Index

_

__init__() (q2m3.core.qmmm_system.QMMMSystem method) (q2m3.core.qpe.QPEEngine method) (q2m3.core.quantum_qmmm.QuantumQMMM method) (q2m3.core.rdm.RDMEstimator method) (q2m3.interfaces.pyscf_pennylane.PySCFPennyLaneConverter method) (q2m3.interfaces.pyscf_pennylane.UnifiedDensityMatrix method) (q2m3.sampling.mm_forcefield.TIP3PForceField method)

A

active space active_electrons (q2m3.molecule.MoleculeConfig attribute) (q2m3.solvation.config.MoleculeConfig attribute) active_indices (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute) active_mo_to_ao_rdm() (q2m3.core.rdm.RDMEstimator method) active_orbitals (q2m3.molecule.MoleculeConfig attribute) (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) (q2m3.solvation.config.MoleculeConfig attribute)

analyze_energy_phases() (in module q2m3.solvation.analysis) analyze_ir_stages() (in module q2m3.profiling.catalyst_ir) Atom (class in q2m3.core.qmmm_system) atoms (q2m3.solvation.solvent.SolventModel attribute)

B

base_coeffs (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) base_time (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) basis (q2m3.core.resource_estimation.EFTQCResources attribute) (q2m3.molecule.MoleculeConfig attribute) (q2m3.solvation.config.MoleculeConfig attribute)

bin_centers (q2m3.solvation.structure_analysis.RadialProfile property) build_operator_index_map() (in module q2m3.core.hamiltonian_utils) (in module q2m3.solvation.circuit_builder) build_qmmm_hamiltonian() (q2m3.interfaces.pyscf_pennylane.PySCFPennyLaneConverter method) build_qpe_circuit() (in module q2m3.solvation.circuit_builder) build_rdm_observables() (q2m3.core.rdm.RDMEstimator method)

C

cache_path_for_config() (in module q2m3.solvation.ir_cache) Catalyst center (q2m3.molecule.MoleculeConfig property) charge (q2m3.molecule.MoleculeConfig attribute) (q2m3.solvation.config.MoleculeConfig attribute) (q2m3.solvation.solvent.SolventAtom attribute) compare_vacuum_solvated() (in module q2m3.core.resource_estimation) compile() (q2m3.core.quantum_solver.QuantumSolver method) compiled_circuit (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) compute_cache_key() (in module q2m3.solvation.ir_cache) compute_coulomb_energy() (q2m3.sampling.mm_forcefield.TIP3PForceField method) compute_delta_corr_pol() (in module q2m3.solvation.analysis) compute_ground_state() (q2m3.core.quantum_qmmm.QuantumQMMM method) compute_hf_energy_solvated() (in module q2m3.solvation.energy) compute_hf_energy_vacuum() (in module q2m3.solvation.energy) compute_lj_energy() (q2m3.sampling.mm_forcefield.TIP3PForceField method) compute_mm_energy() (in module q2m3.solvation.solvent) (q2m3.sampling.mm_forcefield.TIP3PForceField method)

compute_mulliken_charges() (in module q2m3.solvation.energy) compute_optimal_base_time() (q2m3.core.qpe.QPEEngine static method) compute_overlap_integrals() (q2m3.interfaces.pyscf_pennylane.PySCFPennyLaneConverter method) compute_qpe_hf_consistency() (in module q2m3.solvation.analysis) compute_shifted_qpe_params() (q2m3.core.qpe.QPEEngine static method) coordination_by_cutoff() (in module q2m3.solvation.structure_analysis) coords (q2m3.molecule.MoleculeConfig attribute) (q2m3.solvation.config.MoleculeConfig attribute) coords_array (q2m3.molecule.MoleculeConfig property) (q2m3.solvation.config.MoleculeConfig property) copy() (q2m3.sampling.water_molecule.WaterMolecule method) count (q2m3.profiling.timing.ProfilingStats property) create_coefficient_callback() (in module q2m3.solvation.energy) create_hf_corrected_step_callback() (in module q2m3.solvation.energy) create_mc_loop() (in module q2m3.solvation.mc_loop) create_step_callback() (in module q2m3.solvation.energy) create_timing_data_from_result() (in module q2m3.solvation.statistics) create_timing_table() (in module q2m3.solvation.statistics)

