Merge pull request #248 from duartegroup/v1.3.5

V1.3.5

Author: t-young31

.github/pull_request_template.md

@@ -11,3 +11,4 @@ Please replace _#ISSUE_ with just e.g. #12 if this PR resolves issue 12.
 * [ ] The changes include an associated explanation of how/why
 * [ ] Test pass
 * [ ] Documentation has been updated
+* [ ] Changelog has been updated

.github/workflows/catch.yml

@@ -5,6 +5,9 @@ on:
     branches:
       - master
   pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'examples/**'
 
 env:
   BUILD_TYPE: Release

.github/workflows/pytest.yml

@@ -5,6 +5,9 @@ on:
     branches:
       - master
   pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'examples/**'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

.github/workflows/pytest_cov.yml

@@ -4,7 +4,11 @@ on:
   push:
     branches:
       - master
+      - 'v[0-9]+.[0-9]+.[0-9]+'
   pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - 'examples/**'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

autode/__init__.py

@@ -39,7 +39,7 @@
   - Merge when tests pass
 """
 
-__version__ = "1.3.4"
+__version__ = "1.3.5"
 
 
 __all__ = [

autode/hessians.py

@@ -234,9 +234,9 @@ def _mass_weighted(self) -> np.ndarray:
             axis=np.newaxis,
         )
 
-        return Hessian(
-            H / np.sqrt(np.outer(mass_array, mass_array)), units="J m^-2 kg^-1"
-        )
+        return np.array(
+            H / np.sqrt(np.outer(mass_array, mass_array))
+        )  # J Å^-2 kg^-1
 
     @cached_property
     def _proj_mass_weighted(self) -> np.ndarray:

autode/log/log.py

@@ -3,7 +3,7 @@
 
 """
 Set up logging with the standard python logging module. Set the log level with
-$AUTODE_LOG_LEVEL = {'', INFO, WARNING, DEBUG}
+$AUTODE_LOG_LEVEL = {'', ERROR, WARNING, INFO, DEBUG}
 
 i.e. export AUTODE_LOG_LEVEL=DEBUG
 
@@ -36,6 +36,9 @@ def get_log_level():
     if log_level_str == "INFO":
         return logging.INFO
 
+    if log_level_str == "ERROR":
+        return logging.ERROR
+
     return logging.CRITICAL
 
 

autode/units.py

@@ -211,15 +211,15 @@ def energy_unit_from_name(name: str) -> "autode.units.Unit":
 
 
 ha_per_ang = CompositeUnit(
-    ha, per=[ang], aliases=["ha Å-1", "ha Å^-1", "ha/ang"]
+    ha, per=[ang], aliases=["ha / Å", "ha Å-1", "ha Å^-1", "ha/ang"]
 )
 
 ha_per_a0 = CompositeUnit(
-    ha, per=[a0], aliases=["ha a0-1", "ha a0^-1", "ha/bohr"]
+    ha, per=[a0], aliases=["ha / a0", "ha a0-1", "ha a0^-1", "ha/bohr"]
 )
 
 ev_per_ang = CompositeUnit(
-    ev, per=[ang], aliases=["ha a0-1", "ev Å^-1", "ev/ang"]
+    ev, per=[ang], aliases=["ev / Å", "ev Å^-1", "ev/ang"]
 )
 
 kcalmol_per_ang = CompositeUnit(

autode/values.py

@@ -37,9 +37,12 @@
 )
 
 
-def _to(value: Union["Value", "ValueArray"], units: Union[Unit, str]):
+def _to(
+    value: Union["Value", "ValueArray"], units: Union[Unit, str], inplace: bool
+) -> Any:
     """
-    Convert a value or value array to a new unit and return a copy
+    Convert a value or value array to a new unit and return a copy if
+    inplace=False
 
     ---------------------------------------------------------------------------
     Arguments:
@@ -62,26 +65,29 @@ def _to(value: Union["Value", "ValueArray"], units: Union[Unit, str]):
 
     except StopIteration:
         raise TypeError(
-            f"No viable unit conversion from {value.units} " f"-> {units}"
+            f"No viable unit conversion from {value.units} -> {units}"
         )
 
-    # Convert to the base unit, then to the new units
-    c = float(units.conversion / value.units.conversion)
-
-    if isinstance(value, Value):
-        return value.__class__(float(value) * c, units=units)
-
-    elif isinstance(value, ValueArray):
-        value[:] = np.array(value, copy=True) * c
-        value.units = units
-        return value
-
-    else:
+    if not (isinstance(value, Value) or isinstance(value, ValueArray)):
         raise ValueError(
             f"Cannot convert {value} to new units. Must be one of"
             f" Value of ValueArray"
         )
 
