repo stringclasses 454
values | file_path stringlengths 5 201 | extension stringclasses 1
value | content stringlengths 8 509k | num_lines int64 3 16.9k | size_bytes int64 8 511k |
|---|---|---|---|---|---|
scikit-bio | skbio/io/format/tests/test_fasta.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,096 | 48,483 |
scikit-bio | skbio/io/format/tests/test_phylip_dm.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 346 | 15,279 |
scikit-bio | skbio/io/format/tests/test_binary_dm.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 165 | 6,075 |
scikit-bio | skbio/io/tests/test_registry.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 1,765 | 58,616 |
scikit-bio | skbio/io/tests/test_util.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 641 | 23,864 |
scikit-bio | skbio/io/tests/test_descriptors.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 669 | 25,411 |
scikit-bio | skbio/io/tests/test_iosources.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 61 | 1,953 |
scikit-bio | skbio/io/tests/test_format_imports.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 150 | 5,565 |
scikit-bio | doc/metatag.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 69 | 2,023 |
scikit-bio | doc/suburl.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 53 | 1,610 |
scikit-bio | doc/editmap.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 48 | 1,064 |
scikit-bio | doc/source/conf.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 334 | 9,253 |
scikit-bio | doc/source/autoinherit.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 85 | 2,743 |
scikit-bio | web/suburl.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 53 | 1,629 |
scikit-bio | web/conf.py | .py | # ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE.txt, distributed with this software.
# --------------------------------------------... | 121 | 3,170 |
qutip | setup.py | .py | import collections
import os
import pathlib
import subprocess
import sys
import sysconfig
import warnings
# Required third-party imports, must be specified in pyproject.toml.
import packaging.version
from setuptools import setup, Extension
import numpy as np
from Cython.Build import cythonize
from Cython.Distutils imp... | 312 | 11,650 |
qutip | doc/conf.py | .py | #
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import pathlib
import warnings
# -- General configuration ---------... | 398 | 12,486 |
qutip | doc/guide/scripts/ex_steady.py | .py | import numpy as np
import matplotlib.pyplot as plt
import qutip
# Define paramters
N = 20 # number of basis states to consider
a = qutip.destroy(N)
H = a.dag() * a
psi0 = qutip.basis(N, 10) # initial state
kappa = 0.1 # coupling to oscillator
# collapse operators
c_op_list = []
n_th_a = 2 # temperature with aver... | 46 | 1,417 |
qutip | doc/guide/scripts/bloch_ex1.py | .py | import numpy as np
import qutip
b = qutip.Bloch()
th = np.linspace(0, 2*np.pi, 20)
xp = np.cos(th)
yp = np.sin(th)
zp = np.zeros(20)
xz = np.zeros(20)
yz = np.sin(th)
zz = np.cos(th)
b.add_points([xp, yp, zp])
b.add_points([xz, yz, zz])
b.show()
| 18 | 250 |
qutip | doc/guide/scripts/spectrum_ex1.py | .py | import numpy as np
from matplotlib import pyplot
import qutip
N = 4 # number of cavity fock states
wc = wa = 1.0 * 2 * np.pi # cavity and atom frequency
g = 0.1 * 2 * np.pi # coupling strength
kappa = 0.75 # cavity dissipation rate
gamma = 0.25 # atom dissipatio... | 49 | 1,759 |
qutip | doc/guide/scripts/correlation_ex1.py | .py | import numpy as np
import matplotlib.pyplot as plt
import qutip
times = np.linspace(0, 10, 200)
a = qutip.destroy(10)
x = a.dag() + a
H = a.dag() * a
corr1 = qutip.correlation_2op_1t(H, None, times, [np.sqrt(0.5) * a], x, x)
corr2 = qutip.correlation_2op_1t(H, None, times, [np.sqrt(1.0) * a], x, x)
corr3 = qutip.corr... | 18 | 542 |
