Source code for qutip.steadystate

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"""
Module contains functions for solving for the steady state density matrix of
open quantum systems defined by a Liouvillian or Hamiltonian and a list of
collapse operators.
"""

__all__ = ['steadystate', 'steady', 'build_preconditioner',
           'pseudo_inverse']

import warnings
import time
import scipy
import numpy as np
from numpy.linalg import svd
from scipy import prod
import scipy.sparse as sp
import scipy.linalg as la
from scipy.sparse.linalg import (use_solver, splu, spilu, spsolve, eigs,
                                 LinearOperator, gmres, lgmres, bicgstab)
from qutip.qobj import Qobj, issuper, isoper

from qutip.superoperator import liouvillian, vec2mat, spre
from qutip.sparse import sp_permute, sp_bandwidth, sp_reshape, sp_profile

from qutip.superoperator import liouvillian, vec2mat
from qutip.sparse import (sp_permute, sp_bandwidth, sp_reshape,
                          sp_profile)
from qutip.cy.spmath import zcsr_kron
from qutip.graph import reverse_cuthill_mckee, weighted_bipartite_matching
from qutip import (mat2vec, tensor, identity, operator_to_vector)
import qutip.settings as settings
from qutip.utilities import _version2int
from qutip.cy.spconvert import dense2D_to_fastcsr_fmode

import qutip.logging_utils
logger = qutip.logging_utils.get_logger()
logger.setLevel('DEBUG')

# Load MKL spsolve if avaiable
if settings.has_mkl:
    from qutip._mkl.spsolve import (mkl_splu, mkl_spsolve)

# test if scipy is recent enought to get L & U factors from superLU
_scipy_check = _version2int(scipy.__version__) >= _version2int('0.14.0')


def _empty_info_dict():
    def_info = {'perm': [], 'solution_time': None,
                'residual_norm': None,
                'solver': None, 'method': None}

    return def_info


def _default_steadystate_args():
    def_args = {'sparse': True, 'use_rcm': False,
                'use_wbm': False, 'use_precond': False,
                'all_states': False, 'M': None, 'x0': None, 'drop_tol': 1e-4,
                'fill_factor': 100, 'diag_pivot_thresh': None, 'maxiter': 1000,
                'permc_spec': 'COLAMD', 'ILU_MILU': 'smilu_2',
                'restart': 20,
                'max_iter_refine': 10,
                'scaling_vectors': True,
                'weighted_matching': True,
                'return_info': False, 'info': _empty_info_dict(),
                'verbose': False, 'solver': 'scipy', 'weight': None,
                'tol': 1e-12, 'matol': 1e-15, 'mtol': None}
    return def_args


[docs]def steadystate(A, c_op_list=[], method='direct', solver=None, **kwargs): """Calculates the steady state for quantum evolution subject to the supplied Hamiltonian or Liouvillian operator and (if given a Hamiltonian) a list of collapse operators. If the user passes a Hamiltonian then it, along with the list of collapse operators, will be converted into a Liouvillian operator in Lindblad form. Parameters ---------- A : qobj A Hamiltonian or Liouvillian operator. c_op_list : list A list of collapse operators. solver : str {None, 'scipy', 'mkl'} Selects the sparse solver to use. Default is auto-select based on the availability of the MKL library. method : str {'direct', 'eigen', 'iterative-gmres', 'iterative-lgmres', 'iterative-bicgstab', 'svd', 'power', 'power-gmres', 'power-lgmres', 'power-bicgstab'} Method for solving the underlying linear equation. Direct LU solver 'direct' (default), sparse eigenvalue problem 'eigen', iterative GMRES method 'iterative-gmres', iterative LGMRES method 'iterative-lgmres', iterative BICGSTAB method 'iterative-bicgstab', SVD 'svd' (dense), or inverse-power method 'power'. The iterative power methods 'power-gmres', 'power-lgmres', 'power-bicgstab' use the same solvers as their direct counterparts. return_info : bool, optional, default = False Return a dictionary of solver-specific infomation about the solution and how it was obtained. sparse : bool, optional, default = True Solve for the steady state using sparse algorithms. If set to False, the underlying Liouvillian operator will be converted into a dense matrix. Use only for 'smaller' systems. use_rcm : bool, optional, default = False Use reverse Cuthill-Mckee reordering to minimize fill-in in the LU factorization of the Liouvillian. use_wbm : bool, optional, default = False Use Weighted Bipartite Matching reordering to make the Liouvillian diagonally dominant. This is useful for iterative preconditioners only, and is set to ``True`` by default when finding a preconditioner. weight : float, optional Sets the size of the elements used for adding the unity trace condition to the linear solvers. This is set