def test6(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(
test_results_path, "test6_grid" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
instance = self.store_factory()(output_file)
shape = 10, 10, 10
p = Grid(*shape)
p.mass = ([x * 2.0 for x in range(p.size)] | units.kg).reshape(shape)
p.model_time = 2.0 | units.s
instance.store_grid(p.savepoint(1 | units.Myr))
loaded_grid = self.get_version_in_store(instance.load_grid())
self.assertAlmostRelativeEquals(loaded_grid.get_timestamp(),
1 | units.Myr)
self.assertEqual(loaded_grid.shape, shape)
self.assertEqual(loaded_grid[0][0][0].mass, 0 | units.kg)
self.assertAlmostRelativeEquals(loaded_grid[..., 1, 1].mass, p[..., 1,
1].mass)
instance.close()
def test12(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test12" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
shape = 10, 10, 10
p = Grid(*shape)
p.mass = ([x * 2.0 for x in range(p.size)] | units.kg).reshape(shape)
p.model_time = 2.0 | units.s
io.write_set_to_file(p.savepoint(timestamp=2 | units.Myr,
scale=1 | units.kg),
output_file,
"hdf5",
version=self.store_version())
loaded_particles = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version())
loaded_particles = self.get_version_in_store(loaded_particles)
a = loaded_particles.collection_attributes
self.assertAlmostRelativeEquals(a.timestamp, 2 | units.Myr)
self.assertAlmostRelativeEquals(a.scale, 1 | units.kg)
def test20(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test20" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
shape = 10, 10, 10
p = Grid(*shape)
p.mass = (numpy.asarray([x * 2.0
for x in range(p.size)])).reshape(shape)
io.write_set_to_file(p,
output_file,
"hdf5",
version=self.store_version())
loaded = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version())
loaded = self.get_version_in_store(loaded)
self.assertAlmostRelativeEquals(p.mass[0][1][2], 24)
self.assertAlmostRelativeEquals(p[0][1][2].mass, 24)
def test27(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test27" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
instance = self.store_factory()(output_file)
shape = 10,
p = Grid(*shape)
p.mass = ([x * 2.0 for x in range(p.size)] | units.kg).reshape(shape)
p.model_time = 2.0 | units.s
instance.store_grid(p)
loaded_grid = instance.load_grid()
self.assertEqual(loaded_grid.shape, shape)
loaded_mass_in_kg = loaded_grid.mass.value_in(units.kg)
previous_mass_in_kg = p.mass.value_in(units.kg)
for expected, actual in zip(previous_mass_in_kg, loaded_mass_in_kg):
self.assertEqual(expected, actual)
instance.close()
def test54(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test23" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
stars = Particles(2)
stars[0].x = 1.0 | units.km
stars[1].x = 2.0 | units.km
gas = Grid(2, 3)
gas.y = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]] | units.km
stars[0].gas = gas[0][0]
stars[1].gas = gas[1][0]
self.assertAlmostRelativeEquals(stars[0].gas.y, 1.0 | units.km)
self.assertAlmostRelativeEquals(stars[1].gas.y, 4.0 | units.km)
io.write_set_to_file(stars,
output_file,
"hdf5",
version=self.store_version())
loaded_stars = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version())
self.assertAlmostRelativeEquals(loaded_stars[0].gas.y, 1.0 | units.km)
self.assertAlmostRelativeEquals(loaded_stars[1].gas.y, 4.0 | units.km)
def test54b(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test24" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
stars = Particles(2)
stars[0].x = 1.0 | units.km
stars[1].x = 2.0 | units.km
gas = Grid(2, 3)
gas.y = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]] | units.km
gas[0][0].particle = stars[0]
gas[1][2].particle = stars[0]
gas[1][0].particle = stars[1]
#stars[0].gas = gas[0][0]
#stars[1].gas = gas[1][0]
self.assertAlmostRelativeEquals(gas[0][0].particle.x, 1.0 | units.km)
self.assertAlmostRelativeEquals(gas[1][2].particle.x, 1.0 | units.km)
self.assertAlmostRelativeEquals(gas[1][0].particle.x, 2.0 | units.km)
io.write_set_to_file(gas,
output_file,
"hdf5",
version=self.store_version())
loaded_gas = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version())
self.assertAlmostRelativeEquals(loaded_gas[0][0].particle.x,
1.0 | units.km)
self.assertAlmostRelativeEquals(loaded_gas[1][2].particle.x,
1.0 | units.km)
self.assertAlmostRelativeEquals(loaded_gas[1][0].particle.x,
2.0 | units.km)
self.assertEqual(id(loaded_gas[0][0].particle.get_containing_set()),
id(loaded_gas[1][2].particle.get_containing_set()))
self.assertEqual(loaded_gas.particle.shape, loaded_gas.shape)
gas_copy = loaded_gas.copy()
gas_copy[0][0].particle.x = 3 | units.km
self.assertAlmostRelativeEquals(loaded_gas[0][0].particle.x,
1.0 | units.km)
self.assertAlmostRelativeEquals(gas_copy[0][0].particle.x,
3.0 | units.km)
self.assertAlmostRelativeEquals(gas_copy[1][2].particle.x,
3.0 | units.km)
def test29(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test29"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
particles = Grid(10)
particles.attribute1 = "normal"
particles.attribute2 = u"unicode"
io.write_set_to_file(particles,output_file, format='amuse', version = self.store_version())
output = io.read_set_from_file(output_file, format='amuse')
