def save_auxilliary3D(
auxfile,
pressure_m,
rho_m,
temperature,
pbeta,
alfven,
cspeed,
dxB2,
dyB2,
option_pars,
physical_constants,
coords,
Nxyz,
xindex,
rank=0,
collective=False,
):
""" Save auxilliary variables for use in plotting background setup in
hdf5 (gdf default) format after collating the data from mpi sub processes
if necessary.
"""
if rank == 0:
print'writing',auxfile
print'non-SAC 3D auxilliary data for plotting'
grid_dimensions = [Nxyz[0], Nxyz[1], Nxyz[2]]
left_edge = u.Quantity([coords['xmin'],
coords['ymin'],
coords['zmin']]).to(u.m)
right_edge = u.Quantity([coords['xmax'],
coords['ymax'],
coords['zmax']]).to(u.m)
simulation_parameters = gdf.SimulationParameters([
['boundary_conditions', np.zeros(6) + 2],
['cosmological_simulation', 0 ],
['current_iteration', 0 ],
['current_time', 0.0 ],
['dimensionality', 3 ],
['domain_dimensions', grid_dimensions ],
['domain_left_edge', left_edge ],
['domain_right_edge', right_edge ],
['eta', 0.0 ],
['field_ordering', 0 ],
['gamma', physical_constants['gamma'] ],
['gravity0', 0.0 ],
['gravity1', 0.0 ],
['gravity2', physical_constants['gravity']],
['nu', 0.0 ],
['num_ghost_zones', 0 ],
['refine_by', 0 ],
['unique_identifier', 'sacgdf2014' ]
])
if collective:
from mpi4py import MPI
gdf_file = gdf.create_file(h5py.File(auxfile,'w'),
simulation_parameters, grid_dimensions,
driver='mpio', comm=MPI.COMM_WORLD)
else:
gdf_file = gdf.create_file(h5py.File(auxfile,'w'),
simulation_parameters, grid_dimensions)
gdf.write_field(gdf_file,
pressure_m,
'pressure_mhs',
'Background magneto-pressure balance'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file,
rho_m,
'density_mhs',
'Background magneto-density balance'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file,
temperature,
'temperature',
'Background temperature'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file,
pbeta,
'plasma_beta',
'Background plasma beta'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file,
alfven,
'alfven_speed',
'Background Alfven speed'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file,
cspeed,
'sound_speed',
'Background sound speed'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file,
dxB2,
'mag_tension_x',
'x-component background magnetic tension'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file,
dyB2,
'mag_tension_y',
'y-component background magnetic tension'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf_file.close()
if collective:
mpi_save_SACvariables(
auxfile,
((pressure_m,
'pressure_mhs'),
( rho_m,
'density_mhs'),
(temperature,
'temperature'),
(pbeta,
'plasma_beta'),
(alfven,
'alfven_speed'),
(cspeed,
'sound_speed'),
(dxB2,
'mag_tension_x'),
(dyB2,
'mag_tension_y')),
xindex,
)
def save_auxilliary1D(
auxfile,
pressure_Z,
rho_Z,
Rgas_Z,
option_pars,
physical_constants,
coords,
Nxyz,
rank=0,
collective=False,
):
""" Save auxilliary variables for use in plotting background setup in
hdf5 (gdf default) format after collating the data from mpi sub processes
if necessary.