to the average abs value of the Liouvillian elements if not specified by the user. max_iter_refine : int {10} MKL ONLY. Max. number of iterative refinements to perform. scaling_vectors : bool {True, False} MKL ONLY. Scale matrix to unit norm columns and rows. weighted_matching : bool {True, False} MKL ONLY. Use weighted matching to better condition diagonal. x0 : ndarray, optional ITERATIVE ONLY. Initial guess for solution vector. maxiter : int, optional, default=1000 ITERATIVE ONLY. Maximum number of iterations to perform. tol : float, optional, default=1e-12 ITERATIVE ONLY. Tolerance used for terminating solver. mtol : float, optional, default=None ITERATIVE 'power' methods ONLY. Tolerance for lu solve method. If None given then `max(0.1*tol, 1e-15)` is used matol : float, optional, default=1e-15 ITERATIVE ONLY. Absolute tolerance for lu solve method. permc_spec : str, optional, default='COLAMD' ITERATIVE ONLY. Column ordering used internally by superLU for the 'direct' LU decomposition method. Options include 'COLAMD' and 'NATURAL'. If using RCM then this is set to 'NATURAL' automatically unless explicitly specified. use_precond : bool optional, default = False ITERATIVE ONLY. Use an incomplete sparse LU decomposition as a preconditioner for the 'iterative' GMRES and BICG solvers. Speeds up convergence time by orders of magnitude in many cases. M : {sparse matrix, dense matrix, LinearOperator}, optional ITERATIVE ONLY. Preconditioner for A. The preconditioner should approximate the inverse of A. Effective preconditioning can dramatically improve the rate of convergence for iterative methods. If no preconditioner is given and ``use_precond = True``, then one is generated automatically. fill_factor : float, optional, default = 100 ITERATIVE ONLY. Specifies the fill ratio upper bound (>=1) of the iLU preconditioner. Lower values save memory at the cost of longer execution times and a possible singular factorization. drop_tol : float, optional, default = 1e-4 ITERATIVE ONLY. Sets the threshold for the magnitude of preconditioner elements that should be dropped. Can be reduced for a courser factorization at the cost of an increased number of iterations, and a possible singular factorization. diag_pivot_thresh : float, optional, default = None ITERATIVE ONLY. Sets the threshold between [0,1] for which diagonal elements are considered acceptable pivot points when using a preconditioner. A value of zero forces the pivot to be the diagonal element. ILU_MILU : str, optional, default = 'smilu_2' ITERATIVE ONLY. Selects the incomplete LU decomposition method algoithm used in creating the preconditoner. Should only be used by advanced users. Returns ------- dm : qobj Steady state density matrix. info : dict, optional Dictionary containing solver-specific information about the solution. Notes ----- The SVD method works only for dense operators (i.e. small systems). """ if solver is None: solver = 'scipy' if settings.has_mkl: if method in ['direct', 'power']: solver = 'mkl' elif solver == 'mkl' and \ (method not in ['direct', 'power']): raise Exception('MKL solver only for direct or power methods.') elif solver not in ['scipy', 'mkl']: raise Exception('Invalid solver kwarg.') ss_args = _default_steadystate_args() ss_args['method'] = method if solver is not None: ss_args['solver'] = solver ss_args['info']['solver'] = ss_args['solver'] ss_args['info']['method'] = ss_args['method'] for key in kwargs.keys(): if key in ss_args.keys(): ss_args[key] = kwargs[key] else: raise Exception( "Invalid keyword argument '"+key+"' passed to steadystate.") # Set column perm to NATURAL if using RCM and not specified by user if ss_args['use_rcm'] and ('permc_spec' not in kwargs.keys()): ss_args['permc_spec'] = 'NATURAL' # Create & check Liouvillian A = _steadystate_setup(A, c_op_list) # Set weight parameter to avg abs val in L if not set explicitly if 'weight' not in kwargs.keys(): ss_args['weight'] = np.mean(np.abs(A.data.data.max())) ss_args['info']['weight'] = ss_args['weight'] if ss_args['method'] == 'direct': if (ss_args['solver'] == 'scipy' and ss_args['sparse']) \ or ss_args['solver'] == 'mkl': return _steadystate_direct_sparse(A, ss_args) else: return _steadystate_direct_dense(A, ss_args) elif ss_args['method'] == 'eigen': return _steadystate_eigen(A, ss_args) elif ss_args['method'] in ['iterative-gmres', 'iterative-lgmres', 'iterative-bicgstab']: return _steadystate_iterative(A, ss_args) elif ss_args['method'] == 'svd': return _steadystate_svd_dense(A, ss_args) elif ss_args['method'] in ['power', 'power-gmres', 'power-lgmres', 'power-bicgstab']: return _steadystate_power(A, ss_args) else: raise ValueError('Invalid method argument for steadystate.')