qutip | doc/guide/scripts/correlation_ex3.py | .py | import numpy as np
import matplotlib.pyplot as plt
import qutip
N = 15
taus = np.linspace(0,10.0,200)
a = qutip.destroy(N)
H = 2 * np.pi * a.dag() * a
# collapse operator
G1 = 0.75
n_th = 2.00 # bath temperature in terms of excitation number
c_ops = [np.sqrt(G1 * (1 + n_th)) * a, np.sqrt(G1 * n_th) * a.dag()]
# sta... | 34 | 980 |
qutip | doc/guide/scripts/floquet_ex3.py | .py | import numpy as np
from matplotlib import pyplot
import qutip
delta = 0.0 * 2*np.pi
eps0 = 1.0 * 2*np.pi
A = 0.25 * 2*np.pi
omega = 1.0 * 2*np.pi
T = 2*np.pi / omega
tlist = np.linspace(0.0, 20 * T, 301)
psi0 = qutip.basis(2,0)
H0 = - delta/2.0 * qutip.sigmax() - eps0/2.0 * qutip.sigmaz()
H1 = A/2.0 * q... | 53 | 1,600 |
qutip | doc/guide/scripts/ex_bloch_animation.py | .py | import numpy as np
import qutip
def qubit_integrate(w, theta, gamma1, gamma2, psi0, tlist):
# operators and the hamiltonian
sx = qutip.sigmax()
sy = qutip.sigmay()
sz = qutip.sigmaz()
sm = qutip.sigmam()
H = w * (np.cos(theta) * sz + np.sin(theta) * sx)
# collapse operators
c_op_list = ... | 35 | 1,267 |
qutip | doc/guide/scripts/floquet_ex1.py | .py | import numpy as np
from matplotlib import pyplot
import qutip
delta = 0.2 * 2*np.pi
eps0 = 1.0 * 2*np.pi
A = 0.5 * 2*np.pi
omega = 1.0 * 2*np.pi
T = (2*np.pi)/omega
tlist = np.linspace(0.0, 10 * T, 101)
psi0 = qutip.basis(2, 0)
H0 = - delta/2.0 * qutip.sigmax() - eps0/2.0 * qutip.sigmaz()
H1 = A/2.0 * q... | 41 | 1,320 |
qutip | doc/guide/scripts/correlation_ex4.py | .py | import numpy as np
import matplotlib.pyplot as plt
import qutip
N = 25
taus = np.linspace(0, 25.0, 200)
a = qutip.destroy(N)
H = 2 * np.pi * a.dag() * a
kappa = 0.25
n_th = 2.0 # bath temperature in terms of excitation number
c_ops = [np.sqrt(kappa * (1 + n_th)) * a, np.sqrt(kappa * n_th) * a.dag()]
states = [
... | 39 | 1,102 |
qutip | doc/guide/scripts/correlation_ex2.py | .py | import numpy as np
import matplotlib.pyplot as plt
import qutip
times = np.linspace(0, 10.0, 200)
a = qutip.destroy(10)
x = a.dag() + a
H = a.dag() * a
alpha = 2.5
rho0 = qutip.coherent_dm(10, alpha)
corr = qutip.correlation_2op_2t(H, rho0, times, times, [np.sqrt(0.25) * a], x, x)
plt.pcolor(np.real(corr))
plt.xlabel... | 18 | 423 |
qutip | doc/guide/scripts/floquet_ex2.py | .py | import numpy as np
from matplotlib import pyplot
import qutip
delta = 0.0 * 2*np.pi
eps0 = 1.0 * 2*np.pi
A = 0.25 * 2*np.pi
omega = 1.0 * 2*np.pi
T = 2*np.pi / omega
tlist = np.linspace(0.0, 10 * T, 101)
psi0 = qutip.basis(2,0)
H0 = - delta/2.0 * qutip.sigmax() - eps0/2.0 * qutip.sigmaz()
H1 = A/2.0 * q... | 40 | 1,335 |
qutip | qutip/qip.py | .py | """Module replicating the qutip_qip package from within qutip."""
import sys
try:
import qutip_qip
del qutip_qip
sys.modules["qutip.qip"] = sys.modules["qutip_qip"]
except ImportError:
raise ImportError(
"Importing 'qutip.qip' requires the 'qutip_qip' package. Install it "
"with `pip in... | 14 | 416 |
qutip | qutip/partial_transpose.py | .py | __all__ = ['partial_transpose']
import numpy as np
import scipy.sparse as sp
from . import (
Qobj, state_index_number, state_number_index, state_number_enumerate,
)
from .core.dimensions import flatten
def partial_transpose(rho, mask, method='dense'):
"""
Return the partial transpose of a Qobj instance ... | 122 | 3,622 |
qutip | qutip/animation.py | .py | """
Functions to animate results of quantum dynamics simulations,
"""
__all__ = ['anim_wigner_sphere', 'anim_hinton', 'anim_sphereplot',
'anim_matrix_histogram', 'anim_fock_distribution', 'anim_wigner',
'anim_spin_distribution', 'anim_qubism', 'anim_schmidt',
'anim_qfunc']
from . impor... | 639 | 21,100 |
qutip | qutip/random_objects.py | .py | """
This module is a collection of random state and operator generators.