"""
if rank == 0:
print'writing',auxfile
print'non-SAC 1D auxilliary data for plotting'
grid_dimensions = [2, 2, Nxyz[2]] #dims > 1 to be read by yt
left_edge = u.Quantity([coords['xmin'],
coords['ymin'],
coords['zmin']]).to(u.m)
right_edge = u.Quantity([coords['xmax'],
coords['ymax'],
coords['zmax']]).to(u.m)
pressureHS = u.Quantity(np.zeros(grid_dimensions),
unit=pressure_Z.to("Pa").unit)
rhoHS = u.Quantity(np.zeros(grid_dimensions),
unit=rho_Z.to('kg/m**3').unit)
RgasHS = u.Quantity(np.zeros(grid_dimensions),
unit=Rgas_Z.to('m**2/(K s**2)').unit)
pressureHS[:] = pressure_Z
rhoHS[:] = rho_Z
RgasHS[:] = Rgas_Z
simulation_parameters = gdf.SimulationParameters([
['boundary_conditions', np.zeros(6) + 2],
['cosmological_simulation', 0 ],
['current_iteration', 0 ],
['current_time', 0.0 ],
['dimensionality', 3 ],
['domain_dimensions', grid_dimensions ],
['domain_left_edge', left_edge ],
['domain_right_edge', right_edge ],
['eta', 0.0 ],
['field_ordering', 0 ],
['gamma', physical_constants['gamma'] ],
['gravity0', 0.0 ],
['gravity1', 0.0 ],
['gravity2', physical_constants['gravity']],
['nu', 0.0 ],
['num_ghost_zones', 0 ],
['refine_by', 0 ],
['unique_identifier', 'sacgdf2014' ]
])
# import pdb; pdb.set_trace()
gdf_file = gdf.create_file(h5py.File(auxfile,'w'), simulation_parameters, grid_dimensions)
gdf.write_field(gdf_file,
pressureHS,
'pressure_HS',
'Background 1D hydrostatic-pressure'
,collective=collective
)
gdf.write_field(gdf_file,
rhoHS,
'density_HS',
'Background 1D hydrostatic-density'
,collective=collective
)
gdf.write_field(gdf_file,
RgasHS,
'ideal_gas_constant_HS',
'Background 1D hydrostatic-R_gas'
,collective=collective
)
gdf_file.close()
def save_SACvariables(
filename,
rho,
Bx,
By,
Bz,
energy,
option_pars,
physical_constants,
coords,
Nxyz,
xindex,
rank=0,
collective=False,
):
""" Save the background variables for a SAC model in hdf5 (gdf default)
format after collating the data from mpi sub processes if necessary.
"""
if rank == 0:
print'writing',filename
print'SAC background atmosphere'
grid_dimensions = [Nxyz[0], Nxyz[1], Nxyz[2]]
left_edge = u.Quantity([coords['xmin'],
coords['ymin'],
coords['zmin']]).to(u.m)
right_edge = u.Quantity([coords['xmax'],
coords['ymax'],
coords['zmax']]).to(u.m)
gamma = 5./3.
dummy = np.zeros(rho.shape)
simulation_parameters = gdf.SimulationParameters([
['boundary_conditions', np.zeros(6) + 2],
['cosmological_simulation', 0 ],
['current_iteration', 0 ],
['current_time', 0.0 ],
['dimensionality', 3 ],
['domain_dimensions', grid_dimensions ],
['domain_left_edge', left_edge ],
['domain_right_edge', right_edge ],
['eta', 0.0 ],
['field_ordering', 0 ],
['gamma', gamma ],
['gravity0', 0.0 ],
['gravity1', 0.0 ],
['gravity2', physical_constants['gravity'] ],
['nu', 0.0 ],
['num_ghost_zones', 0 ],
['refine_by', 0 ],
['unique_identifier', 'sacgdf2014' ]
])
if collective:
from mpi4py import MPI
gdf_file = gdf.create_file(h5py.File(filename,'w'),
simulation_parameters, grid_dimensions,
driver='mpio', comm=MPI.COMM_WORLD)
else:
gdf_file = gdf.create_file(h5py.File(filename,'w'), simulation_parameters, grid_dimensions)
gdf.write_field(gdf_file, rho,
'density_bg',
'Background Density'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, dummy*u.Unit('kg/m**3'),
'density_pert',
'Perturbation Density'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file,
energy,
'internal_energy_bg',
'Background Internal Energy'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, dummy*u.Unit('kg/(m s**2)'),
'internal_energy_pert',
'Perturbation Internal Energy'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, Bx,
'mag_field_x_bg',
'x Component of Background Magnetic Field'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, dummy*u.Unit('T'),
'mag_field_x_pert',
'x Component of Pertubation Magnetic Field'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, By,
'mag_field_y_bg',
'y Component of Background Magnetic Field'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, dummy*u.Unit('T'),
'mag_field_y_pert',
'y Component of Pertubation Magnetic Field'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, Bz,
'mag_field_z_bg',
'z Component of Background Magnetic Field'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, dummy*u.Unit('T'),
'mag_field_z_pert',
'z Component of Pertubation Magnetic Field'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, dummy*u.Unit('m/s'),
'velocity_x',
'x Component of Velocity'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, dummy*u.Unit('m/s'),
'velocity_y',
'y Component of Velocity'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file, dummy*u.Unit('m/s'),
'velocity_z',
'z Component of Velocity'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf_file.close()
if collective:
mpi_save_SACvariables(
filename,
((rho, 'density_bg' ),
(energy,'internal_energy_bg'),
(Bx, 'mag_field_x_bg' ),
(By, 'mag_field_y_bg' ),
(Bz, 'mag_field_z_bg' )),
xindex,
)
def save_SACsources(
sourcesfile,
Fx,
Fy,
option_pars,
physical_constants,
coords,
Nxyz,
xindex,
rank=0,
collective=False,
):
""" Save the balancing forces for a SAC model with multiple flux tubes in
hdf5 (gdf default) format after collating the data from mpi sub processes
if necessary.
