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fix no solvent #334

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merged 2 commits into from
Apr 19, 2024
Merged

fix no solvent #334

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2125c4f
fix qrc solvent
t-young31 Apr 14, 2024
4cc3951
Update pytest_cov.yml
t-young31 Apr 14, 2024
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3 changes: 2 additions & 1 deletion .github/workflows/pytest_cov.yml
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Expand Up @@ -56,7 +56,8 @@ jobs:
run: |
pytest --cov=./ --cov-report=xml

- uses: codecov/codecov-action@v3
- uses: codecov/codecov-action@v4
with:
flags: unittests
fail_ci_if_error: true
token: ${{ secrets.CODECOV_TOKEN }} # required
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Thanks for this, I was wondering why all the codecov runs were failing!

8 changes: 1 addition & 7 deletions autode/transition_states/base.py
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Expand Up @@ -463,13 +463,7 @@ def displaced_species_along_mode(

disp_coords -= (disp_factor / 20) * mode_disp_coords

# Create a new species from the initial
disp_species = Species(
name=f"{species.name}_disp",
atoms=species.atoms.copy(),
charge=species.charge,
mult=species.mult,
)
disp_species = species.new_species(name=f"{species.name}_disp")
disp_species.coordinates = disp_coords

return disp_species
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2 changes: 1 addition & 1 deletion doc/changelog.rst
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Expand Up @@ -11,7 +11,7 @@ Functionality improvements

Bug Fixes
*********
- ...
- Fixes no solvent being added in QRC calculations

Usability improvements/Changes
******************************
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17 changes: 16 additions & 1 deletion tests/test_ts/test_mode_checking.py
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@@ -1,3 +1,7 @@
import os
import numpy as np

from autode.species.molecule import Molecule
from autode.calculations import Calculation
from autode.transition_states.base import TSbase
from autode.transition_states.base import imag_mode_generates_other_bonds
Expand All @@ -8,7 +12,6 @@
from autode.bond_rearrangement import BondRearrangement
from autode.methods import ORCA
from .. import testutils
import os

here = os.path.dirname(os.path.abspath(__file__))
orca = ORCA()
Expand Down Expand Up @@ -70,6 +73,18 @@ def test_graph_no_other_bonds():
)


def test_disp_molecule_has_same_solvent():
mol = Molecule(smiles="[H][H]", solvent_name="water")
mol.hessian = np.eye(3 * mol.n_atoms, 3 * mol.n_atoms)

disp_mol = displaced_species_along_mode(
species=mol,
mode_number=1,
)
assert disp_mol.solvent is not None
assert disp_mol.solvent == mol.solvent


def has_correct_mode(name, fbonds, bbonds):
calc = Calculation(
name=name,
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