13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. Use for local quantum-dynamics work where physical assumptions, dimensions, and numerical convergence must be explicit.
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill qutip --agent claude-code
Codex
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qutip -a codex -y
Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qutip -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qutip -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qutip -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qutip -a opencode -y
Windsurf
$ npx skills add K-Dense-AI/scientific-agent-skills --skill qutip -a windsurf -y
name: qutip description: Simulate and audit closed and open quantum-system models with QuTiP 5, including deterministic, trajectory, steady-state, spectral, and phase-space workflows. Use for local quantum-dynamics work where physical assumptions, dimensions, and numerical convergence must be explicit. license: MIT compatibility: Requires Python 3.11+, uv, and qutip==5.3.1 for executable simulations. Bundled planners and all script help run with the Python standard library; plotting requires the graphics extra. No network service or credentials are used. metadata: version: "1.4" skill-author: K-Dense Inc. last-reviewed: "2026-10-01"
Use QuTiP for finite-dimensional quantum mechanics, quantum optics, Lindblad dynamics, trajectories, weak-coupling Bloch-Redfield models, and specialized Floquet, HEOM, and permutational-invariance methods. It is not a hardware execution SDK. Circuit and control functionality moved to separate QuTiP family packages.
This skill targets **QuTiP 5.3.1**, released 2026-08-04. QuTiP 5.3 requires Python 3.11 or newer. Its required distributions are NumPy (`>=1.23.2`), SciPy (`>=1.9.2`, excluding `1.16.0` and `1.17.0`), and `packaging`.
Create a dedicated environment and pin every direct distribution:
uv venv --python 3.11 uv pip install "qutip==5.3.1"
For plots:
uv pip install "qutip[graphics]==5.3.1"
Optional QuTiP family packages are independently versioned:
uv pip install "qutip-qip==0.4.2" uv pip install "qutip-qtrl==0.2.0" uv pip install "qutip-jax==0.1.1"
noisy-device simulation package. Import from `qutip_qip`, not `qutip.qip`.
control**. It is not a trajectory viewer. Import from `qutip_qtrl`, not `qutip.control`; PyPI still classifies it pre-alpha.
automatic-differentiation experiments. It is explicitly pre-alpha.
release and its own README says it is not officially released. Do not put an unreleased Git install into a reproducible workflow.
Use a project lockfile or a hash-generating `uv pip compile` workflow when transitive dependency identity must also be frozen.
Core tests cover small native CPU systems with known solutions. Optional JAX checks cover CPU conversion/evolution and differentiation only; GPU/MPI, large HEOM hierarchies, and experimentally realistic physics are unvalidated. Snippets with placeholders such as `H`, `rho0`, or `c_ops` are illustrative fragments to adapt after defining a consistent model.
Before solving, record:
1. **Units and convention.** QuTiP equations normally set \(\hbar=1\). Hamiltonian entries are angular frequencies and rates have reciprocal-time units. A decay rate specified as `1/T1` needs no `2*pi` factor. Convert cyclic frequency with \(2\pi f\); never mix Hz and rad/s. 2. **Subsystem order.** `tensor(A, B, C)` fixes subsystem indices `0, 1, 2`. Preserve that order in every state, operator, collapse channel, and partial trace. `obj.ptrace([0, 2])` keeps those subsystems; it does not trace them. 3. **State validity.** Check ket norm or density-matrix Hermiticity, unit trace, and eigenvalues above a stated negative tolerance. Tiny negative values may be numerical; material negativity invalidates a claimed state. 4. **Generator meaning.** A Lindblad channel with rate `gamma` is represented by `sqrt(gamma) * A`, not `gamma * A`. Define what each rate measures. For example, `sqrt(gamma_phi / 2) * sigmaz()` gives coherence decay `exp(-gamma_phi * t)`. 5. **Approximations.** State rotating-wave, Born-Markov, secular, weak-coupling, bath-equilibrium, truncation, symmetry, and initial-factorization assumptions wherever used. 6. **Numerics.** Justify Hilbert truncation, output grid, integration method, tolerances, trajectory count, and random seeds. Report `result.stats`. 7. **Convergence.** Sweep every artificial cutoff: Fock dimension, time/frequency window and spacing, ODE tolerances, trajectories, Floquet harmonics, HEOM depth and bath exponents, or PIQS representation as applicable.
Prefer explicit imports and inspect both shape and structured dimensions:
from qutip import basis, qeye, sigmaz, tensor psi = tensor(basis(2, 0), basis(3, 1)) z_on_first = tensor(sigmaz(), qeye(3)) assert psi.shape == (6, 1) assert psi.dims == [[2, 3], [1]] assert z_on_first.dims == [[2, 3], [2, 3]] rho_first = psi.proj().ptrace(0) # keep subsystem 0
Matrix shape alone is insufficient: two objects can both be 6-by-6 but encode different tensor factorizations. Read `references/core_concepts.md` before building composite, superoperator, or channel models.
| Model | Current API | Required justification | |---|---|---| | Closed, pure, unitary | `sesolve` | Hermitian Hamiltonian; no dissipation | | Lindblad/open or mixed | `mesolve` | Markovian completely positive model and channel rates | | Quantum jumps | `mcsolve` | Unravelling, trajectory convergence, seeds | | Microscopic weak bath | `brmesolve` | Born-Markov/weak coupling, spectra, secular choice | | Diffusive measurement | `ssesolve`, `smesolve` | monitored versus unmonitored channels | | Periodic drive | `FloquetBasis`, `fsesolve`, `fmmesolve` | verified period and Floquet convergence | | Structured non-Markovian bath | `qutip.solver.heom` | bath expansion and hierarchy convergence | | Symmetric spin ensemble | `qutip.piqs` | permutation symmetry and basis choice |
Do not select a more specialized solver merely because it exists.
QuTiP 5.3 uses ordinary
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