Docs: replace xyz files with xyz strings

docs/source/_static/examples/cpp/active_space_selector.cpp

@@ -27,9 +27,15 @@ int main() {
   // --------------------------------------------------------------------------------------------
 
   // --------------------------------------------------------------------------------------------
+  // docs:xyz ../data/water.structure.xyz
   // start-cell-run
-  // Load a molecular structure (water molecule) from XYZ file
-  auto structure = Structure::from_xyz_file("../data/water.structure.xyz");
+  // Load a molecular structure (water molecule) from inline XYZ file
+  auto structure = Structure::from_xyz(R"(3
+Water molecule
+O    0.000000    0.000000    0.000000
+H    0.758602    0.000000    0.504284
+H   -0.758602    0.000000    0.504284
+)");
   int charge = 0;
 
   // First, run SCF to get molecular orbitals

docs/source/_static/examples/cpp/ansatz.cpp

@@ -4,6 +4,7 @@
 
 // Ansatz usage examples.
 // --------------------------------------------------------------------------------------------
+// docs:xyz ../data/h2.structure.xyz
 // start-cell-create
 #include <iostream>
 #include <qdk/chemistry.hpp>
@@ -12,8 +13,12 @@ using namespace qdk::chemistry::data;
 using namespace qdk::chemistry::algorithms;
 
 int main() {
-  // Load H2 structure from XYZ file
-  auto structure = Structure::from_xyz_file("../data/h2.structure.xyz");
+  // Load H2 structure from inline XYZ file
+  auto structure = Structure::from_xyz(R"(2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+)");
 
   // SCF
   auto scf_solver = ScfSolverFactory::create();

docs/source/_static/examples/cpp/dynamical_correlation.cpp

@@ -24,9 +24,14 @@ auto mp2_calculator =
 // -----------------------------------------------------------------------------
 
 // -----------------------------------------------------------------------------
+// docs:xyz ../data/h2.structure.xyz
 // start-cell-run
-// Load H2 structure from XYZ file
-auto structure = Structure::from_xyz_file("../data/h2.structure.xyz");
+// Load H2 structure from inline XYZ file
+auto structure = Structure::from_xyz(R"(2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+)");
 
 // Run initial SCF to get reference wavefunction
 auto scf_solver = ScfSolverFactory::create();

docs/source/_static/examples/cpp/hamiltonian.cpp

@@ -4,9 +4,15 @@
 
 // Hamiltonian usage examples.
 // --------------------------------------------------------------------------------------------
+// docs:xyz ../data/water.structure.xyz
 // start-cell-hamiltonian-creation
-// Load structure from XYZ file
-auto structure = Structure::from_xyz_file("../data/water.structure.xyz");
+// Load structure from inline XYZ file
+auto structure = Structure::from_xyz(R"(3
+Water molecule
+O    0.000000    0.000000    0.000000
+H    0.758602    0.000000    0.504284
+H   -0.758602    0.000000    0.504284
+)");
 
 // Run initial SCF to get orbitals
 auto scf_solver = ScfSolverFactory::create();

docs/source/_static/examples/cpp/hamiltonian_constructor.cpp

@@ -25,10 +25,14 @@ hamiltonian_constructor->settings().set("eri_method", "direct");
 // --------------------------------------------------------------------------------------------
 
 // --------------------------------------------------------------------------------------------
+// docs:xyz ../data/h2.structure.xyz
 // start-cell-construct
-// Load structure from XYZ file
-auto structure = std::make_shared<Structure>(
-    Structure::from_xyz_file("../data/h2.structure.xyz"));
+// Load structure from inline XYZ file
+auto structure = std::make_shared<Structure>(Structure::from_xyz(R"(2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+)"));
 
 // Run a SCF to get orbitals
 auto scf_solver = ScfSolverFactory::create();

docs/source/_static/examples/cpp/localizer.cpp

@@ -28,9 +28,15 @@ int main() {
   // --------------------------------------------------------------------------------------------
 
   // --------------------------------------------------------------------------------------------
+  // docs:xyz ../data/water.structure.xyz
   // start-cell-localize
-  // Load H2O molecule from XYZ file
-  auto structure = Structure::from_xyz_file("../data/water.structure.xyz");
+  // Load H2O molecule from inline XYZ file
+  auto structure = Structure::from_xyz(R"(3
+Water molecule
+O    0.000000    0.000000    0.000000
+H    0.758602    0.000000    0.504284
+H   -0.758602    0.000000    0.504284
+)");
 
