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Docs: replace xyz files with xyz strings #545

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51c50cf
Docs: replace xyz files with xyz strings
eimrek Jun 23, 2026
9aa340b
Revert "Docs: replace xyz files with xyz strings"
eimrek Jun 24, 2026
73818ed
docs: inline xyz files at build time (opt-in)
eimrek Jun 24, 2026
3577cab
add warning if .xyz file not accessible
eimrek Jun 24, 2026
115f09a
examples: duplicate xyz strings to fscripts; test for consistency
eimrek Jun 25, 2026
890d561
Potential fix for pull request finding
eimrek Jun 25, 2026
6b5563a
update comments
eimrek Jun 25, 2026
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8 changes: 7 additions & 1 deletion docs/source/_static/examples/cpp/active_space_selector.cpp
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Expand Up @@ -27,9 +27,15 @@ int main() {
// --------------------------------------------------------------------------------------------

// --------------------------------------------------------------------------------------------
// docs:xyz ../data/water.structure.xyz
// start-cell-run
// Load a molecular structure (water molecule) from XYZ file
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auto structure = Structure::from_xyz_file("../data/water.structure.xyz");
auto structure = Structure::from_xyz(R"(3
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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
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7 changes: 6 additions & 1 deletion docs/source/_static/examples/cpp/ansatz.cpp
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Expand Up @@ -4,6 +4,7 @@

// Ansatz usage examples.
// --------------------------------------------------------------------------------------------
// docs:xyz ../data/h2.structure.xyz
// start-cell-create
#include <iostream>
#include <qdk/chemistry.hpp>
Expand All @@ -13,7 +14,11 @@ using namespace qdk::chemistry::algorithms;

int main() {
// Load H2 structure from XYZ file
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auto structure = Structure::from_xyz_file("../data/h2.structure.xyz");
auto structure = Structure::from_xyz(R"(2
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H2 molecule
H 0.000000 0.000000 0.000000
H 0.000000 0.000000 0.740848
)");

// SCF
auto scf_solver = ScfSolverFactory::create();
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7 changes: 6 additions & 1 deletion docs/source/_static/examples/cpp/dynamical_correlation.cpp
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Expand Up @@ -24,9 +24,14 @@ auto mp2_calculator =
// -----------------------------------------------------------------------------

// -----------------------------------------------------------------------------
// docs:xyz ../data/h2.structure.xyz
// start-cell-run
// Load H2 structure from XYZ file
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auto structure = Structure::from_xyz_file("../data/h2.structure.xyz");
auto structure = Structure::from_xyz(R"(2
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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();
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8 changes: 7 additions & 1 deletion docs/source/_static/examples/cpp/hamiltonian.cpp
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Expand Up @@ -4,9 +4,15 @@

// Hamiltonian usage examples.
// --------------------------------------------------------------------------------------------
// docs:xyz ../data/water.structure.xyz
// start-cell-hamiltonian-creation
// Load structure from XYZ file
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auto structure = Structure::from_xyz_file("../data/water.structure.xyz");
auto structure = Structure::from_xyz(R"(3
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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();
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8 changes: 6 additions & 2 deletions docs/source/_static/examples/cpp/hamiltonian_constructor.cpp
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Expand Up @@ -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
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auto structure = std::make_shared<Structure>(
Structure::from_xyz_file("../data/h2.structure.xyz"));
auto structure = std::make_shared<Structure>(Structure::from_xyz(R"(2
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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();
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8 changes: 7 additions & 1 deletion docs/source/_static/examples/cpp/localizer.cpp
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Expand Up @@ -28,9 +28,15 @@ int main() {
// --------------------------------------------------------------------------------------------

// --------------------------------------------------------------------------------------------
// docs:xyz ../data/water.structure.xyz
// start-cell-localize
// Load H2O molecule from XYZ file
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auto structure = Structure::from_xyz_file("../data/water.structure.xyz");
auto structure = Structure::from_xyz(R"(3
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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();
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7 changes: 6 additions & 1 deletion docs/source/_static/examples/cpp/orbitals.cpp
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Expand Up @@ -4,6 +4,7 @@

// Orbitals usage examples.
// --------------------------------------------------------------------------------------------
// docs:xyz ../data/h2.structure.xyz
// start-cell-create
#include <iostream>
#include <qdk/chemistry.hpp>
Expand All @@ -14,7 +15,11 @@ using namespace qdk::chemistry::algorithms;
int main() {
// Obtain orbitals from a SCF calculation
// Load H2 molecule from XYZ file
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auto structure = Structure::from_xyz_file("../data/h2.structure.xyz");
auto structure = Structure::from_xyz(R"(2
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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();
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17 changes: 15 additions & 2 deletions docs/source/_static/examples/cpp/quickstart.cpp
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Expand Up @@ -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
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auto structure = std::make_shared<data::Structure>(
data::Structure::from_xyz_file("../data/para_benzyne.structure.xyz"));
auto structure =
std::make_shared<data::Structure>(data::Structure::from_xyz(R"(10
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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;
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7 changes: 6 additions & 1 deletion docs/source/_static/examples/cpp/scf_solver.cpp
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Expand Up @@ -27,9 +27,14 @@ int main() {
// --------------------------------------------------------------------------------------------

