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Initial electrostatics framework #970

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merged 8 commits into from
Jun 21, 2022

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Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
For example some methods only do CHONF, or other limited types
.. so don't show them to the user.

Also helpful for some materials potentials (e.g., silver-only)

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
Class handles electrostatics from atomic partial charges
(e.g., Mulliken from a quantum program, or Gasteiger from Open Babel)

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
Includes element filtering / masking
(e.g., this method only supports some elements)

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
@ghutchis ghutchis requested a review from aerkiaga June 20, 2022 17:43
@ghutchis ghutchis changed the title Electrostatics WIP: Electrostatics Jun 20, 2022
Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
Array<double> potentials(points.size(), 0.0);
for(unsigned int i = 0; i < points.size(); ++i)
potentials[i] = potential(mol, points[i]);
return potentials;

Check notice

Code scanning

Reference to local variable returned.

Reference to local variable returned.
return search->second; // value from the map
} else {
MatrixX charges(atomCount(), 1);
return charges;

Check notice

Code scanning

Reference to local variable returned.

Reference to local variable returned.
if (m_identifiers.find(identifier) != m_identifiers.end()) {
MatrixX charges(molecule.atomCount(),
1); // we have to return something, so zeros
return charges;

Check notice

Code scanning

Reference to local variable returned.

Reference to local variable returned.

if (m_identifiers.find(identifier) != m_identifiers.end()) {
Core::Array<double> potentials(points.size(), 0.0);
return potentials;

Check notice

Code scanning

Reference to local variable returned.

Reference to local variable returned.

ChargeManager& ChargeManager::instance()
{
static ChargeManager instance;

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Code scanning

Local static object: instance

Local static object: instance
avogadro/calc/defaultmodel.cpp Fixed Show fixed Hide fixed
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Here are the build results
macOS-arm64.dmg
Artifacts will only be retained for 90 days.

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
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Here are the build results
macOS-arm64.dmg
Artifacts will only be retained for 90 days.

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
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Here are the build results
macOS-arm64.dmg
Artifacts will only be retained for 90 days.

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Here are the build results
Avogadro2.AppImage
macOS.dmg
Win64.exe
Artifacts will only be retained for 90 days.

avogadro/core/molecule.h Outdated Show resolved Hide resolved
avogadro/calc/chargemanager.cpp Outdated Show resolved Hide resolved
avogadro/calc/chargemanager.cpp Show resolved Hide resolved
Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
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Here are the build results
macOS-arm64.dmg
Artifacts will only be retained for 90 days.

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Here are the build results
Avogadro2.AppImage
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

@ghutchis ghutchis changed the title WIP: Electrostatics Initial electrostatics framework Jun 21, 2022
@ghutchis ghutchis added the enhancement feature changes / API changes label Jun 21, 2022
@ghutchis ghutchis merged commit ad7ebe7 into OpenChemistry:master Jun 21, 2022
@ghutchis ghutchis deleted the electrostatics branch June 21, 2022 15:24
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Here are the build results
Avogadro2.AppImage
macOS.dmg
Ubuntu-2004.tar.gz
Win64.exe
Artifacts will only be retained for 90 days.

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avo-bot commented Jun 23, 2022

This pull request has been mentioned on Avogadro Discussion. There might be relevant details there:

https://discuss.avogadro.cc/t/june-2022-development-update/3879/1

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