Merge pull request #378 from tovrstra/fchk-ref-energy

Fchk ref energy

Author: tovrstra

.github/workflows/pytest.yaml

@@ -27,7 +27,7 @@ jobs:
         if: ${{ matrix.python-version == '3.9'}}
         # Ensure changes to these dependencies are reflected
         # in pyproject.toml and docs/install.rst
-        run: pip install numpy==1.22 scipy==1.11.1 attrs==21.3.0
+        run: pip install numpy==1.26.4 scipy==1.13.1 attrs==21.3.0
       - name: Install development version
         run: pip install -e .[dev]
       # If some tests are slow against expectations, pytest will abort due to timeout.

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: 'iodata/test/data/.*'
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.6.0
+  rev: v5.0.0
   hooks:
     - id: check-added-large-files
       args: ["--maxkb=100"]
@@ -29,11 +29,11 @@ repos:
     - id: remove-crlf
       exclude_types: [binary]
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.28.5
+  rev: 0.31.3
   hooks:
     - id: check-github-workflows
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.4.9
+  rev: v0.10.0
   hooks:
     - id: ruff-format
     - id: ruff

docs/gen_formats.py

@@ -21,7 +21,7 @@
 
 from iodata.api import FORMAT_MODULES
 
-__all__ = ("format_words", "print_section", "main")
+__all__ = ("format_words", "main", "print_section")
 
 
 HEADER = """

docs/install.rst

@@ -34,7 +34,7 @@ In addition, IOData has the following dependencies:
     Ensure changes to these dependencies are reflected
     in pyproject.toml and .github/workflows/pytest.yaml
 
-- numpy >= 1.22: https://numpy.org/
+- numpy >= 1.26.4: https://numpy.org/
 - scipy >= 1.11.1: https://scipy.org/
 - attrs >= 21.3.0: https://www.attrs.org/en/stable/index.html
 

iodata/__init__.py

@@ -28,4 +28,4 @@
 from .api import dump_many, dump_one, load_many, load_one, write_input
 from .iodata import IOData
 
-__all__ = ("IOData", "load_one", "load_many", "dump_one", "dump_many", "write_input")
+__all__ = ("IOData", "dump_many", "dump_one", "load_many", "load_one", "write_input")

iodata/api.py

@@ -37,7 +37,7 @@
     WriteInputError,
 )
 
-__all__ = ("load_one", "load_many", "dump_one", "dump_many", "write_input")
+__all__ = ("dump_many", "dump_one", "load_many", "load_one", "write_input")
 
 
 def _find_format_modules():

iodata/basis.py

@@ -33,7 +33,7 @@
 
 from .attrutils import convert_array_to, validate_shape
 
-__all__ = ("angmom_sti", "angmom_its", "Shell", "MolecularBasis")
+__all__ = ("MolecularBasis", "Shell", "angmom_its", "angmom_sti")
 
 ANGMOM_CHARS = "spdfghiklmnoqrtuvwxyzabce"
 

iodata/convert.py

@@ -31,12 +31,12 @@
 from .orbitals import MolecularOrbitals
 
 __all__ = (
-    "convert_conventions",
-    "iter_cart_alphabet",
-    "HORTON2_CONVENTIONS",
     "CCA_CONVENTIONS",
-    "convert_to_unrestricted",
+    "HORTON2_CONVENTIONS",
+    "convert_conventions",
     "convert_to_segmented",
+    "convert_to_unrestricted",
+    "iter_cart_alphabet",
 )
 
 

iodata/docstrings.py

@@ -21,10 +21,10 @@
 from typing import Callable, Optional
 
 __all__ = (
-    "document_load_one",
-    "document_load_many",
-    "document_dump_one",
     "document_dump_many",
+    "document_dump_one",
+    "document_load_many",
+    "document_load_one",
     "document_write_input",
 )
 
@@ -188,8 +188,7 @@ def _document_dump(
     def decorator(func):
         if optional:
             optional_sentence = (
-                " If the following attributes are present, they are also dumped "
-                "into the file: {}."
+                " If the following attributes are present, they are also dumped into the file: {}."
             ).format(", ".join(f"``{word}``" for word in optional))
         else:
             optional_sentence = ""

iodata/formats/fchk.py

@@ -348,12 +348,13 @@ def load_many(lit: LineIterator) -> Iterator[dict]:
                 ),
                 stacklevel=2,
             )
+        reference_energy = fchk.get("Optimization Reference Energy", 0.0)
         for istep, (energy, recor, atcoords, gradients) in enumerate(trajectory):
             data = {
                 "title": fchk["title"],
                 "atnums": fchk["Atomic numbers"],
                 "atcorenums": fchk["Nuclear charges"],
-                "energy": energy,
+                "energy": energy + reference_energy,
                 "atcoords": atcoords,
                 "atgradient": gradients,
                 "extra": {