self.assertEquals(output[0].attribute2, u"unicode")
def load(self):
dataset = Dataset(self.filename)
shape = ()
order = dict()
for i, (key, d) in enumerate(dataset.dimensions.items()):
shape += (len(d), )
order[key] = i
grid = Grid(*shape[0:2])
for s in dataset.ncattrs():
setattr(grid.collection_attributes, s, getattr(dataset, s))
for name, var in dataset.variables.items():
perm = [order[x] for x in var.dimensions]
if hasattr(var, "units"):
unit = units_lookup[var.units]
else:
unit = units.none
setattr(grid, name, numpy.array(var).transpose(tuple(perm)) | unit)
self.dataset = dataset
return grid
def result(self):
grid = Grid.create(self.dimensions,
self.box_size.as_vector_with_length(3))
zero = numpy.zeros(self.dimensions).flatten() | units.m / units.s
rho, rhovx, rhovy, rhovz, rhoe = self.sph_code.get_hydro_state_at_point(
grid.x.flatten() - self.box_offset,
grid.y.flatten() - self.box_offset,
grid.z.flatten() - self.box_offset, zero, zero, zero)
grid.rho = rho.reshape(self.dimensions)
grid.rhovx = rhovx.reshape(self.dimensions)
grid.rhovy = rhovy.reshape(self.dimensions)
grid.rhovz = rhovz.reshape(self.dimensions)
grid.energy = rhoe.reshape(self.dimensions)
if self.do_scale:
grid.rho *= self.sph_code.gas_particles.total_mass() / (grid.rho.sum() * grid.cellsize().prod())
total_sph_momentum = (self.sph_code.gas_particles.mass.reshape((-1,1)) * self.sph_code.gas_particles.velocity).sum(axis=0)
total_grid_momentum = grid.momentum.reshape((-1,3)).sum(axis=0)
grid.momentum += total_sph_momentum / grid.cellsize().prod() - total_grid_momentum
grid.energy *= self.sph_code.thermal_energy / (grid.energy.sum() * grid.cellsize().prod())
return grid
def result(self):
grid = Grid.create(self.dimensions,
self.box_size.as_vector_with_length(3))
grid.add_vector_attribute("momentum", ["rhovx","rhovy","rhovz"])
zero = numpy.zeros(self.dimensions).flatten() | units.m / units.s
rho, rhovx, rhovy, rhovz, rhoe = self.sph_code.get_hydro_state_at_point(
grid.x.flatten() - self.box_offset,
grid.y.flatten() - self.box_offset,
grid.z.flatten() - self.box_offset, zero, zero, zero)
grid.rho = rho.reshape(self.dimensions)
grid.rhovx = rhovx.reshape(self.dimensions)
grid.rhovy = rhovy.reshape(self.dimensions)
grid.rhovz = rhovz.reshape(self.dimensions)
grid.energy = rhoe.reshape(self.dimensions)
if self.do_scale:
grid.rho *= self.sph_code.gas_particles.total_mass() / (grid.rho.sum() * grid.cellsize().prod())
total_sph_momentum = (self.sph_code.gas_particles.mass.reshape((-1,1)) * self.sph_code.gas_particles.velocity).sum(axis=0)
total_grid_momentum = grid.momentum.reshape((-1,3)).sum(axis=0)
grid.momentum += total_sph_momentum / grid.cellsize().prod() - total_grid_momentum
grid.energy *= self.sph_code.thermal_energy / (grid.energy.sum() * grid.cellsize().prod())
return grid
def __init__(self, filename, nx, ny):
self.filename = filename
import os.path
import sys
if not os.path.isfile(filename):
sys.exit("Error: No such file " + filename)
raw = numpy.fromfile(filename).newbyteorder('S')
grid = raw.reshape((7, ny, nx))
# lats=grid[0,:,:]/numpy.pi*180
# lons=grid[1,:,:]/numpy.pi*180
self.lat = lats = grid[0, :, :]
self.lon = lons = grid[1, :, :]
self.htn = htn = grid[2, :, :]
self.hte = hte = grid[3, :, :]
self.hus = hus = grid[4, :, :]
self.huw = huw = grid[5, :, :]
self.angle = angle = grid[6, :, :]
#nodes is the U-grid
self.nodes = nodes = Grid(ny * nx)
nodes.lats = lats | units.rad
nodes.lons = lons | units.rad
def setup_simple_grid(self):
test_grid = Grid.create((4,3,2), [1.0, 1.0, 1.0] | units.m)
test_grid.rho = numpy.linspace(1.0, 2.0, num=24).reshape(test_grid.shape) | units.kg/units.m**3
test_grid.rhovx = test_grid.rho * (3.0 | units.m/units.s)
test_grid.rhovy = test_grid.rho * (4.0 | units.m/units.s)
test_grid.rhovz = test_grid.rho * (0.0 | units.m/units.s)
test_grid.energy = test_grid.rho * ((1.0 | (units.m/units.s)**2) + 0.5 * (5.0 | units.m/units.s)**2)
return test_grid
def make_grid(number_of_grid_cells, length, constant_hydrogen_density, inner_radius, outer_radius):
grid = Grid.create([number_of_grid_cells] * 3, length.as_vector_with_length(3))
grid.radius = grid.position.lengths()
grid.hydrogen_density = constant_hydrogen_density
grid.hydrogen_density[grid.radius <= inner_radius] = 0 | units.cm ** -3
grid.hydrogen_density[grid.radius >= outer_radius] = 0 | units.cm ** -3
return grid
def make_grid(number_of_grid_cells, length, constant_hydrogen_density, inner_radius, outer_radius):
grid = Grid.create([number_of_grid_cells] * 3, length.as_vector_with_length(3))
grid.radius = grid.position.lengths()
grid.hydrogen_density = constant_hydrogen_density
grid.hydrogen_density[grid.radius <= inner_radius] = 0 | units.cm ** -3
grid.hydrogen_density[grid.radius >= outer_radius] = 0 | units.cm ** -3
return grid
def hydro_plot(view, hydro_code, image_size, figname):
"""
view: the (physical) region to plot [xmin, xmax, ymin, ymax]
hydro_code: hydrodynamics code in which the gas to be plotted is defined
image_size: size of the output image in pixels (x, y)
"""
shape = (image_size[0], image_size[1], 1)
size = image_size[0] * image_size[1]
axis_lengths = [0.0, 0.0, 0.0] | units.m
axis_lengths[0] = view[1] - view[0]
axis_lengths[1] = view[3] - view[2]