"""
__all__ = [
'rand_herm',
'rand_unitary',
'rand_dm',
'rand_stochastic',
'rand_ket',
'rand_kraus_map',
'rand_super',
"rand_super_bcsz",
]
import numpy as np
from numpy.random import Generator, SeedSequence, defa... | 907 | 31,664 |
qutip | qutip/entropy.py | .py | __all__ = ['entropy_vn', 'entropy_linear', 'entropy_mutual', 'negativity',
'concurrence', 'entropy_conditional', 'entangling_power',
'entropy_relative']
from .core.numpy_backend import np
from .partial_transpose import partial_transpose
from . import (ptrace, tensor, sigmay, ket2dm,
... | 386 | 11,101 |
qutip | qutip/measurement.py | .py | """
Module for measuring quantum objects.
"""
__all__ = [
'measurement_statistics_povm',
'measurement_statistics_observable',
'measure_observable',
'measure_povm',
'measurement_statistics',
'measure'
]
import numpy as np
from . import Qobj, expect, qeye_like, settings
def _verify_input(op, ... | 448 | 14,593 |
qutip | qutip/visualization.py | .py | """
Functions for visualizing results of quantum dynamics simulations,
visualizations of quantum states and processes.
"""
__all__ = ['plot_wigner_sphere', 'hinton', 'sphereplot',
'matrix_histogram', 'plot_energy_levels', 'plot_fock_distribution',
'plot_wigner', 'plot_qfunc', 'plot_expectation_va... | 2,115 | 65,494 |
qutip | qutip/distributions.py | .py | """
This module provides classes and functions for working with spatial
distributions, such as Wigner distributions, etc.
.. note::
Experimental.
"""
__all__ = ['Distribution', 'HarmonicOscillatorWaveFunction',
'HarmonicOscillatorProbabilityFunction']
import numpy as np
from numpy.typing import Arra... | 533 | 18,209 |
qutip | qutip/fileio.py | .py | __all__ = ['file_data_store', 'file_data_read', 'qsave', 'qload']
import pickle
import numpy as np
from .core import Qobj
from pathlib import Path
# -----------------------------------------------------------------------------
# Write matrix data to a file
#
def file_data_store(filename, data, numtype="complex", num... | 236 | 7,117 |
qutip | qutip/ipynbtools.py | .py | """
This module contains utility functions for using QuTiP with IPython notebooks.
"""
from qutip.ui.progressbar import HTMLProgressBar
from .settings import _blas_info, available_cpu_count
import IPython
from IPython.display import HTML, display
import matplotlib.pyplot as plt
from matplotlib import animation
from ba... | 317 | 10,033 |
qutip | qutip/utilities.py | .py | """
This module contains utility functions that are commonly needed in other
qutip modules.
"""
# Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['n_thermal', 'clebsch', 'convert_unit', 'iterated_fit']
import math
from fractions import Fraction
from typing import Call... | 1,019 | 31,492 |
qutip | qutip/bloch.py | .py | __all__ = ['Bloch']
from pathlib import Path
from typing import Literal
import numpy as np
from numpy import cos, ones, outer, sin
from packaging.version import parse as parse_version
from . import Qobj, expect, sigmax, sigmay, sigmaz
try:
import matplotlib
import matplotlib.pyplot as plt
from matplotli... | 1,055 | 40,243 |
qutip | qutip/matplotlib_utilities.py | .py | """
This module contains utility functions that enhance Matplotlib
in one way or another.
"""
__all__ = ['wigner_cmap', 'MidpointNorm', 'complex_phase_cmap']
import numpy as np
try:
import matplotlib as mpl
from matplotlib import cm
from matplotlib.colors import Normalize, ColorConverter
except ImportEr... | 156 | 5,594 |
qutip | qutip/wigner.py | .py | __all__ = [
'wigner', 'qfunc', 'QFunc', 'spin_q_function', 'spin_wigner',
'wigner_transform',
]
import numpy as np
import warnings
from numpy import (
zeros, array, arange, exp, real, conj, pi, copy, sqrt, meshgrid, cos, sin,
)
import scipy.sparse as sp
import scipy.fftpack as ft
import scipy.linalg as la
... | 1,111 | 38,676 |
qutip | qutip/testing.py | .py | from .about import about
from .settings import settings as qset
def run(full=False):
"""
Run the test scripts for QuTiP.
