def evolve_model(self, time):
self.code.stopping_conditions.number_of_steps_detection.disable()
self.code.stopping_conditions.number_of_steps_detection.enable()
epsilon = 1e-12 | units.s
while self.code.model_time + epsilon < time:
self.code.evolve_model(time)
if 0: # plot for debugging
phi = self.code.grid.gravitational_potential[:, :, 0]
figure = pyplot.figure(figsize=(10, 5))
plot = figure.add_subplot(1, 1, 1)
plot.imshow(phi.value_in(units.m**2 / units.s**2))
pyplot.show()
print phi[:, 1][0:10]
self.P0 = phi
def main():
number_of_grid_points = 400
name_of_the_code = "athena"
model = CalculateKelvinHelmholtzInstability(
number_of_grid_points=number_of_grid_points, number_of_workers=1, name_of_the_code=name_of_the_code
)
if not IS_PLOT_AVAILABLE:
return
grids = model.get_solution_at_time(1.0 | time)
rho = grids[0].rho[..., ..., 0].value_in(density)
figure = pyplot.figure(figsize=(20, 20))
plot = figure.add_subplot(1, 1, 1)
plot.imshow(rho, origin="lower")
figure.savefig("kelvin_helmholtz_{0}_{1}.png".format(name_of_the_code, number_of_grid_points))
pyplot.show()
def evolve_model(self, time):
self.code.stopping_conditions.number_of_steps_detection.disable()
self.code.stopping_conditions.number_of_steps_detection.enable()
epsilon = 1e-12 | units.s
while self.code.model_time + epsilon < time:
self.code.evolve_model(time)
if 0: # plot for debugging
phi = self.code.grid.gravitational_potential[:, :, 0]
figure = pyplot.figure(figsize=(10, 5))
plot = figure.add_subplot(1, 1, 1)
plot.imshow(phi.value_in(units.m**2 / units.s**2))
pyplot.show()
print(phi[:, 1][0:10])
self.P0 = phi
def main():
number_of_grid_points = 400
name_of_the_code = 'athena'
model = CalculateKelvinHelmholtzInstability(
number_of_grid_points=number_of_grid_points,
number_of_workers=1,
name_of_the_code=name_of_the_code)
if not IS_PLOT_AVAILABLE:
return
grids = model.get_solution_at_time(1.0 | time)
rho = grids[0].rho[..., ..., 0].value_in(density)
figure = pyplot.figure(figsize=(20, 20))
plot = figure.add_subplot(1, 1, 1)
plot.imshow(rho, origin='lower')
figure.savefig('kelvin_helmholtz_{0}_{1}.png'.format(
name_of_the_code, number_of_grid_points))
pyplot.show()
def gravity_for_code(self, field, grid):
x = field.x.flatten()
y = field.y.flatten()
z = field.z.flatten()
rho = field.rho.flatten()
cell_size = (self.length_scale / self.ncells)
cell_volume = cell_size * cell_size * (1 | units.cm)
epsilon_squared = cell_size ** 2
cell_mass = rho * cell_volume
for cell in grid.iter_cells():
dx = x - cell.x
dy = y - cell.y
dz = z - cell.z
r_squared = (dx**2 + dy**2 + dz**2 + epsilon_squared)
r = r_squared.sqrt()
cell.potential = constants.G * (cell_mass / r).sum()
phi = grid.potential[:, :, 0]
figure = pyplot.figure(figsize=(10, 5))
plot = figure.add_subplot(1, 1, 1)
plot.imshow(phi.value_in(units.m**2 / units.s**2))
pyplot.show()
def gravity_for_code(self, field, grid):
x = field.x.flatten()
y = field.y.flatten()
z = field.z.flatten()
rho = field.rho.flatten()
cell_size = (self.length_scale / self.ncells)
cell_volume = cell_size * cell_size * (1 | units.cm)
epsilon_squared = cell_size ** 2
cell_mass = rho * cell_volume
for cell in grid.iter_cells():
dx = x - cell.x
dy = y - cell.y
dz = z - cell.z
r_squared = (dx**2 + dy**2 + dz**2 + epsilon_squared)
r = r_squared.sqrt()
cell.potential = constants.G * (cell_mass / r).sum()
phi = grid.potential[:, :, 0]
figure = pyplot.figure(figsize=(10, 5))
plot = figure.add_subplot(1, 1, 1)
plot.imshow(phi.value_in(units.m**2 / units.s**2))
pyplot.show()
def calculate_potential_for_grid(self, grid, field):
x = field.x.flatten()
x = field.x[:, 0, 0]
y = field.y[0, :, 0]
# we assume constant grid spacing so
# we just create a sample space using
# the number of points in x and y
nx = len(x)
ny = len(y)
dx = x[1] - x[0]
dy = y[1] - y[0]
#
# wavenumbers from online examples
# kx = (2 * numpy.pi) * numpy.fft.fftfreq(nx, d = dx ) * (1 | units.m)
# ky = (2 * numpy.pi) * numpy.fft.fftfreq(ny, d = dy ) * (1 | units.m)
#
# wavenumbers as calculated in athena
dkx = 2.0*numpy.pi/nx
dky = 2.0*numpy.pi/ny
kx = ((((2.0*numpy.cos(numpy.arange(nx) * dkx))-2.0)/(dx**2))
).value_in(units.m**-2)
ky = ((((2.0*numpy.cos(numpy.arange(ny) * dky))-2.0)/(dy**2))
).value_in(units.m**-2)
kx_grid, ky_grid = numpy.meshgrid(kx, ky)
# convert rho to 2d field
rho = field.rho[:, :, 0]
# use rho0 as mean, should be equal to rho.mean()
# but we are comparing with athena and
# want the most accurate solution
rho_mean = self.rho0 # field.rho.mean()
# to remove division by zero
kx_grid[0][0] = 1
ky_grid[0][0] = 1
# for poisson solver the source term (gravity)
# has to sum to zero over the field
# we can ensure this by subtracting the mean from rho
rho -= rho_mean
gravity_function = 4 * numpy.pi * constants.G * rho
gravity_function = gravity_function.value_in(units.s ** -2)
gravity_function_fourier_space = numpy.fft.fftn(gravity_function)
phi_fourier_space = gravity_function_fourier_space / \
(kx_grid + ky_grid)
# 0,0 was divided by zero, should just be zero
phi_fourier_space[0, 0] = 0
phi = numpy.fft.ifftn(phi_fourier_space).real
# we removed the units for fft, replace these
phi = phi | units.m**2 / units.s**2
if 0: # plot for debugging
phi_delta = phi # - self.P0
figure = pyplot.figure(figsize=(10, 5))
plot = figure.add_subplot(1, 2, 1)
plot.imshow(phi_delta.value_in(units.m**2 / units.s**2)[1:, 1:])
plot = figure.add_subplot(1, 2, 2)
plot.imshow(
(phi - self.P0).value_in(units.m**2 / units.s**2)[1:, 1:])
pyplot.show()
print phi[:, 1][0:10]
print (phi[:, 1][0:10] - self.P0[:, 1][0:10]) / phi[:, 1][0:10]
def calculate_potential_for_grid(self, grid, field):
x = field.x.flatten()
x = field.x[:, 0, 0]
y = field.y[0, :, 0]
# we assume constant grid spacing so
# we just create a sample space using
# the number of points in x and y
nx = len(x)
ny = len(y)
dx = x[1] - x[0]
dy = y[1] - y[0]
#
# wavenumbers from online examples
# kx = (2 * numpy.pi) * numpy.fft.fftfreq(nx, d = dx ) * (1 | units.m)
# ky = (2 * numpy.pi) * numpy.fft.fftfreq(ny, d = dy ) * (1 | units.m)
#
# wavenumbers as calculated in athena
dkx = 2.0*numpy.pi/nx
dky = 2.0*numpy.pi/ny
kx = ((((2.0*numpy.cos(numpy.arange(nx) * dkx))-2.0)/(dx**2))
).value_in(units.m**-2)
ky = ((((2.0*numpy.cos(numpy.arange(ny) * dky))-2.0)/(dy**2))
).value_in(units.m**-2)
kx_grid, ky_grid = numpy.meshgrid(kx, ky)
# convert rho to 2d field
rho = field.rho[:, :, 0]
# use rho0 as mean, should be equal to rho.mean()
# but we are comparing with athena and
# want the most accurate solution
rho_mean = self.rho0 # field.rho.mean()
# to remove division by zero
kx_grid[0][0] = 1
ky_grid[0][0] = 1
# for poisson solver the source term (gravity)
# has to sum to zero over the field
# we can ensure this by subtracting the mean from rho
rho -= rho_mean
gravity_function = 4 * numpy.pi * constants.G * rho
gravity_function = gravity_function.value_in(units.s ** -2)
gravity_function_fourier_space = numpy.fft.fftn(gravity_function)
phi_fourier_space = gravity_function_fourier_space / \
(kx_grid + ky_grid)
# 0,0 was divided by zero, should just be zero
phi_fourier_space[0, 0] = 0
phi = numpy.fft.ifftn(phi_fourier_space).real
# we removed the units for fft, replace these
phi = phi | units.m**2 / units.s**2
if 0: # plot for debugging
phi_delta = phi # - self.P0
figure = pyplot.figure(figsize=(10, 5))
plot = figure.add_subplot(1, 2, 1)
plot.imshow(phi_delta.value_in(units.m**2 / units.s**2)[1:, 1:])
plot = figure.add_subplot(1, 2, 2)
plot.imshow(
(phi - self.P0).value_in(units.m**2 / units.s**2)[1:, 1:])
pyplot.show()
print(phi[:, 1][0:10])
print((phi[:, 1][0:10] - self.P0[:, 1][0:10]) / phi[:, 1][0:10])