grid = Grid.create(shape, axis_lengths)
grid.x += view[0]
grid.y += view[2]
speed = grid.z.reshape(size) * (0 | 1 / units.s)
rho, rhovx, rhovy, rhovz, rhoe = \
hydro_code.get_hydro_state_at_point(
grid.x.reshape(size),
grid.y.reshape(size),
grid.z.reshape(size),
speed, speed, speed)
min_v = 800.0 | units.km / units.s
max_v = 3000.0 | units.km / units.s
min_rho = 3.0e-4 | units.g / units.cm**3
max_rho = 0.1 | units.g / units.cm**3
min_E = 1.0e11 | units.J / units.kg
max_E = 1.0e13 | units.J / units.kg
v_sqr = (rhovx**2 + rhovy**2 + rhovz**2) / rho**2
E = rhoe / rho
log_v = numpy.log((v_sqr / min_v**2)) / numpy.log((max_v**2 / min_v**2))
log_rho = numpy.log((rho / min_rho)) / numpy.log((max_rho / min_rho))
log_E = numpy.log((E / min_E)) / numpy.log((max_E / min_E))
red = numpy.minimum(numpy.ones_like(rho.number),
numpy.maximum(numpy.zeros_like(rho.number),
log_rho)).reshape(shape)
green = numpy.minimum(numpy.ones_like(rho.number),
numpy.maximum(numpy.zeros_like(rho.number),
log_v)).reshape(shape)
blue = numpy.minimum(numpy.ones_like(rho.number),
numpy.maximum(numpy.zeros_like(rho.number),
log_E)).reshape(shape)
alpha = numpy.minimum(
numpy.ones_like(log_v),
numpy.maximum(numpy.zeros_like(log_v), numpy.log(
(rho / (10 * min_rho))))).reshape(shape)
rgba = numpy.concatenate((red, green, blue, alpha), axis=2)
pyplot.figure(figsize=(image_size[0] / 100.0, image_size[1] / 100.0),
dpi=100)
im = pyplot.figimage(rgba, origin='lower')
pyplot.savefig(figname, transparent=True, dpi=100)
print("\nHydroplot was saved to: ", figname)
pyplot.close()
def hydro_plot(view, hydro_code, image_size, figname):
"""
view: the (physical) region to plot [xmin, xmax, ymin, ymax]
hydro_code: hydrodynamics code in which the gas to be plotted is defined
image_size: size of the output image in pixels (x, y)
"""
if not HAS_MATPLOTLIB:
return
shape = (image_size[0], image_size[1], 1)
size = image_size[0] * image_size[1]
axis_lengths = [0.0, 0.0, 0.0] | units.m
axis_lengths[0] = view[1] - view[0]
axis_lengths[1] = view[3] - view[2]
grid = Grid.create(shape, axis_lengths)
grid.x += view[0]
grid.y += view[2]
speed = grid.z.reshape(size) * (0 | 1/units.s)
rho, rhovx, rhovy, rhovz, rhoe = hydro_code.get_hydro_state_at_point(
grid.x.reshape(size),
grid.y.reshape(size),
grid.z.reshape(size), speed, speed, speed)
min_v = 800.0 | units.km / units.s
max_v = 3000.0 | units.km / units.s
min_rho = 3.0e-9 | units.g / units.cm**3
max_rho = 1.0e-5 | units.g / units.cm**3
min_E = 1.0e11 | units.J / units.kg
max_E = 1.0e13 | units.J / units.kg
v_sqr = (rhovx**2 + rhovy**2 + rhovz**2) / rho**2
E = rhoe / rho
log_v = numpy.log((v_sqr / min_v**2)) / numpy.log((max_v**2 / min_v**2))
log_rho = numpy.log((rho / min_rho)) / numpy.log((max_rho / min_rho))
log_E = numpy.log((E / min_E)) / numpy.log((max_E / min_E))
red = numpy.minimum(numpy.ones_like(rho.number), numpy.maximum(
numpy.zeros_like(rho.number), log_rho)).reshape(shape)
green = numpy.minimum(numpy.ones_like(rho.number), numpy.maximum(
numpy.zeros_like(rho.number), log_v)).reshape(shape)
blue = numpy.minimum(numpy.ones_like(rho.number), numpy.maximum(
numpy.zeros_like(rho.number), log_E)).reshape(shape)
alpha = numpy.minimum(
numpy.ones_like(log_v),
numpy.maximum(
numpy.zeros_like(log_v),
numpy.log((rho / (10*min_rho)))
)
).reshape(shape)
rgba = numpy.concatenate((red, green, blue, alpha), axis=2)
pyplot.figure(figsize=(image_size[0]/100.0, image_size[1]/100.0), dpi=100)
im = pyplot.figimage(rgba, origin='lower')
pyplot.savefig(figname, transparent=True, dpi=100,
facecolor='k', edgecolor='k')
print "\nHydroplot was saved to: ", figname
pyplot.close()
def setup_particles_in_nbodycode(self):
staggered_grid_shape = numpy.asarray(self.gridcode.grid.shape) + 2
corner0 = self.gridcode.grid[0][0][0].position
corner1 = self.gridcode.grid[-1][-1][-1].position
delta = self.gridcode.grid[1][1][1].position - corner0
print delta.prod()
self.volume = delta.prod()
staggered_corner0 = corner0 - delta
staggered_corner1 = corner1
self.staggered_grid = Grid.create(
staggered_grid_shape,
staggered_corner1 - staggered_corner0 + delta)
# self.staggered_grid.x += staggered_corner0.x
# self.staggered_grid.y += staggered_corner0.x
# self.staggered_grid.z += staggered_corner0.x
# self.staggered_grid.p000 = 0.0 | mass
# self.staggered_grid.p100 = 0.0 | mass
# self.staggered_grid.p010 = 0.0 | mass
# self.staggered_grid.p110 = 0.0 | mass
# self.staggered_grid.p000 = 0.0 | mass
# self.staggered_grid.p100 = 0.0 | mass
# self.staggered_grid.p011 = 0.0 | mass
# self.staggered_grid.p111 = 0.0 | mass
# self.staggered_grid.p001 = 0.0 | mass
# self.staggered_grid.p101 = 0.0 | mass
self.normal_grid = Grid.create(
self.gridcode.grid.shape, corner1 - corner0 + delta)
particles = Particles(self.normal_grid.size)
particles.mass = 0.0 | mass
particles.x = self.grid.x.flatten()
particles.y = self.grid.y.flatten()
particles.z = self.grid.z.flatten()
particles.vx = 0.0 | speed
particles.vy = 0.0 | speed
particles.vz = 0.0 | speed
particles.radius = 0.0 | length
self.nbodycode.particles.add_particles(particles)
self.from_model_to_nbody = particles.new_channel_to(
self.nbodycode.particles)
self.nbodycode.commit_particles()
self.particles = particles