Parameters
----------
full: bool
If True run all test (30 min). Otherwise skip few variants of the
slowest tests.
"""
# Call about to get all version inf... | 35 | 1,016 |
qutip | qutip/continuous_variables.py | .py | """
This module contains a collection functions for calculating continuous variable
quantities from fock-basis representation of the state of multi-mode fields.
"""
__all__ = ['correlation_matrix', 'covariance_matrix',
'correlation_matrix_field', 'correlation_matrix_quadrature',
'wigner_covarianc... | 260 | 8,524 |
qutip | qutip/control.py | .py | """Module replicating the qutip_qtrl package from within qutip."""
import sys
try:
import qutip_qtrl
del qutip_qtrl
sys.modules["qutip.control"] = sys.modules["qutip_qtrl"]
except ImportError:
raise ImportError(
"Importing 'qutip.control' requires the 'qutip_qtrl' package. "
"Install it... | 14 | 431 |
qutip | qutip/tomography.py | .py | __all__ = ['qpt_plot', 'qpt_plot_combined', 'qpt']
from numpy import hstack, real, imag
import scipy.linalg as la
from . import tensor, spre, spost, stack_columns, unstack_columns
from .visualization import matrix_histogram
import itertools
try:
import matplotlib.pyplot as plt
except ImportError:
pass
def _... | 190 | 5,326 |
qutip | qutip/cite.py | .py | """
Citation generator for QuTiP
"""
from pathlib import Path
__all__ = ['cite']
def cite(save=False, path=None):
"""
Citation information and bibtex generator for QuTiP
Parameters
----------
save: bool
The flag specifying whether to save the .bib file.
path: str
The complet... | 55 | 1,413 |
qutip | qutip/settings.py | .py | """
This module contains settings for the QuTiP graphics, multiprocessing, and
tidyup functionality, etc.
"""
import os
import sys
from ctypes import cdll, CDLL
import platform
from glob import glob
from pathlib import Path
import numpy as np
import scipy
__all__ = ['settings']
def _blas_info_pre_1_26():
config ... | 362 | 10,593 |
qutip | qutip/typing.py | .py | from typing import Sequence, Union, Any, Protocol, Callable, TypeVar
from numbers import Number, Real
import numpy as np
import scipy.interpolate
__all__ = ["QobjEvoLike", "CoefficientLike", "LayerType"]
class QEvoProtocol(Protocol):
def __call__(self, t: Real, **kwargs) -> "Qobj":
...
class CoeffProt... | 56 | 1,050 |
qutip | qutip/about.py | .py | """
Command line output of information on QuTiP and dependencies.
"""
__all__ = ['about']
import sys
import importlib.metadata
import platform
from pathlib import Path
import numpy
import scipy
import inspect
import qutip
from qutip.settings import _blas_info, settings
def about():
"""
About box for QuTiP. G... | 99 | 3,147 |
qutip | qutip/simdiag.py | .py | __all__ = ['simdiag']
import numpy as np
import scipy.linalg as la
from . import Qobj
from .core import data as _data
def _degen(tol, vecs, ops, i=0):
"""
Private function that finds eigen vals and vecs for degenerate matrices..
"""
if len(ops) == i:
return vecs
# New eigenvectors are so... | 135 | 4,334 |
qutip | qutip/solver/options.py | .py | __all__ = []
import warnings
import weakref
class _SolverOptions(dict):
"""
Class to hold options for solver and integrator.
Parameters
----------
default : dict
Default dict, only keys in this will be accepted.
on_update : callable, ``f(keys : set) -> None``, optional
Functi... | 117 | 3,472 |
qutip | qutip/solver/brmesolve.py | .py | """
This module provides solvers for the Lindblad master equation and von Neumann
equation.
"""
# Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['brmesolve', 'BRSolver']
from typing import Any
import warnings
import numpy as np
from numpy.typing import ArrayLike
impor... | 419 | 15,988 |
qutip | qutip/solver/mesolve.py | .py | """
This module provides solvers for the Lindblad master equation and von Neumann
equation.