D

decompose_hamiltonian() (in module q2m3.core.hamiltonian_utils) (in module q2m3.solvation.circuit_builder) default_cache_dir() (in module q2m3.solvation.ir_cache) delta_core_constant_ha (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute) delta_corr-pol delta_gates_percent (q2m3.core.resource_estimation.ResourceComparisonResult attribute) delta_h_diag_fro (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute) delta_h_hermitian_max_abs (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute) delta_h_offdiag_fro (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute) delta_h_offdiag_to_diag (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute)

delta_h_trace_ha (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute) delta_lambda_percent (q2m3.core.resource_estimation.ResourceComparisonResult attribute) delta_nuclear_mm_ha (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute) DeltaCorrPolResult (class in q2m3.solvation.analysis) derive_t_resources() (in module q2m3.core.resource_estimation) detect_equilibration() (in module q2m3.solvation.analysis) device_seed (q2m3.solvation.config.QPEConfig attribute) draw_circuits() (q2m3.core.quantum_qmmm.QuantumQMMM method) draw_qpe_circuit() (q2m3.core.qpe.QPEEngine method) draw_rdm_circuit() (q2m3.core.rdm.RDMEstimator method)

E

EFTQC EFTQCResources (class in q2m3.core.resource_estimation) embedding_diagnostics (q2m3.core.resource_estimation.EFTQCResources attribute) embedding_mode (q2m3.core.resource_estimation.EFTQCResources attribute) (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) (q2m3.solvation.config.SolvationConfig attribute) EmbeddingDiagnostics (class in q2m3.core.resource_estimation) energy (q2m3.core.quantum_solver.SolverResult attribute) energy_range (q2m3.solvation.config.QPEConfig attribute) energy_shift (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) EnergyPhaseResult (class in q2m3.solvation.analysis)

enforce_physical_constraints() (q2m3.core.rdm.RDMEstimator method) EquilibrationResult (class in q2m3.solvation.analysis) estimate_eftqc_runtime() (in module q2m3.core.resource_estimation) estimate_ground_state_energy() (q2m3.core.qpe.QPEEngine method) estimate_qpe_resources() (q2m3.interfaces.pyscf_pennylane.PySCFPennyLaneConverter method) estimate_resources() (in module q2m3.core.resource_estimation) euler_angles (q2m3.sampling.water_molecule.WaterMolecule attribute) (q2m3.solvation.solvent.SolventMolecule attribute) extract_energy_from_probs() (in module q2m3.solvation.phase_extraction) extract_energy_from_shots() (in module q2m3.solvation.phase_extraction) extract_molecular_orbitals() (q2m3.interfaces.pyscf_pennylane.PySCFPennyLaneConverter method)

F

fixed_mo (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute)

from_quantum_state() (q2m3.interfaces.pyscf_pennylane.UnifiedDensityMatrix method) from_state_vector() (q2m3.solvation.solvent.SolventMolecule class method)

G

get_atom_coords() (q2m3.sampling.water_molecule.WaterMolecule method) (q2m3.solvation.solvent.SolventMolecule method) get_best_available_device() (in module q2m3.core.device_utils) get_catalyst_backend_info() (in module q2m3.core.device_utils) get_catalyst_effective_backend() (in module q2m3.core.device_utils) get_charges() (q2m3.sampling.water_molecule.WaterMolecule method) (q2m3.solvation.solvent.SolventMolecule method)

get_effective_catalyst_device_label() (in module q2m3.core.device_utils) get_embedding_potential() (q2m3.core.qmmm_system.QMMMSystem method) get_lj_params() (q2m3.solvation.solvent.SolventModel method) get_mm_embedding_data() (in module q2m3.solvation.solvent) get_mm_embedding_data_bohr() (in module q2m3.solvation.solvent) get_qm_coords() (q2m3.core.qmmm_system.QMMMSystem method) get_total_charge() (q2m3.core.qmmm_system.QMMMSystem method)