def setup_particles_in_nbodycode(self):
staggered_grid_shape = numpy.asarray(self.gridcode.grid.shape) + 2
corner0 = self.gridcode.grid[0][0][0].position
corner1 = self.gridcode.grid[-1][-1][-1].position
delta = self.gridcode.grid[1][1][1].position - corner0
print delta.prod()
self.volume = delta.prod()
staggered_corner0 = corner0 - delta
staggered_corner1 = corner1
self.staggered_grid = Grid.create(
staggered_grid_shape,
staggered_corner1 - staggered_corner0 + delta)
#self.staggered_grid.x += staggered_corner0.x
#self.staggered_grid.y += staggered_corner0.x
#self.staggered_grid.z += staggered_corner0.x
#self.staggered_grid.p000 = 0.0 | mass
#self.staggered_grid.p100 = 0.0 | mass
#self.staggered_grid.p010 = 0.0 | mass
#self.staggered_grid.p110 = 0.0 | mass
#self.staggered_grid.p000 = 0.0 | mass
#self.staggered_grid.p100 = 0.0 | mass
#self.staggered_grid.p011 = 0.0 | mass
#self.staggered_grid.p111 = 0.0 | mass
#self.staggered_grid.p001 = 0.0 | mass
#self.staggered_grid.p101 = 0.0 | mass
self.normal_grid = Grid.create(self.gridcode.grid.shape,
corner1 - corner0 + delta)
particles = Particles(self.normal_grid.size)
particles.mass = 0.0 | mass
particles.x = self.grid.x.flatten()
particles.y = self.grid.y.flatten()
particles.z = self.grid.z.flatten()
particles.vx = 0.0 | speed
particles.vy = 0.0 | speed
particles.vz = 0.0 | speed
particles.radius = 0.0 | length
self.nbodycode.particles.add_particles(particles)
self.from_model_to_nbody = particles.new_channel_to(
self.nbodycode.particles)
self.nbodycode.commit_particles()
self.particles = particles
def test20(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test20"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
shape = 10, 10, 10
p = Grid(*shape)
p.mass = (numpy.asarray([x * 2.0 for x in range(p.size)])).reshape(shape)
io.write_set_to_file(p, output_file, "hdf5", version = self.store_version())
loaded = io.read_set_from_file(output_file, "hdf5", version = self.store_version())
loaded = self.get_version_in_store(loaded)
self.assertAlmostRelativeEquals(p.mass[0][1][2], 24)
self.assertAlmostRelativeEquals(p[0][1][2].mass, 24)
def test12(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test12"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
shape = 10, 10, 10
p = Grid(*shape)
p.mass = ([x * 2.0 for x in range(p.size)] | units.kg).reshape(shape)
p.model_time = 2.0 | units.s
io.write_set_to_file(p.savepoint(timestamp = 2 | units.Myr, scale = 1 | units.kg), output_file, "hdf5", version = self.store_version())
loaded_particles = io.read_set_from_file(output_file, "hdf5", version = self.store_version())
loaded_particles = self.get_version_in_store(loaded_particles)
a = loaded_particles.collection_attributes
self.assertAlmostRelativeEquals(a.timestamp, 2 | units.Myr)
self.assertAlmostRelativeEquals(a.scale, 1 | units.kg)
def test26(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test26"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
p = Grid(20)
io.write_set_to_file(p, output_file, format='amuse', version = self.store_version())
os.remove(output_file)
def setup_simple_grid(self):
test_grid = Grid.create((4, 3, 2), [1.0, 1.0, 1.0] | units.m)
test_grid.rho = numpy.linspace(1.0, 2.0, num=24).reshape(
test_grid.shape) | units.kg / units.m**3
test_grid.rhovx = test_grid.rho * (3.0 | units.m / units.s)
test_grid.rhovy = test_grid.rho * (4.0 | units.m / units.s)
test_grid.rhovz = test_grid.rho * (0.0 | units.m / units.s)
test_grid.energy = test_grid.rho * ((1.0 |
(units.m / units.s)**2) + 0.5 *
(5.0 | units.m / units.s)**2)
return test_grid
def test53(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test53"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
stars = Particles(2)
stars[0].x = 1.0 | units.km
stars[1].x = 2.0 | units.km
gas = Grid(2,3)
gas.y = [[1.0, 2.0, 3.0], [4.0,5.0,6.0]] | units.km
stars[0].gas = gas
io.write_set_to_file(stars, output_file, "hdf5", version = self.store_version())
loaded_stars = io.read_set_from_file(output_file, "hdf5", version = self.store_version())
self.assertAlmostRelativeEquals(loaded_stars[0].gas[0][0].y,1.0 | units.km)
self.assertAlmostRelativeEquals(loaded_stars[0].gas[0][2].y,3.0 | units.km)
self.assertEquals(loaded_stars[1].gas, None)
def test54b(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test24"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
stars = Particles(2)
stars[0].x = 1.0 | units.km
stars[1].x = 2.0 | units.km
gas = Grid(2,3)
gas.y = [[1.0, 2.0, 3.0], [4.0,5.0,6.0]] | units.km
gas[0][0].particle = stars[0]
gas[1][2].particle = stars[0]
gas[1][0].particle = stars[1]
#stars[0].gas = gas[0][0]
#stars[1].gas = gas[1][0]
self.assertAlmostRelativeEquals(gas[0][0].particle.x,1.0 | units.km)
self.assertAlmostRelativeEquals(gas[1][2].particle.x,1.0 | units.km)
self.assertAlmostRelativeEquals(gas[1][0].particle.x,2.0 | units.km)
io.write_set_to_file(gas, output_file, "hdf5", version = self.store_version())
loaded_gas = io.read_set_from_file(output_file, "hdf5", version = self.store_version())
self.assertAlmostRelativeEquals(loaded_gas[0][0].particle.x, 1.0 | units.km)
self.assertAlmostRelativeEquals(loaded_gas[1][2].particle.x, 1.0 | units.km)
self.assertAlmostRelativeEquals(loaded_gas[1][0].particle.x, 2.0 | units.km)