"""
# Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['mesolve', 'MESolver']
from numpy.typing import ArrayLike
from typing import Any
from time import time
from .. import Qobj... | 306 | 11,773 |
qutip | qutip/solver/_feedback.py | .py | from qutip.core.cy.qobjevo import QobjEvo, _Feedback
from qutip.core.dimensions import Dimensions, Field, SuperSpace
import qutip.core.data as _data
from qutip.core.qobj import Qobj
import numpy as np
class _ExpectFeedback(_Feedback):
def __init__(self, oper, default=0.):
self.oper = QobjEvo(oper)
... | 151 | 4,542 |
qutip | qutip/solver/floquet.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = [
"FloquetBasis",
"floquet_tensor",
"fsesolve",
"fmmesolve",
"FMESolver",
]
from typing import Any, overload, TypeVar, Literal, Callable
import warnings
import numpy as np
from numpy.typing import Arr... | 1,045 | 33,994 |
qutip | qutip/solver/sesolve.py | .py | """
This module provides solvers for the unitary Schrodinger equation.
"""
# Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['sesolve', 'SESolver']
from numpy.typing import ArrayLike
from time import time
from typing import Any, Callable
from .. import Qobj, QobjEvo
f... | 239 | 8,749 |
qutip | qutip/solver/parallel.py | .py | """
This module provides functions for parallel execution of loops and function
mappings, using the builtin Python module multiprocessing or the loky parallel
execution library.
"""
__all__ = ['parallel_map', 'serial_map', 'loky_pmap', 'mpi_pmap']
import multiprocessing
import os
import sys
import time
import threadin... | 560 | 21,085 |
qutip | qutip/solver/solver_base.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['Solver']
from numpy.typing import ArrayLike
from numbers import Number
from typing import Any, Callable
from .. import Qobj, QobjEvo, ket2dm
from .options import _SolverOptions
from ..core import stack_columns, unstack... | 513 | 17,920 |
qutip | qutip/solver/krylovsolve.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['krylovsolve']
from .. import QobjEvo, Qobj
from .mesolve import mesolve
from .result import Result
from numpy.typing import ArrayLike
from qutip.typing import QobjEvoLike
from typing import Any, Callable
def krylovso... | 128 | 5,356 |
qutip | qutip/solver/spectrum.py | .py | __all__ = ['spectrum', 'spectrum_correlation_fft']
import numpy as np
import scipy.fftpack
from .steadystate import steadystate
from ..core import liouvillian, spre, expect
from ..core import data as _data
from qutip.settings import settings
def spectrum(H, wlist, c_ops, a_op, b_op, solver="es"):
r"""
Calcul... | 189 | 6,193 |
qutip | qutip/solver/multitraj.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
from .result import Result
from .multitrajresult import MultiTrajResult
from .parallel import _get_map
from time import time
from .solver_base import Solver
from ..core import QobjEvo, Qobj
from ..core.numpy_backend import np
from ... | 524 | 20,126 |
qutip | qutip/solver/result.py | .py | """ Class for solve function results"""
# Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
from typing import TypedDict, Any, Callable
from ..core.numpy_backend import np
from numpy.typing import ArrayLike
from ..core import Qobj, QobjEvo, expect
__all__ = ["Result"]
class _Qob... | 523 | 16,829 |
qutip | qutip/solver/floquet_bwcomp.py | .py | """ Floquet solver compatibility functions that behave like the corresponding
functions from QuTiP 4.7.
These functions are indented to be used when porting code from QuTiP 4.7 to
QuTiP 5. They are deprecated and will be removed in QuTiP 5.1.
"""
__all__ = [
"floquet_modes",
"floquet_modes_t",
"floquet_mo... | 245 | 7,660 |
qutip | qutip/solver/countstat.py | .py | """
This module contains functions for calculating current and current noise using
the counting statistics formalism.
