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Adjusts XYZ to Mol and XYZ File to Mol modules to assume angstrom and convert to bohr #9

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Merged
ryanmrichard merged 3 commits into from
Oct 8, 2025
Merged

Adjusts XYZ to Mol and XYZ File to Mol modules to assume angstrom and convert to bohr #9

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b3c51b8
clang-format changes
jlheflin Oct 5, 2025
36e971c
clang format changes
jlheflin Oct 8, 2025
663530e
added testing for the x and y components instead of just the z compon…
jlheflin Oct 8, 2025
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14 changes: 11 additions & 3 deletions src/cxx/nux/xyz_to_mol.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -24,10 +24,16 @@ MODULE_CTOR(XYZToMolecule) {
satisfies_property_type<simde::MoleculeFromString>();
add_submodule<simde::ZFromSymbol>("Z from symbol");
add_submodule<simde::AtomFromZ>("Atom from z");
add_input<double>("Unit scaling factor")
.set_default(1.0)
.set_description(
"Sets the unit scaling factor, default 1.0 for bohr input units")
.set_default(1.0);
}

MODULE_RUN(XYZToMolecule) {
const auto& [xyz_data] = simde::MoleculeFromString::unwrap_inputs(inputs);
auto unit_scale = inputs.at("Unit scaling factor").value<double>();
auto& z_from_sym = submods.at("Z from symbol");
auto& atom_from_z = submods.at("Atom from z");

Expand Down Expand Up @@ -66,9 +72,11 @@ MODULE_RUN(XYZToMolecule) {

auto Z = z_from_sym.run_as<simde::ZFromSymbol>(atom_string);
auto atom = atom_from_z.run_as<simde::AtomFromZ>(Z);
atom.x() = x;
atom.y() = y;
atom.z() = z;

// Assumes that the XYZ coordnates given are in angstroms
atom.x() = x * unit_scale;
atom.y() = y * unit_scale;
atom.z() = z * unit_scale;

mol.push_back(atom);
}
Expand Down
22 changes: 22 additions & 0 deletions tests/cxx/unit_tests/xyz_to_mol.cpp
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Expand Up @@ -65,4 +65,26 @@ TEST_CASE("XYZToMolecule") {

REQUIRE(mol == test_mol);
}

SECTION("XYZ to Molecule Unit Scaling: Angstroms to Bohr") {
auto atom0{make_atoms(1)};
auto atom1{make_atoms(1)};
atom1.x() = 1.8897259886;
atom1.y() = 1.8897259886;
atom1.z() = 1.8897259886;

simde::type::molecule test_mol{atom0, atom1};

std::stringstream xyz_data;
xyz_data << "2\n";
xyz_data << "This is a comment!\n";
xyz_data << "H 0 0 0\n";
xyz_data << "H 1 1 1\n";

xyz_mod.change_input("Unit scaling factor", 1.8897259886);

auto mol = xyz_mod.run_as<simde::MoleculeFromString>(xyz_data.str());

REQUIRE(mol == test_mol);
}
}