"""
if rank == 0:
print'writing',sourcesfile
print'SAC background source terms'
grid_dimensions = [Nxyz[0], Nxyz[1], Nxyz[2]]
left_edge = u.Quantity([coords['xmin'],
coords['ymin'],
coords['zmin']]).to(u.m)
right_edge = u.Quantity([coords['xmax'],
coords['ymax'],
coords['zmax']]).to(u.m)
simulation_parameters = gdf.SimulationParameters([
['boundary_conditions', np.zeros(6) + 2],
['cosmological_simulation', 0 ],
['current_iteration', 0 ],
['current_time', 0.0 ],
['dimensionality', 3 ],
['domain_dimensions', grid_dimensions ],
['domain_left_edge', left_edge ],
['domain_right_edge', right_edge ],
['eta', 0.0 ],
['field_ordering', 0 ],
['gamma', physical_constants['gamma'] ],
['gravity0', 0.0 ],
['gravity1', 0.0 ],
['gravity2', physical_constants['gravity']],
['nu', 0.0 ],
['num_ghost_zones', 0 ],
['refine_by', 0 ],
['unique_identifier', 'sacgdf2014' ]
])
if collective:
from mpi4py import MPI
gdf_file = gdf.create_file(h5py.File(sourcesfile,'w'),
simulation_parameters, grid_dimensions,
driver='mpio', comm=MPI.COMM_WORLD)
else:
gdf_file = gdf.create_file(h5py.File(sourcesfile,'w'),
simulation_parameters, grid_dimensions)
gdf.write_field(gdf_file,
Fx,
'balancing_force_x_bg',
'x Component of Background Balancing Force'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf.write_field(gdf_file,
Fy,
'balancing_force_y_bg',
'y Component of Background Balancing Force'
,field_shape=grid_dimensions
,arr_slice=xindex
,collective=collective
)
gdf_file.close()
if collective:
mpi_save_SACvariables(
sourcesfile,
((Fx,'balancing_force_x_bg'),
(Fy,'balancing_force_y_bg')),
xindex,
)
def save_auxilliary3D(
auxfile,
pressure_m,
rho_m,
temperature,
pbeta,
alfven,
cspeed,
dxB2,
dyB2,
option_pars,
physical_constants,
coords,
Nxyz
):
""" Save auxilliary variables for use in plotting background setup in
hdf5 (gdf default) format after collating the data from mpi sub processes
if necessary.
"""
rank = 0
if option_pars['l_mpi']:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
gather_vars = [
pressure_m,
rho_m,
temperature,
pbeta,
alfven,
cspeed,
dxB2,
dyB2
]
concat_vars = []
for var in gather_vars:
concat_vars.append(comm.gather(var, root=0))
if rank == 0:
out_vars = []
for cvar in concat_vars:
out_vars.append(np.concatenate(cvar, axis=0))
pressure_m, rho_m, temperature, pbeta,\
alfven, cspeed, dxB2, dyB2 = out_vars
if rank == 0:
print'writing',auxfile
print'non-SAC 3D auxilliary data for plotting'
grid_dimensions = [Nxyz[0], Nxyz[1], Nxyz[2]]
left_edge = u.Quantity([coords['xmin'],
coords['ymin'],
coords['zmin']]).to(u.m)
right_edge = u.Quantity([coords['xmax'],
coords['ymax'],
coords['zmax']]).to(u.m)
simulation_parameters = gdf.SimulationParameters([
['boundary_conditions', np.zeros(6) + 2],
['cosmological_simulation', 0 ],
['current_iteration', 0 ],
['current_time', 0.0 ],
['dimensionality', 3 ],
['domain_dimensions', grid_dimensions ],
['domain_left_edge', left_edge ],
['domain_right_edge', right_edge ],
['eta', 0.0 ],
['field_ordering', 0 ],
['gamma', physical_constants['gamma'] ],
['gravity0', 0.0 ],
['gravity1', 0.0 ],
['gravity2', physical_constants['gravity']],
['nu', 0.0 ],
['num_ghost_zones', 0 ],
['refine_by', 0 ],
