repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
value |
|---|---|---|---|---|---|---|
finmag | finmag-master/examples/nmag_example_2/__init__.py | 0 | 0 | 0 | py | |
finmag | finmag-master/examples/nmag_example_2/callgraph.py | #!/usr/bin/env python
try:
from pycallgraph import PyCallGraph
from pycallgraph import Config
from pycallgraph import GlobbingFilter
from pycallgraph import Grouper
from pycallgraph.output import GraphvizOutput
except ImportError:
print "You need to install pycallgraph (for instance with `pip i... | 911 | 26.636364 | 90 | py |
finmag | finmag-master/examples/nmag_example_2/test_nmag_example_2.py | import os
import pytest
import subprocess as sp
import numpy as np
import run_finmag
from finmag.util.fileio import Tablereader
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
@pytest.mark.slow
def test_against_nmag():
cwd_backup = os.getcwd()
os.chdir(MODULE_DIR)
try:
cmd = ['make', 'cl... | 1,218 | 27.348837 | 68 | py |
finmag | finmag-master/examples/spatially-varying-anisotropy/run.py | """
Demonstrating spatially varying anisotropy. Example with anisotropy vectors as follows:
-----------------------------------
--> --> --> --> --> --> --> --> -->
--> --> --> --> --> --> --> --> -->
--> --> --> --> --> --> --> --> -->
-----------------------------------
^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^ ^
| | | ... | 2,709 | 29.111111 | 97 | py |
finmag | finmag-master/examples/precession/run.py | import os
import numpy as np
import dolfin as df
import matplotlib.pyplot as plt
from finmag import Simulation
from finmag.energies import Demag, Exchange
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
IMAGE = os.path.join(MODULE_DIR, 'precession.png')
ts = np.linspace(0, 3e-10)
def run_simulation(do_preces... | 1,201 | 28.317073 | 82 | py |
finmag | finmag-master/examples/exchange_1D/1d_plot.py | import numpy
import finmag.util.helpers as helpers
from mayavi import mlab
"""
Visualise the final configuration of the magnetisation.
"""
x = numpy.genfromtxt("1d_coord.txt")
y = numpy.zeros(len(x))
z = numpy.zeros(len(x))
Ms = numpy.genfromtxt("1d_M.txt")
Mx, My, Mz = helpers.components(Ms[-1])
figure = mlab.fig... | 474 | 18 | 55 | py |
finmag | finmag-master/examples/exchange_1D/1d_anim.py | import numpy
import finmag.util.helpers as helpers
from mayavi import mlab
"""
Visualise the evolution of the vector field M over time.
"""
x = numpy.genfromtxt("1d_coord.txt")
y = numpy.zeros(len(x))
z = numpy.zeros(len(x))
Ms = numpy.genfromtxt("1d_M.txt")
u, v, w = helpers.components(Ms[0])
figure = mlab.figure... | 769 | 20.388889 | 56 | py |
finmag | finmag-master/examples/exchange_1D/run_visual.py | """ Attempt to visualise some dynimacs using python's visual module.
Visualisation probably okay, but some convergence problem in the time
integration means this does not look smooth at all, and is very slow.
"""
import dolfin
import numpy
from scipy.integrate import odeint
from finmag.physics.llg import LLG
"""
Co... | 1,412 | 24.232143 | 97 | py |
finmag | finmag-master/examples/exchange_1D/1d_angles.py | import numpy
import pylab
from finmag.util.helpers import vectors, norm, angle
# Load the data which dolfin has created and odeint has integrated.
Ms = numpy.genfromtxt("1d_M.txt")
# Each entry in ys is M for a particular moment in time.
# Each M is all the x-values of M on the mesh, followed by the y and z-values.
... | 994 | 25.184211 | 78 | py |
finmag | finmag-master/examples/exchange_1D/1d_dynamics.py | import numpy
import pylab
from finmag.util.helpers import norm, angle, components, \
vectors, rows_to_columns
# Load the data which dolfin has created and odeint has integrated.
Ms = numpy.genfromtxt("1d_M.txt")
# Each entry in ys is M for a particular moment in time.
# Each M is all the x-values of M on the... | 838 | 30.074074 | 78 | py |
finmag | finmag-master/examples/exchange_1D/1d_run.py | import dolfin
import numpy
from scipy.integrate import odeint
from finmag.physics.llg import LLG
from finmag.energies import Exchange
"""
Compute the behaviour of a one-dimensional strip of magnetic material,
with exchange interaction.
"""
A = 1.3e-11
Ms = 8.6e5
length = 20e-9 # in meters
simplexes = 10
mesh = dolf... | 1,018 | 22.159091 | 70 | py |
finmag | finmag-master/examples/macrospin/test_macrospin.py | import dolfin
import os
import py
import numpy
import pytest
from finmag import Simulation
from finmag.energies import Zeeman
from finmag.util.macrospin import make_analytic_solution
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
"""
The analytical solution of the LLG equation for a constant
applied field, b... | 4,033 | 29.330827 | 89 | py |
finmag | finmag-master/examples/macrospin/test_macrospin_alpha_rtol.py | import py
import os
import dolfin
import numpy
import logging
import matplotlib.pyplot as plt
from finmag import Simulation
from finmag.energies import Zeeman
from test_macrospin import make_analytic_solution
from scipy.integrate import odeint
log = logging.getLogger(name='finmag')
log.setLevel(logging.WARNING)
"""
W... | 3,160 | 37.54878 | 110 | py |
finmag | finmag-master/examples/demag/run_nmag.py | import os
import nmag, sys
from nmag import SI
try:
meshfile = sys.argv[1]
datafile = sys.argv[2]
except IndexError:
print 'Usage: nmsim %s meshfile outputdatafile' % sys.argv[0]
sys.exit(1)
#create simulation object
sim = nmag.Simulation()
# define magnetic material
Py = nmag.MagMaterial(name = 'Py',
... | 1,149 | 22.469388 | 74 | py |
finmag | finmag-master/examples/demag/test_field.py | import os
import dolfin as df
from numpy import average
from finmag.energies import Demag
from finmag.field import Field
from finmag.util.meshes import from_geofile
TOL = 1e-3
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
Ms = 1e6
def test_field():
"""
Test the demag field.
H_demag should be eq... | 1,648 | 27.929825 | 80 | py |
finmag | finmag-master/examples/demag/short_nmag_comp_tests2.py | ##import io
import os
import sys
import time
import subprocess
import numpy as np
import dolfin as df
from finmag.field import Field
from finmag.util.meshes import from_geofile
from finmag.energies import Demag
from finmag.energies.demag.solver_gcr import FemBemGCRSolver
import pylab as p
import finmag.energies.demag.s... | 12,237 | 32.165312 | 149 | py |
finmag | finmag-master/examples/demag/test_energy.py | import os
import py
import pytest
import logging
import dolfin as df
from numpy import pi, sqrt
from finmag.energies import Demag
from finmag.field import Field
from finmag.util.meshes import from_geofile
from finmag.util.consts import mu0
log = logging.getLogger("finmag")
MODULE_DIR = os.path.dirname(os.path.abspath(... | 1,339 | 25.8 | 81 | py |
finmag | finmag-master/examples/varying_alpha/run.py | import dolfin as df
from finmag.physics.llg import LLG
x0 = 0; x1 = 100e-9; xn = 50;
y0 = 0; y1 = 10e-9; yn = 5;
nanowire = df.RectangleMesh(df.Point(x0, y0), df.Point(x1, y1), xn, yn, "left/right")
S1 = df.FunctionSpace(nanowire, "Lagrange", 1)
S3 = df.VectorFunctionSpace(nanowire, "Lagrange", 1, dim=3)
llg = LLG(S1... | 687 | 28.913043 | 89 | py |
finmag | finmag-master/examples/cubic_anisotropy/sim.py | import math
import numpy as np
from finmag import Simulation
from finmag.energies import CubicAnisotropy, Demag, Exchange, Zeeman
from finmag.util.consts import flux_density_to_field_strength
from finmag.util.meshes import cylinder
ps = 1e-12
# Mesh
mesh = cylinder(r=10, h=2.5, maxh=3.0, filename='disk')
unit_length... | 1,560 | 25.016667 | 68 | py |
finmag | finmag-master/examples/cubic_anisotropy/nmag_original.py | import os, sys, math
from nsim.netgen import netgen_mesh_from_string
from nmag.common import SI, degrees_per_ns, Tesla, mu0, at, every
from nmag.nmag5 import Simulation, MagMaterial, cubic_anisotropy
from nsim.model import Value
ps = SI(1e-12, "s"); nm = SI(1e-9, "m") # Useful definitions
t... | 2,157 | 13.882759 | 133 | py |
finmag | finmag-master/examples/cubic_anisotropy/hysteresis.py | import numpy as np
import dolfin as df
from finmag import Simulation
from finmag.energies import Exchange, CubicAnisotropy
from finmag.util.consts import mu0
mesh = df.BoxMesh(df.Point(0, 0, 0), df.Point(1, 1, 40), 1, 1, 40)
Ms = 876626 # A/m
A = 1.46e-11 # J/m
K1 = -8608726
K2 = -13744132
K3 = 1100269
u1 = (0, -... | 1,144 | 28.358974 | 111 | py |
finmag | finmag-master/examples/boost_python/demo2_classdef/demo2.py | import demo2_module
c = demo2_module.console()
c.print_line("Hello World - demo2")
c.print_line()
| 102 | 10.444444 | 35 | py |
finmag | finmag-master/examples/boost_python/demo3_numpy/demo3_exceptions.py | import numpy as np
import sys
import traceback
import demo3_module
a = np.array([[1, 2], [3, 4]], dtype=float)
print "Providing a vector instead of a matrix as an argument\n"
try:
demo3_module.trace(a[0])
raise Exception("An exception has not been raised")
except:
traceback.print_exception(*sys.exc_info(... | 531 | 23.181818 | 63 | py |
finmag | finmag-master/examples/boost_python/demo3_numpy/demo3.py | import numpy as np
import demo3_module
a = np.array([[1, 2], [3, 4]], dtype=float)
print "Trace of a:", demo3_module.trace(a)
| 128 | 17.428571 | 43 | py |
finmag | finmag-master/examples/boost_python/demo4_dolfin/demo4.py | import dolfin as df
import demo4_module
mesh = df.UnitCubeMesh(5, 5, 5)
print "Number of vertices:", demo4_module.get_num_vertices(mesh)
| 138 | 22.166667 | 64 | py |
finmag | finmag-master/examples/boost_python/demo4_dolfin/demo4_swig_objects.py | import dolfin as df
mesh = df.UnitCubeMesh(5,5,5)
print "mesh = ", mesh, ", type(mesh) =", type(mesh)
print "mesh.this = ", mesh.this, ", type(mesh.this) =", type(mesh.this)
| 176 | 24.285714 | 71 | py |
finmag | finmag-master/examples/boost_python/petsc/demo5.py | import dolfin as df
import demo5_module
mesh = df.UnitCubeMesh(5, 5, 5)
print "Number of vertices:", demo5_module.get_num_vertices(mesh)
V = df.FunctionSpace(mesh, 'Lagrange', 1)
expr = df.Expression('sin(x[0])', degree=1)
M = df.interpolate(expr, V)
print 'vector length',demo5_module.get_vector_local_size(M.vector... | 324 | 24 | 68 | py |
finmag | finmag-master/examples/boost_python/demo1_helloworld/demo1.py | import demo1_module
demo1_module.print_line("Hello World!")
| 61 | 14.5 | 39 | py |
finmag | finmag-master/src/setup-native.py | #!/usr/bin/env python
# Run native_compiler.make_modules() as part of the distribution
# process.
# See
# http://stackoverflow.com/questions/279237/python-import-a-module-from-a-folder
# for info on this addition before the import line, which works for modules in
# arbitrary directories (here, "finmag/util")
import ... | 606 | 29.35 | 138 | py |
finmag | finmag-master/src/print_tarball_name.py | import os
import sys
from finmag.util.helpers import binary_tarball_name
try:
revision = sys.argv[1]
suffix = sys.argv[2]
destdir = sys.argv[3]
except IndexError:
print "Usage: print_tarball_name REVISION SUFFIX DESTDIR"
sys.exit(0)
name = binary_tarball_name(repo=os.curdir, revision=revision, suf... | 368 | 22.0625 | 76 | py |
finmag | finmag-master/src/setup-cython.py | # build script for compiled version of finmag
# change this as needed
libincludedir = "."
import sys
import os
from distutils.core import setup
from distutils.extension import Extension
# we'd better have Cython installed, or it's a no-go
try:
from Cython.Distutils import build_ext
except:
print "You don't ... | 3,236 | 33.43617 | 109 | py |
finmag | finmag-master/src/distcp.py | import os
import shutil
import argparse
directories_to_ignore = ['build', '__pycache__']
def cp_file(sourcedir, filename, targetdir):
# The only relevant case is if we have a .so file for a given .py,
# then don't copy .py if the .so file is __init__.py, we need to
# copy an empty __init__.py
# Crea... | 4,398 | 34.192 | 85 | py |
finmag | finmag-master/src/finmag/field.py | """
Representation of scalar and vector fields, as well as
operations on them backed by a dolfin function.
This module exists because things like per-node operations or exporting of
field values to convenient formats are awkward to do in dolfin currently.
Additionally, some things are non-trivial to get right, especia... | 29,357 | 38.406711 | 126 | py |
finmag | finmag-master/src/finmag/field_test.py | import dolfin as df
import numpy as np
import functools
import pytest
import os
from field import Field, associated_scalar_space
class TestField(object):
def setup(self):
self.create_meshes()
self.define_tolerances()
# All created function spaces are CG (Lagrange)
# with degree=1 ... | 74,170 | 46.637123 | 177 | py |
finmag | finmag-master/src/finmag/setup2.py | # build script for compiled version of finmag
# change this as needed
libincludedir = "."
import sys
import os
from distutils.core import setup
from distutils.extension import Extension
# we'd better have Cython installed, or it's a no-go
try:
from Cython.Distutils import build_ext
except:
print "You don't ... | 1,728 | 25.6 | 89 | py |
finmag | finmag-master/src/finmag/init.py | # FinMag - a thin layer on top of FEniCS to enable micromagnetic multi-physics simulations
# Copyright (C) 2012 University of Southampton
# Do not distribute
#
# CONTACT: [email protected]
from __future__ import division
import logging
logger = logging.getLogger("finmag")
# no need to propagate up to root handler,... | 5,083 | 37.80916 | 90 | py |
finmag | finmag-master/src/finmag/__init__.py | # FinMag
# Copyright (C) 2012 University of Southampton
# Do not distribute
#
# CONTACT: [email protected]
#
from init import *
from __version__ import __version__
# dolfin 1.1.0 re-orders the degrees of freedom
# to speed up some iterative algorithms. However,
# this means that the ordering doesn't correspond
# t... | 554 | 28.210526 | 49 | py |
finmag | finmag-master/src/finmag/distcp.py | #files_to_ignore = ['llg.py']
directories_to_ignore = ['build']
directories_for_straight_copy_only = ['native']
import os
import shutil
import argparse
def cp_file(sourcedir, filename, targetdir):
# only relevant case is if we have a .so file for a given .py, then don't copy .py
# if the .so file is __init_... | 2,146 | 31.530303 | 86 | py |
finmag | finmag-master/src/finmag/field_setters_test.py | """
Ensure that field values can be set using a wide range of types and make sure
we don't assign a new dolfin function, but only overwrite the values of the
existing function.
"""
import dolfin as df
import numpy as np
import pytest
from .field import Field
EPSILON = 1e-14
@pytest.fixture
def setup():
mesh = d... | 4,917 | 29.171779 | 94 | py |
finmag | finmag-master/src/finmag/scheduler/timeevent.py | from finmag.scheduler.event import Event
EPSILON = 1e-15 # Time precision, used to compare two time values.
def same_time(t0, t1):
"""
This function compares time values and returns True or False to denote
comparison.
"""
return (t0 is not None) and (t1 is not None) and abs(t0 - t1) < EPSILON
... | 3,027 | 34.209302 | 79 | py |
finmag | finmag-master/src/finmag/scheduler/event.py | # Event states are as follows:
# EV_ACTIVE: Event intends to trigger eventually if integration continues.
# EV_DONE: Event does not intent to trigger again. Should be removed by the
# scheduler.
# EV_REQUESTS_STOP_INTEGRATION: Event wishes the scheduler to stop the
# integration. This does n... | 2,435 | 37.0625 | 79 | py |
finmag | finmag-master/src/finmag/scheduler/scheduler.py | import atexit
import logging
import functools
from numbers import Number
from datetime import datetime, timedelta
from finmag.scheduler.derivedevents import SingleTimeEvent, RepeatingTimeEvent
from finmag.scheduler.timeevent import same_time
from finmag.scheduler.event import EV_DONE, EV_REQUESTS_STOP_INTEGRATION
# Thi... | 9,526 | 34.681648 | 136 | py |
finmag | finmag-master/src/finmag/scheduler/scheduler_test.py | import pytest
from timeevent import TimeEvent
from derivedevents import SingleTimeEvent, RepeatingTimeEvent
from scheduler import Scheduler
class Counter(object):
cnt_every = 0
cnt_at = 0
def inc_every(self):
self.cnt_every += 1
def inc_at(self):
self.cnt_at += 1
def reset(self)... | 7,883 | 23.184049 | 79 | py |
finmag | finmag-master/src/finmag/scheduler/__init__.py | # This file is needed just os that python recognises
# the contents as a module, but we're not actually
# exposing any names here.
| 131 | 32 | 52 | py |
finmag | finmag-master/src/finmag/scheduler/derivedevents.py | import logging
from finmag.scheduler.timeevent import TimeEvent, same_time, EPSILON
# Import the possible states of events.
from finmag.scheduler.event import EV_ACTIVE, EV_DONE
from finmag.scheduler.event import EV_REQUESTS_STOP_INTEGRATION
log = logging.getLogger(name="finmag")
class SingleTimeEvent(TimeEvent):
... | 3,767 | 32.945946 | 79 | py |
finmag | finmag-master/src/finmag/physics/effective_field.py | import logging
import numpy as np
from finmag.field import Field
from finmag.util.helpers import vector_valued_function
from finmag.energies import TimeZeeman
from finmag.physics.errors import UnknownInteraction
logger = logging.getLogger(name="finmag")
class EffectiveField(object):
def __init__(self, m, Ms, un... | 5,424 | 30.911765 | 76 | py |
finmag | finmag-master/src/finmag/physics/errors.py | class UnknownInteraction(KeyError):
def __init__(self, unknown_interaction, known_interactions):
self.unknown = unknown_interaction
self.known = known_interactions
super(UnknownInteraction, self).__init__()
def __str__(self):
message = ("Couldn't find interaction with name {}. ... | 434 | 35.25 | 76 | py |
finmag | finmag-master/src/finmag/physics/neb_cartesian_modified.py | import os
import numpy as np
import dolfin as df
# import inspect
from aeon import timer
# import finmag.util.consts as consts
# from finmag.util import helpers
# from finmag.physics.effective_field import EffectiveField
from finmag.util.vtk_saver import VTKSaver
from finmag import Simulation
# from finmag.field impo... | 22,197 | 34.5168 | 117 | py |
finmag | finmag-master/src/finmag/physics/physics.py | """
Derives physical quantities from the primary simulation state.
"""
import logging
import numpy as np
import dolfin as df
import finmag.util.consts as consts
from finmag.field import Field
from effective_field import EffectiveField
from equation import Equation
logger = logging.getLogger(name="finmag")
class Phy... | 6,484 | 34.054054 | 195 | py |
finmag | finmag-master/src/finmag/physics/neb_cartesian.py | import os
import dolfin as df
import numpy as np
# import inspect
from aeon import timer
# import finmag.util.consts as consts
# from finmag.util import helpers
# from finmag.physics.effective_field import EffectiveField
from finmag.util.vtk_saver import VTKSaver
from finmag import Simulation
# from finmag.field impor... | 21,007 | 33.839138 | 94 | py |
finmag | finmag-master/src/finmag/physics/llg.py | import logging
import numpy as np
import dolfin as df
import finmag.util.consts as consts
from aeon import timer
from finmag.field import Field
from finmag.physics.effective_field import EffectiveField
from finmag.native import llg as native_llg
from finmag.util import helpers
from finmag.util.meshes import nodal_volum... | 21,056 | 36.137566 | 195 | py |
finmag | finmag-master/src/finmag/physics/llg_stt.py | import dolfin as df
import numpy as np
import inspect
from aeon import timer
import finmag.util.consts as consts
from finmag.field import Field
from finmag.util import helpers
from finmag.physics.effective_field import EffectiveField
from finmag.util.meshes import nodal_volume
from finmag.native import llg as native_l... | 9,776 | 30.236422 | 112 | py |
finmag | finmag-master/src/finmag/physics/equation.py | """
This module solves the LLG equation or one of its many variants.
Using native code tied in by instant, it allows to specify parameters
and the terms of the equation that are to be used and then solves for dm/dt.
No effective field computation, no saving of magnetisation to file or
whatever, just straight up solvi... | 5,606 | 37.9375 | 102 | py |
finmag | finmag-master/src/finmag/physics/__init__.py | 0 | 0 | 0 | py | |
finmag | finmag-master/src/finmag/physics/neb.py | import os
import dolfin as df
import numpy as np
import inspect
from aeon import timer
import finmag.util.consts as consts
from finmag.util import helpers
from finmag.physics.effective_field import EffectiveField
from finmag.util.vtk_saver import VTKSaver
from finmag import Simulation
# from finmag.field import Field ... | 30,649 | 31.263158 | 104 | py |
finmag | finmag-master/src/finmag/physics/tests/test_effective_field.py | import numpy as np
import dolfin as df
import pytest
import os
from finmag.example import barmini
def test_effective_field_compute_returns_copy(tmpdir):
"""
Regression test to ensure that the value returned by
EffectiveField.compute() does not change as a simulation
progresses. This used to happen sin... | 733 | 27.230769 | 70 | py |
finmag | finmag-master/src/finmag/physics/tests/test_terms.py | import pytest
from os import path
import dolfin as df
import finmag.physics.equation as eqn
@pytest.fixture
def terms_module():
MODULE_DIR = path.dirname(path.abspath(__file__))
SOURCE_DIR = path.join(MODULE_DIR, "..", "native")
with open(path.join(SOURCE_DIR, "terms.h"), "r") as header:
code = he... | 1,460 | 30.76087 | 101 | py |
finmag | finmag-master/src/finmag/physics/tests/test_equation.py | import pytest
import numpy as np
import dolfin as df
from finmag.physics.equation import Equation
@pytest.fixture
def setup():
mesh = df.UnitIntervalMesh(3)
V = df.FunctionSpace(mesh, "CG", 1)
alpha = df.Function(V)
alpha.assign(df.Constant(1))
W = df.VectorFunctionSpace(mesh, "CG", 1, dim=3)
... | 4,598 | 32.086331 | 86 | py |
finmag | finmag-master/src/finmag/physics/tests/neb/microspin.py | import os
import dolfin as df
import numpy as np
import matplotlib as mpl
mpl.use("Agg")
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.colors import colorConverter
from matplotlib.collections import PolyCollection, LineCollection
from finmag import Simulation as Sim
from fin... | 1,477 | 22.09375 | 73 | py |
finmag | finmag-master/src/finmag/physics/tests/neb/neb_test.py | import os
import dolfin as df
import numpy as np
import matplotlib as mpl
mpl.use("Agg")
import matplotlib.pyplot as plt
from finmag import Simulation as Sim
from finmag.energies import Exchange, UniaxialAnisotropy
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
def test_compute_dm():
from finmag.physi... | 1,245 | 20.482759 | 68 | py |
finmag | finmag-master/src/finmag/physics/llb/sllg.py | import time
import numpy as np
import dolfin as df
import finmag.util.consts as consts
import finmag.native.llb as native_llb
from finmag.field import Field
from finmag.util import helpers
from finmag.physics.effective_field import EffectiveField
from finmag.util.meshes import mesh_volume, nodal_volume
from finmag.uti... | 9,355 | 28.514196 | 107 | py |
finmag | finmag-master/src/finmag/physics/llb/exchange.py | import logging
import dolfin as df
from aeon import timer
from finmag.energies.energy_base import EnergyBase
from finmag.util.consts import mu0
from finmag.physics.llb.material import Material
logger = logging.getLogger('finmag')
class ExchangeStd(EnergyBase):
"""
Compute the exchange field for LLB case.
... | 4,723 | 25.840909 | 82 | py |
finmag | finmag-master/src/finmag/physics/llb/llb_test.py | import os
import pytest
import dolfin as df
import numpy as np
import matplotlib as mpl
mpl.use("Agg")
import matplotlib.pyplot as plt
from finmag.physics.llb.llb import LLB
from finmag.physics.llb.exchange import Exchange
from finmag.energies import Zeeman
from finmag.energies import Demag
from finmag.physics.llb.mate... | 4,687 | 22.44 | 76 | py |
finmag | finmag-master/src/finmag/physics/llb/material.py | import logging
import numpy as np
import dolfin as df
import finmag.util.consts as consts
import finmag.native.llb as native_llb
from finmag.util import helpers
from finmag.field import Field
logger = logging.getLogger(name='finmag')
class Material(object):
"""
The aim to define this class is to collect mat... | 6,255 | 32.816216 | 106 | py |
finmag | finmag-master/src/finmag/physics/llb/__init__.py | # FinMag - a thin layer on top of FEniCS to enable micromagnetic multi-physics simulations
# Copyright (C) 2012 University of Southampton
# Do not distribute
#
# CONTACT: [email protected]
#
# AUTHOR(S) OF THIS FILE: Dmitri Chernyshenko ([email protected])
| 270 | 32.875 | 90 | py |
finmag | finmag-master/src/finmag/physics/llb/llb.py | import dolfin as df
import numpy as np
import inspect
from aeon import timer
from finmag.native import sundials
import finmag.native.llb as native_llb
from finmag.energies import Zeeman
from finmag.energies import Demag
from finmag.physics.llb.exchange import Exchange
from finmag.physics.llb.material import Material
fr... | 13,787 | 30.124153 | 93 | py |
finmag | finmag-master/src/finmag/physics/llb/anisotropy.py | import dolfin as df
import logging
from aeon import timer
from finmag.energies.energy_base import EnergyBase
from material import Material
logger = logging.getLogger('finmag')
class LLBAnisotropy(EnergyBase):
"""
Compute the anisotropy field for LLB case
H = -(m_x e_x + m_y e_y)/chi_perp
==>
E... | 2,072 | 23.104651 | 77 | py |
finmag | finmag-master/src/finmag/physics/llb/sllg_test.py | import os
import dolfin as df
import numpy as np
import matplotlib as mpl
mpl.use("Agg")
import matplotlib.pyplot as plt
from finmag.physics.llb.sllg import SLLG
from finmag.energies import Zeeman
from finmag.energies import Demag
MODULE_DIR = os.path.dirname(os.path.abspath(__file__))
def plot_random_number():
... | 1,150 | 22.979167 | 76 | py |
finmag | finmag-master/src/finmag/physics/llb/tests/__init__.py | # FinMag - a thin layer on top of FEniCS to enable micromagnetic multi-physics simulations
# Copyright (C) 2012 University of Southampton
# Do not distribute
#
# CONTACT: [email protected]
#
# AUTHOR(S) OF THIS FILE: Dmitri Chernyshenko ([email protected])
| 270 | 32.875 | 90 | py |
finmag | finmag-master/src/finmag/drivers/llg_integrator.py | import logging
from finmag.field import Field
from finmag.drivers.sundials_integrator import SundialsIntegrator
from finmag.drivers.scipy_integrator import ScipyIntegrator
log = logging.getLogger(name='finmag')
def llg_integrator(llg, m0, backend="sundials", **kwargs):
# XXX TODO: Passing the tablewriter argumen... | 1,284 | 41.833333 | 93 | py |
finmag | finmag-master/src/finmag/drivers/sundials_integrator.py | import logging
from finmag.native import sundials
EPSILON = 1e-15
log = logging.getLogger(name='finmag')
class SundialsIntegrator(object):
"""
Sundials time integrator. We always start integration from t = 0.
Attributes:
cur_t The time up to which integration has been carried out.
""... | 7,695 | 38.875648 | 101 | py |
finmag | finmag-master/src/finmag/drivers/__init__.py | 0 | 0 | 0 | py | |
finmag | finmag-master/src/finmag/drivers/scipy_integrator.py | import logging
import numpy as np
from scipy.integrate import ode
EPSILON = 1e-15
log = logging.getLogger(name="finmag")
class ScipyIntegrator(object):
def __init__(self, llg, m0, reltol=1e-6, abstol=1e-6, nsteps=10000, method="bdf", tablewriter=None, **kwargs):
self.m_field = m0
self.solve_for =... | 1,359 | 31.380952 | 114 | py |
finmag | finmag-master/src/finmag/drivers/tests/test_integrator_raises_exception_on_exceed_maxsteps.py | import os
import pytest
import finmag
steps = 10
def test_can_change_maxsteps():
sim = finmag.example.barmini()
sim.create_integrator()
sim.integrator.max_steps = steps
assert sim.integrator.max_steps == steps
def test_time_run_until():
sim = finmag.example.barmini()
sim.create_integrator()... | 1,301 | 24.529412 | 70 | py |
finmag | finmag-master/src/finmag/drivers/tests/test_relaxation.py | import os
import numpy as np
import dolfin as df
import matplotlib.pyplot as plt
from finmag import Simulation
from finmag.energies import Zeeman, Exchange, Demag
from finmag.util.consts import ONE_DEGREE_PER_NS
MODULE_DIR = os.path.abspath(os.path.dirname(__file__))
def test_easy_relaxation(do_plot=False):
"""
... | 2,025 | 30.65625 | 154 | py |
finmag | finmag-master/src/finmag/drivers/tests/test_scipy.py | import dolfin as df
from finmag import Simulation
def _test_scipy_advance_time():
mesh = df.UnitIntervalMesh(10)
sim = Simulation(mesh, Ms=1, unit_length=1e-9, integrator_backend="scipy")
sim.set_m((1, 0, 0))
sim.advance_time(1e-12)
sim.advance_time(2e-12)
sim.advance_time(2e-12)
sim.advan... | 723 | 25.814815 | 78 | py |
finmag | finmag-master/src/finmag/drivers/tests/sundials_nsteps_test.py | import finmag
import os
def test_integrator_get_set_max_steps(tmpdir):
"""
Tests setting and getting of nsteps
"""
os.chdir(str(tmpdir))
sim = finmag.example.barmini()
sim.run_until(0) # create integrator object
steps = sim.integrator.max_steps
assert steps != 42 # would be an odd d... | 1,747 | 28.133333 | 76 | py |
finmag | finmag-master/src/finmag/drivers/tests/test_relax_two_times.py | import dolfin as df
from finmag import Simulation
from finmag.energies import Zeeman
def test_relax_two_times():
"""
Test whether we can call the relax method on Sim two times in a row.
"""
mesh = df.BoxMesh(df.Point(0, 0, 0), df.Point(10, 10, 10), 2, 2, 2)
Ms = 0.86e6
sim = Simulation(mesh,... | 656 | 22.464286 | 72 | py |
finmag | finmag-master/src/finmag/drivers/tests/test_integrators.py | # FinMag - a thin layer on top of FEniCS to enable micromagnetic multi-physics simulations
# Copyright (C) 2012 University of Southampton
# Do not distribute
#
# CONTACT: [email protected]
#
# AUTHOR(S) OF THIS FILE: Dmitri Chernyshenko ([email protected])
import unittest
from finmag.tests.jacobean.domain... | 1,632 | 31.019608 | 96 | py |
finmag | finmag-master/src/finmag/drivers/tests/sundials_reinit_test.py | # FinMag - a thin layer on top of FEniCS to enable micromagnetic multi-physics simulations
# Copyright (C) 2012 University of Southampton
# Do not distribute
#
# CONTACT: [email protected]
#
# AUTHOR(S) OF THIS FILE: Hans Fangohr (copied template from Dmitri for
# integrator tests)
"""The purpose of this file is ... | 4,324 | 33.055118 | 90 | py |
finmag | finmag-master/src/finmag/energies/test_energies_in_regions.py | from __future__ import division
import numpy as np
import dolfin as df
import pytest
import os
import finmag
from finmag.field import Field
#from finmag.energies import Zeeman, TimeZeeman, DiscreteTimeZeeman, OscillatingZeeman
from finmag.energies import Zeeman
#from finmag.util.consts import mu0
from finmag.util.meshe... | 4,938 | 34.278571 | 89 | py |
finmag | finmag-master/src/finmag/energies/energy_base.py | import logging
import dolfin as df
import numpy as np
from aeon import timer
from finmag.util.meshes import nodal_volume
from finmag.util import helpers
from finmag.util.consts import mu0
from finmag.field import Field
logger = logging.getLogger('finmag')
class EnergyBase(object):
"""
Computes a field for a... | 9,254 | 34.190114 | 81 | py |
finmag | finmag-master/src/finmag/energies/cubic_anisotropy.py | import logging
import numpy as np
import dolfin as df
from aeon import timer
from finmag.field import Field
from energy_base import EnergyBase
from finmag.util import helpers
from finmag.util.consts import mu0
from finmag.native import llg as native_llg
logger = logging.getLogger('finmag')
class CubicAnisotropy(Ener... | 4,052 | 33.347458 | 102 | py |
finmag | finmag-master/src/finmag/energies/exchange.py | import logging
import dolfin as df
from aeon import timer
from energy_base import EnergyBase
from finmag.field import Field
logger = logging.getLogger('finmag')
class Exchange(EnergyBase):
"""
Compute the exchange field.
.. math::
E_{\\text{exch}} = \\int_\\Omega A (\\nabla M)^2 dx
*Argu... | 2,933 | 26.942857 | 76 | py |
finmag | finmag-master/src/finmag/energies/anisotropy_test.py | import pytest
import textwrap
import dolfin as df
import numpy as np
from finmag.field import Field
from finmag.energies import UniaxialAnisotropy
from finmag.util.consts import mu0
TOLERANCE = 1e-12
@pytest.fixture(scope="module")
def fixt():
"""
Create an UniaxialAnisotropy object that will be re-used duri... | 4,795 | 32.538462 | 93 | py |
finmag | finmag-master/src/finmag/energies/dw_fixed_energy.py | import os
import textwrap
import dolfin as df
import numpy as np
from demag import Demag
class FixedEnergyDW(object):
def __init__(self, left=(1, 0, 0), right=(-1, 0, 0), repeat_time=5, name='FixedEnergyDW'):
self.left = left
self.right = right
self.repeat_time = repeat_time
self.... | 5,152 | 33.817568 | 96 | py |
finmag | finmag-master/src/finmag/energies/cubic_anisotropy_test.py | import dolfin as df
import numpy as np
from finmag.field import Field
from finmag.energies import CubicAnisotropy
from finmag.util.meshes import mesh_volume
import pytest
unit_length = 1e-9
Ms = 876626 # A/m
K1 = -8608726
K2 = -13744132
K3 = 1100269
u1 = (0, -0.7071, 0.7071)
u2 = (0, 0.7071, 0.7071)
u3 = (-1, 0, 0)... | 1,514 | 27.584906 | 86 | py |
finmag | finmag-master/src/finmag/energies/dmi_test.py | import pytest
import numpy as np
import dolfin as df
from math import pi
from finmag.energies import DMI, Exchange
from finmag import Simulation
from finmag.field import Field
from finmag.util.helpers import vector_valued_function
from finmag.util.pbc2d import PeriodicBoundary2D
def test_dmi_uses_unit_length_2dmesh()... | 3,797 | 29.878049 | 86 | py |
finmag | finmag-master/src/finmag/energies/exchange_test.py | import pytest
import numpy as np
import dolfin as df
from finmag.energies import Exchange
from finmag.field import Field
from math import sqrt, pi
from finmag.util.consts import mu0
from finmag.util.pbc2d import PeriodicBoundary2D
@pytest.fixture
def fixt():
"""
Create an Exchange object that will be re-used d... | 6,795 | 29.475336 | 84 | py |
finmag | finmag-master/src/finmag/energies/init.py | import logging
from demag import Demag, Demag2D, MacroGeometry
from energy_base import EnergyBase
from exchange import Exchange
from anisotropy import UniaxialAnisotropy
from cubic_anisotropy import CubicAnisotropy
from zeeman import Zeeman, TimeZeeman, DiscreteTimeZeeman, OscillatingZeeman, TimeZeemanPython
from dmi i... | 466 | 34.923077 | 94 | py |
finmag | finmag-master/src/finmag/energies/zeeman_test.py | from __future__ import division
import numpy as np
import dolfin as df
import pytest
import os
import finmag
import logging
from finmag.field import Field
from finmag import sim_with
from finmag.energies import Zeeman, TimeZeeman, DiscreteTimeZeeman, OscillatingZeeman
from finmag.util.consts import mu0
from finmag.util... | 15,728 | 33.953333 | 97 | py |
finmag | finmag-master/src/finmag/energies/dmi.py | import logging
import dolfin as df
from aeon import timer
from finmag.field import Field
from energy_base import EnergyBase
from finmag.util.helpers import times_curl
logger = logging.getLogger('finmag')
class DMI(EnergyBase):
"""
Compute the Dzyaloshinskii-Moriya Interaction (DMI) field.
.. math::
... | 5,280 | 29.703488 | 101 | py |
finmag | finmag-master/src/finmag/energies/random_thermal.py | import numpy as np
import dolfin as df
from finmag.util.consts import mu0, k_B
from finmag.util.meshes import mesh_volume
class RandomThermal(object):
"""
Thermal field from Simone,
E. Martínez, L. López-Díaz, L. Torres and C.J. García-Cervera.
Minimizing cell size dependence in micromagnetics simu... | 1,736 | 28.948276 | 99 | py |
finmag | finmag-master/src/finmag/energies/thin_film_demag.py | import logging
import numpy as np
import dolfin as df
logger = logging.getLogger('finmag')
class ThinFilmDemag(object):
"""
Demagnetising field for thin films in the i-direction.
Hj = Hk = 0 and Hi = - Mi.
"""
def __init__(self, direction="z", field_strength=None, in_jacobian=False, name='Thin... | 1,491 | 30.083333 | 100 | py |
finmag | finmag-master/src/finmag/energies/magnetostatic_field_test.py | import numpy as np
from finmag.util.consts import mu0
from finmag.energies.magnetostatic_field import MagnetostaticField
def test_magnetostatic_field_for_uniformly_magnetised_sphere():
"""
Our favourite test when it comes to demag!
"""
Ms = 1
m = np.array((1, 0, 0))
Nxx = Nyy = Nzz = 1.0 / 3.... | 1,372 | 32.487805 | 106 | py |
finmag | finmag-master/src/finmag/energies/__init__.py | from init import *
| 19 | 9 | 18 | py |
finmag | finmag-master/src/finmag/energies/magnetostatic_field.py | import numpy as np
from finmag.util.consts import mu0
EPS = 1e-15
class MagnetostaticField(object):
"""
Magnetostatic field for uniform magnetisation.
The magnetostatic energy density for a uniform magnetisation can
be written as:
.. math::
U_{\\text{ms}} =
\\frac{1}{2} \\... | 2,238 | 29.671233 | 89 | py |
finmag | finmag-master/src/finmag/energies/thin_film_demag_test.py | import pytest
import numpy as np
import dolfin as df
from finmag import Simulation as Sim
from finmag.energies import ThinFilmDemag, Demag
Ms = 8.6e5
def test_interaction_accepts_name():
"""
Check that the interaction accepts a 'name' argument and has a 'name' attribute.
"""
demag = ThinFilmDemag()
... | 2,383 | 31.657534 | 91 | py |
finmag | finmag-master/src/finmag/energies/anisotropy.py | import logging
import dolfin as df
import numpy as np
from aeon import timer
from energy_base import EnergyBase
from finmag.field import Field
from finmag.util import helpers
from finmag.util.consts import mu0
from finmag.native import llg as native_llg
from finmag.field import Field
logger = logging.getLogger('finmag... | 4,846 | 30.888158 | 100 | py |
finmag | finmag-master/src/finmag/energies/zeeman.py | import logging
import dolfin as df
import numpy as np
from finmag.field import Field
from finmag.util.consts import mu0
from finmag.util.meshes import nodal_volume
from finmag.util import helpers
from math import pi, cos
log = logging.getLogger("finmag")
class Zeeman(object):
def __init__(self, H, name='Zeeman'... | 15,581 | 37.474074 | 276 | py |
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