def _steadystate_setup(A, c_op_list): """Build Liouvillian (if necessary) and check input. """ if isoper(A): if len(c_op_list) > 0: return liouvillian(A, c_op_list) raise TypeError('Cannot calculate the steady state for a ' + 'non-dissipative system ' + '(no collapse operators given)') elif issuper(A): return A else: raise TypeError('Solving for steady states requires ' + 'Liouvillian (super) operators') def _steadystate_LU_liouvillian(L, ss_args, has_mkl=0): """Creates modified Liouvillian for LU based SS methods. """ perm = None perm2 = None rev_perm = None n = int(np.sqrt(L.shape[0])) form = 'csr' if has_mkl: L = L.data + sp.csr_matrix( (ss_args['weight']*np.ones(n), (np.zeros(n), [nn * (n + 1) for nn in range(n)])), shape=(n ** 2, n ** 2)) else: form = 'csc' L = L.data.tocsc() + sp.csc_matrix( (ss_args['weight']*np.ones(n), (np.zeros(n), [nn * (n + 1) for nn in range(n)])), shape=(n ** 2, n ** 2)) if settings.debug: old_band = sp_bandwidth(L)[0] old_pro = sp_profile(L)[0] logger.debug('Orig. NNZ: %i' % L.nnz) if ss_args['use_rcm']: logger.debug('Original bandwidth: %i' % old_band) if ss_args['use_wbm']: if settings.debug: logger.debug('Calculating Weighted Bipartite Matching ordering...') _wbm_start = time.time() perm = weighted_bipartite_matching(L) _wbm_end = time.time() L = sp_permute(L, perm, [], form) ss_args['info']['perm'].append('wbm') ss_args['info']['wbm_time'] = _wbm_end-_wbm_start if settings.debug: wbm_band = sp_bandwidth(L)[0] logger.debug('WBM bandwidth: %i' % wbm_band) if ss_args['use_rcm']: if settings.debug: logger.debug('Calculating Reverse Cuthill-Mckee ordering...') _rcm_start = time.time() perm2 = reverse_cuthill_mckee(L) _rcm_end = time.time() rev_perm = np.argsort(perm2) L = sp_permute(L, perm2, perm2, form) ss_args['info']['perm'].append('rcm') ss_args['info']['rcm_time'] = _rcm_end-_rcm_start if settings.debug: rcm_band = sp_bandwidth(L)[0] rcm_pro = sp_profile(L)[0] logger.debug('RCM bandwidth: %i' % rcm_band) logger.debug('Bandwidth reduction factor: %f' % (old_band/rcm_band)) logger.debug('Profile reduction factor: %f' % (old_pro/rcm_pro)) L.sort_indices() return L, perm, perm2, rev_perm, ss_args def steady(L, maxiter=10, tol=1e-12, itertol=1e-15, method='solve', use_precond=False): """ Deprecated. See steadystate instead. """ message = "steady has been deprecated, use steadystate instead" warnings.warn(message, DeprecationWarning) return steadystate(L, [], maxiter=maxiter, tol=tol, use_precond=use_precond) def _steadystate_direct_sparse(L, ss_args): """ Direct solver that uses scipy sparse matrices """ if settings.debug: logger.debug('Starting direct LU solver.') dims = L.dims[0] n = int(np.sqrt(L.shape[0])) b = np.zeros(n ** 2, dtype=complex) b[0] = ss_args['weight'] if ss_args['solver'] == 'mkl': has_mkl = 1 else: has_mkl = 0 ss_lu_liouv_list = _steadystate_LU_liouvillian(L, ss_args, has_mkl) L, perm, perm2, rev_perm, ss_args = ss_lu_liouv_list if np.any(perm): b = b[np.ix_(perm,)] if np.any(perm2): b = b[np.ix_(perm2,)] if ss_args['solver'] == 'scipy': ss_args['info']['permc_spec'] = ss_args['permc_spec'] ss_args['info']['drop_tol'] = ss_args['drop_tol'] ss_args['info']['diag_pivot_thresh'] = ss_args['diag_pivot_thresh'] ss_args['info']['fill_factor'] = ss_args['fill_factor'] ss_args['info']['ILU_MILU'] = ss_args['ILU_MILU'] if not ss_args['solver'] == 'mkl': # Use superLU solver orig_nnz = L.nnz _direct_start = time.time() lu = splu(L, permc_spec=ss_args['permc_spec'], diag_pivot_thresh=ss_args['diag_pivot_thresh'], options=dict(ILU_MILU=ss_args['ILU_MILU'])) v = lu.solve(b) _direct_end = time.time() ss_args['info']['solution_time'] = _direct_end - _direct_start if (settings.debug or ss_args['return_info']) and _scipy_check: L_nnz = lu.L.nnz U_nnz = lu.U.nnz ss_args['info']['l_nnz'] = L_nnz ss_args['info']['u_nnz'] = U_nnz ss_args['info']['lu_fill_factor'] = (L_nnz + U_nnz)/L.nnz if settings.debug: logger.debug('L NNZ: %i ; U NNZ: %i' % (L_nnz, U_nnz)) logger.debug('Fill factor: %f' % ((L_nnz + U_nnz)/orig_nnz)) else: # Use MKL solver if len(ss_args['info']['perm']) != 0: in_perm = np.arange(n**2, dtype=np.int32) else: in_perm = None _direct_start = time.time() v = mkl_spsolve(L, b, perm=in_perm, verbose=ss_args['verbose'], max_iter_refine=ss_args['max_iter_refine'], scaling_vectors=ss_args['scaling_vectors'], weighted_matching=ss_args['weighted_matching']) _direct_end = time.time() ss_args['info']['solution_time'] = _direct_end-_direct_start if ss_args['return_info']: ss_args['info']['residual_norm'] = la.norm(b - L*v, np.inf) ss_args['info']['max_iter_refine'] = ss_args['max_iter_refine'] ss_args['info']['scaling_vectors'] = ss_args['scaling_vectors'] ss_args['info']['weighted_matching'] = ss_args['weighted_matching'] if