   // Obtain orbitals from SCF calculation
   auto scf_solver = ScfSolverFactory::create();

docs/source/_static/examples/cpp/orbitals.cpp

@@ -4,6 +4,7 @@
 
 // Orbitals usage examples.
 // --------------------------------------------------------------------------------------------
+// docs:xyz ../data/h2.structure.xyz
 // start-cell-create
 #include <iostream>
 #include <qdk/chemistry.hpp>
@@ -13,8 +14,12 @@ using namespace qdk::chemistry::algorithms;
 
 int main() {
   // Obtain orbitals from a SCF calculation
-  // Load H2 molecule from XYZ file
-  auto structure = Structure::from_xyz_file("../data/h2.structure.xyz");
+  // Load H2 molecule from inline XYZ file
+  auto structure = Structure::from_xyz(R"(2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+)");
 
   // Obtain orbitals from a SCF calculation
   auto scf_solver = ScfSolverFactory::create();

docs/source/_static/examples/cpp/quickstart.cpp

@@ -24,10 +24,23 @@ using namespace qdk::chemistry;
 
 int main() {
   // ---------------------------------------------------------------------------
+  // docs:xyz ../data/para_benzyne.structure.xyz
   // start-cell-structure
-  // Load para-benzyne structure from XYZ file
-  auto structure = std::make_shared<data::Structure>(
-      data::Structure::from_xyz_file("../data/para_benzyne.structure.xyz"));
+  // Load para-benzyne structure from inline XYZ file
+  auto structure =
+      std::make_shared<data::Structure>(data::Structure::from_xyz(R"(10
+para-Benzyne
+C    0.000000    1.396000    0.000000
+C    1.209077    0.698000    0.000000
+C    1.209077   -0.698000    0.000000
+C    0.000000   -1.396000    0.000000
+C   -1.209077   -0.698000    0.000000
+C   -1.209077    0.698000    0.000000
+H    2.151000    1.242000    0.000000
+H    2.151000   -1.242000    0.000000
+H   -2.151000   -1.242000    0.000000
+H   -2.151000    1.242000    0.000000
+)"));
 
   std::cout << "Created structure with " << structure->get_num_atoms()
             << " atoms" << std::endl;

docs/source/_static/examples/cpp/scf_solver.cpp

@@ -27,9 +27,14 @@ int main() {
   // --------------------------------------------------------------------------------------------
 
   // --------------------------------------------------------------------------------------------
+  // docs:xyz ../data/h2.structure.xyz
   // start-cell-run
-  // Load structure from XYZ file
-  auto structure = Structure::from_xyz_file("../data/h2.structure.xyz");
+  // Load structure from inline XYZ file
+  auto structure = Structure::from_xyz(R"(2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+)");
 
   // Run the SCF calculation
   auto [E_scf, wfn] = scf_solver->run(structure, 0, 1, "def2-tzvpp");

docs/source/_static/examples/cpp/serialization.cpp

@@ -4,16 +4,20 @@
 
 // Serialization usage examples.
 // --------------------------------------------------------------------------------------------
+// docs:xyz ../data/h2.structure.xyz
 // start-cell-json
 #include <filesystem>
 #include <qdk/chemistry.hpp>
 using namespace qdk::chemistry::data;
 
 int main() {
-  // Load structure from XYZ file (the file uses Angstrom, converted to Bohr
-  // internally)
-  Structure structure_from_file =
-      Structure::from_xyz_file("../data/h2.structure.xyz");
+  // Load structure from inline XYZ file (the data uses Angstrom, converted to
+  // Bohr internally)
+  Structure structure_from_file = Structure::from_xyz(R"(2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+)");
 
   // For demonstration: create a structure with custom masses and charges
   // (requires explicit coordinates, here in Bohr)

docs/source/_static/examples/python/active_space_selector.py

@@ -25,14 +25,18 @@
 ################################################################################
 
 ################################################################################
+# docs:xyz ../data/water.structure.xyz
 # start-cell-run
-from pathlib import Path
 from qdk_chemistry.data import Structure
 
-# Load a molecular structure (water molecule) from XYZ file
-structure = Structure.from_xyz_file(
-    Path(__file__).parent / "../data/water.structure.xyz"
-)
+# Load a molecular structure (water molecule) from inline XYZ file
+structure = Structure.from_xyz("""\
+3
+Water molecule
+O    0.000000    0.000000    0.000000
+H    0.758602    0.000000    0.504284
+H   -0.758602    0.000000    0.504284
+""")
 charge = 0
 
 # First, run SCF to get molecular orbitals

docs/source/_static/examples/python/ansatz.py

@@ -6,13 +6,18 @@
 # --------------------------------------------------------------------------------------------
 
 ################################################################################
+# docs:xyz ../data/h2.structure.xyz
 # start-cell-create
-from pathlib import Path
 from qdk_chemistry.data import Ansatz, Structure
 from qdk_chemistry.algorithms import create
 
-# Load H2 molecule structure from XYZ file
-structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
+# Load H2 molecule structure from inline XYZ file
+structure = Structure.from_xyz("""\
+2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+""")
 