"""
__all__ = ['countstat_current', 'countstat_current_noise']
import numpy as np
from itertools import product
from ..core import (
sprepost, spre, qeye_like, Qobj, operator_to_vector, CoreOption... | 333 | 11,304 |
qutip | qutip/solver/scattering.py | .py | """
Photon scattering in quantum optical systems
This module includes a collection of functions for numerically computing photon
scattering in driven arbitrary systems coupled to some configuration of output
waveguides. The implementation of these functions closely follows the
mathematical treatment given in K.A. Fisc... | 303 | 11,346 |
qutip | qutip/solver/mcsolve.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['mcsolve', "MCSolver"]
from ..core.numpy_backend import np
from numpy.typing import ArrayLike
from numpy.random import SeedSequence
from time import time
from typing import Any
import warnings
from .. import settings
f... | 986 | 39,590 |
qutip | qutip/solver/dysolve_propagator.py | .py | from qutip import Qobj, qeye_like
from .cy.dysolve import cy_compute_integrals
from numpy.typing import ArrayLike
import numpy as np
import scipy as sp
from numbers import Number
import itertools
__all__ = ['DysolvePropagator', 'dysolve_propagator']
class DysolvePropagator:
"""
A generator of propagator usi... | 373 | 10,952 |
qutip | qutip/solver/stochastic.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ["smesolve", "SMESolver", "ssesolve", "SSESolver"]
import numpy as np
from numpy.typing import ArrayLike
from numpy.random import SeedSequence
from typing import Any, Callable, Literal, overload
from functools import par... | 1,136 | 41,390 |
qutip | qutip/solver/steadystate.py | .py | from qutip import liouvillian, lindblad_dissipator, Qobj, qzero_like, qeye_like
from qutip import vector_to_operator, operator_to_vector, hilbert_dist
from qutip import settings, CoreOptions
import qutip.core.data as _data
import numpy as np
import scipy.sparse.csgraph
import scipy.sparse.linalg
from warnings import wa... | 613 | 21,055 |
qutip | qutip/solver/propagator.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['Propagator', 'propagator', 'propagator_steadystate']
import numbers
import numpy as np
from .. import Qobj, qeye, qeye_like, unstack_columns, QobjEvo, liouvillian
from ..core import data as _data
from ..typing import ... | 435 | 14,504 |
qutip | qutip/solver/correlation.py | .py | __all__ = [
'correlation_3op',
'correlation_2op_1t', 'correlation_2op_2t', 'correlation_3op_1t',
'correlation_3op_2t', 'coherence_function_g1', 'coherence_function_g2'
]
import numpy as np
from ..core import (
Qobj, QobjEvo, liouvillian, spre, unstack_columns, stack_columns,
tensor, expect, qeye_l... | 631 | 23,204 |
qutip | qutip/solver/nm_mcsolve.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['nm_mcsolve', 'NonMarkovianMCSolver']
import numbers
from typing import Any
from collections.abc import Sequence
import numpy as np
from numpy.typing import ArrayLike
from numpy.random import SeedSequence
import scipy
... | 687 | 27,288 |
qutip | qutip/solver/multitrajresult.py | .py | """
This module provides result classes for multi-trajectory solvers.
Note that single trajectories are described by regular `Result` objects from the
`qutip.solver.result` module.
"""
# Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
from typing import TypedDict
from ..core.numpy... | 1,796 | 64,101 |
qutip | qutip/solver/heom/bofin_baths.py | .py | """
This module provides utilities for describing baths when using the HEOM
(hierarchy equations of motion) to model system-bath interactions. See the
``qutip.nonmarkov.bofin_solvers`` module for the associated solver.
The implementation is derived from the BoFiN library (see
https://github.com/tehruhn/bofin) which wa... | 803 | 29,136 |
qutip | qutip/solver/heom/__init__.py | .py | """
This module provides solvers for system-bath evolution using the
HEOM (hierarchy equations of motion).
See https://en.wikipedia.org/wiki/Hierarchical_equations_of_motion for a very
basic introduction to the technique.
The implementation is derived from the BoFiN library (see
https://github.com/tehruhn/bofin) whic... | 56 | 1,314 |
qutip | qutip/solver/heom/bofin_solvers.py | .py | """
This module provides solvers for system-bath evoluation using the
HEOM (hierarchy equations of motion).
See https://en.wikipedia.org/wiki/Hierarchical_equations_of_motion for a very
basic introduction to the technique.
The implementation is derived from the BoFiN library (see
https://github.com/tehruhn/bofin) whi... | 1,411 | 52,376 |
qutip | qutip/solver/integrator/integrator.py | .py | """ `Integrator`: ODE solver wrapper to use in qutip's Solver """
import numpy as np
from collections.abc import Iterator, Callable
from qutip.core import QobjEvo
from ._rhs import RHS
from qutip.core.data import Data
__all__ = ['Integrator', 'IntegratorException']
class IntegratorException(Exception):
"""Error ... | 241 | 7,804 |
qutip | qutip/solver/integrator/verner7efficient.py | .py | """
Provide a cython implimentation verner 'most-efficient'
order 7 runge-Kutta method.