ss_args['use_rcm']: v = v[np.ix_(rev_perm,)] data = dense2D_to_fastcsr_fmode(vec2mat(v), n, n) data = 0.5 * (data + data.H) if ss_args['return_info']: return Qobj(data, dims=dims, isherm=True), ss_args['info'] else: return Qobj(data, dims=dims, isherm=True) def _steadystate_direct_dense(L, ss_args): """ Direct solver that use numpy dense matrices. Suitable for small system, with a few states. """ if settings.debug: logger.debug('Starting direct dense solver.') dims = L.dims[0] n = int(np.sqrt(L.shape[0])) b = np.zeros(n ** 2) b[0] = ss_args['weight'] L = L.data.todense() L[0, :] = np.diag(ss_args['weight']*np.ones(n)).reshape((1, n ** 2)) _dense_start = time.time() v = np.linalg.solve(L, b) _dense_end = time.time() ss_args['info']['solution_time'] = _dense_end-_dense_start if ss_args['return_info']: ss_args['info']['residual_norm'] = la.norm(b - L*v, np.inf) data = vec2mat(v) data = 0.5 * (data + data.conj().T) return Qobj(data, dims=dims, isherm=True) def _steadystate_eigen(L, ss_args): """ Internal function for solving the steady state problem by finding the eigenvector corresponding to the zero eigenvalue of the Liouvillian using ARPACK. """ ss_args['info'].pop('weight', None) if settings.debug: logger.debug('Starting Eigen solver.') dims = L.dims[0] L = L.data.tocsc() if ss_args['use_rcm']: ss_args['info']['perm'].append('rcm') if settings.debug: old_band = sp_bandwidth(L)[0] logger.debug('Original bandwidth: %i' % old_band) perm = reverse_cuthill_mckee(L) rev_perm = np.argsort(perm) L = sp_permute(L, perm, perm, 'csc') if settings.debug: rcm_band = sp_bandwidth(L)[0] logger.debug('RCM bandwidth: %i' % rcm_band) logger.debug('Bandwidth reduction factor: %f' % (old_band/rcm_band)) _eigen_start = time.time() eigval, eigvec = eigs(L, k=1, sigma=1e-15, tol=ss_args['tol'], which='LM', maxiter=ss_args['maxiter']) _eigen_end = time.time() ss_args['info']['solution_time'] = _eigen_end - _eigen_start if ss_args['return_info']: ss_args['info']['residual_norm'] = la.norm(L*eigvec, np.inf) if ss_args['use_rcm']: eigvec = eigvec[np.ix_(rev_perm,)] _temp = vec2mat(eigvec) data = dense2D_to_fastcsr_fmode(_temp, _temp.shape[0], _temp.shape[1]) data = 0.5 * (data + data.H) out = Qobj(data, dims=dims, isherm=True) if ss_args['return_info']: return out/out.tr(), ss_args['info'] else: return out/out.tr() def _iterative_precondition(A, n, ss_args): """ Internal function for preconditioning the steadystate problem for use with iterative solvers. """ if settings.debug: logger.debug('Starting preconditioner.') _precond_start = time.time() try: P = spilu(A, permc_spec=ss_args['permc_spec'], drop_tol=ss_args['drop_tol'], diag_pivot_thresh=ss_args['diag_pivot_thresh'], fill_factor=ss_args['fill_factor'], options=dict(ILU_MILU=ss_args['ILU_MILU'])) P_x = lambda x: P.solve(x) M = LinearOperator((n ** 2, n ** 2), matvec=P_x) _precond_end = time.time() ss_args['info']['permc_spec'] = ss_args['permc_spec'] ss_args['info']['drop_tol'] = ss_args['drop_tol'] ss_args['info']['diag_pivot_thresh'] = ss_args['diag_pivot_thresh'] ss_args['info']['fill_factor'] = ss_args['fill_factor'] ss_args['info']['ILU_MILU'] = ss_args['ILU_MILU'] ss_args['info']['precond_time'] = _precond_end-_precond_start if settings.debug or ss_args['return_info']: if settings.debug: logger.debug('Preconditioning succeeded.') logger.debug('Precond. time: %f' % (_precond_end - _precond_start)) if _scipy_check: L_nnz = P.L.nnz U_nnz = P.U.nnz ss_args['info']['l_nnz'] = L_nnz ss_args['info']['u_nnz'] = U_nnz ss_args['info']['ilu_fill_factor'] = (L_nnz+U_nnz)/A.nnz e = np.ones(n ** 2, dtype=int) condest = la.norm(M*e, np.inf) ss_args['info']['ilu_condest'] = condest if settings.debug: logger.debug('L NNZ: %i ; U NNZ: %i' % (L_nnz, U_nnz)) logger.debug('Fill factor: %f' % ((L_nnz+U_nnz)/A.nnz)) logger.debug('iLU condest: %f' % condest) except: raise Exception("Failed to build preconditioner. Try increasing " + "fill_factor and/or drop_tol.") return M, ss_args def _steadystate_iterative(L, ss_args): """ Iterative steady state solver using the GMRES, LGMRES, or BICGSTAB algorithm and a sparse incomplete LU preconditioner. """ ss_iters = {'iter': 0} def _iter_count(r): ss_iters['iter'] += 1 return if settings.debug: logger.debug('Starting %s solver.' % ss_args['method']) dims = L.dims[0] n = int(np.sqrt(L.shape[0])) b = np.zeros(n ** 2) b[0] = ss_args['weight'] L, perm, perm2, rev_perm, ss_args = _steadystate_LU_liouvillian(L, ss_args) if np.any(perm): b = b[np.ix_(perm,)] if np.any(perm2): b = b[np.ix_(perm2,)] use_solver(assumeSortedIndices=True) if ss_args['M'] is None and ss_args['use_precond']: ss_args['M'], ss_args = _iterative_precondition(L, n, ss_args) if ss_args['M'] is None: warnings.warn("Preconditioning failed. Continuing without.", UserWarning) # Select iterative solver type _iter_start = time.time() # FIXME: These atol keyword except checks can be removed once scipy 1.1 # is a minimum requirement extra = {"callback_type": 'legacy'} if scipy.