 # SCF
 scf_solver = create("scf_solver")

docs/source/_static/examples/python/basis_set.py

@@ -6,15 +6,20 @@
 # --------------------------------------------------------------------------------------------
 
 ################################################################################
+# docs:xyz ../data/water.structure.xyz
 # start-cell-loading
 import numpy as np
 from pathlib import Path
 from qdk_chemistry.data import AOType, BasisSet, OrbitalType, Shell, Structure
 
-# Load a water molecule structure from XYZ file
-structure = Structure.from_xyz_file(
-    Path(__file__).parent / "../data/water.structure.xyz"
-)
+# Load a water molecule structure from inline XYZ file
+structure = Structure.from_xyz("""\
+3
+Water molecule
+O    0.000000    0.000000    0.000000
+H    0.758602    0.000000    0.504284
+H   -0.758602    0.000000    0.504284
+""")
 
 # Create basis sets from the library using basis set name
 basis_from_name = BasisSet.from_basis_name("sto-3g", structure)

docs/source/_static/examples/python/design_principles.py

@@ -7,7 +7,6 @@
 
 ################################################################################
 # start-cell-scf-create
-from pathlib import Path
 
 from qdk_chemistry.algorithms import create
 from qdk_chemistry.data import Structure
@@ -24,9 +23,15 @@
 ################################################################################
 
 ################################################################################
+# docs:xyz ../data/h2.structure.xyz
 # start-cell-data-flow
-# Load a Structure from file (data classes in QDK/Chemistry are immutable by design)
-structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
+# Load a Structure from inline XYZ file (data classes in QDK/Chemistry are immutable by design)
+structure = Structure.from_xyz("""\
+2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+""")
 
 # Configure and run SCF calculation
 scf_solver = create("scf_solver")

docs/source/_static/examples/python/dynamical_correlation.py

@@ -22,13 +22,18 @@
 ################################################################################
 
 ################################################################################
+# docs:xyz ../data/h2.structure.xyz
 # start-cell-run
-from pathlib import Path
 
 from qdk_chemistry.data import Ansatz, Structure
 
-# Load H2 structure from XYZ file
-structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
+# Load H2 structure from inline XYZ file
+structure = Structure.from_xyz("""\
+2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+""")
 
 # Run initial SCF to get reference wavefunction
 scf_solver = create("scf_solver")

docs/source/_static/examples/python/factory_pattern.py

@@ -6,13 +6,18 @@
 # --------------------------------------------------------------------------------------------
 
 ################################################################################
+# docs:xyz ../data/h2.structure.xyz
 # start-cell-scf-localizer
-from pathlib import Path
 from qdk_chemistry.algorithms import create
 from qdk_chemistry.data import Structure
 
-# Load H2 molecule from XYZ file
-structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
+# Load H2 molecule from inline XYZ file
+structure = Structure.from_xyz("""\
+2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+""")
 
 # Create a SCF solver using the default implementation
 scf_solver = create("scf_solver")

docs/source/_static/examples/python/hamiltonian.py

@@ -6,15 +6,19 @@
 # --------------------------------------------------------------------------------------------
 
 ################################################################################
+# docs:xyz ../data/water.structure.xyz
 # start-cell-hamiltonian-creation
-from pathlib import Path
 from qdk_chemistry.algorithms import create
 from qdk_chemistry.data import Structure, SpinChannel
 
-# Load a structure from XYZ file
-structure = Structure.from_xyz_file(
-    Path(__file__).parent / "../data/water.structure.xyz"
-)
+# Load a structure from inline XYZ file
+structure = Structure.from_xyz("""\
+3
+Water molecule
+O    0.000000    0.000000    0.000000
+H    0.758602    0.000000    0.504284
+H   -0.758602    0.000000    0.504284
+""")
 
 # Run initial SCF to get orbitals
 scf_solver = create("scf_solver")

docs/source/_static/examples/python/hamiltonian_constructor.py

@@ -4,7 +4,6 @@
 # Copyright (c) Microsoft Corporation. All rights reserved.
 # Licensed under the MIT License. See LICENSE.txt in the project root for license information.
 # --------------------------------------------------------------------------------------------
-from pathlib import Path
 
 from qdk_chemistry.algorithms import available, create
 from qdk_chemistry.data import Structure
@@ -31,9 +30,15 @@
 ################################################################################
 
 ################################################################################
+# docs:xyz ../data/h2.structure.xyz
 # start-cell-construct
-# Load a structure from XYZ file
-structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
+# Load a structure from inline XYZ file
+structure = Structure.from_xyz("""\
+2
+H2 molecule
+H    0.000000    0.000000    0.000000
+H    0.000000    0.000000    0.740848
+""")
 
 # Run a SCF to get orbitals
 scf_solver = create("scf_solver")