See https://www.sfu.ca/~jverner/
"""
# Verner 7 Efficient
# https://www.sfu.ca/~jverner/RKV76.IIa.Efficient.00001675585.081206.CoeffsOnlyFLOAT
__all__ = ["vern7_coeff"]
import numpy as np
order = 7
rk_step = 10
rk_extra_step = 16
de... | 334 | 11,985 |
qutip | qutip/solver/integrator/krylov.py | .py | import numpy as np
from qutip.core import data as _data
from ..integrator import IntegratorException, Integrator
from ..sesolve import SESolver
from ..mesolve import MESolver
__all__ = ["IntegratorKrylov"]
class IntegratorKrylov(Integrator):
"""
Evolve the state ("rho0") finding an approximation for the tim... | 345 | 12,577 |
qutip | qutip/solver/integrator/tsit5.py | .py | """
Tsitouras's 5/4 order Runge-Kutta method
Runge–Kutta pairs of order 5(4) satisfying only the first column
simplifying assumption,
Ch. Tsitouras,
Computers & Mathematics with Applications, Vol 62, Issue 2, 770-775
Jan 2011
"""
__all__ = ["tsit5_coeff"]
import numpy as np
order = 5
rk_step = 7
a = np.zeros((rk_ste... | 104 | 2,241 |
qutip | qutip/solver/integrator/qutip_integrator.py | .py | from ..integrator import IntegratorException, Integrator
from ..solver_base import Solver
from .explicit_rk import Explicit_RungeKutta
import numpy as np
from qutip import data as _data
from .verner7efficient import vern7_coeff
from .verner9efficient import vern9_coeff
from .tsit5 import tsit5_coeff
__all__ = [
'I... | 256 | 7,667 |
qutip | qutip/solver/integrator/verner9efficient.py | .py | """
Provide a cython implimentation verner 'most-efficient'
order 9 runge-Kutta method.
See https://www.sfu.ca/~jverner/
"""
# Verner 9 Efficient
# https://www.sfu.ca/~jverner/
__all__ = ["vern9_coeff"]
import numpy as np
order = 9
rk_step = 16
rk_extra_step = 26
denseout_order = 9
bh = np.zeros(rk_step, dtype=np.flo... | 707 | 24,555 |
qutip | qutip/solver/integrator/scipy_integrator.py | .py | """ODE integrator from scipy."""
__all__ = [
'IntegratorScipyAdams',
'IntegratorScipyBDF',
'IntegratorScipyDop853',
'IntegratorScipylsoda',
]
import numpy as np
from scipy.integrate import ode
from scipy.integrate._ode import zvode
from qutip.core import data as _data
from qutip.core.data.reshape impo... | 537 | 18,739 |
qutip | qutip/solver/sode/sode.py | .py | import numpy as np
import warnings
from . import _sode
from ..integrator.integrator import Integrator
from ..stochastic import StochasticSolver, SMESolver
from ._noise import Wiener, PreSetWiener
__all__ = ["SIntegrator", "PlatenSODE", "PredCorr_SODE"]
class SIntegrator(Integrator):
"""
A wrapper around stoc... | 312 | 9,356 |
qutip | qutip/solver/sode/rouchon.py | .py | import numpy as np
import warnings
from qutip import unstack_columns, stack_columns
from qutip.core import data as _data
from ..stochastic import StochasticSolver
from .sode import SIntegrator
from ..integrator.integrator import Integrator
from ._noise import Wiener
__all__ = ["RouchonSODE"]
class RouchonSODE(SInte... | 206 | 6,638 |
qutip | qutip/solver/sode/_noise.py | .py | import numpy as np
__all__ = ["Wiener", "PreSetWiener"]
class Wiener:
"""
Wiener process.
"""
def __init__(self, t0, dt, generator, shape):
self.t0 = t0
self.dt = dt
self.shape = shape
self.generator = generator
self.noise = np.zeros((0,) + shape, dtype=float)
... | 145 | 4,447 |
qutip | qutip/solver/sode/itotaylor.py | .py | from . import _sode
from .sode import _Explicit_Simple_Integrator, _Implicit_Simple_Integrator
from ..stochastic import StochasticSolver, SMESolver
__all__ = [
"EulerSODE", "Milstein_SODE", "Taylor1_5_SODE", "Explicit1_5_SODE",
"Implicit_Milstein_SODE", "Implicit_Taylor1_5_SODE"
]
class EulerSODE(_Explicit_... | 171 | 5,193 |
qutip | qutip/solver/nonmarkov/transfertensor.py | .py | # @author: Arne L. Grimsmo
# @email1: arne.grimsmo@gmail.com
# @organization: University of Sherbrooke
"""
This module contains an implementation of the non-Markovian transfer tensor
method (TTM), introduced in [1].