__version__ >= "1.4" else {} if ss_args['method'] == 'iterative-gmres': try: v, check = gmres(L, b, tol=ss_args['tol'], atol=ss_args['matol'], M=ss_args['M'], x0=ss_args['x0'], restart=ss_args['restart'], maxiter=ss_args['maxiter'], callback=_iter_count, **extra) except TypeError as e: if "unexpected keyword argument 'atol'" in str(e): v, check = gmres(L, b, tol=ss_args['tol'], M=ss_args['M'], x0=ss_args['x0'], restart=ss_args['restart'], maxiter=ss_args['maxiter'], callback=_iter_count) elif ss_args['method'] == 'iterative-lgmres': try: v, check = lgmres(L, b, tol=ss_args['tol'], atol=ss_args['matol'], M=ss_args['M'], x0=ss_args['x0'], maxiter=ss_args['maxiter'], callback=_iter_count) except TypeError as e: if "unexpected keyword argument 'atol'" in str(e): v, check = lgmres(L, b, tol=ss_args['tol'], M=ss_args['M'], x0=ss_args['x0'], maxiter=ss_args['maxiter'], callback=_iter_count) elif ss_args['method'] == 'iterative-bicgstab': try: v, check = bicgstab(L, b, tol=ss_args['tol'], atol=ss_args['matol'], M=ss_args['M'], x0=ss_args['x0'], maxiter=ss_args['maxiter'], callback=_iter_count) except TypeError as e: if "unexpected keyword argument 'atol'" in str(e): v, check = bicgstab(L, b, tol=ss_args['tol'], M=ss_args['M'], x0=ss_args['x0'], maxiter=ss_args['maxiter'], callback=_iter_count) else: raise Exception("Invalid iterative solver method.") _iter_end = time.time() ss_args['info']['iter_time'] = _iter_end - _iter_start if 'precond_time' in ss_args['info'].keys(): ss_args['info']['solution_time'] = (ss_args['info']['iter_time'] + ss_args['info']['precond_time']) else: ss_args['info']['solution_time'] = ss_args['info']['iter_time'] ss_args['info']['iterations'] = ss_iters['iter'] if ss_args['return_info']: ss_args['info']['residual_norm'] = la.norm(b - L*v, np.inf) if settings.debug: logger.debug('Number of Iterations: %i' % ss_iters['iter']) logger.debug('Iteration. time: %f' % (_iter_end - _iter_start)) if check > 0: raise Exception("Steadystate error: Did not reach tolerance after " + str(ss_args['maxiter']) + " steps." + "\nResidual norm: " + str(ss_args['info']['residual_norm'])) elif check < 0: raise Exception( "Steadystate error: Failed with fatal error: " + str(check) + ".") if ss_args['use_rcm']: v = v[np.ix_(rev_perm,)] data = vec2mat(v) data = 0.5 * (data + data.conj().T) if ss_args['return_info']: return Qobj(data, dims=dims, isherm=True), ss_args['info'] else: return Qobj(data, dims=dims, isherm=True) def _steadystate_svd_dense(L, ss_args): """ Find the steady state(s) of an open quantum system by solving for the nullspace of the Liouvillian. """ ss_args['info'].pop('weight', None) atol = 1e-12 rtol = 1e-12 if settings.debug: logger.debug('Starting SVD solver.') _svd_start = time.time() u, s, vh = svd(L.full(), full_matrices=False) tol = max(atol, rtol * s[0]) nnz = (s >= tol).sum() ns = vh[nnz:].conj().T _svd_end = time.time() ss_args['info']['solution_time'] = _svd_end-_svd_start if ss_args['all_states']: rhoss_list = [] for n in range(ns.shape[1]): rhoss = Qobj(vec2mat(ns[:, n]), dims=L.dims[0]) rhoss_list.append(rhoss / rhoss.tr()) if ss_args['return_info']: return rhoss_list, ss_args['info'] else: if ss_args['return_info']: return rhoss_list, ss_args['info'] else: return rhoss_list else: rhoss = Qobj(vec2mat(ns[:, 0]), dims=L.dims[0]) return rhoss / rhoss.tr() def _steadystate_power_liouvillian(L, ss_args, has_mkl=0): """Creates modified Liouvillian for power based SS methods. """ perm = None perm2 = None rev_perm = None n = L.shape[0] if ss_args['solver'] == 'mkl': L = L.data - (1e-15) * sp.eye(n, n, format='csr') kind = 'csr' else: L = L.data.tocsc() - (1e-15) * sp.eye(n, n, format='csc') kind = 'csc' orig_nnz = L.nnz if settings.debug: old_band = sp_bandwidth(L)[0] old_pro = sp_profile(L)[0] logger.debug('Original bandwidth: %i' % old_band) logger.debug('Original profile: %i' % old_pro) if ss_args['use_wbm']: if settings.debug: logger.debug('Calculating Weighted Bipartite Matching ordering...') _wbm_start = time.time() perm = weighted_bipartite_matching(L) _wbm_end = time.time() L = sp_permute(L, perm, [], kind) ss_args['info']['perm'].append('wbm') ss_args['info']['wbm_time'] = _wbm_end-_wbm_start if settings.debug: wbm_band = sp_bandwidth(L)[0] wbm_pro = sp_profile(L)[0] logger.debug('WBM bandwidth: %i' % wbm_band) logger.debug('WBM profile: %i' % wbm_pro) if ss_args['use_rcm']: if