+    if isinstance(value, Value) and inplace:
+        raise ValueError(
+            "Cannot modify a value inplace as floats are immutable"
+        )
+
+    # Convert to the base unit, then to the new units
+    c = float(units.conversion / value.units.conversion)
+
+    new_value = value if inplace else value.copy()
+    new_value *= c
+    new_value.units = units
+
+    return None if inplace else new_value
+
 
 def _units_init(value, units: Union[Unit, str, None]):
     """Initialise the units of this value
@@ -171,6 +177,11 @@ def _other_same_units(self, other):
 
         return other.to(self.units)
 
+    def _like_self_from_float(self, value: float) -> "Value":
+        new_value = self.__class__(value, units=self.units)
+        new_value.__dict__.update(self.__dict__)
+        return new_value
+
     def __eq__(self, other) -> bool:
         """Equality of two values, which may be in different units"""
 
@@ -210,20 +221,26 @@ def __add__(self, other) -> "Value":
         if isinstance(other, np.ndarray):
             return other + float(self)
 
-        return self.__class__(
-            float(self) + self._other_same_units(other), units=self.units
+        return self._like_self_from_float(
+            float(self) + self._other_same_units(other)
         )
 
-    def __mul__(self, other) -> "Value":
+    def __mul__(self, other) -> Union[float, "Value"]:
         """Multiply this value with another"""
         if isinstance(other, np.ndarray):
             return other * float(self)
 
-        return self.__class__(
-            float(self) * self._other_same_units(other), units=self.units
+        if isinstance(other, Value):
+            logger.warning(
+                "Multiplying autode.Value returns a float with no units"
+            )
+            return float(self) * self._other_same_units(other)
+
+        return self._like_self_from_float(
+            float(self) * self._other_same_units(other)
         )
 
-    def __rmul__(self, other) -> "Value":
+    def __rmul__(self, other) -> Union[float, "Value"]:
         return self.__mul__(other)
 
     def __radd__(self, other) -> "Value":
@@ -232,16 +249,13 @@ def __radd__(self, other) -> "Value":
     def __sub__(self, other) -> "Value":
         return self.__add__(-other)
 
-    def __floordiv__(self, other):
-        raise NotImplementedError(
-            "Integer division is not supported by " "autode.values.Value"
-        )
+    def __floordiv__(self, other) -> Union[float, "Value"]:
+        x = float(self) // self._other_same_units(other)
+        return x if isinstance(other, Value) else self._like_self_from_float(x)
 
-    def __truediv__(self, other) -> "Value":
-        return self.__class__(
-            float(self) / float(self._other_same_units(other)),
-            units=self.units,
-        )
+    def __truediv__(self, other) -> Union[float, "Value"]:
+        x = float(self) / self._other_same_units(other)
+        return x if isinstance(other, Value) else self._like_self_from_float(x)
 
     def __abs__(self) -> "Value":
         """Absolute value"""
@@ -260,7 +274,7 @@ def to(self, units):
         Raises:
             (TypeError):
         """
-        return _to(self, units)
+        return _to(self, units, inplace=False)
 
 
 class Energy(Value):
@@ -643,7 +657,21 @@ def to(self, units) -> Any:
         Raises:
             (TypeError):
         """
-        return _to(self, units)
+        return _to(self, units, inplace=False)
+
+    def to_(self, units) -> None:
+        """
+        Convert this array into a set of new units, inplace. This will not copy
+        the array
+
+        -----------------------------------------------------------------------
+        Returns:
+            (None)
+
+        Raises:
+            (TypeError):
+        """
+        _to(self, units, inplace=True)
 
     def __array_finalize__(self, obj):
         """See https://numpy.org/doc/stable/user/basics.subclassing.html"""

autode/wrappers/QChem.py

@@ -158,17 +158,24 @@ def coordinates_from(self, calc: "CalculationExecutor") -> Coordinates:
                 "Non-optimisation calculation performed - no change"
                 " to geometry"
             )
-            return calc.molecule.atoms
+            return calc.molecule.coordinates
+
+        if calc.molecule.n_atoms == 1:
+            # Coordinate of a single atom will not change
+            return calc.molecule.coordinates
 
         coords = []
 
         for i, line in enumerate(calc.output.file_lines):
 