// --------------------------------------------------------------------------------------------
// docs:xyz ../data/h2.structure.xyz
// start-cell-run
// Load structure from XYZ file
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auto structure = Structure::from_xyz_file("../data/h2.structure.xyz");
auto structure = Structure::from_xyz(R"(2
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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");
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8 changes: 6 additions & 2 deletions docs/source/_static/examples/cpp/serialization.cpp
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Expand Up @@ -4,6 +4,7 @@

// Serialization usage examples.
// --------------------------------------------------------------------------------------------
// docs:xyz ../data/h2.structure.xyz
// start-cell-json
#include <filesystem>
#include <qdk/chemistry.hpp>
Expand All @@ -12,8 +13,11 @@ using namespace qdk::chemistry::data;
int main() {
// Load structure from XYZ file (the file uses Angstrom, converted to Bohr
// internally)
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Structure structure_from_file =
Structure::from_xyz_file("../data/h2.structure.xyz");
Structure structure_from_file = Structure::from_xyz(R"(2
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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)
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12 changes: 8 additions & 4 deletions docs/source/_static/examples/python/active_space_selector.py
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Expand Up @@ -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
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structure = Structure.from_xyz_file(
Path(__file__).parent / "../data/water.structure.xyz"
)
structure = Structure.from_xyz("""\
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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
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9 changes: 7 additions & 2 deletions docs/source/_static/examples/python/ansatz.py
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Expand Up @@ -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
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structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
structure = Structure.from_xyz("""\
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2
H2 molecule
H 0.000000 0.000000 0.000000
H 0.000000 0.000000 0.740848
""")

# SCF
scf_solver = create("scf_solver")
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11 changes: 8 additions & 3 deletions docs/source/_static/examples/python/basis_set.py
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Expand Up @@ -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
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structure = Structure.from_xyz_file(
Path(__file__).parent / "../data/water.structure.xyz"
)
structure = Structure.from_xyz("""\
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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)
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9 changes: 7 additions & 2 deletions docs/source/_static/examples/python/design_principles.py
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Expand Up @@ -7,7 +7,6 @@

################################################################################
# start-cell-scf-create
from pathlib import Path

from qdk_chemistry.algorithms import create
from qdk_chemistry.data import Structure
Expand All @@ -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)
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structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
structure = Structure.from_xyz("""\
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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")
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9 changes: 7 additions & 2 deletions docs/source/_static/examples/python/dynamical_correlation.py
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Expand Up @@ -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
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structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
structure = Structure.from_xyz("""\
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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")
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9 changes: 7 additions & 2 deletions docs/source/_static/examples/python/factory_pattern.py
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Expand Up @@ -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
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structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
structure = Structure.from_xyz("""\
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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")
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12 changes: 8 additions & 4 deletions docs/source/_static/examples/python/hamiltonian.py
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Expand Up @@ -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
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structure = Structure.from_xyz_file(
Path(__file__).parent / "../data/water.structure.xyz"
)
structure = Structure.from_xyz("""\
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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")
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9 changes: 7 additions & 2 deletions docs/source/_static/examples/python/hamiltonian_constructor.py
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Expand Up @@ -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
Expand All @@ -31,9 +30,15 @@
################################################################################

################################################################################
# docs:xyz ../data/h2.structure.xyz
# start-cell-construct
# Load a structure from XYZ file
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structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
structure = Structure.from_xyz("""\
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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")
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9 changes: 7 additions & 2 deletions docs/source/_static/examples/python/interfaces.py
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Expand Up @@ -6,13 +6,18 @@
# --------------------------------------------------------------------------------------------

################################################################################
# docs:xyz ../data/h2.structure.xyz
# start-cell-scf
from pathlib import Path
from qdk_chemistry.algorithms import available, create
from qdk_chemistry.data import Structure

# Load H2 molecule from XYZ file
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structure = Structure.from_xyz_file(Path(__file__).parent / "../data/h2.structure.xyz")
structure = Structure.from_xyz("""\
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2
H2 molecule
H 0.000000 0.000000 0.000000
H 0.000000 0.000000 0.740848
""")

# Create a SCF solver using the factory
scf_solver = create("scf_solver", "pyscf")
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