settings.debug: logger.debug('Calculating Reverse Cuthill-Mckee ordering...') ss_args['info']['perm'].append('rcm') _rcm_start = time.time() perm2 = reverse_cuthill_mckee(L) _rcm_end = time.time() ss_args['info']['rcm_time'] = _rcm_end-_rcm_start rev_perm = np.argsort(perm2) L = sp_permute(L, perm2, perm2, kind) if settings.debug: new_band = sp_bandwidth(L)[0] new_pro = sp_profile(L)[0] logger.debug('RCM bandwidth: %i' % new_band) logger.debug('Bandwidth reduction factor: %f' % (old_band/new_band)) logger.debug('RCM profile: %i' % new_pro) logger.debug('Profile reduction factor: %f' % (old_pro/new_pro)) L.sort_indices() return L, perm, perm2, rev_perm, ss_args def _steadystate_power(L, ss_args): """ Inverse power method for steady state solving. """ ss_args['info'].pop('weight', None) if settings.debug: logger.debug('Starting iterative inverse-power method solver.') tol = ss_args['tol'] mtol = ss_args['mtol'] if mtol is None: mtol = max(0.1*tol, 1e-15) maxiter = ss_args['maxiter'] use_solver(assumeSortedIndices=True) rhoss = Qobj() sflag = issuper(L) if sflag: rhoss.dims = L.dims[0] else: rhoss.dims = [L.dims[0], 1] n = L.shape[0] # Build Liouvillian if ss_args['solver'] == 'mkl' and ss_args['method'] == 'power': has_mkl = 1 else: has_mkl = 0 L, perm, perm2, rev_perm, ss_args = _steadystate_power_liouvillian(L, ss_args, has_mkl) orig_nnz = L.nnz # start with all ones as RHS v = np.ones(n, dtype=complex) if ss_args['use_rcm']: v = v[np.ix_(perm2,)] # Do preconditioning if ss_args['solver'] == 'scipy': if ss_args['M'] is None and ss_args['use_precond'] and \ ss_args['method'] in ['power-gmres', 'power-lgmres', 'power-bicgstab']: ss_args['M'], ss_args = _iterative_precondition(L, int(np.sqrt(n)), ss_args) if ss_args['M'] is None: warnings.warn("Preconditioning failed. Continuing without.", UserWarning) ss_iters = {'iter': 0} def _iter_count(r): ss_iters['iter'] += 1 return _power_start = time.time() # Get LU factors if ss_args['method'] == 'power': if ss_args['solver'] == 'mkl': lu = mkl_splu(L, max_iter_refine=ss_args['max_iter_refine'], scaling_vectors=ss_args['scaling_vectors'], weighted_matching=ss_args['weighted_matching']) else: lu = splu(L, permc_spec=ss_args['permc_spec'], diag_pivot_thresh=ss_args['diag_pivot_thresh'], options=dict(ILU_MILU=ss_args['ILU_MILU'])) if settings.debug and _scipy_check: L_nnz = lu.L.nnz U_nnz = lu.U.nnz logger.debug('L NNZ: %i ; U NNZ: %i' % (L_nnz, U_nnz)) logger.debug('Fill factor: %f' % ((L_nnz+U_nnz)/orig_nnz)) it = 0 # FIXME: These atol keyword except checks can be removed once scipy 1.1 # is a minimum requirement while (la.norm(L * v, np.inf) > tol) and (it < maxiter): check = 0 if ss_args['method'] == 'power': v = lu.solve(v) elif ss_args['method'] == 'power-gmres': try: v, check = gmres(L, v, tol=mtol, atol=ss_args['matol'], M=ss_args['M'], x0=ss_args['x0'], restart=ss_args['restart'], maxiter=ss_args['maxiter'], callback=_iter_count) except TypeError as e: if "unexpected keyword argument 'atol'" in str(e): v, check = gmres(L, v, tol=mtol, M=ss_args['M'], x0=ss_args['x0'], restart=ss_args['restart'], maxiter=ss_args['maxiter'], callback=_iter_count) elif ss_args['method'] == 'power-lgmres': try: v, check = lgmres(L, v, tol=mtol, atol=ss_args['matol'], M=ss_args['M'], x0=ss_args['x0'], maxiter=ss_args['maxiter'], callback=_iter_count) except TypeError as e: if "unexpected keyword argument 'atol'" in str(e): v, check = lgmres(L, v, tol=mtol, M=ss_args['M'], x0=ss_args['x0'], maxiter=ss_args['maxiter'], callback=_iter_count) elif ss_args['method'] == 'power-bicgstab': try: v, check = bicgstab(L, v, tol=mtol, atol=ss_args['matol'], M=ss_args['M'], x0=ss_args['x0'], maxiter=ss_args['maxiter'], callback=_iter_count) except TypeError as e: if "unexpected keyword argument 'atol'" in str(e): v, check = bicgstab(L, v, tol=mtol, M=ss_args['M'], x0=ss_args['x0'], maxiter=ss_args['maxiter'], callback=_iter_count) else: raise Exception("Invalid iterative solver method.") if check > 0: raise Exception("{} failed to find solution in " "{} iterations.".format(ss_args['method'], check)) if check < 0: raise Exception("Breakdown in {}".format(ss_args['method'])) v = v / la.norm(v, np.inf) it += 1 if ss_args['method'] == 'power' and ss_args['solver'] == 'mkl': lu.delete() if ss_args['return_info']: ss_args['info']['max_iter_refine'] = ss_args['max_iter_refine'] ss_args['info']['scaling_vectors'] = ss_args['scaling_vectors'] ss_args['info']['weighted_matching'] = ss_args['weighted_matching'] if it >= maxiter: raise Exception('Failed to find steady state after ' + str(maxiter) + ' iterations') _power_end = time.time() ss_args['info']['solution_time'] = _power_end-_power_start ss_args['info']['iterations'] = it if ss_args['return_info']: ss_args['info']['residual_norm'] = la.norm(L*v, np.inf) if settings.debug: logger.debug('Number of iterations: %i' % it) if ss_args['use_rcm']: v = v[np.ix_(rev_perm,)] # normalise according to type of problem if sflag: trow = v[::rhoss.shape[0]+1] data = v / np.sum(trow) else: data = data / la.norm(v) data = dense2D_to_fastcsr_fmode(vec2mat(data), rhoss.shape[0], rhoss.shape[0]) rhoss.data = 0.5 * (data + data.H) rhoss.isherm = True if ss_args['return_info']: return rhoss, ss_args['info'] else: return rhoss