H

Hamiltonian 1-norm hamiltonian_1norm (q2m3.core.resource_estimation.EFTQCResources attribute)

hamiltonian_mode (q2m3.solvation.config.SolvationConfig attribute) Hartree

I

initial_water_distance (q2m3.solvation.config.SolvationConfig attribute) initialize_solvent_ring() (in module q2m3.solvation.solvent) IR cache ir_cache_dir (q2m3.solvation.config.SolvationConfig attribute)

ir_cache_enabled (q2m3.solvation.config.SolvationConfig attribute) ir_cache_force_recompile (q2m3.solvation.config.SolvationConfig attribute) ir_output_dir() (in module q2m3.profiling.catalyst_ir) is_cache_available() (in module q2m3.solvation.ir_cache) is_fixed_circuit (q2m3.solvation.circuit_builder.QPECircuitBundle attribute)

K

kcal/mol

kt (q2m3.solvation.config.SolvationConfig property)

L

lj_epsilon (q2m3.solvation.solvent.SolventAtom attribute) lj_sigma (q2m3.solvation.solvent.SolventAtom attribute) load_config() (in module q2m3.utils.io) load_state_trajectory_csv() (in module q2m3.solvation.structure_analysis)

load_xyz() (in module q2m3.utils.io) local_coord (q2m3.solvation.solvent.SolventAtom attribute) local_coords (q2m3.solvation.solvent.SolventModel property) logical_qubits (q2m3.core.resource_estimation.EFTQCResources attribute)

M

max (q2m3.profiling.timing.ProfilingStats property) MCResult (class in q2m3.solvation.mc_loop) mean (q2m3.profiling.timing.ProfilingStats property) measure_1rdm() (q2m3.core.rdm.RDMEstimator method) measure_rdm_from_qpe_state() (in module q2m3.core.rdm) measurement_mode (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) MemorySnapshot (class in q2m3.profiling.memory) MemoryTimeline (class in q2m3.profiling.memory) metadata (q2m3.core.quantum_solver.SolverResult attribute) min (q2m3.profiling.timing.ProfilingStats property) MM embedding ModeComparisonResult (class in q2m3.solvation.analysis) model (q2m3.solvation.solvent.SolventMolecule attribute) module q2m3 q2m3.constants q2m3.core.device_utils q2m3.core.hamiltonian_utils q2m3.core.qmmm_system q2m3.core.qpe q2m3.core.quantum_qmmm q2m3.core.quantum_solver q2m3.core.rdm q2m3.core.resource_estimation q2m3.interfaces.pyscf_pennylane q2m3.molecule q2m3.profiling.catalyst_ir q2m3.profiling.memory q2m3.profiling.orchestrator q2m3.profiling.qpe_profiler q2m3.profiling.timing q2m3.sampling.mm_forcefield q2m3.sampling.water_molecule q2m3.solvation.analysis q2m3.solvation.circuit_builder q2m3.solvation.config q2m3.solvation.energy q2m3.solvation.ir_cache q2m3.solvation.mc_loop q2m3.solvation.orchestrator q2m3.solvation.phase_extraction q2m3.solvation.plotting q2m3.solvation.solvent q2m3.solvation.statistics q2m3.solvation.structure_analysis q2m3.utils.io q2m3.utils.plotting

molecule (q2m3.solvation.config.SolvationConfig attribute) MoleculeConfig (class in q2m3.molecule) (class in q2m3.solvation.config) molecules_to_state_array() (in module q2m3.solvation.solvent)

N

n_atoms (q2m3.molecule.MoleculeConfig property) n_estimation_wires (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) (q2m3.solvation.config.QPEConfig attribute) n_mc_steps (q2m3.solvation.config.SolvationConfig attribute) n_mm_charges (q2m3.core.resource_estimation.EFTQCResources attribute) n_qpe_evaluations (q2m3.solvation.config.SolvationConfig property) n_shots (q2m3.solvation.config.QPEConfig attribute) n_system_qubits (q2m3.core.resource_estimation.EFTQCResources attribute) (q2m3.solvation.circuit_builder.QPECircuitBundle attribute)

n_terms (q2m3.core.resource_estimation.EFTQCResources attribute) n_trotter_steps (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) (q2m3.solvation.config.QPEConfig attribute) n_waters (q2m3.solvation.config.SolvationConfig attribute) name (q2m3.molecule.MoleculeConfig attribute) (q2m3.solvation.config.MoleculeConfig attribute) (q2m3.solvation.solvent.SolventModel attribute)

