@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/qutip/references/advanced.md

@@ -0,0 +1,555 @@
+# QuTiP Advanced Features
+
+## Floquet Theory
+
+For time-periodic Hamiltonians H(t + T) = H(t).
+
+### Floquet Modes and Quasi-Energies
+
+```python
+from qutip import *
+import numpy as np
+
+# Time-periodic Hamiltonian
+w_d = 1.0  # Drive frequency
+T = 2 * np.pi / w_d  # Period
+
+H0 = sigmaz()
+H1 = sigmax()
+H = [H0, [H1, 'cos(w*t)']]
+args = {'w': w_d}
+
+# Calculate Floquet modes and quasi-energies
+f_modes, f_energies = floquet_modes(H, T, args)
+
+print("Quasi-energies:", f_energies)
+print("Floquet modes:", f_modes)
+```
+
+### Floquet States at Time t
+
+```python
+# Get Floquet state at specific time
+t = 1.0
+f_states_t = floquet_states(f_modes, f_energies, t)
+```
+
+### Floquet State Decomposition
+
+```python
+# Decompose initial state in Floquet basis
+psi0 = basis(2, 0)
+f_coeff = floquet_state_decomposition(f_modes, f_energies, psi0)
+```
+
+### Floquet-Markov Master Equation
+
+```python
+# Time evolution with dissipation
+c_ops = [np.sqrt(0.1) * sigmam()]
+tlist = np.linspace(0, 20, 200)
+
+result = fmmesolve(H, psi0, tlist, c_ops, e_ops=[sigmaz()], T=T, args=args)
+
+# Plot results
+import matplotlib.pyplot as plt
+plt.plot(tlist, result.expect[0])
+plt.xlabel('Time')
+plt.ylabel('⟨σz⟩')
+plt.show()
+```
+
+### Floquet Tensor
+
+```python
+# Floquet tensor (generalized Bloch-Redfield)
+A_ops = [[sigmaz(), lambda w: 0.1 * w if w > 0 else 0]]
+
+# Build Floquet tensor
+R, U = floquet_markov_mesolve(H, psi0, tlist, A_ops, e_ops=[sigmaz()],
+                               T=T, args=args)
+```
+
+### Effective Hamiltonian
+
+```python
+# Time-averaged effective Hamiltonian
+H_eff = floquet_master_equation_steadystate(H, c_ops, T, args)
+```
+
+## Hierarchical Equations of Motion (HEOM)
+
+For non-Markovian open quantum systems with strong system-bath coupling.
+
+### Basic HEOM Setup
+
+```python
+from qutip import heom
+
+# System Hamiltonian
+H_sys = sigmaz()
+
+# Bath correlation function (exponential)
+Q = sigmax()  # System-bath coupling operator
+ck_real = [0.1]  # Coupling strengths
+vk_real = [0.5]  # Bath frequencies
+
+# HEOM bath
+bath = heom.BosonicBath(Q, ck_real, vk_real)
+
+# Initial state
+rho0 = basis(2, 0) * basis(2, 0).dag()
+
+# Create HEOM solver
+max_depth = 5
+hsolver = heom.HEOMSolver(H_sys, [bath], max_depth=max_depth)
+
+# Time evolution
+tlist = np.linspace(0, 10, 100)
+result = hsolver.run(rho0, tlist)
+
+# Extract reduced system density matrix
+rho_sys = [r.extract_state(0) for r in result.states]
+```
+
+### Multiple Baths
+
+```python
+# Define multiple baths
+bath1 = heom.BosonicBath(sigmax(), [0.1], [0.5])
+bath2 = heom.BosonicBath(sigmay(), [0.05], [1.0])
+
+hsolver = heom.HEOMSolver(H_sys, [bath1, bath2], max_depth=5)
+```
+
+### Drude-Lorentz Spectral Density
+
+```python
+# Common in condensed matter physics
+from qutip.nonmarkov.heom import DrudeLorentzBath
+
+lam = 0.1  # Reorganization energy
+gamma = 0.5  # Bath cutoff frequency
+T = 1.0  # Temperature (in energy units)
+Nk = 2  # Number of Matsubara terms
+
+bath = DrudeLorentzBath(Q, lam, gamma, T, Nk)
+```
+
+### HEOM Options
+
+```python
+options = heom.HEOMSolver.Options(
+    nsteps=2000,
+    store_states=True,
+    rtol=1e-7,
+    atol=1e-9
+)
+
+hsolver = heom.HEOMSolver(H_sys, [bath], max_depth=5, options=options)
+```
+
+## Permutational Invariance
+
+For identical particle systems (e.g., spin ensembles).