[docs]def build_preconditioner(A, c_op_list=[], **kwargs): """Constructs a iLU preconditioner necessary for solving for the steady state density matrix using the iterative linear solvers in the 'steadystate' function. Parameters ---------- A : qobj A Hamiltonian or Liouvillian operator. c_op_list : list A list of collapse operators. return_info : bool, optional, default = False Return a dictionary of solver-specific infomation about the solution and how it was obtained. use_rcm : bool, optional, default = False Use reverse Cuthill-Mckee reordering to minimize fill-in in the LU factorization of the Liouvillian. use_wbm : bool, optional, default = False Use Weighted Bipartite Matching reordering to make the Liouvillian diagonally dominant. This is useful for iterative preconditioners only, and is set to ``True`` by default when finding a preconditioner. weight : float, optional Sets the size of the elements used for adding the unity trace condition to the linear solvers. This is set to the average abs value of the Liouvillian elements if not specified by the user. method : str, default = 'iterative' Tells the preconditioner what type of Liouvillian to build for iLU factorization. For direct iterative methods use 'iterative'. For power iterative methods use 'power'. permc_spec : str, optional, default='COLAMD' Column ordering used internally by superLU for the 'direct' LU decomposition method. Options include 'COLAMD' and 'NATURAL'. If using RCM then this is set to 'NATURAL' automatically unless explicitly specified. fill_factor : float, optional, default = 100 Specifies the fill ratio upper bound (>=1) of the iLU preconditioner. Lower values save memory at the cost of longer execution times and a possible singular factorization. drop_tol : float, optional, default = 1e-4 Sets the threshold for the magnitude of preconditioner elements that should be dropped. Can be reduced for a courser factorization at the cost of an increased number of iterations, and a possible singular factorization. diag_pivot_thresh : float, optional, default = None Sets the threshold between [0,1] for which diagonal elements are considered acceptable pivot points when using a preconditioner. A value of zero forces the pivot to be the diagonal element. ILU_MILU : str, optional, default = 'smilu_2' Selects the incomplete LU decomposition method algoithm used in creating the preconditoner. Should only be used by advanced users. Returns ------- lu : object Returns a SuperLU object representing iLU preconditioner. info : dict, optional Dictionary containing solver-specific information. """ ss_args = _default_steadystate_args() ss_args['method'] = 'iterative' for key in kwargs.keys(): if key in ss_args.keys(): ss_args[key] = kwargs[key] else: raise Exception("Invalid keyword argument '" + key + "' passed to steadystate.") # Set column perm to NATURAL if using RCM and not specified by user if ss_args['use_rcm'] and ('permc_spec' not in kwargs.keys()): ss_args['permc_spec'] = 'NATURAL' L = _steadystate_setup(A, c_op_list) # Set weight parameter to avg abs val in L if not set explicitly if 'weight' not in kwargs.keys(): ss_args['weight'] = np.mean(np.abs(L.data.data.max())) ss_args['info']['weight'] = ss_args['weight'] n = int(np.sqrt(L.shape[0])) if ss_args['method'] == 'iterative': ss_list = _steadystate_LU_liouvillian(L, ss_args) L, perm, perm2, rev_perm, ss_args = ss_list elif ss_args['method'] == 'power': ss_list = _steadystate_power_liouvillian(L, ss_args) L, perm, perm2, rev_perm, ss_args = ss_list else: raise Exception("Invalid preconditioning method.") M, ss_args = _iterative_precondition(L, n, ss_args) if ss_args['return_info']: return M, ss_args['info'] else: return M
