Set up your lab notebook
########################

The cumulative assignment uses a Markdown lab notebook to record the inputs, decisions, results, and interpretations that lead to the final ground-state energy estimate.
The lab notebook is a note-taking document, not a Jupyter notebook, and it does not contain executable code.
Each required chapter adds information to the same record.
The completed lab notebook should make the calculation reproducible and should distinguish changes in the molecular model from errors introduced by the quantum algorithm.

How to use the lab notebook
===========================

1. Download :download:`the blank Markdown template <../../_static/examples/ground_state_qpe_lab_notebook_template.md>` and save a working copy in the tutorial folder, or copy its headings into your preferred note-taking format.
2. Complete only :ref:`lab-notebook-setup` now, using the result from the setup check in :doc:`Before you begin <00_before_you_begin>`.
3. Leave the remaining sections blank until a chapter links to them.
4. Record values with units, enough significant figures to support later comparisons, and the settings associated with each result.
5. Keep observations separate from interpretations, and do not overwrite earlier results when a later chapter changes an approximation or algorithm setting.

After recording the package version and setup-check result, continue to :doc:`Energy and accuracy <01_energy_and_accuracy>`.

Template field guide
====================

The remainder of this page previews and explains the headings and prompts in the downloaded template.
You do not need to complete them now; each required chapter links directly to the section used for that stage of the calculation.

.. _lab-notebook-setup:

Setup and provenance
====================

Record the package version used for the tutorial and whether the setup check passed.

- :term:`QDK`/Chemistry version:
- Built-in implementation verification result:

.. _lab-notebook-goal:

Calculation goal and reference plan
===================================

State what the tutorial calculates and how each comparison will be interpreted.

- Molecular system:
- Target quantity:
- Teaching target:
- Basis-set comparison (which related calculations will be compared, and what does their difference measure?):
- Active-space comparison (which molecular models will be compared, and what changes between them?):
- Quantum-algorithm reference (which classical energy for the same selected-space Hamiltonian will validate the final result?):
- Error sources that remain outside the final algorithmic comparison:

.. _lab-notebook-molecule:

Molecular input and mean-field calculation
==========================================

Record the molecular definition and the first electronic-structure results.

- Geometry source:
- Nitrogen--nitrogen distance and units:
- Molecular charge:
- Spin multiplicity:
- First basis set:
- First Hartree--Fock energy and units:
- Second basis set:
- Second Hartree--Fock energy and units:
- Basis-set sensitivity and units:
- Interpretation of the basis-set sensitivity:

.. _lab-notebook-active-space:

Active-space model
==================

Record how the correlated molecular model was chosen.

- Orbital representation used for selection:
- Initial active electrons and spatial orbitals:
- Initial correlated method:
- Orbital entropies and entropy-gap evidence used for active-space selection:
- Selected active electrons and spatial orbitals:
- Selected active-space energy and units:
- Comparison with the initial active space:
- Interpretation of the active-space energy change and size tradeoff:
- Algorithmic reference energy and units:

.. _lab-notebook-qubits:

Qubit representation
====================

Record how the selected electronic Hamiltonian was represented on qubits.
The :ref:`compute register <tutorial-compute-register>` contains the qubits that store the encoded active-space fermionic state.
Each qubit in this register is a compute-register qubit.
Ancilla qubits assist with algorithmic tasks such as control, workspace, or readout and are recorded separately.

- Fermion-to-qubit encoding:
- Number of active spatial orbitals:
- Number of active spin orbitals:
- Number of compute-register qubits:
- Number of Pauli terms in the qubit Hamiltonian:
- :ref:`Fixed-electron-number subspace <tutorial-fixed-electron-number-subspace>` (:math:`n_\alpha`, :math:`n_\beta`, and number of basis states):
- Core energy and units:
- Mapped active-space ground-state energy and units:
- Mapped selected-space total energy and units:
- Difference from the :ref:`selected-space algorithmic reference <tutorial-selected-space-reference>` and units:
- Interpretation of the energy comparison:
- Quantities excluded from the compute-register qubit count:

.. _lab-notebook-trial-state:

Trial state
===========

Record the approximation prepared on the compute register.

- Source wavefunction:
- Leading reference determinants, amplitudes, weights, and cumulative weights:
- Determinant-selection rule used before :term:`PMC` re-optimization:
- Determinant counts compared:
- Fidelity for each trial state:
- State-preparation method:
- Compute qubits for each trial state:
- Preparation logical gate count and logical gate-family counts for each trial state:
- Interpretation of the fidelity and circuit cost:
- Trial state selected for IQPE and rationale:

.. _lab-notebook-phase-estimation:

Phase-estimation calculation
============================

Record the algorithm settings and final result.

- Evolution time and units:
- Hamiltonian-simulation method and settings:
- Number of phase bits:
- Shots per bit:
- Number of complete IQPE runs:
- Readout ancillas:
- Simulator seed range:
- Complete-run bitstring counts:
- Modal bitstring:
- Measured active-space energy and units:
- Core energy added after phase estimation:
- Total molecular energy estimate and units:
- Difference from the algorithmic reference and units:
- Result relative to the :math:`1\ \mathrm{m}E_{\mathrm{h}}` teaching target:
- Observed runtime:

.. _lab-notebook-conclusion:

Conclusion
==========

Explain what the final comparison establishes and what it does not establish.

- Main result:
- Evidence that supports the result:
- Basis-set limitations:
- Active-space limitations:
- Quantum-algorithm limitations:
- One change that would strengthen the calculation:
