keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
2D | dean0x7d/pybinding | pybinding/pltutils.py | .py | 14,833 | 517 | """Collection of utility functions for matplotlib"""
import warnings
from contextlib import contextmanager, suppress
import numpy as np
import matplotlib as mpl
import matplotlib.style as mpl_style
import matplotlib.pyplot as plt
from .utils import with_defaults
__all__ = ['cm2inch', 'colorbar', 'despine', 'despine_... | Python |
2D | dean0x7d/pybinding | pybinding/chebyshev.py | .py | 22,251 | 583 | """Computations based on Chebyshev polynomial expansion
The kernel polynomial method (KPM) can be used to approximate various functions by expanding them
in a series of Chebyshev polynomials.
"""
import warnings
import numpy as np
import scipy
from . import _cpp
from . import results
from .model import Model
from .s... | Python |
2D | dean0x7d/pybinding | pybinding/modifier.py | .py | 18,397 | 538 | """Modifier function decorators
Used to create functions which express some feature of a tight-binding model,
such as various fields, defects or geometric deformations.
"""
import inspect
import functools
import warnings
import numpy as np
from . import _cpp
from .system import Sites
from .support.inspect import get... | Python |
2D | dean0x7d/pybinding | pybinding/model.py | .py | 5,858 | 163 | """Main model definition interface"""
import numpy as np
from scipy.sparse import csr_matrix
from . import _cpp
from . import results
from .system import System, decorate_structure_plot
from .lattice import Lattice
from .leads import Leads
__all__ = ['Model']
class Model(_cpp.Model):
"""Builds a Hamiltonian fro... | Python |
2D | dean0x7d/pybinding | pybinding/shape.py | .py | 10,808 | 345 | """System shape and symmetry"""
import numpy as np
import matplotlib.pyplot as plt
from . import _cpp
from . import pltutils
from .utils import with_defaults
__all__ = ['FreeformShape', 'Polygon', 'CompositeShape',
'circle', 'line', 'primitive', 'rectangle', 'regular_polygon',
'translational_sym... | Python |
2D | dean0x7d/pybinding | pybinding/results.py | .py | 36,387 | 1,051 | """Processing and presentation of computed data
Result objects hold computed data and offer postprocessing and plotting functions
which are specifically adapted to the nature of the stored data.
"""
from copy import copy
import numpy as np
import matplotlib.pyplot as plt
from . import pltutils
from .utils import wit... | Python |
2D | dean0x7d/pybinding | pybinding/__init__.py | .py | 3,159 | 79 | from .__about__ import (__author__, __copyright__, __doc__, __email__, __license__, __summary__,
__title__, __url__, __version__)
import os
import sys
if sys.platform.startswith("linux"):
# When the _pybinding C++ extension is compiled with MKL, it requires specific
# dlopen flags on Li... | Python |
2D | dean0x7d/pybinding | pybinding/solver.py | .py | 17,892 | 489 | """Eigensolvers with a few extra computation methods
The :class:`.Solver` class is the main interface for dealing with eigenvalue problems. It
is made to work specifically with pybinding's :class:`.Model` objects, but it may use any
eigensolver algorithm under the hood.
A few different algorithms are provided out of ... | Python |
2D | dean0x7d/pybinding | pybinding/constants.py | .py | 749 | 28 | """A few useful physical constants
Note that energy is expressed in units of eV.
"""
from math import pi
import numpy as np
c = 299792458 #: [m/s] speed of light
e = 1.602 * 10**-19 #: [C] electron charge
epsilon0 = 8.854 * 10**-12 #: [F/m] vacuum permittivity
hbar = 6.58211899 * 10**-16 #: [eV*s] reduced Plank c... | Python |
2D | dean0x7d/pybinding | pybinding/lattice.py | .py | 20,663 | 559 | """Crystal lattice specification"""
import itertools
import warnings
from copy import deepcopy
from math import pi, atan2, sqrt
import numpy as np
import matplotlib.pyplot as plt
from . import _cpp
from . import pltutils
from .utils import x_pi, with_defaults, rotate_axes
from .support.deprecated import LoudDeprecati... | Python |
2D | dean0x7d/pybinding | pybinding/system.py | .py | 19,487 | 526 | """Structural information and utilities"""
import functools
import itertools
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from . import _cpp
from . import pltutils
from .lattice import Lattice
from .utils import with_defaults, rotate_axes
from .support.alias imp... | Python |
2D | dean0x7d/pybinding | pybinding/greens.py | .py | 577 | 22 | """Green's function computation and related methods
Deprecated: use the chebyshev module instead
"""
import warnings
from . import chebyshev
from .support.deprecated import LoudDeprecationWarning
__all__ = ['Greens', 'kpm', 'kpm_cuda']
Greens = chebyshev.KPM
def kpm(*args, **kwargs):
warnings.warn("Use pb.kpm(... | Python |
2D | dean0x7d/pybinding | pybinding/leads.py | .py | 7,279 | 198 | """Lead interface for scattering models
The only way to create leads is using the :meth:`.Model.attach_lead` method.
The classes represented here are the final product of that process, listed
in :attr:`.Model.leads`.
"""
import numpy as np
import matplotlib.pyplot as plt
from math import pi
from scipy.sparse import cs... | Python |
2D | dean0x7d/pybinding | pybinding/parallel.py | .py | 13,695 | 428 | """Multi-threaded functions for parameter sweeps"""
import sys
import inspect
import itertools
from copy import copy
from functools import partial
import numpy as np
import matplotlib.pyplot as plt
from pybinding.support.inspect import get_call_signature
from . import _cpp
from .utils import cpuinfo, progressbar, dec... | Python |
2D | dean0x7d/pybinding | pybinding/repository/__init__.py | .py | 0 | 0 | null | Python |
2D | dean0x7d/pybinding | pybinding/repository/group6_tmd.py | .py | 4,432 | 112 | """Tight-binding models for group 6 transition metal dichalcogenides (TMD)."""
import re
import math
import pybinding as pb
_default_3band_params = { # from https://doi.org/10.1103/PhysRevB.88.085433
# -> a, eps1, eps2, t0, t1, t2, t11, t12, t22
"MoS2": [0.3190, 1.046, 2.104, -0... | Python |
2D | dean0x7d/pybinding | pybinding/repository/phosphorene.py | .py | 2,298 | 64 | """A single layer of black phosphorus"""
from math import pi, sin, cos
import pybinding as pb
def monolayer_4band(num_hoppings=5):
"""Monolayer phosphorene lattice using the four-band model
Parameters
----------
num_hoppings : int
Number of hopping terms to consider: from t2 to t5.
"""
... | Python |
2D | dean0x7d/pybinding | pybinding/repository/examples.py | .py | 1,000 | 50 | """Example components: lattices, shapes and modifiers
Components which aren't very useful for simulations,
but great for examples and testing.
"""
import pybinding as pb
def chain_lattice(a=1, t=-1, v=0):
"""1D lattice
Parameters
----------
a : float
Unit cell length.
t : float
H... | Python |
2D | dean0x7d/pybinding | pybinding/repository/graphene/shape.py | .py | 1,168 | 32 | import math
import pybinding as pb
from .constants import a, a_cc
__all__ = ['hexagon_ac']
def hexagon_ac(side_width, lattice_offset=(-a/2, 0)):
"""A graphene-specific shape which guaranties armchair edges on all sides
Parameters
----------
side_width : float
Hexagon side width. It may be ad... | Python |
2D | dean0x7d/pybinding | pybinding/repository/graphene/__init__.py | .py | 178 | 7 | """A one-atom thick layer of carbon in a honeycomb structure"""
from . import utils
from .constants import *
from .lattice import *
from .modifiers import *
from .shape import *
| Python |
2D | dean0x7d/pybinding | pybinding/repository/graphene/constants.py | .py | 319 | 9 | from pybinding.constants import hbar
a = 0.24595 #: [nm] unit cell length
a_cc = 0.142 #: [nm] carbon-carbon distance
t = -2.8 #: [eV] nearest neighbor hopping
t_nn = 0.1 #: [eV] next-nearest neighbor hopping
vf = 3 / (2 * hbar) * abs(t) * a_cc #: [nm/s] Fermi velocity
beta = 3.37 #: strain hopping modulation
| Python |
2D | dean0x7d/pybinding | pybinding/repository/graphene/lattice.py | .py | 5,652 | 196 | import pybinding as pb
__all__ = ['monolayer', 'monolayer_alt', 'monolayer_4atom', 'bilayer']
def monolayer(nearest_neighbors=1, onsite=(0, 0), **kwargs):
"""Monolayer graphene lattice up to `nearest_neighbors` hoppings
Parameters
----------
nearest_neighbors : int
Number of nearest neighbor... | Python |
2D | dean0x7d/pybinding | pybinding/repository/graphene/utils.py | .py | 273 | 9 | from math import sqrt
from .constants import hbar, vf
def landau_level(magnetic_field: float, n: int):
""" Calculate the energy of Landau level n in the given magnetic field. """
lb = sqrt(hbar / magnetic_field)
return hbar * (vf * 10**-9) / lb * sqrt(2 * n)
| Python |
2D | dean0x7d/pybinding | pybinding/repository/graphene/modifiers.py | .py | 3,680 | 138 | import numpy as np
import pybinding as pb
from pybinding.constants import pi, phi0, hbar
__all__ = ['mass_term', 'coulomb_potential', 'constant_magnetic_field',
'triaxial_strain', 'gaussian_bump']
def mass_term(delta):
"""Break sublattice symmetry, make massive Dirac electrons, open a band gap
On... | Python |
2D | dean0x7d/pybinding | pybinding/utils/misc.py | .py | 3,785 | 151 | import os
from functools import wraps
from contextlib import contextmanager
import numpy as np
from ..support.inspect import get_call_signature
def to_tuple(o):
try:
return tuple(o)
except TypeError:
return (o,) if o is not None else ()
def to_list(o):
try:
return list(o)
e... | Python |
2D | dean0x7d/pybinding | pybinding/utils/progressbar.py | .py | 5,796 | 224 | import datetime
import io
import os
import sys
def percentage(template="{:3.0%}"):
def widget(pbar):
return template.format(pbar.percent)
return widget
def bar(marker='/', left='[', right=']', fill=' '):
def widget(pbar, width):
width -= len(left) + len(right)
marked = marker * i... | Python |
2D | dean0x7d/pybinding | pybinding/utils/__init__.py | .py | 75 | 4 | from . import cpuinfo, progressbar
from .misc import *
from .time import *
| Python |
2D | dean0x7d/pybinding | pybinding/utils/cpuinfo.py | .py | 1,702 | 65 | import os
from .. import _cpp
_cached_info = None
def cpu_info():
"""Forwarded from `cpuinfo.get_cpu_info()`"""
global _cached_info
if not _cached_info:
try:
from cpuinfo import get_cpu_info
except ImportError:
def get_cpu_info():
return {}
... | Python |
2D | dean0x7d/pybinding | pybinding/utils/time.py | .py | 2,669 | 116 | import time
__all__ = ['tic', 'toc', 'timed', 'pretty_duration']
_tic_times = []
def tic():
"""Set a start time"""
global _tic_times
_tic_times.append(time.time())
def toc(message=""):
"""Print the elapsed time from the last :func:`.tic`
Parameters
----------
message : str
Pri... | Python |
2D | dean0x7d/pybinding | pybinding/support/kwant.py | .py | 3,368 | 105 | """Kwant compatibility layer"""
import warnings
import numpy as np
try:
from kwant.system import FiniteSystem, InfiniteSystem
kwant_installed = True
except ImportError:
FiniteSystem = InfiniteSystem = object
kwant_installed = False
def _warn_if_not_empty(args, params):
if args or params:
... | Python |
2D | dean0x7d/pybinding | pybinding/support/pickle.py | .py | 2,912 | 110 | """Utility functions for getting data to/from files"""
import gzip
import os
import pathlib
import pickle
from ..utils import decorator_decorator
__all__ = ['pickleable', 'save', 'load']
def _normalize(file):
"""Convenience function to support path objects."""
if 'Path' in type(file).__name__:
retur... | Python |
2D | dean0x7d/pybinding | pybinding/support/fuzzy_set.py | .py | 1,002 | 45 | import copy
import numpy as np
__all__ = ['FuzzySet']
class FuzzySet:
def __init__(self, iterable=None, rtol=1.e-3, atol=1.e-5):
self.data = []
self.rtol = rtol
self.atol = atol
if iterable:
for item in iterable:
self.add(item)
def __getitem__(sel... | Python |
2D | dean0x7d/pybinding | pybinding/support/deprecated.py | .py | 112 | 5 |
class LoudDeprecationWarning(UserWarning):
"""Python's DeprecationWarning is silent by default"""
pass
| Python |
2D | dean0x7d/pybinding | pybinding/support/__init__.py | .py | 0 | 0 | null | Python |
2D | dean0x7d/pybinding | pybinding/support/inspect.py | .py | 4,158 | 123 | import inspect
from collections import OrderedDict
__all__ = ['CallSignature', 'get_call_signature']
class CallSignature:
"""Holds a function and the arguments it was called with"""
def __init__(self, function: callable, positional: OrderedDict,
args: tuple, keyword_only: OrderedDict, kwargs... | Python |
2D | dean0x7d/pybinding | pybinding/support/collections.py | .py | 3,143 | 85 | import numpy as np
from matplotlib.collections import Collection
from matplotlib.artist import allow_rasterization
# noinspection PyAbstractClass
class CircleCollection(Collection):
"""Custom circle collection
The default matplotlib `CircleCollection` creates circles based on their
area in screen units. ... | Python |
2D | dean0x7d/pybinding | pybinding/support/structure.py | .py | 6,913 | 244 | from abc import ABCMeta, abstractmethod
from collections import namedtuple
import numpy as np
from numpy import ma
from scipy.sparse import csr_matrix, coo_matrix
def _slice_csr_matrix(csr, idx):
"""Return a slice of a CSR matrix matching the given indices (applied to both rows and cols"""
from copy import c... | Python |
2D | dean0x7d/pybinding | pybinding/support/alias.py | .py | 6,352 | 233 | import numpy as np
from scipy.sparse import csr_matrix
class AliasArray(np.ndarray):
"""An ndarray with a mapping of values to user-friendly names -- see example
This ndarray subclass enables comparing sub_id and hop_id arrays directly with
their friendly string identifiers. The mapping parameter transla... | Python |
2D | dean0x7d/pybinding | docs/test_examples.py | .py | 710 | 24 | import pytest
import pathlib
import warnings
docs = pathlib.Path(__file__).parent
examples = list(docs.glob("tutorial/**/*.py")) + list(docs.glob("examples/**/*.py"))
assert len(examples) != 0
@pytest.fixture(scope='module', ids=[e.stem for e in examples], params=examples)
def example_file(request):
"""An examp... | Python |
2D | dean0x7d/pybinding | docs/conf.py | .py | 12,076 | 361 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import os
import shutil
import filecmp
import sphinx_rtd_theme
from recommonmark.parser import CommonMarkParser
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative... | Python |
2D | dean0x7d/pybinding | docs/benchmarks/system_build.py | .py | 6,109 | 173 | #! /usr/bin/env python3
"""Tight-binding system construction benchmark
Usage: Make sure you have all the requirements and then run this script using python3.
