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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 @@ -20,6 +20,12 @@

namespace nux {

double ang2bohr(double ang_value) {
// Converts a anstrom-based value to a bohr-based value
double bohr_value = ang_value * 1.8897259886;
return bohr_value;
}

MODULE_CTOR(XYZToMolecule) {
satisfies_property_type<simde::MoleculeFromString>();
add_submodule<simde::ZFromSymbol>("Z from symbol");
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() = ang2bohr(x);
atom.y() = ang2bohr(y);
atom.z() = ang2bohr(z);

mol.push_back(atom);
}
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2 changes: 1 addition & 1 deletion tests/cxx/unit_tests/xyz_file_to_mol.cpp
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Expand Up @@ -47,7 +47,7 @@ TEST_CASE("XYZFileToMolecule") {
SECTION("Full XYZ To Molecule run: File") {
auto atom0{make_atoms(1)};
auto atom1{make_atoms(1)};
atom1.z() = 1;
atom1.z() = 1.8897259886;

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

Expand Down
2 changes: 1 addition & 1 deletion tests/cxx/unit_tests/xyz_to_mol.cpp
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Expand Up @@ -51,7 +51,7 @@ TEST_CASE("XYZToMolecule") {
SECTION("Full XYZ To Molecule run: Data") {
auto atom0{make_atoms(1)};
auto atom1{make_atoms(1)};
atom1.z() = 1;
atom1.z() = 1.8897259886;

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

Expand Down