+
+### Dicke States
+
+```python
+from qutip import dicke
+
+# Dicke state |j, m⟩ for N spins
+N = 10  # Number of spins
+j = N/2  # Total angular momentum
+m = 0   # z-component
+
+psi = dicke(N, j, m)
+```
+
+### Permutation-Invariant Operators
+
+```python
+from qutip.piqs import jspin
+
+# Collective spin operators
+N = 10
+Jx = jspin(N, 'x')
+Jy = jspin(N, 'y')
+Jz = jspin(N, 'z')
+Jp = jspin(N, '+')
+Jm = jspin(N, '-')
+```
+
+### PIQS Dynamics
+
+```python
+from qutip.piqs import Dicke
+
+# Setup Dicke model
+N = 10
+emission = 1.0
+dephasing = 0.5
+pumping = 0.0
+collective_emission = 0.0
+
+system = Dicke(N=N, emission=emission, dephasing=dephasing,
+               pumping=pumping, collective_emission=collective_emission)
+
+# Initial state
+psi0 = dicke(N, N/2, N/2)  # All spins up
+
+# Time evolution
+tlist = np.linspace(0, 10, 100)
+result = system.solve(psi0, tlist, e_ops=[Jz])
+```
+
+## Non-Markovian Monte Carlo
+
+Quantum trajectories with memory effects.
+
+```python
+from qutip import nm_mcsolve
+
+# Non-Markovian bath correlation
+def bath_correlation(t1, t2):
+    tau = abs(t2 - t1)
+    return np.exp(-tau / 2.0) * np.cos(tau)
+
+# System setup
+H = sigmaz()
+c_ops = [sigmax()]
+psi0 = basis(2, 0)
+tlist = np.linspace(0, 10, 100)
+
+# Solve with memory
+result = nm_mcsolve(H, psi0, tlist, c_ops, sc_ops=[],
+                     bath_corr=bath_correlation, ntraj=500,
+                     e_ops=[sigmaz()])
+```
+
+## Stochastic Solvers with Measurements
+
+### Continuous Measurement
+
+```python
+# Homodyne detection
+sc_ops = [np.sqrt(0.1) * destroy(N)]  # Measurement operator
+
+result = ssesolve(H, psi0, tlist, sc_ops=sc_ops,
+                   e_ops=[num(N)], ntraj=100,
+                   noise=11)  # 11 for homodyne
+
+# Heterodyne detection
+result = ssesolve(H, psi0, tlist, sc_ops=sc_ops,
+                   e_ops=[num(N)], ntraj=100,
+                   noise=12)  # 12 for heterodyne
+```
+
+### Photon Counting
+
+```python
+# Quantum jump times
+result = mcsolve(H, psi0, tlist, c_ops, ntraj=50,
+                 options=Options(store_states=True))
+
+# Extract measurement times
+for i, jump_times in enumerate(result.col_times):
+    print(f"Trajectory {i} jump times: {jump_times}")
+    print(f"Which operator: {result.col_which[i]}")
+```
+
+## Krylov Subspace Methods
+
+Efficient for large systems.
+
+```python
+from qutip import krylovsolve
+
+# Use Krylov solver
+result = krylovsolve(H, psi0, tlist, krylov_dim=10, e_ops=[num(N)])
+```
+
+## Bloch-Redfield Master Equation
+
+For weak system-bath coupling.