O

op_index_map (q2m3.solvation.circuit_builder.QPECircuitBundle attribute)

ops (q2m3.solvation.circuit_builder.QPECircuitBundle attribute) oxygen_position (q2m3.sampling.water_molecule.WaterMolecule property)

P

ParentSideMonitor (class in q2m3.profiling.memory) peak_hwm_mb (q2m3.profiling.memory.ParentSideMonitor property) peak_smaps (q2m3.profiling.memory.MemoryTimeline property) phase (q2m3.core.quantum_solver.SolverResult attribute) phase wrapping plot_acceptance_rate() (in module q2m3.solvation.plotting) plot_energy_comparison() (in module q2m3.utils.plotting) plot_energy_trajectory() (in module q2m3.solvation.plotting) position (q2m3.sampling.water_molecule.WaterMolecule attribute) (q2m3.solvation.solvent.SolventMolecule attribute) precompute_vacuum_cache() (in module q2m3.solvation.energy)

print_time_statistics() (in module q2m3.solvation.statistics) profile_execution() (in module q2m3.profiling.qpe_profiler) profile_function() (in module q2m3.profiling.timing) profile_hamiltonian_build() (in module q2m3.profiling.qpe_profiler) profile_qjit_compilation() (in module q2m3.profiling.qpe_profiler) profile_qjit_compilation_fixed() (in module q2m3.profiling.qpe_profiler) profile_section() (in module q2m3.profiling.timing) ProfileResult (class in q2m3.profiling.memory) ProfilingStats (class in q2m3.profiling.timing) pyscf_to_pennylane_hamiltonian() (q2m3.interfaces.pyscf_pennylane.PySCFPennyLaneConverter method) pyscf_to_pennylane_hamiltonian_with_mm() (q2m3.interfaces.pyscf_pennylane.PySCFPennyLaneConverter method) PySCFPennyLaneConverter (class in q2m3.interfaces.pyscf_pennylane)

Q

q2m3 module q2m3.constants module q2m3.core.device_utils module q2m3.core.hamiltonian_utils module q2m3.core.qmmm_system module q2m3.core.qpe module q2m3.core.quantum_qmmm module q2m3.core.quantum_solver module q2m3.core.rdm module q2m3.core.resource_estimation module q2m3.interfaces.pyscf_pennylane module q2m3.molecule module q2m3.profiling.catalyst_ir module q2m3.profiling.memory module q2m3.profiling.orchestrator module q2m3.profiling.qpe_profiler module q2m3.profiling.timing module q2m3.sampling.mm_forcefield module q2m3.sampling.water_molecule module

q2m3.solvation.analysis module q2m3.solvation.circuit_builder module q2m3.solvation.config module q2m3.solvation.energy module q2m3.solvation.ir_cache module q2m3.solvation.mc_loop module q2m3.solvation.orchestrator module q2m3.solvation.phase_extraction module q2m3.solvation.plotting module q2m3.solvation.solvent module q2m3.solvation.statistics module q2m3.solvation.structure_analysis module q2m3.utils.io module q2m3.utils.plotting module QM/MM QMMMSystem (class in q2m3.core.qmmm_system) QPE qpe_config (q2m3.solvation.config.SolvationConfig attribute) qpe_interval (q2m3.solvation.config.QPEConfig attribute) QPECircuitBundle (class in q2m3.solvation.circuit_builder) QPEConfig (class in q2m3.solvation.config) QPEEngine (class in q2m3.core.qpe) QPEHFConsistencyResult (class in q2m3.solvation.analysis) QuantumQMMM (class in q2m3.core.quantum_qmmm) QuantumSolver (class in q2m3.core.quantum_solver)

