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Fix anglescan when the two molecules are different #458

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merged 4 commits into from
Oct 31, 2024
Merged

Fix anglescan when the two molecules are different #458

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b5ac8c2
Add trace log
mlund Oct 24, 2024
4331755
Fix error and simplify ranges operations
mlund Oct 29, 2024
67ec3b9
Clang format
mlund Oct 29, 2024
c479456
Minor refactoring
mlund Oct 29, 2024
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15 changes: 10 additions & 5 deletions src/actions.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,10 @@ void AngularScan::Molecule::initialize(const Space::GroupVector& groups, int mol
if (group.isAtomic()) {
throw ConfigurationError("{}: group {} is not molecular", NAME, index);
}
auto as_centered_position = [&](auto& particle) -> Point {

faunus_logger->trace("{}: initizalizing group {}", NAME, index);

auto as_centered_position = [&](const auto& particle) -> Point {
return particle.pos - group.mass_center;
};
ref_positions = group | rv::transform(as_centered_position) | ranges::to_vector;
Expand All @@ -72,14 +75,17 @@ ParticleVector AngularScan::Molecule::getRotatedReference(const Space::GroupVect
auto particles = ParticleVector(group.begin(), group.end()); // copy particles from Space
auto positions =
ref_positions | rv::transform([&](const auto& pos) -> Point { return q * pos; });
std::copy(positions.begin(), positions.end(),
std::ranges::copy(positions,
(particles | rv::transform(&Particle::pos)).begin());
return particles;
}

void AngularScan::report(const Group& group1, const Group& group2, const Eigen::Quaterniond& q1,
const Eigen::Quaterniond& q2, Energy::NonbondedBase& nonbonded)
{
using ranges::views::concat;
using std::views::transform;

const auto energy = nonbonded.groupGroupEnergy(group1, group2);
if (energy >= max_energy) {
return;
Expand All @@ -95,8 +101,7 @@ void AngularScan::report(const Group& group1, const Group& group2, const Eigen::
*stream << format(q1) << format(q2)
<< fmt::format("{:8.4f} {:>10.3E}\n", group2.mass_center.z(), energy / 1.0_kJmol);
if (trajectory) {
auto positions = ranges::views::concat(group1, group2) |
std::views::transform(&Particle::pos);
auto positions = concat(group1, group2) | transform(&Particle::pos);
trajectory->writeNext({500, 500, 500}, positions.begin(), positions.end());
}
}
Expand All @@ -119,7 +124,7 @@ void AngularScan::operator()(Space& spc, Energy::Hamiltonian& hamiltonian)

#pragma omp parallel for
for (const auto& q1 : angles.quaternions_1) {
auto particles1 = molecules.second.getRotatedReference(spc.groups, q1);
auto particles1 = molecules.first.getRotatedReference(spc.groups, q1);
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Source of the problem!

auto group1 = Group(0, particles1.begin(), particles1.end());
group1.updateMassCenter(spc.geometry.getBoundaryFunc(), {0, 0, 0});

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