+
+```python
+# Bath spectral density
+def ohmic_spectrum(w):
+    if w >= 0:
+        return 0.1 * w  # Ohmic
+    else:
+        return 0
+
+# Coupling operators and spectra
+a_ops = [[sigmax(), ohmic_spectrum]]
+
+# Solve
+result = brmesolve(H, psi0, tlist, a_ops, e_ops=[sigmaz()])
+```
+
+### Temperature-Dependent Bath
+
+```python
+def thermal_spectrum(w):
+    # Bose-Einstein distribution
+    T = 1.0  # Temperature
+    if abs(w) < 1e-10:
+        return 0.1 * T
+    n_th = 1 / (np.exp(abs(w)/T) - 1)
+    if w >= 0:
+        return 0.1 * w * (n_th + 1)
+    else:
+        return 0.1 * abs(w) * n_th
+
+a_ops = [[sigmax(), thermal_spectrum]]
+result = brmesolve(H, psi0, tlist, a_ops, e_ops=[sigmaz()])
+```
+
+## Superoperators and Quantum Channels
+
+### Superoperator Representations
+
+```python
+# Liouvillian
+L = liouvillian(H, c_ops)
+
+# Convert between representations
+from qutip import (spre, spost, sprepost,
+                    super_to_choi, choi_to_super,
+                    super_to_kraus, kraus_to_super)
+
+# Superoperator forms
+L_spre = spre(H)  # Left multiplication
+L_spost = spost(H)  # Right multiplication
+L_sprepost = sprepost(H, H.dag())
+
+# Choi matrix
+choi = super_to_choi(L)
+
+# Kraus operators
+kraus = super_to_kraus(L)
+```
+
+### Quantum Channels
+
+```python
+# Depolarizing channel
+p = 0.1  # Error probability
+K0 = np.sqrt(1 - 3*p/4) * qeye(2)
+K1 = np.sqrt(p/4) * sigmax()
+K2 = np.sqrt(p/4) * sigmay()
+K3 = np.sqrt(p/4) * sigmaz()
+
+kraus_ops = [K0, K1, K2, K3]
+E = kraus_to_super(kraus_ops)
+
+# Apply channel
+rho_out = E * operator_to_vector(rho_in)
+rho_out = vector_to_operator(rho_out)
+```
+
+### Amplitude Damping
+
+```python
+# T1 decay
+gamma = 0.1
+K0 = Qobj([[1, 0], [0, np.sqrt(1 - gamma)]])
+K1 = Qobj([[0, np.sqrt(gamma)], [0, 0]])
+
+E_damping = kraus_to_super([K0, K1])
+```
+
+### Phase Damping
+
+```python
+# T2 dephasing
+gamma = 0.1
+K0 = Qobj([[1, 0], [0, np.sqrt(1 - gamma/2)]])
+K1 = Qobj([[0, 0], [0, np.sqrt(gamma/2)]])
+
+E_dephasing = kraus_to_super([K0, K1])
+```
+
+## Quantum Trajectories Analysis
+
+### Extract Individual Trajectories
+
+```python
+options = Options(store_states=True, store_final_state=False)
+result = mcsolve(H, psi0, tlist, c_ops, ntraj=100, options=options)
+
+# Access individual trajectories
+for i in range(len(result.states)):
+    trajectory = result.states[i]  # List of states for trajectory i
+    # Analyze trajectory
+```
+
+### Trajectory Statistics
+
+```python
+# Mean and standard deviation
+result = mcsolve(H, psi0, tlist, c_ops, e_ops=[num(N)], ntraj=500)
+
+n_mean = result.expect[0]
+n_std = result.std_expect[0]
+
+# Photon number distribution at final time
+final_states = [result.states[i][-1] for i in range(len(result.states))]
+```
+
+## Time-Dependent Terms Advanced
+
+### QobjEvo
+
+```python
+from qutip import QobjEvo
+
+# Time-dependent Hamiltonian with QobjEvo
+def drive(t, args):
+    return args['A'] * np.exp(-t/args['tau']) * np.sin(args['w'] * t)
+
+H0 = num(N)
+H1 = destroy(N) + create(N)
+args = {'A': 1.0, 'w': 1.0, 'tau': 5.0}
+