The considered system sizes can be changed in the `__name__ == '__main__'` section at
the bottom.
Requires Python >= 3.6 and the following packages which can be... | Python |
2D | dean0x7d/pybinding | docs/tutorial/strain_example.py | .py | 1,268 | 49 | """Strain a triangular system by pulling on its vertices"""
import pybinding as pb
import numpy as np
import matplotlib.pyplot as plt
from pybinding.repository import graphene
from math import pi
pb.pltutils.use_style()
def triaxial_strain(c):
"""Strain-induced displacement and hopping energy modification"""
... | Python |
2D | dean0x7d/pybinding | docs/tutorial/fields_example.py | .py | 1,518 | 58 | """PN junction and broken sublattice symmetry in a graphene nanoribbon"""
import pybinding as pb
import matplotlib.pyplot as plt
from pybinding.repository import graphene
from math import pi, sqrt
pb.pltutils.use_style()
def mass_term(delta):
"""Break sublattice symmetry with opposite A and B onsite energy"""
... | Python |
2D | dean0x7d/pybinding | docs/tutorial/shape_symmetry_example.py | .py | 1,480 | 55 | """Model an infinite nanoribbon consisting of graphene rings"""
import pybinding as pb
import numpy as np
import matplotlib.pyplot as plt
from pybinding.repository import graphene
from math import pi
pb.pltutils.use_style()
def ring(inner_radius, outer_radius):
"""A simple ring shape"""
def contains(x, y, z)... | Python |
2D | dean0x7d/pybinding | docs/tutorial/twisted_heterostructures.py | .py | 6,393 | 192 | """Construct a circular flake of twisted bilayer graphene (arbitrary angle)"""
import numpy as np
import matplotlib.pyplot as plt
import math
import pybinding as pb
from scipy.spatial import cKDTree
from pybinding.repository import graphene
c0 = 0.335 # [nm] graphene interlayer spacing
def two_graphene_monolayers(... | Python |
2D | dean0x7d/pybinding | docs/tutorial/bands_example.py | .py | 835 | 27 | """Calculate and plot the band structure of monolayer graphene"""
import pybinding as pb
import matplotlib.pyplot as plt
from math import sqrt, pi
from pybinding.repository import graphene
pb.pltutils.use_style()
model = pb.Model(
graphene.monolayer(), # predefined lattice from the material repository
pb.tr... | Python |
2D | dean0x7d/pybinding | docs/tutorial/finite_example.py | .py | 892 | 34 | """Model a graphene ring structure and calculate the local density of states"""
import pybinding as pb
import numpy as np
import matplotlib.pyplot as plt
from pybinding.repository import graphene
pb.pltutils.use_style()
def ring(inner_radius, outer_radius):
"""A simple ring shape"""
def contains(x, y, z):
... | Python |
2D | dean0x7d/pybinding | docs/tutorial/lattice_example.py | .py | 965 | 44 | """Create and plot a monolayer graphene lattice and it's Brillouin zone"""
import pybinding as pb
import matplotlib.pyplot as plt
from math import sqrt
pb.pltutils.use_style()
def monolayer_graphene():
"""Return the lattice specification for monolayer graphene"""
a = 0.24595 # [nm] unit cell length
a_c... | Python |
2D | dean0x7d/pybinding | docs/examples/ribbons/bilayer_graphene.py | .py | 1,484 | 48 | """Bilayer graphene nanoribbon with zigzag edges"""
import pybinding as pb
import matplotlib.pyplot as plt
from pybinding.repository import graphene
from math import pi, sqrt
pb.pltutils.use_style()
def bilayer_graphene():
"""Bilayer lattice in the AB-stacked form (Bernal-stacked)"""
lat = pb.Lattice(a1=[gra... | Python |
2D | dean0x7d/pybinding | docs/examples/lattice/monolayer_graphene_soc.py | .py | 2,087 | 71 | """Calculate the band structure of graphene with Rashba spin-orbit coupling"""
import pybinding as pb
import numpy as np