-            if "Coordinates (Angstroms)" not in line:
+            if "Coordinates (Angstroms)" in line:
+                start_idx = i + 2
+            elif "Standard Nuclear Orientation (Angstroms)" in line:
+                start_idx = i + 3
+            else:
                 continue
 
-            """e.g.
-            
+            """e.g.            
                                Coordinates (Angstroms)
              ATOM                X               Y               Z
               1  O         0.0003489977   -0.1403224128    0.0000000000
@@ -177,7 +184,6 @@ def coordinates_from(self, calc: "CalculationExecutor") -> Coordinates:
             Point Group: cs    Number of degrees of freedom:     3
             """
 
-            start_idx = i + 2
             end_idx = start_idx + calc.molecule.n_atoms
             coords = []
             for cline in calc.output.file_lines[start_idx:end_idx]:

autode/wrappers/XTB.py

@@ -50,29 +50,31 @@ def print_cartesian_constraints(self, inp_file, molecule):
         if molecule.constraints.cartesian is None:
             return None
 
-        constrained_atom_idxs = [i + 1 for i in molecule.constraints.cartesian]
-        list_of_ranges, used_atoms = [], []
-
-        for i in constrained_atom_idxs:
-            atom_range = []
-            if i not in used_atoms:
-                while i in constrained_atom_idxs:
-                    used_atoms.append(i)
-                    atom_range.append(i)
-                    i += 1
-                if len(atom_range) in (1, 2):
-                    list_of_ranges += str(atom_range)
-                else:
-                    list_of_ranges.append(f"{atom_range[0]}-{atom_range[-1]}")
+        atom_idxs = list(
+            sorted(int(i) + 1 for i in molecule.constraints.cartesian)
+        )
+        list_of_ranges = []
 
+        for atom_idx in atom_idxs:
+            last_range = (
+                list_of_ranges[-1] if len(list_of_ranges) > 0 else None
+            )
+            if last_range is not None and atom_idx - 1 == last_range[-1]:
+                last_range.append(atom_idx)
+            else:
+                list_of_ranges.append([atom_idx])
+
+        list_of_ranges_str = [
+            f"{idxs[0]}-{idxs[-1]}" if len(idxs) > 1 else str(idxs[0])
+            for idxs in list_of_ranges
+        ]
         print(
             f"$constrain\n"
             f"force constant={self.force_constant}\n"
-            f'atoms: {",".join(list_of_ranges)}\n'
+            f'atoms: {",".join(list_of_ranges_str)}\n'
             f"$",
             file=inp_file,
         )
-
         return None
 
     @staticmethod

doc/changelog.rst

@@ -1,6 +1,30 @@
 Changelog
 =========
 
+1.3.5
+--------
+----------
+
+
+Usability improvements/Changes
+******************************
+- :code:`autode.value.ValueArray.to()` now defaults to copying the object rather than inplace modification
+
+
+Functionality improvements
+**************************
+- Adds a :code:`to_` method to :code:`autode.value.ValueArray` for explicit inplace modification of the array
+
+
+Bug Fixes
+*********
+- Fixes :code:`ERROR` logging level being ignored from environment variable :code:`AUTODE_LOG_LEVEL`
+- Fixes :code:`autode.values.Value` instances generating items with units on division, and throw a warning if multiplying
+- Fixes the printing of cartesian constraints in XTB input files, meaning they are no longer ignored
+- Fixes :code:`Hessian` instances changing units when normal modes are calculated
+- Fixes an incorrect alias for :code:`ev_per_ang`
+
+
 1.3.4
 --------
 ----------
@@ -10,7 +34,6 @@ Feature additions.
 Usability improvements/Changes
 ******************************
 * Throw useful exception for invalid :code:`ade.Config.ts_template_folder_path`
-* Adds the reaction temperature to the unique reaction hash
 
 
 Functionality improvements
@@ -22,7 +45,7 @@ Functionality improvements
 
 Bug Fixes
 *********
--
+- Fixes calculation :code:`clean_up()` failing with a null filename
 
 
 1.3.3

doc/config.rst

@@ -136,7 +136,7 @@ to see all the options.
 Logging
 -------
 
-To set the logging level to one of {INFO, WARNING, ERROR} set the :code:`AUTODE_LOG_LEVEL`
+To set the logging level to one of {DEBUG, INFO, WARNING, ERROR} set the :code:`AUTODE_LOG_LEVEL`
 environment variable, in bash::
 
     $ export AUTODE_LOG_LEVEL=INFO