Xyz to mol

.clang-format

@@ -0,0 +1,110 @@
+# Copyright 2022 NWChemEx-Project
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+---
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.gitignore

@@ -20,6 +20,7 @@
 # These are directories used by IDEs for storing settings
 .idea/
 .vscode/
+.cache/
 
 # These are common Python virtual enviornment directory names
 venv/

src/cxx/nux/nux.cpp

@@ -21,6 +21,7 @@ namespace nux {
 
 void load_modules(pluginplay::ModuleManager &mm) {
   mm.add_module<BOApproximation>("Born-Oppenheimer Approximation");
+  mm.add_module<XYZToMolecule>("XYZ To Molecule");
 }
 
-} // namespace nux
+} // namespace nux

src/cxx/nux/nux_modules.hpp

@@ -20,5 +20,6 @@
 namespace nux {
 
 DECLARE_MODULE(BOApproximation);
+DECLARE_MODULE(XYZToMolecule);
 
-}
+}

src/cxx/nux/xyz_to_mol.cpp

@@ -0,0 +1,77 @@
+/*
+ * Copyright 2025 NWChemEx-Project
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+#include "nux_modules.hpp"
+#include <fstream>
+#include <sstream>
+#include <string>
+#include <vector>
+
+namespace nux {
+
+  MODULE_CTOR(XYZToMolecule) {
+    satisfies_property_type<simde::MoleculeFromString>();
+    add_submodule<simde::ZFromSymbol>("Z from symbol");
+    add_submodule<simde::AtomFromZ>("Atom from z");
+  }
+
+  MODULE_RUN(XYZToMolecule) {
+    const auto& [filename] = simde::MoleculeFromString::unwrap_inputs(inputs);
+
+    auto& z_from_sym = submods.at("Z from symbol");
+    auto& atom_from_z = submods.at("Atom from z");
+
+    chemist::Molecule mol;
+
+    std::ifstream xyz_file(filename);
+
+    if (!xyz_file) {
+      throw std::runtime_error("File not found: " + filename);
+    }
+
+    std::string line;
+
+    // Skips the 1st line of the file, associated with the number of
+    // atoms in the file, and the 2nd line, the comment line.
+    std::getline(xyz_file, line);
+    std::getline(xyz_file, line);
+
+    while (std::getline(xyz_file, line)) {
+      std::istringstream iss(line);
+      std::vector<std::string> tokens;
+      std::string token;
+      while (std::getline(iss, token, ' ')) {
+        if (token.size()) { tokens.emplace_back(token); }
+      }
+      auto Z = z_from_sym.run_as<simde::ZFromSymbol>(tokens.at(0));
+      auto x = std::stod(tokens.at(1));
+      auto y = std::stod(tokens.at(2));
+      auto z = std::stod(tokens.at(3));
+
+      auto atm = atom_from_z.run_as<simde::AtomFromZ>(Z);
+      atm.x()  = x;
+      atm.y()  = y;
+      atm.z()  = z;
+      mol.push_back(atm);
+    }
+
+    xyz_file.close();
+
+    auto rv = results();
+    return simde::MoleculeFromString::wrap_results(rv, mol);
+  }
+
+} // namespace nux

tests/cxx/unit_tests/xyz_to_mol.cpp

@@ -0,0 +1,71 @@
+/*
+ * Copyright 2024 NWChemEx-Project
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+#include "../test_nux.hpp"
+#include <nux/nux.hpp>
+
+TEST_CASE("XYZToMolecule") {
+    pluginplay::ModuleManager mm;
+    nux::load_modules(mm);
+
+    auto make_atoms = [=](auto&& Z) {
+      REQUIRE(Z == 1);
+      double h_mass = 1837.4260218693814;
+      return simde::type::atom{"H", 1, h_mass, 0.0, 0.0, 0.0};
+    };
+
+    auto atom_mod = pluginplay::make_lambda<simde::AtomFromZ>(make_atoms);
+
+    auto z_mod = pluginplay::make_lambda<simde::ZFromSymbol>([=](auto&& symbol) {
+        return simde::type::atomic_number{1};
+    });
+
+    auto& xyz_mod = mm.at("XYZ To Molecule");
+    xyz_mod.change_submod("Z from symbol", z_mod);
+    xyz_mod.change_submod("Atom from z", atom_mod);
+
+  SECTION("No XYZ file found") {
+    std::string file = "file.xyz";
+    REQUIRE_THROWS_AS(xyz_mod.run_as<simde::MoleculeFromString>(file), std::runtime_error);
+  }
+
+  SECTION("Full XYZ To Molecule run") {
+    auto atom0{make_atoms(1)};
+    auto atom1{make_atoms(1)};
+    atom1.z() = 1;
+
+    simde::type::molecule test_mol{atom0, atom1};
+
+    std::ofstream xyz_file;
+    xyz_file.open("h2.xyz");
+
+    xyz_file << "2\n";
+    xyz_file << "This is a comment!\n";
+    xyz_file << "H 0 0 0\n";
+    xyz_file << "H 0 0 1\n";
+    xyz_file.close();
+
+    std::string filename = "h2.xyz";
+
+    auto mol = xyz_mod.run_as<simde::MoleculeFromString>(filename);
+
+    remove("h2.xyz");
+    std::ifstream del_file("h2.xyz");
+
+    REQUIRE(mol == test_mol);
+    REQUIRE(del_file.good() == false);
+  }
+}