import matplotlib.pyplot as plt
from math import pi, sqrt
def monolayer_graphene_soc():
"""Return the lattice specification for monolayer graphene with Rashba SOC,
see http://doi.org/10.... | Python |
2D | dean0x7d/pybinding | docs/examples/lattice/trestle.py | .py | 737 | 38 | """One dimensional lattice with complex hoppings"""
import pybinding as pb
import matplotlib.pyplot as plt
pb.pltutils.use_style()
def trestle(d=0.2, t1=0.8 + 0.6j, t2=2):
lat = pb.Lattice(a1=1.3*d)
lat.add_sublattices(
('A', [0, 0], 0),
('B', [d/2, d], 0)
)
lat.add_hoppings(
... | Python |
2D | dean0x7d/pybinding | docs/examples/lattice/monolayer_graphene.py | .py | 1,445 | 61 | """Create and plot a monolayer graphene lattice, its Brillouin zone and band structure"""
import pybinding as pb
import matplotlib.pyplot as plt
from math import sqrt, pi
pb.pltutils.use_style()
def monolayer_graphene():
"""Return the lattice specification for monolayer graphene"""
a = 0.24595 # [nm] unit ... | Python |
2D | dean0x7d/pybinding | docs/examples/lattice/phosphorene.py | .py | 2,236 | 91 | """Create and plot a phosphorene lattice, its Brillouin zone and band structure"""
import pybinding as pb
import matplotlib.pyplot as plt
from math import pi, sin, cos
pb.pltutils.use_style()
def phosphorene_4band():
"""Monolayer phosphorene lattice using the four-band model"""
a = 0.222
ax = 0.438
a... | Python |
2D | dean0x7d/pybinding | docs/examples/lattice/checkerboard.py | .py | 801 | 36 | """Two dimensional checkerboard lattice with real hoppings"""
import pybinding as pb
import matplotlib.pyplot as plt
from math import pi
pb.pltutils.use_style()
def checkerboard(d=0.2, delta=1.1, t=0.6):
lat = pb.Lattice(a1=[d, 0], a2=[0, d])
lat.add_sublattices(
('A', [0, 0], -delta),
('B', ... | Python |
2D | dean0x7d/pybinding | docs/examples/lattice/bilayer_graphene.py | .py | 1,728 | 68 | """Build the simplest model of bilayer graphene and compute its band structure"""
import pybinding as pb
import matplotlib.pyplot as plt
from math import sqrt, pi
pb.pltutils.use_style()
def bilayer_graphene():
"""Bilayer lattice in the AB-stacked form (Bernal-stacked)
This is the simplest model with just a... | Python |
2D | dean0x7d/pybinding | docs/examples/lattice/monolayer_graphene_nn.py | .py | 1,535 | 60 | """Monolayer graphene with next-nearest hoppings"""
import pybinding as pb
import matplotlib.pyplot as plt
from math import sqrt, pi
pb.pltutils.use_style()
def monolayer_graphene_nn():
a = 0.24595 # [nm] unit cell length
a_cc = 0.142 # [nm] carbon-carbon distance
t = -2.8 # [eV] nearest neighbou... | Python |
2D | dean0x7d/pybinding | docs/examples/finite/line.py | .py | 951 | 42 | """1D lattice chains - finite dimension are imposed using builtin `pb.line` shape"""
import pybinding as pb
import matplotlib.pyplot as plt
pb.pltutils.use_style()
def simple_chain_lattice(a=1, t=-1):
"""Very simple 1D lattice"""
lat = pb.Lattice(a)
lat.add_one_sublattice('A', [0, 0])
lat.add_one_hop... | Python |
2D | dean0x7d/pybinding | docs/examples/finite/shapes.py | .py | 632 | 32 | """Several finite-sized systems created using builtin lattices and shapes"""
import pybinding as pb
from pybinding.repository import graphene
import matplotlib.pyplot as plt
from math import pi
pb.pltutils.use_style()
model = pb.Model(
graphene.monolayer(),
pb.rectangle(x=2, y=1.2)
)
model.plot()
plt.show()
... | Python |
2D | dean0x7d/pybinding | docs/_ext/generate.py | .py | 5,931 | 156 | """Adapted from sphinx.ext.autosummary.generate
Modified to only consider module members listed in `__all__` and
only class members listed in `autodoc_allowed_special_members`.
Copyright 2007-2016 by the Sphinx team, https://github.com/sphinx-doc/sphinx/blob/master/AUTHORS
License: BSD, see https://github.com/sphinx-... | Python |
2D | dean0x7d/pybinding | docs/_ext/nbexport.py | .py | 9,303 | 289 | import os
import itertools
import posixpath
from sphinx import addnodes, roles
from docutils import nodes, writers
import nbformat
from nbconvert.preprocessors import ExecutePreprocessor
from nbconvert.preprocessors.execute import CellExecutionError
def _finilize_markdown_cells(nb):
markdown_cells = (c for c in... | Python |
2D | dean0x7d/pybinding | docs/advanced/kwant_example.py | .py | 5,647 | 167 | #! /usr/bin/env python3
"""Transport through a barrier
The `main()` function builds identical models in pybinding and kwant and then calculates
the transmission using `kwant.smatrix`. The results are plotted to verify that they are
identical.
The `measure_and_plot()` function compares transport calculation time for v... | Python |
2D | dean0x7d/pybinding | tests/test_model.py | .py | 5,050 | 155 | import pytest
import numpy as np
import pybinding as pb
from pybinding.repository import graphene
from scipy.sparse import csr_matrix
def point_to_same_memory(a, b):
"""Check if two numpy arrays point to the same data in memory"""
return a.data == b.data
@pytest.fixture(scope='module')
def model():
ret... | Python |
2D | dean0x7d/pybinding | tests/test_kpm.py | .py | 7,527 | 198 | import pytest
import numpy as np
import pybinding as pb
from pybinding.repository import graphene, group6_tmd
models = {
'graphene-pristine': [graphene.monolayer(), pb.rectangle(15)],
'graphene-pristine-oversized': [graphene.monolayer(), pb.rectangle(20)],
'graphene-const_potential': [graphene.monolayer()... | Python |
2D | dean0x7d/pybinding | tests/test_system.py | .py | 3,047 | 77 | import pytest
import numpy as np
import pybinding as pb
from pybinding.repository import graphene, group6_tmd
models = {
'graphene-monolayer': [graphene.monolayer(), graphene.hexagon_ac(1)],
'graphene-monolayer-alt': [graphene.monolayer_alt(), pb.rectangle(1.6, 1.4)],
'graphene-monolayer-4atom': [graphene... | Python |
2D | dean0x7d/pybinding | tests/test_kwant.py | .py | 4,093 | 110 | import pytest
import numpy as np
import pybinding as pb
from pybinding.support.kwant import kwant_installed
from pybinding.repository import graphene, group6_tmd
if not kwant_installed:
def test_kwant_error():
"""Raise an exception if kwant isn't installed"""
model = pb.Model(graphene.monolayer(... | Python |
2D | dean0x7d/pybinding | tests/test_parallel.py | .py | 1,675 | 53 | import pytest
import numpy as np
import pybinding as pb
from pybinding.repository import graphene
def silence_parallel_output(factory):
factory.hooks.status.clear()
factory.config.pbar_fd = None
factory.config.filename = None
def test_sweep(baseline, plot_if_fails):
@pb.parallelize(v=np.linspace(0,... | Python |
2D | dean0x7d/pybinding | tests/test_results.py | .py | 3,741 | 118 | import pytest
import pickle
import numpy as np
import pybinding as pb
from pybinding.repository import graphene
@pytest.fixture(scope='module')
def model():
return pb.Model(graphene.monolayer(), pb.rectangle(1))
def test_sweep():
x0 = np.arange(3)
y0 = np.arange(-1, 2)
data0 = np.arange(9).reshape... | Python |
2D | dean0x7d/pybinding | tests/__init__.py | .py | 0 | 0 | null | Python |
2D | dean0x7d/pybinding | tests/test_shape.py | .py | 3,216 | 95 | import pytest
import math
import numpy as np
import pybinding as pb
from pybinding.repository import graphene, examples
polygons = {
'triangle': pb.regular_polygon(3, radius=1.1),
'triangle90': pb.regular_polygon(3, radius=1.1, angle=math.pi/2),
'diamond': pb.regular_polygon(4, radius=1),
'square': p... | Python |
2D | dean0x7d/pybinding | tests/test_pickle.py | .py | 915 | 43 | import pytest
import pathlib
import pybinding as pb
mock_data = list(range(10))
def round_trip(obj, file):
pb.save(obj, file)
return pb.load(file) == obj
def test_path_type(tmpdir):
# str
file = str(tmpdir / 'file')
assert round_trip(mock_data, file)
# py.path.local object
file = tmpd... | Python |
2D | dean0x7d/pybinding | tests/test_wrapper.py | .py | 525 | 20 | import numpy as np
from _pybinding import wrapper_tests
def test_variant_caster():
assert wrapper_tests.variant_cast() == (5, "Hello")
assert wrapper_tests.variant_load(1) == "int"
assert wrapper_tests.variant_load("1") == "std::string"
def test_array_ref():
r = wrapper_tests.TestArrayRef()
as... | Python |
2D | dean0x7d/pybinding | tests/test_modifiers.py | .py | 23,419 | 663 | import pytest
import numpy as np
import pybinding as pb
from pybinding.repository import graphene
one, zero = np.ones(1), np.zeros(1)
complex_one = np.ones(1, dtype=np.complex64)
def build_model(*params):
model = pb.Model(graphene.monolayer(), *params)
model.report()
return model
def test_modifier_fu... | Python |
2D | dean0x7d/pybinding | tests/test_lattice.py | .py | 11,364 | 308 | import pytest
import numpy as np
import pybinding as pb
from pybinding.repository import graphene
from pybinding.support.deprecated import LoudDeprecationWarning
lattices = {
"graphene-monolayer": graphene.monolayer(),
"graphene-monolayer-nn": graphene.monolayer(2),
"graphene-monolayer-4atom": graphene.mo... | Python |
2D | dean0x7d/pybinding | tests/test_solver.py | .py | 3,071 | 92 | import pytest
import numpy as np
import pybinding as pb
from pybinding.repository import graphene
solvers = ['arpack']
if hasattr(pb._cpp, 'FEAST'):
solvers.append('feast')
models = {
'graphene-magnetic_field': {'model': [graphene.monolayer(), pb.rectangle(6),
graphe... | Python |
2D | dean0x7d/pybinding | tests/test_leads.py | .py | 3,665 | 107 | import pytest
import numpy as np
import pybinding as pb
from pybinding.repository import graphene, examples
@pytest.fixture
def ring_model():
def ring(inner_radius, outer_radius):
def contains(x, y, _):
r = np.sqrt(x**2 + y**2)
return np.logical_and(inner_radius < r, r < outer_rad... | Python |
2D | dean0x7d/pybinding | tests/conftest.py | .py | 3,408 | 109 | import pytest
from contextlib import suppress
import matplotlib as mpl
mpl.use('Agg') # disable `plt.show()` popup window during testing
import matplotlib.pyplot as plt
import pybinding as pb
from .utils.path import path_from_fixture
from .utils.compare_figures import CompareFigure
from .utils.fuzzy_equal import F... | Python |
2D | dean0x7d/pybinding | tests/utils/fuzzy_equal.py | .py | 5,396 | 160 | import math
import numbers
from functools import singledispatch, update_wrapper
import numpy as np
from scipy.sparse import csr_matrix, coo_matrix
import pybinding as pb
def _assertdispatch(func):
"""Adapted `@singledispatch` for custom assertions
* Works with methods instead of functions
* Keeps track... | Python |
2D | dean0x7d/pybinding | tests/utils/__init__.py | .py | 0 | 0 | null | Python |
2D | dean0x7d/pybinding | tests/utils/compare_figures.py | .py | 4,392 | 130 | import os
import shutil
import tempfile
import warnings
from contextlib import suppress
import matplotlib as mpl
import matplotlib.style
import matplotlib.units
import matplotlib.pyplot as plt
from matplotlib.testing.compare import compare_images
import pybinding.pltutils as pltutils
from .path import path_from_fixt... | Python |
2D | dean0x7d/pybinding | tests/utils/path.py | .py | 1,192 | 37 | import pathlib
def path_from_fixture(request, prefix, variant='', ext='', override_group=''):
"""Use a fixture's `request` argument to create a unique file path
The final return path will look like:
prefix/module_name/test_name[fixture_param]variant.ext
Parameters
----------
request
... | Python |
2D | AbbasHub/Improved_Phase-Field_LBM_2D | Improved_phase-field_Periodic_2D.f90 | .f90 | 12,048 | 486 | !****************************************************************
!
! Improved conservative phase-field LBM solver
! for two-phase flows in a periodic domain (2D)
!
!----------------------------------------------------------------
! Based on the following paper:
!