+H_td = QobjEvo([H0, [H1, drive]], args=args)
+
+# Can update args without recreating
+H_td.arguments({'A': 2.0, 'w': 1.5, 'tau': 10.0})
+```
+
+### Compiled Time-Dependent Terms
+
+```python
+# Fastest method (requires Cython)
+H = [num(N), [destroy(N) + create(N), 'A * exp(-t/tau) * sin(w*t)']]
+args = {'A': 1.0, 'w': 1.0, 'tau': 5.0}
+
+# QuTiP compiles this for speed
+result = sesolve(H, psi0, tlist, args=args)
+```
+
+### Callback Functions
+
+```python
+# Advanced control
+def time_dependent_coeff(t, args):
+    # Access solver state if needed
+    return complex_function(t, args)
+
+H = [H0, [H1, time_dependent_coeff]]
+```
+
+## Parallel Processing
+
+### Parallel Map
+
+```python
+from qutip import parallel_map
+
+# Define task
+def simulate(gamma):
+    c_ops = [np.sqrt(gamma) * destroy(N)]
+    result = mesolve(H, psi0, tlist, c_ops, e_ops=[num(N)])
+    return result.expect[0]
+
+# Run in parallel
+gamma_values = np.linspace(0, 1, 20)
+results = parallel_map(simulate, gamma_values, num_cpus=4)
+```
+
+### Serial Map (for debugging)
+
+```python
+from qutip import serial_map
+
+# Same interface but runs serially
+results = serial_map(simulate, gamma_values)
+```
+
+## File I/O
+
+### Save/Load Quantum Objects
+
+```python
+# Save
+H.save('hamiltonian.qu')
+psi.save('state.qu')
+
+# Load
+H_loaded = qload('hamiltonian.qu')
+psi_loaded = qload('state.qu')
+```
+
+### Save/Load Results
+
+```python
+# Save simulation results
+result = mesolve(H, psi0, tlist, c_ops, e_ops=[num(N)])
+result.save('simulation.dat')
+
+# Load results
+from qutip import Result
+loaded_result = Result.load('simulation.dat')
+```
+
+### Export to MATLAB
+
+```python
+# Export to .mat file
+H.matlab_export('hamiltonian.mat', 'H')
+```
+
+## Solver Options
+
+### Fine-Tuning Solvers
+
+```python
+options = Options()
+
+# Integration parameters
+options.nsteps = 10000  # Max internal steps
+options.rtol = 1e-8     # Relative tolerance
+options.atol = 1e-10    # Absolute tolerance
+
+# Method selection
+options.method = 'adams'  # Non-stiff (default)
+# options.method = 'bdf'  # Stiff problems
+
+# Storage options
+options.store_states = True
+options.store_final_state = True
+
+# Progress
+options.progress_bar = True
+
+# Random number seed (for reproducibility)
+options.seeds = 12345
+
+result = mesolve(H, psi0, tlist, c_ops, options=options)
+```
+
+### Debugging
+
+```python
+# Enable detailed output
+options.verbose = True
+
+# Memory tracking
+options.num_cpus = 1  # Easier debugging
+```
+
+## Performance Tips
+
+1. **Use sparse matrices**: QuTiP does this automatically
+2. **Minimize Hilbert space**: Truncate when possible
+3. **Choose right solver**:
+   - Pure states: `sesolve` faster than `mesolve`
+   - Stochastic: `mcsolve` for quantum jumps
+   - Periodic: Floquet methods
+4. **Time-dependent terms**: String format fastest
+5. **Expectation values**: Only compute needed observables
+6. **Parallel trajectories**: `mcsolve` uses all CPUs
+7. **Krylov methods**: For very large systems
+8. **Memory**: Use `store_final_state` instead of `store_states` when possible