def _pseudo_inverse_dense(L, rhoss, w=None, **pseudo_args): """ Internal function for computing the pseudo inverse of an Liouvillian using dense matrix methods. See pseudo_inverse for details. """ rho_vec = np.transpose(mat2vec(rhoss.full())) tr_mat = tensor([identity(n) for n in L.dims[0][0]]) tr_vec = np.transpose(mat2vec(tr_mat.full())) N = np.prod(L.dims[0][0]) I = np.identity(N * N) P = np.kron(np.transpose(rho_vec), tr_vec) Q = I - P if w is None: L = L else: L = 1.0j*w*spre(tr_mat)+L if pseudo_args['method'] == 'direct': try: LIQ = np.linalg.solve(L.full(), Q) except: LIQ = np.linalg.lstsq(L.full(), Q)[0] R = np.dot(Q, LIQ) return Qobj(R, dims=L.dims) elif pseudo_args['method'] == 'numpy': return Qobj(np.dot(Q, np.dot(np.linalg.pinv(L.full()), Q)), dims=L.dims) elif pseudo_args['method'] == 'scipy': # return Qobj(la.pinv(L.full()), dims=L.dims) return Qobj(np.dot(Q, np.dot(la.pinv(L.full()), Q)), dims=L.dims) elif pseudo_args['method'] == 'scipy2': # return Qobj(la.pinv2(L.full()), dims=L.dims) return Qobj(np.dot(Q, np.dot(la.pinv2(L.full()), Q)), dims=L.dims) else: raise ValueError("Unsupported method '%s'. Use 'direct' or 'numpy'" % method) def _pseudo_inverse_sparse(L, rhoss, w=None, **pseudo_args): """ Internal function for computing the pseudo inverse of an Liouvillian using sparse matrix methods. See pseudo_inverse for details. """ N = np.prod(L.dims[0][0]) rhoss_vec = operator_to_vector(rhoss) tr_op = tensor([identity(n) for n in L.dims[0][0]]) tr_op_vec = operator_to_vector(tr_op) P = zcsr_kron(rhoss_vec.data, tr_op_vec.data.T) I = sp.eye(N*N, N*N, format='csr') Q = I - P if w is None: L = 1.0j*(1e-15)*spre(tr_op) + L else: if w != 0.0: L = 1.0j*w*spre(tr_op) + L else: L = 1.0j*(1e-15)*spre(tr_op) + L if pseudo_args['use_rcm']: perm = reverse_cuthill_mckee(L.data) A = sp_permute(L.data, perm, perm) Q = sp_permute(Q, perm, perm) else: if ss_args['solver'] == 'scipy': A = L.data.tocsc() A.sort_indices() if pseudo_args['method'] == 'splu': if settings.has_mkl: A = L.data.tocsr() A.sort_indices() LIQ = mkl_spsolve(A, Q.toarray()) else: pspec = pseudo_args['permc_spec'] diag_p_thresh = pseudo_args['diag_pivot_thresh'] pseudo_args = pseudo_args['ILU_MILU'] lu = sp.linalg.splu(A, permc_spec=pspec, diag_pivot_thresh=diag_p_thresh, options=dict(ILU_MILU=pseudo_args)) LIQ = lu.solve(Q.toarray()) elif pseudo_args['method'] == 'spilu': lu = sp.linalg.spilu(A, permc_spec=pseudo_args['permc_spec'], fill_factor=pseudo_args['fill_factor'], drop_tol=pseudo_args['drop_tol']) LIQ = lu.solve(Q.toarray()) else: raise ValueError("unsupported method '%s'" % method) R = sp.csr_matrix(Q * LIQ) if pseudo_args['use_rcm']: rev_perm = np.argsort(perm) R = sp_permute(R, rev_perm, rev_perm, 'csr') return Qobj(R, dims=L.dims) def pseudo_inverse(L, rhoss=None, w=None, sparse=True, **kwargs): """ Compute the pseudo inverse for a Liouvillian superoperator, optionally given its steady state density matrix (which will be computed if not given). Returns ------- L : Qobj A Liouvillian superoperator for which to compute the pseudo inverse. rhoss : Qobj A steadystate density matrix as Qobj instance, for the Liouvillian superoperator L. w : double frequency at which to evaluate pseudo-inverse. Can be zero for dense systems and large sparse systems. Small sparse systems can fail for zero frequencies. sparse : bool Flag that indicate whether to use sparse or dense matrix methods when computing the pseudo inverse. method : string Name of method to use. For sparse=True, allowed values are 'spsolve', 'splu' and 'spilu'. For sparse=False, allowed values are 'direct' and 'numpy'. kwargs : dictionary Additional keyword arguments for setting parameters for solver methods. Returns ------- R : Qobj Returns a Qobj instance representing the pseudo inverse of L. Note ---- In general the inverse of a sparse matrix will be dense. If you are applying the inverse to a density matrix then it is better to cast the problem as an Ax=b type problem where the explicit calculation of the inverse is not required. See page 67 of "Electrons in nanostructures" C. Flindt, PhD Thesis available online: http://orbit.dtu.dk/fedora/objects/orbit:82314/datastreams/ file_4732600/content Note also that the definition of the pseudo-inverse herein is different from numpys pinv() alone, as it includes pre and post projection onto the subspace defined by the projector Q. """ pseudo_args = _default_steadystate_args() for key in kwargs.keys(): if key in pseudo_args.keys(): pseudo_args[key] = kwargs[key] else: raise Exception( "Invalid keyword argument '"+key+"' passed to pseudo_inverse.") if 'method' not in kwargs.keys(): pseudo_args['method'] = 'splu' # Set column perm to NATURAL if using RCM and not specified by user if pseudo_args['use_rcm'] and ('permc_spec' not in kwargs.keys()): pseudo_args['permc_spec'] = 'NATURAL' if rhoss is None: rhoss = steadystate(L, **pseudo_args) if sparse: return _pseudo_inverse_sparse(L, rhoss, w=w, **pseudo_args) else: if pseudo_args['method'] != 'splu': pseudo_args['method'] = pseudo_args['method'] else: pseudo_args['method'] = 'direct' return _pseudo_inverse_dense(L, rhoss, w=w, **pseudo_args)