! A. Fakhari, T. Mitchell, C. Leonardi, and D. Bolster,... | Fortran |
2D | cheminfo/nmrium | CHANGELOG.md | .md | 187,750 | 1,835 | # Changelog
## [1.10.1](https://github.com/cheminfo/nmrium/compare/v1.10.0...v1.10.1) (2025-12-12)
### Bug Fixes
* display molecule when no active tab ([bc903f7](https://github.com/cheminfo/nmrium/commit/bc903f77a5fbc35b0a52d6fb5c7d48781d62c301))
## [1.10.0](https://github.com/cheminfo/nmrium/compare/v1.9.0...v1.1... | Markdown |
2D | lherron2/thermomaps-ising | thermomaps_ising.ipynb | .ipynb | 453,636 | 1,411 | {
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"provenance": [],
"gpuType": "T4",
"authorship_tag": "ABX9TyOLqvU13qBmIUH3Vd3sPTRK",
"include_colab_link": true
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
},
"language_info"... | Unknown |
2D | lherron2/thermomaps-ising | thermomaps-root/setup.py | .py | 719 | 27 | from setuptools import setup, find_packages
import os
setup(
name="thermomaps",
version="0.1",
packages=find_packages(),
install_requires=[],
author="Lukas",
author_email="lherron@umd.edu",
description="A Python module to study molecular dynamics simulations using Thermodynamic Maps",
c... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/cli/tm_cli.py | .py | 4,080 | 99 | import os
import numpy as np
# import matplotlib.pyplot as plt
from slurmflow.serializer import ObjectSerializer
from data.generic import Summary
import argparse
import logging
# logging.getLogger('matplotlib').setLevel(logging.WARNING)
logging.getLogger('tm.core.DiffusionModel').setLevel(logging.INFO)
logging.getLo... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/cli/ising_cli.py | .py | 6,656 | 117 | import numpy as np
import os
from slurmflow.config import ConfigParser
from slurmflow.serializer import ObjectSerializer
from slurmflow.driver import SlurmDriver
from ising.base import IsingModel
from ising.samplers import SwendsenWangSampler, SingleSpinFlipSampler
from ising.observables import Energy, Magnetization
... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/cli/__init__.py | .py | 14 | 2 | import pprint
| Python |
2D | lherron2/thermomaps-ising | thermomaps-root/cli/thermomap.py | .py | 10,407 | 332 | import os
import torch
import argparse
import numpy as np
from tm.core.backbone import ConvBackbone
from tm.core.diffusion_model import DiffusionTrainer, SteeredDiffusionSampler
from tm.core.diffusion_process import VPDiffusion
from tm.core.loader import Loader
from tm.core.prior import LocalEquilibriumHarmonicPrior, G... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/ising/samplers.py | .py | 5,609 | 166 | import numpy as np
import random
from typing import Callable, Dict, List, Type
from abc import ABC, abstractmethod
from ising.base import IsingModel
import logging
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
class Sampler(ABC):
"""
Abstract base class for samplers in the Ising model.
... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/ising/swedsen_wang_simulator.py | .py | 14,503 | 375 | import numpy as np
import random
from typing import Callable, Dict, List
from abc import ABC, abstractmethod
class Observable(ABC):
"""
Abstract base class for observables in the Ising model.
An observable is a physical quantity that can be measured in a simulation.
Attributes:
name (str): Th... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/ising/__init__.py | .py | 0 | 0 | null | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/ising/base.py | .py | 3,147 | 84 | import numpy as np
import random
import sys
from typing import Callable, Dict, List, Type
from abc import ABC, abstractmethod
from data.trajectory import EnsembleIsingTrajectory
from data.generic import Summary
from ising.observables import Energy, Magnetization
from slurmflow.serializer import ObjectSerializer
impor... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/ising/observables.py | .py | 3,640 | 112 | import numpy as np
from abc import ABC, abstractmethod
from data.observables import Observable
import logging
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
class Energy(Observable):
"""
Class for calculating the energy of a lattice.
Energy is defined as the sum of the interaction ene... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/tm/__init__.py | .py | 0 | 0 | null | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/tm/core/FluctuationDataset.py | .py | 6,436 | 190 | import numpy as np
from inspect import signature
from scipy.optimize import curve_fit
import types
def safe_index(arr, idx):
if idx < len(arr):
return arr[idx]
else:
return arr[-1]
def linear_fit(x, a, b):
return x*a + b
class Fluctuation:
"""
A class for performing fluctuation a... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/tm/core/Directory.py | .py | 3,276 | 124 | import os
class Directory:
"""
Reads relevant paths from a YAML file defined for an experiment.
"""
def __init__(
self,
pdb: str,
expid: str,
iter: str,
identifier: str,
device: str,
num_devices: int,
**paths
):
"""
I... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/tm/core/backbone.py | .py | 7,574 | 237 | import torch.nn as nn
import torch
from torch.optim.lr_scheduler import MultiStepLR
import os
from tm.core.utils import Interpolater, default
import logging
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
class Backbone(nn.Module):
"""
Diffusion wrapper for instances of deep learning archit... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/tm/core/diffusion_model.py | .py | 17,506 | 530 | import torch
import os
import numpy as np
import logging
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
def temperature_density_rescaling(std_temp, ref_temp):
"""
Calculate temperature density rescaling factor.
Args:
std_temp (float): The standard temperature.
ref_temp... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/tm/core/diffusion_process.py | .py | 8,409 | 267 | import torch
from torch import vmap
import logging
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
def polynomial_noise(t, alpha_max, alpha_min, s=1e-5, **kwargs):
"""
Generate polynomial noise schedule used in Hoogeboom et. al.
Args:
t (torch.Tensor): Time steps.
alph... | Python |
2D | lherron2/thermomaps-ising | thermomaps-root/tm/core/prior.py | .py | 3,435 | 69 | import torch
import numpy as np
from typing import Any, Callable, Dict, List
import sys
import logging
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
logger.addHandler(logging.StreamHandler(sys.stdout))
class UnitNormalPrior:
def __init__(self, shape, channels_info):
self.channels_info ... | Python |
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