[1] Javier Cerrillo and Jianshu Cao, Phys. Rev. Lett 112, 110401 (2014)
"""
import numpy as np
import... | 176 | 5,420 |
qutip | qutip/core/direct_sum.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
from . import data as _data
from .cy.qobjevo import QobjEvo
from .dimensions import Dimensions, Field, SumSpace
from .operators import qzero
from .qobj import Qobj
from .superoperator import operator_to_vector
from .. import setti... | 704 | 25,315 |
qutip | qutip/core/options.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
from ..settings import settings
from .numpy_backend import np as qt_np
import numpy
from typing import overload, Literal, Any
import types
__all__ = ["CoreOptions"]
class QutipOptions:
"""
Class for basic functionality f... | 269 | 8,893 |
qutip | qutip/core/blochredfield.py | .py | # Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
import os
import inspect
import numpy as np
from typing import overload, Union
from qutip.settings import settings as qset
from . import Qobj, QobjEvo, liouvillian, coefficient, sprepost
from ._brtools import SpectraCoefficient, _... | 428 | 15,144 |
qutip | qutip/core/numpy_backend.py | .py | from ..settings import settings
class NumpyBackend:
__slots__ = (
"_qt_np",
"abs",
"angle",
"arccos",
"array",
"ceil",
"conj",
"cos",
"cumsum",
"diff",
"e",
"histogram",
"imag",
"inf",
"inner",
... | 52 | 934 |
qutip | qutip/core/tensor.py | .py | """
Module for the creation of composite quantum objects via the tensor product.
"""
__all__ = [
'tensor', 'super_tensor', 'composite', 'tensor_swap', 'tensor_contract',
'expand_operator'
]
from collections.abc import Iterable
from functools import partial
from typing import TypeVar, overload
import numpy as ... | 518 | 17,164 |
qutip | qutip/core/environment.py | .py | """
Classes that describe environments of open quantum systems
"""
# Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = ['BosonicEnvironment',
'DrudeLorentzEnvironment',
'UnderDampedEnvironment',
'OhmicEnvironment',
'ExponentialB... | 3,039 | 100,827 |
qutip | qutip/core/superoperator.py | .py | __all__ = [
'liouvillian', 'lindblad_dissipator', 'operator_to_vector',
'vector_to_operator', 'stack_columns', 'unstack_columns', 'stacked_index',
'unstacked_index', 'spost', 'spre', 'sprepost', 'reshuffle', 'scommutator',
'santicommutator'
]
import functools
from typing import TypeVar, overload
import... | 598 | 19,322 |
qutip | qutip/core/local_matmul.py | .py | from .qobj import Qobj
from .data.local_matmul import target_mode_matmul, target_mode_matmul_super
__all__ = ["local_matmul"]
def local_matmul(
operator: Qobj,
state: Qobj,
modes: int | list[int],
dual: bool = False
) -> Qobj:
"""
Applies an operator to specific modes of a quantum state or o... | 188 | 6,372 |
qutip | qutip/core/superop_reps.py | .py | #
# This module was initially contributed by Ben Criger.
#
"""
This module implements transformations between superoperator representations,
including supermatrix, Kraus, Choi and Chi (process) matrix formalisms.
"""
from __future__ import annotations
__all__ = [
'kraus_to_choi', 'kraus_to_super', 'to_superpauli',... | 613 | 19,894 |
qutip | qutip/core/operators.py | .py | """
This module contains functions for generating Qobj representation of a variety
of commonly occuring quantum operators.
"""
# Required for Sphinx to follow autodoc_type_aliases
from __future__ import annotations
__all__ = [
'jmat', 'spin_Jx', 'spin_Jy', 'spin_Jz', 'spin_Jm', 'spin_Jp',
'spin_J_set', 'sigmap... | 1,317 | 35,255 |
qutip | qutip/core/semidefinite.py | .py | """
This module implements internal-use functions for semidefinite programming.
"""
import collections
import functools
import numpy as np
import scipy.sparse as sp
# Conditionally import CVXPY
try:
import cvxpy
__all__ = ["dnorm_problem", "dnorm_sparse_problem"]
except ImportError:
cvxpy = None
__al... | 162 | 4,886 |
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