R

radial_density_profile() (in module q2m3.solvation.structure_analysis) radial_profile_to_rows() (in module q2m3.solvation.structure_analysis) RadialProfile (class in q2m3.solvation.structure_analysis) random_seed (q2m3.solvation.config.SolvationConfig attribute) raw_measurements (q2m3.core.quantum_solver.SolverResult attribute) RDM RDMEstimator (class in q2m3.core.rdm) read_proc_status() (in module q2m3.profiling.memory) read_smaps_rollup() (in module q2m3.profiling.memory) record() (q2m3.profiling.timing.ProfilingStats method)

reference (q2m3.solvation.solvent.SolventModel attribute) replay_quantum_trajectory() (in module q2m3.solvation.orchestrator) resolve_compiled_circuit() (in module q2m3.solvation.ir_cache) ResourceComparisonResult (class in q2m3.core.resource_estimation) rotation_step (q2m3.solvation.config.SolvationConfig attribute) run_both_modes() (in module q2m3.profiling.orchestrator) run_mode_comparison() (in module q2m3.solvation.analysis) run_single_profile() (in module q2m3.profiling.orchestrator) run_single_profile_in_subprocess() (in module q2m3.profiling.orchestrator) run_solvation() (in module q2m3.solvation.orchestrator) run_sweep() (in module q2m3.profiling.orchestrator)

S

save_json_results() (in module q2m3.utils.io) select_device() (in module q2m3.core.device_utils) select_random_snapshot_indices() (in module q2m3.solvation.structure_analysis) select_representative_snapshot_indices() (in module q2m3.solvation.structure_analysis) shell_counts_per_frame() (in module q2m3.solvation.structure_analysis) solute_center() (in module q2m3.solvation.structure_analysis) solvated (q2m3.core.resource_estimation.ResourceComparisonResult attribute) SolvationConfig (class in q2m3.solvation.config) solve() (q2m3.core.quantum_solver.QuantumSolver method) SolventAtom (class in q2m3.solvation.solvent)

SolventModel (class in q2m3.solvation.solvent) SolventMolecule (class in q2m3.solvation.solvent) SolverResult (class in q2m3.core.quantum_solver) spin_to_spatial_rdm() (q2m3.core.rdm.RDMEstimator method) state_array_to_molecules() (in module q2m3.solvation.solvent) state_to_symbols_coords() (in module q2m3.solvation.structure_analysis) StepResult (class in q2m3.solvation.energy) summary() (q2m3.profiling.timing.ProfilingStats method) symbol (q2m3.solvation.solvent.SolventAtom attribute) symbols (q2m3.molecule.MoleculeConfig attribute) (q2m3.solvation.config.MoleculeConfig attribute)

T

take_snapshot() (in module q2m3.profiling.memory) target_error (q2m3.core.resource_estimation.EFTQCResources attribute) target_resolution (q2m3.solvation.config.QPEConfig attribute) temperature (q2m3.solvation.config.SolvationConfig attribute) TimingData (class in q2m3.solvation.statistics) TIP3PForceField (class in q2m3.sampling.mm_forcefield) to_pennylane_observable() (q2m3.interfaces.pyscf_pennylane.UnifiedDensityMatrix method)

to_pyscf_mol() (q2m3.core.qmmm_system.QMMMSystem method) to_state_vector() (q2m3.solvation.solvent.SolventMolecule method) toffoli_gates (q2m3.core.resource_estimation.EFTQCResources attribute) total (q2m3.profiling.timing.ProfilingStats property) translation_step (q2m3.solvation.config.SolvationConfig attribute) Trotterization two_electron_tensor_fixed (q2m3.core.resource_estimation.EmbeddingDiagnostics attribute)

U

UnifiedDensityMatrix (class in q2m3.interfaces.pyscf_pennylane)

V

vacuum (q2m3.core.resource_estimation.ResourceComparisonResult attribute) validate() (q2m3.molecule.MoleculeConfig method) (q2m3.solvation.config.MoleculeConfig method) (q2m3.solvation.config.SolvationConfig method)

validate_state_trajectory() (in module q2m3.solvation.structure_analysis) verbose (q2m3.solvation.config.SolvationConfig attribute)

W

water_oxygen_distances() (in module q2m3.solvation.structure_analysis) WaterMolecule (class in q2m3.sampling.water_molecule)

write_state_trajectory_csv() (in module q2m3.solvation.structure_analysis) write_xyz_snapshot() (in module q2m3.solvation.structure_analysis)

X

xyz_atom_count() (in module q2m3.solvation.structure_analysis)