Merge pull request #308 from duartegroup/v1.4.1

V1.4.1

Author: t-young31

.github/workflows/pytest.yml

@@ -35,15 +35,19 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         activate-environment: test
-        mamba-version: "*"
         channels: conda-forge
 
+    - name: Install mamba solver
+      run: |
+        conda install -n base conda-libmamba-solver
+
     - name: Install
       run: |
-        mamba install \
+        conda install \
           --file requirements.txt \
           --file tests/requirements.txt \
-          --channel conda-forge
+          --channel conda-forge \
+          --solver=libmamba
         python -m pip install . --no-deps
 
     - name: Test

.github/workflows/pytest_cov.yml

@@ -36,15 +36,19 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         activate-environment: test
-        mamba-version: "*"
         channels: conda-forge
 
+    - name: Install mamba solver
+      run: |
+        conda install -n base conda-libmamba-solver
+
     - name: Install
       run: |
-        mamba install \
+        conda install \
           --file requirements.txt \
           --file tests/requirements.txt \
-          --channel conda-forge
+          --channel conda-forge \
+          --solver=libmamba
         source .github/scripts/install_xtb_ci.sh
         python -m pip install . --no-deps
 

.pre-commit-config.yaml

@@ -1,18 +1,18 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
+    rev: v4.4.0
     hooks:
       - id: trailing-whitespace
       - id: mixed-line-ending
 
   - repo: https://github.com/psf/black
-    rev: 22.10.0
+    rev: 23.9.1
     hooks:
       - id: black
         language_version: python3
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.0.1
+    rev: v1.5.1
     hooks:
     - id: mypy
       exclude: "tests/|doc/|examples/"

autode/__init__.py

@@ -1,3 +1,5 @@
+import importlib.metadata
+
 from autode import methods
 from autode import geom
 from autode import pes
@@ -25,14 +27,10 @@
 from autode.utils import temporary_config
 
 """
-Bumping the version number requires following the release proceedure:
-
-- Update changelog (doc/changelog.rst)
+Bumping the version number requires following the release procedure:
 
 - Run tests/benchmark.py with both organic and organometallic sets
 
-- Change __version__ here and in setup.py
-
 - Release on conda-forge
   - Fork https://github.com/conda-forge/autode-feedstock
   - Make a local branch
@@ -41,8 +39,7 @@
   - Merge when tests pass
 """
 
-__version__ = "1.4.0"
-
+__version__ = importlib.metadata.version("autode")
 
 __all__ = [
     "KeywordsSet",

autode/atoms.py

@@ -219,7 +219,6 @@ def group(self) -> int:
         """
 
         for group_idx in range(1, 18):
-
             if self.label in PeriodicTable.group(group_idx):
                 return group_idx
 
@@ -242,7 +241,6 @@ def period(self) -> int:
         """
 
         for period_idx in range(1, 7):
-
             if self.label in PeriodicTable.period(period_idx):
                 return period_idx
 
@@ -692,7 +690,6 @@ def moi(self) -> MomentOfInertia:
         moi = MomentOfInertia(np.zeros(shape=(3, 3)), units="amu Å^2")
 
         for atom in self:
-
             mass, (x, y, z) = atom.mass, atom.coord
 
             moi[0, 0] += mass * (y**2 + z**2)
@@ -887,7 +884,6 @@ def are_planar(self, distance_tol: Distance = Distance(1e-3, "Å")) -> bool:
         normal_vec = np.cross(arr[1, :] - x0, arr[2, :] - x0)
 
         for i in range(3, len(self)):
-
             # Calculate the 0->i atomic vector, which must not have any
             # component in the direction in the normal if the atoms are planar
             if np.dot(normal_vec, arr[i, :] - x0) > distance_tol_float:
@@ -1253,7 +1249,6 @@ def dihedral(self, w: int, x: int, y: int, z: int) -> Angle:
 
 
 class PeriodicTable:
-
     # fmt: off
     table = np.array(
         [['H',    '',   '',   '',   '',  '',    '',   '',   '',   '',   '',   '',   '',   '',   '',   '',   '', 'He'],

autode/bond_rearrangement.py

@@ -246,7 +246,6 @@ def add_bond_rearrangment(bond_rearrangs, reactant, product, fbonds, bbonds):
     bbond_atoms = [atom for bbond in bbonds for atom in bbond]
     for fbond in fbonds:
         for idx in fbond:
-
             if (
                 reactant.graph.degree(idx)
                 == reactant.atoms[idx].maximal_valance
@@ -358,7 +357,6 @@ def get_fbonds_bbonds_2b(
         for bbond1, bbond2 in itertools.product(
             all_possible_bbonds[0], all_possible_bbonds[1]
         ):
-
             possible_brs = add_bond_rearrangment(
                 possible_brs, reac, prod, fbonds=[], bbonds=[bbond1, bbond2]
             )
@@ -672,7 +670,6 @@ def strip_equiv_bond_rearrs(possible_brs, mol, depth=6):
 
         # Compare bond_rearrang to all those already considered to be unique,
         for unique_br in unique_brs:
-
             if unique_br.get_active_atom_neighbour_lists(
                 species=mol, depth=depth
             ) == br.get_active_atom_neighbour_lists(species=mol, depth=depth):
@@ -736,7 +733,6 @@ def prune_small_ring_rearrs(possible_brs, mol):
 
         # Check against all other rearrangements
         for j, other_br in enumerate(possible_brs):
-
             # Only consider brs with the same set of elements
             if elems[i] != elems[j]:
                 continue

autode/bracket/base.py

@@ -76,10 +76,8 @@ def converged(self) -> bool:
         """Whether the bracketing method has converged or not"""
         assert self.imgpair is not None, "Must have an image pair"
 
-        # NOTE: In bracketing methods, usually the geometry
-        # optimisation is done in separate micro-iterations,
-        # which means that the gradient tolerance is checked
-        # elsewhere, and only distance criteria is checked here
+        # NOTE: Usually geometry optimisation is done in separate
+        # micro-iters, so gradient is checked elsewhere
         return self.imgpair.dist <= self._dist_tol
 
     @property
@@ -175,6 +173,7 @@ def _calculate(
             self._step()
 
             if self.imgpair.has_jumped_over_barrier:
+                # TODO: implement image pair regeneration
                 logger.error(
                     "One image has probably jumped over the barrier, in"
                     f" {self._name} TS search. Please check the"
@@ -209,7 +208,7 @@ def _calculate(
 
         self.print_geometries()
         self.plot_energies()
-        if self.ts_guess is not None:
+        if self.converged and self.ts_guess is not None:
             self.ts_guess.print_xyz_file(filename=f"{self._name}_ts_guess.xyz")
         return None
 

autode/bracket/dhs.py

@@ -715,6 +715,9 @@ def _get_dhs_step(self, side: ImageSide) -> CartesianCoordinates:
             gs_step = np.zeros_like(dhs_step)
             # hack to ensure the first step is 100% DHS (as GS is not possible)
             dhs_step = dhs_step / (1 - self._gs_mix)
+        else:
+            # rescale GS step as well so that one vector doesn't dominate
+            gs_step *= self._step_size / np.linalg.norm(gs_step)
 
         old_coord = self.imgpair.get_coord_by_side(side)
         new_coord = (