self.assertEquals(id(loaded_gas[0][0].particle.get_containing_set()), id(loaded_gas[1][2].particle.get_containing_set()))
self.assertEqual(loaded_gas.particle.shape, loaded_gas.shape)
gas_copy = loaded_gas.copy()
gas_copy[0][0].particle.x = 3 | units.km
self.assertAlmostRelativeEquals(loaded_gas[0][0].particle.x, 1.0 | units.km)
self.assertAlmostRelativeEquals(gas_copy[0][0].particle.x, 3.0 | units.km)
self.assertAlmostRelativeEquals(gas_copy[1][2].particle.x, 3.0 | units.km)
def test56(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path,
"test26" + self.store_version() + ".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
number_of_particles = 10
p = Particles(number_of_particles)
p.mass = [x * 2.0 for x in range(number_of_particles)] | units.kg
p.model_time = 2.0 | units.s
gas = Grid(2, 3)
gas.y = [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]] | units.km
io.write_set_to_file(p,
output_file,
"hdf5",
particle=p[1],
particles=p,
gridpoint=gas[0][0],
grid=gas,
version=self.store_version())
loaded_particles = io.read_set_from_file(output_file,
"hdf5",
version=self.store_version(),
copy_history=False,
close_file=False)
attributes = loaded_particles.collection_attributes
self.assertAlmostRelativeEquals(attributes.particle.mass,
loaded_particles[1].mass)
self.assertEquals(attributes.particle.key, loaded_particles[1].key)
self.assertEquals(id(attributes.particles), id(loaded_particles))
self.assertAlmostRelativeEquals(attributes.gridpoint.y, 1.0 | units.km)
self.assertAlmostRelativeEquals(attributes.grid[0][0].y,
1.0 | units.km)
def test6(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test6_grid"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
instance = self.store_factory()(output_file)
shape = 10, 10, 10
p = Grid(*shape)
p.mass = ([x * 2.0 for x in range(p.size)] | units.kg).reshape(shape)
p.model_time = 2.0 | units.s
instance.store_grid(p.savepoint(1| units.Myr))
loaded_grid = self.get_version_in_store(instance.load_grid())
self.assertAlmostRelativeEquals(loaded_grid.get_timestamp(), 1| units.Myr)
self.assertEquals(loaded_grid.shape, shape)
self.assertEquals(loaded_grid[0][0][0].mass, 0 | units.kg)
self.assertAlmostRelativeEquals(loaded_grid[...,1,1].mass, p[...,1,1].mass)
instance.close()
def test56(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test26"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
number_of_particles = 10
p = Particles(number_of_particles)
p.mass = [x * 2.0 for x in range(number_of_particles)] | units.kg
p.model_time = 2.0 | units.s
gas = Grid(2,3)
gas.y = [[1.0, 2.0, 3.0], [4.0,5.0,6.0]] | units.km
io.write_set_to_file(
p,
output_file,
"hdf5",
particle = p[1],
particles = p,
gridpoint = gas[0][0],
grid = gas,
version = self.store_version()
)
loaded_particles = io.read_set_from_file(
output_file,
"hdf5",
version = self.store_version()
)
attributes = loaded_particles.collection_attributes
self.assertAlmostRelativeEquals(attributes.particle.mass, loaded_particles[1].mass)
self.assertAlmostRelativeEquals(attributes.particle.key, loaded_particles[1].key)
self.assertEquals(id(attributes.particles), id(loaded_particles))
self.assertAlmostRelativeEquals(attributes.gridpoint.y, 1.0 | units.km)
self.assertAlmostRelativeEquals(attributes.grid[0][0].y, 1.0 | units.km)
def test27(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test27"+self.store_version()+".hdf5")
if os.path.exists(output_file):
os.remove(output_file)
instance = self.store_factory()(output_file)
shape = 10,
p = Grid(*shape)
p.mass = ([x * 2.0 for x in range(p.size)] | units.kg).reshape(shape)
p.model_time = 2.0 | units.s
instance.store_grid(p)
loaded_grid = instance.load_grid()
self.assertEquals(loaded_grid.shape, shape)
loaded_mass_in_kg = loaded_grid.mass.value_in(units.kg)
previous_mass_in_kg = p.mass.value_in(units.kg)
for expected, actual in zip(previous_mass_in_kg, loaded_mass_in_kg):
self.assertEquals(expected, actual)
instance.close()
def test59(self):
test_results_path = self.get_path_to_results()
output_file = os.path.join(test_results_path, "test59"+self.store_version()+".h5")
if os.path.exists(output_file):
os.remove(output_file)
g=Grid(10,10)
p=Particles(2)
p[0].sub=g[0:5]
io.write_set_to_file(p, output_file,"amuse", version=self.store_version())
z = io.read_set_from_file(output_file,"amuse")
os.remove(output_file)
def new_grid(self):
density = mass / length**3
density = density
momentum = speed * density
energy = mass / (time**2 * length)
grid = Grid.create(self.dimensions_of_mesh, (10.0, 10.0, 10.0) | length)
grid.rho = self.rho_medium
grid.rhovx = 0.0 | momentum
grid.rhovy = 0.0 | momentum
grid.rhovz = 0.0 | momentum
grid.energy = 0.0 | energy
return grid
def test_evolve_w_plot(sysfac,
tend=1. | units.hour,
dt=3600. | units.s,
dtplot=None):
sys = sysfac()
if dtplot is None:
dtplot = dt
pyplot.ion()
f = pyplot.figure(figsize=(10, 10))
pyplot.show()
i = 0
Lx = sys.parameters.Lx
grid = Grid.create((400, 400), (Lx, Lx))
dx, dy = grid.cellsize()
Lx = Lx.value_in(1000 * units.km)
x = grid.x.flatten()
y = grid.y.flatten()
while sys.model_time < tend - dtplot / 2:
i = i + 1
sys.evolve_model(sys.model_time + dtplot, dt=dt)
psi, dpsi = sys.get_psi_dpsidt(dx + 0. * x, x, y)
psi = psi.reshape(grid.shape)
# psi=sys.grid[:,:,0].psi
f.clf()
f1 = pyplot.subplot(111)
f1.imshow(psi.transpose() / psi.max(),
vmin=0,
vmax=1,
extent=[0, Lx, 0, Lx],
origin="lower")
f1.set_xlabel("x (x1000 km)")
pyplot.draw()
pyplot.savefig("test_bc.png")
if i % 100 == 25:
print("wait")
raw_input()
print("done")
raw_input()
def new_grid(self):
density = mass / length**3
density = density
momentum = speed * density
energy = mass / (time**2 * length)
grid = Grid.create(self.dimensions_of_mesh,
(10.0, 10.0, 10.0) | length)
grid.rho = self.rho_medium
grid.rhovx = 0.0 | momentum
grid.rhovy = 0.0 | momentum
grid.rhovz = 0.0 | momentum
grid.energy = 0.0 | energy
return grid
def derive_stellar_structure(self):
sorted = self.sph_particles.pressure.argsort()[::-1]
binned = sorted.reshape((-1, self.particles_per_zone))
stellar_model = Grid(binned.shape[0])
stellar_model.dmass = self.sph_particles.mass[binned].sum(axis=1)
stellar_model.mass = stellar_model.dmass.accumulate()
stellar_model.pressure = self.sph_particles.pressure[binned].sum(
axis=1)
stellar_model.rho = stellar_model.dmass / (
self.sph_particles.mass /
self.sph_particles.density)[binned].sum(axis=1)
stellar_model.radius = (
(3 / (4 * numpy.pi)) * stellar_model.dmass /
stellar_model.rho).accumulate()**(1.0 / 3.0) * 1
stellar_model.temperature = (
(self.sph_particles.mass * self.sph_particles.u *
self.sph_particles.mu)[binned].sum(axis=1) /
(1.5 * constants.kB * stellar_model.dmass)).as_quantity_in(units.K)
zeros = numpy.zeros(len(stellar_model.dmass))
stellar_model.luminosity = zeros - 1 | units.LSun
attribute_names = self.sph_particles.get_attribute_names_defined_in_store(
)
for attribute, name in [("h1", "X_H"), ("he4", "X_He"), ("c12", "X_C"),
("n14", "X_N"), ("o16", "X_O"),
("ne20", "X_Ne"), ("mg24", "X_Mg"),
("si28", "X_Si"), ("fe56", "X_Fe")]:
if attribute in attribute_names:
setattr(
stellar_model, name, (self.sph_particles.mass * getattr(
self.sph_particles, attribute))[binned].sum(axis=1) /
stellar_model.dmass)
else:
setattr(stellar_model, name, zeros)
return stellar_model
def derive_stellar_structure(self):
sorted = self.sph_particles.pressure.argsort()[::-1]
binned = sorted.reshape((-1, self.particles_per_zone))
stellar_model = Grid(binned.shape[0])
stellar_model.dmass = self.sph_particles.mass[binned].sum(axis=1)
stellar_model.mass = stellar_model.dmass.accumulate()
stellar_model.pressure= self.sph_particles.pressure[binned].sum(axis=1)
stellar_model.rho = stellar_model.dmass / (self.sph_particles.mass / self.sph_particles.density)[binned].sum(axis=1)
stellar_model.radius = ((3 / (4 * numpy.pi)) * stellar_model.dmass / stellar_model.rho).accumulate()**(1.0/3.0) * 1
stellar_model.temperature = ((self.sph_particles.mass * self.sph_particles.u * self.sph_particles.mu)[binned].sum(axis=1) /
(1.5 * constants.kB * stellar_model.dmass)).as_quantity_in(units.K)
zeros = numpy.zeros(len(stellar_model.dmass))
stellar_model.luminosity = zeros - 1 | units.LSun
attribute_names = self.sph_particles.get_attribute_names_defined_in_store()
for attribute, name in [("h1", "X_H"), ("he4", "X_He"), ("c12", "X_C"), ("n14", "X_N"),
("o16", "X_O"), ("ne20", "X_Ne"), ("mg24", "X_Mg"), ("si28", "X_Si"), ("fe56", "X_Fe")]:
if attribute in attribute_names:
setattr(stellar_model, name, (self.sph_particles.mass * getattr(self.sph_particles, attribute))[binned].sum(axis=1) / stellar_model.dmass)
else:
setattr(stellar_model, name, zeros)
return stellar_model
def generate_grid(self,n=10,m=10, FI0=-80. | units.deg, FI1=80. | units.deg,
L0=0. | units.deg, L1=360. | units.deg,
dFI=None, dL=None):
if dFI is None:
dFI=(FI1-FI0)/n
if dL is None:
dL=(L1-L0)/m
FI,L=numpy.mgrid[in_deg(FI0):in_deg(FI1):in_deg(dFI),
in_deg(L0):in_deg(L1):in_deg(dL)]
FI=FI|units.deg
L=L|units.deg
n,m=FI.shape
fi,l=self.forward_transform(FI,L)
grid=Grid((n,m))
grid.FI=FI
grid.L=L
grid.lat=to_deg(fi)
grid.lon=to_deg(l)
return grid
def get_sets(self):
nodes=Grid(self.parameters["NP"])
if self.coordinates=="cartesian":
nodes.x=self.p[:,0] | units.m
nodes.y=self.p[:,1] | units.m
else:
nodes.lon=self.p[:,0] | units.deg
nodes.lat=self.p[:,1] | units.deg
nodes.depth=self.p[:,2] | units.m
elements=Grid(self.parameters["NE"])
elements.nodes=[(x[1]-1,x[2]-1,x[3]-1) for x in self.t]
elev_boundary=[]
for type_,seg in self.elev_spec_boundary_seg:
indices=seg-1
b=Grid(len(indices))
b.nodes=indices
b.type=type_
elev_boundary.append(b)
flow_boundary=[]
for type_,seg in self.flow_spec_boundary_seg:
indices=seg-1
b=Grid(len(indices))
b.nodes=indices
b.type=type_
flow_boundary.append(b)
return nodes,elements,elev_boundary,flow_boundary
def get_sets(self):
nodes = Grid(self.parameters["NP"])
if self.coordinates == "cartesian":
nodes.x = self.p[:, 0] | units.m
nodes.y = self.p[:, 1] | units.m
else:
nodes.lon = self.p[:, 0] | units.deg
nodes.lat = self.p[:, 1] | units.deg
nodes.vmark = self.vmark
elements = Grid(self.parameters["NE"])
elements.n1 = [(x[0]) for x in self.t]
elements.n2 = [(x[1]) for x in self.t]
elements.n3 = [(x[2]) for x in self.t]
return nodes, elements #,elev_boundary,flow_boundary
def hydro_plot(view, hydro_code, image_size, time, figname):
"""
Produce a series of images suitable for conversion into a movie.
view: the (physical) region to plot [xmin, xmax, ymin, ymax]
hydro_code: hydrodynamics code in which the gas to be plotted is defined
image_size: size of the output image in pixels (x, y)
time: current hydro code time
"""
if not HAS_MATPLOTLIB:
return
shape = (image_size[0], image_size[1], 1)
size = image_size[0] * image_size[1]
axis_lengths = [0.0, 0.0, 0.0] | units.m
axis_lengths[0] = view[1] - view[0]
axis_lengths[1] = view[3] - view[2]
grid = Grid.create(shape, axis_lengths)
grid.x += view[0]
grid.y += view[2]
speed = grid.z.reshape(size) * (0 | 1 / units.s)
rho, rhovx, rhovy, rhovz, rhoe \
= hydro_code.get_hydro_state_at_point(
grid.x.reshape(size), grid.y.reshape(size), grid.z.reshape(size),
speed, speed, speed)
min_v = 800.0 | units.km / units.s
max_v = 3000.0 | units.km / units.s
min_rho = 3.0e-9 | units.g / units.cm**3
max_rho = 1.0e-5 | units.g / units.cm**3
min_E = 1.0e11 | units.J / units.kg
max_E = 1.0e13 | units.J / units.kg
v_sqr = (rhovx**2 + rhovy**2 + rhovz**2) / rho**2
E = rhoe / rho
log_v = numpy.log((v_sqr / min_v**2)) / numpy.log((max_v**2 / min_v**2))
log_rho = numpy.log((rho / min_rho)) / numpy.log((max_rho / min_rho))
log_E = numpy.log((E / min_E)) / numpy.log((max_E / min_E))
red = numpy.minimum(numpy.ones_like(rho.number),
numpy.maximum(numpy.zeros_like(rho.number),
log_rho)).reshape(shape)
green = numpy.minimum(numpy.ones_like(rho.number),
numpy.maximum(numpy.zeros_like(rho.number),
log_v)).reshape(shape)
blue = numpy.minimum(numpy.ones_like(rho.number),
numpy.maximum(numpy.zeros_like(rho.number),
log_E)).reshape(shape)
alpha = numpy.minimum(
numpy.ones_like(log_v),
numpy.maximum(numpy.zeros_like(log_v), numpy.log(
(rho / (10 * min_rho))))).reshape(shape)
rgba = numpy.concatenate((red, green, blue, alpha), axis=2)
pyplot.figure(figsize=(image_size[0] / 100.0, image_size[1] / 100.0),
dpi=100)
im = pyplot.figimage(rgba, origin='lower')
pyplot.savefig(figname,
transparent=True,
dpi=100,
facecolor='k',
edgecolor='k')
print("Saved hydroplot at time", time, "in file")
print(' ', figname)
pyplot.close()
def new_grid(self):
grid = Grid.create(self.dimensions_of_mesh, [1, 1, 1] | length)
self.clear_grid(grid)
return grid
def new_grid():
grid = Grid.create(DIMENSIONS_OF_MESH, [1, 1, 1] | length)
clear_grid(grid)
return grid
def initialize_grid(grid, magentic_field_grid):
temp = [1,1,1] | length
l = 1.0 | length;
A_grid = Grid.create(DIMENSIONS_OF_A_MESH, temp + grid.cellsize()*[2,2,0])
A_grid.position -= A_grid.cellsize()*[0.5,0.5,0.0]
A_grid.Az = (
B0*l/(4.0*PI)*numpy.cos(4.0*PI/l*A_grid.x) +
B0*l/(2.0*PI)*numpy.cos(2.0*PI/l*A_grid.y))
assert grid.cellsize().x == A_grid.cellsize().x
assert grid.cellsize().y == A_grid.cellsize().y
# assert grid.dim[0] == A_grid.dim[0]
magentic_field_grid.B1i = (A_grid.Az[:-1,1:,...] - A_grid.Az[:-1,:-1,...])/A_grid.cellsize().y;
magentic_field_grid.B2i = -(A_grid.Az[1:,:-1,...] - A_grid.Az[:-1,:-1,...])/A_grid.cellsize().x;
magentic_field_grid.B3i = 0.0 | magnetic_field;
#magentic_field_grid.B1i[-1,...,...] = magentic_field_grid.B1i[0,...,...]
