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Don't bond Noble gases #1357

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merged 3 commits into from
Sep 29, 2023
Merged

Don't bond Noble gases #1357

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72391c2
Don't bond Noble gas atoms (e.g., Ar-Ar clusters)
ghutchis Sep 29, 2023
fadd005
Add the snapshot date to the DMG
ghutchis Sep 29, 2023
a934b18
Make sure to remove any old DMG before running cpack
ghutchis Sep 29, 2023
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1 change: 1 addition & 0 deletions .github/workflows/build_cmake.yml
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Expand Up @@ -262,6 +262,7 @@ jobs:
if [ -z "${P12_PASSWORD}" ]; then
unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign
fi
[[ ! "${GITHUB_REF}" =~ "tags" ]] && export SNAPSHOT_DATE=`date -j "+%d-%m-%y"`
cpack ${{ matrix.config.cpack_flags }}
working-directory: ${{ runner.workspace }}/build/avogadroapp
env:
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3 changes: 3 additions & 0 deletions .github/workflows/build_m1.yml
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Expand Up @@ -145,13 +145,16 @@ jobs:
# signing occurs via avogadroapp cpack instructions
fi # certificate exists
fi # password exists
# remove any previous DMG in case they're still around
rm -f avogadroapp/*.dmg

- name: Create Mac and Windows Packages
shell: bash
run: |
if [ -z "${P12_PASSWORD}" ]; then
unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign
fi
[[ ! "${GITHUB_REF}" =~ "tags" ]] && export SNAPSHOT_DATE=`date -j "+%d-%m-%y"`
cpack ${{ matrix.config.cpack_flags }}
working-directory: ${{ runner.workspace }}/build/avogadroapp
env:
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22 changes: 22 additions & 0 deletions avogadro/core/molecule.cpp
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Expand Up @@ -1055,6 +1055,28 @@ void Molecule::perceiveBondsSimple(const double tolerance, const double min)
Vector3 jpos = m_positions3d[j];
Vector3 diff = jpos - ipos;

// Don't automatically bond nobel gases to anything
switch (atomicNumber(i)) {
case 2: // He
case 10: // Ne
case 18: // Ar
case 36: // Kr
continue;
default:
break;
}

// now for the other atom
switch (atomicNumber(j)) {
case 2: // He
case 10: // Ne
case 18: // Ar
case 36: // Kr
continue;
default:
break;
}

if (std::fabs(diff[0]) > cutoff || std::fabs(diff[1]) > cutoff ||
std::fabs(diff[2]) > cutoff ||
(atomicNumber(i) == 1 && atomicNumber(j) == 1))
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