes]]:

tests/integration_tests/test_terachem_integration.py

@@ -197,3 +197,20 @@ def test_terachem_hessian():
         ),
         atol=1e-6,
     )
+
+
+@pytest.mark.integration
+@skipif_program_not_available("terachem")
+def test_terachem_optimization(water):
+    # Modify keywords
+    energy_inp = ProgramInput(
+        structure=water,
+        calctype=CalcType.gradient,
+        model={"method": "hf", "basis": "sto-3g"},
+        keywords={"purify": "no", "new_minimizer": "yes"},
+    )
+
+    program = "terachem"
+    output = compute(program, energy_inp)
+    assert output.input_data == energy_inp
+    assert output.provenance.program == program