#magentic_field_grid.B2i[...,-1,...] = magentic_field_grid.B2i[...,0,...]
magentic_field_grid.B1c = 0.0 | magnetic_field;
magentic_field_grid.B2c = 0.0 | magnetic_field;
magentic_field_grid.B3c = 0.0 | magnetic_field;
magentic_field_grid.divB = 0.0 | (magnetic_field / length)
magentic_field_grid.B1c[:-1,...,...] = (magentic_field_grid.B1i[:-1,...,...] + magentic_field_grid.B1i[1:,...,...])*0.5
magentic_field_grid.B2c[...,:-1,...] = (magentic_field_grid.B2i[...,:-1,...] + magentic_field_grid.B2i[...,1:,...])*0.5
magentic_field_grid.B3c = magentic_field_grid.B3i
# magentic_field_grid.B1c[-1,...,...] = magentic_field_grid.B1c[0,...,...]
# magentic_field_grid.B2c[...,-1,...] = magentic_field_grid.B2c[...,0,...]
mu0 = 1.0 | (mass*length/time**2/current**2)
magentic_field_grid.divB[0:-1,0:-1,...] = (
(magentic_field_grid.B1i[:-1,:-1,...] - magentic_field_grid.B1i[1:,:-1,...])/grid.cellsize().x +
(magentic_field_grid.B2i[:-1,:-1,...] - magentic_field_grid.B2i[:-1,1:,...])/grid.cellsize().y
)
assert (abs(magentic_field_grid.divB[:-1,:-1,:-1]) < 1.0e-10 | magentic_field_grid.divB.unit).all()
assert magentic_field_grid.B1i.unit == magnetic_field
grid.rho = D0
grid.rhovx = -D0*V0*numpy.sin(2.0*PI/l*grid.y)
grid.rhovy = D0*V0*numpy.sin(2.0*PI/l*grid.x)
grid.rhovz = 0.0 | momentum
print("sum rho vx:", grid.rhovx.sum())
print("sum rho vy:",grid.rhovy.sum())
print("sum rho vz:",grid.rhovz.sum())
grid.energy = (
P0 / (GAMMA - 1) +
0.5 * (grid.rhovx**2 + grid.rhovy**2 + grid.rhovz**2)/grid.rho +
0.5 * (magentic_field_grid.B1c[:-1,:-1,:-1]**2 + magentic_field_grid.B2c[:-1,:-1,:-1]**2 + magentic_field_grid.B3c[:-1,:-1,:-1]**2)/mu0
)
def initialize_grid(grid, magentic_field_grid):
temp = [1, 1, 1] | length
l = 1.0 | length
A_grid = Grid.create(DIMENSIONS_OF_A_MESH,
temp + grid.cellsize() * [2, 2, 0])
A_grid.position -= A_grid.cellsize() * [0.5, 0.5, 0.0]
A_grid.Az = (B0 * l / (4.0 * PI) * numpy.cos(4.0 * PI / l * A_grid.x) +
B0 * l / (2.0 * PI) * numpy.cos(2.0 * PI / l * A_grid.y))
assert grid.cellsize().x == A_grid.cellsize().x
assert grid.cellsize().y == A_grid.cellsize().y
# assert grid.dim[0] == A_grid.dim[0]
magentic_field_grid.B1i = (A_grid.Az[:-1, 1:, ...] -
A_grid.Az[:-1, :-1, ...]) / A_grid.cellsize().y
magentic_field_grid.B2i = (
-(A_grid.Az[1:, :-1, ...] - A_grid.Az[:-1, :-1, ...]) /
A_grid.cellsize().x)
magentic_field_grid.B3i = 0.0 | magnetic_field
# magentic_field_grid.B1i[-1,...,...] = magentic_field_grid.B1i[0,...,...]
# magentic_field_grid.B2i[...,-1,...] = magentic_field_grid.B2i[...,0,...]
magentic_field_grid.B1c = 0.0 | magnetic_field
magentic_field_grid.B2c = 0.0 | magnetic_field
magentic_field_grid.B3c = 0.0 | magnetic_field
magentic_field_grid.divB = 0.0 | (magnetic_field / length)
magentic_field_grid.B1c[:-1, ..., ...] = (
magentic_field_grid.B1i[:-1, ..., ...] +
magentic_field_grid.B1i[1:, ..., ...]) * 0.5
magentic_field_grid.B2c[
..., :-1, ...] = (magentic_field_grid.B2i[..., :-1, ...] +
magentic_field_grid.B2i[..., 1:, ...]) * 0.5
magentic_field_grid.B3c = magentic_field_grid.B3i
# magentic_field_grid.B1c[-1,...,...] = magentic_field_grid.B1c[0,...,...]
# magentic_field_grid.B2c[...,-1,...] = magentic_field_grid.B2c[...,0,...]
mu0 = 1.0 | (mass * length / time**2 / current**2)
magentic_field_grid.divB[0:-1, 0:-1, ...] = (
(magentic_field_grid.B1i[:-1, :-1, ...] -
magentic_field_grid.B1i[1:, :-1, ...]) / grid.cellsize().x +
(magentic_field_grid.B2i[:-1, :-1, ...] -
magentic_field_grid.B2i[:-1, 1:, ...]) / grid.cellsize().y)
assert (abs(magentic_field_grid.divB[:-1, :-1, :-1]) <
1.0e-10 | magentic_field_grid.divB.unit).all()
assert magentic_field_grid.B1i.unit == magnetic_field
grid.rho = D0
grid.rhovx = -D0 * V0 * numpy.sin(2.0 * PI / l * grid.y)
grid.rhovy = D0 * V0 * numpy.sin(2.0 * PI / l * grid.x)
grid.rhovz = 0.0 | momentum
print("sum rho vx:", grid.rhovx.sum())
print("sum rho vy:", grid.rhovy.sum())
print("sum rho vz:", grid.rhovz.sum())
grid.energy = (P0 / (GAMMA - 1) + 0.5 *
(grid.rhovx**2 + grid.rhovy**2 + grid.rhovz**2) / grid.rho +
0.5 * (magentic_field_grid.B1c[:-1, :-1, :-1]**2 +
magentic_field_grid.B2c[:-1, :-1, :-1]**2 +
magentic_field_grid.B3c[:-1, :-1, :-1]**2) / mu0)
def create_grid(*arg):
grid = Grid.create(*arg)
grid.add_vector_attribute("momentum", ["rhovx", "rhovy", "rhovz"])
return grid
def new_grid(self):
grid = Grid.create(self.dimensions_of_mesh, [1,1,1] | length)
self.clear_grid(grid)
return grid
def new_grid():
grid = Grid.create(DIMENSIONS_OF_MESH, [1,1,1] | length)
clear_grid(grid)
return grid