['unique_identifier', 'sacgdf2014' ]
])
gdf_file = gdf.create_file(h5py.File(auxfile,'w'), simulation_parameters, grid_dimensions)
gdf.write_field(gdf_file,
pressure_m,
'pressure_mhs',
'Background magneto-pressure balance'
)
gdf.write_field(gdf_file,
rho_m,
'density_mhs',
'Background magneto-density balance'
)
gdf.write_field(gdf_file,
temperature.to(u.K),
'temperature',
'Background temperature'
)
gdf.write_field(gdf_file,
pbeta,
'plasma_beta',
'Background plasma beta'
)
gdf.write_field(gdf_file,
alfven,
'alfven_speed',
'Background Alfven speed'
)
gdf.write_field(gdf_file,
cspeed,
'sound_speed',
'Background sound speed'
)
gdf.write_field(gdf_file,
dxB2,
'mag_tension_x',
'x-component background magnetic tension'
)
gdf.write_field(gdf_file,
dyB2,
'mag_tension_y',
'y-component background magnetic tension'
)
gdf_file.close()
def save_SACvariables(
filename,
rho,
Bx,
By,
Bz,
energy,
option_pars,
physical_constants,
coords,
Nxyz
):
""" Save the background variables for a SAC model in hdf5 (gdf default)
format after collating the data from mpi sub processes if necessary.
"""
rank = 0
if option_pars['l_mpi']:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
gather_vars = [
rho.to(u.Unit('kg/m**3')),
Bx.to(u.Unit('T')),
By.to(u.Unit('T')),
Bz.to(u.Unit('T')),
energy.to(u.Unit('kg/(m s**2)'))
]
concat_vars = []
for var in gather_vars:
concat_vars.append(comm.gather(var, root=0))
if rank == 0:
out_vars = []
for cvar in concat_vars:
out_vars.append(np.concatenate(cvar, axis=0))
rho,Bx,By,Bz,energy = out_vars
if rank == 0:
print'writing',filename
print'SAC background atmosphere'
grid_dimensions = [Nxyz[0], Nxyz[1], Nxyz[2]]
left_edge = u.Quantity([coords['xmin'],
coords['ymin'],
coords['zmin']]).to(u.m)
right_edge = u.Quantity([coords['xmax'],
coords['ymax'],
coords['zmax']]).to(u.m)
g0 = physical_constants['gravity']
gamma = 5./3.
dummy = np.zeros(rho.shape)
simulation_parameters = gdf.SimulationParameters([
['boundary_conditions', np.zeros(6) + 2],
['cosmological_simulation', 0 ],
['current_iteration', 0 ],
['current_time', 0.0 ],
['dimensionality', 3 ],
['domain_dimensions', grid_dimensions ],
['domain_left_edge', left_edge ],
['domain_right_edge', right_edge ],
['eta', 0.0 ],
['field_ordering', 0 ],
['gamma', gamma ],
['gravity0', 0.0 ],
['gravity1', 0.0 ],
['gravity2', g0 ],
['nu', 0.0 ],
['num_ghost_zones', 0 ],
['refine_by', 0 ],
['unique_identifier', 'sacgdf2014' ]
])
gdf_file = gdf.create_file(h5py.File(filename,'w'), simulation_parameters, grid_dimensions)
gdf.write_field(gdf_file, rho,
'density_bg',
'Background Density'
)
gdf.write_field(gdf_file, dummy*u.Unit('kg/m**3'),
'density_pert',
'Perturbation Density'
)
gdf.write_field(gdf_file,
energy,
'internal_energy_bg',
'Background Internal Energy'
)
gdf.write_field(gdf_file, dummy*u.Unit('kg/(m s**2)'),
'internal_energy_pert',
'Perturbation Internal Energy'
)
gdf.write_field(gdf_file, Bx,
'mag_field_x_bg',
'x Component of Background Magnetic Field'
)
gdf.write_field(gdf_file, dummy*u.Unit('T'),
'mag_field_x_pert',
'x Component of Pertubation Magnetic Field'
)
gdf.write_field(gdf_file, By,
'mag_field_y_bg',
'y Component of Background Magnetic Field'
)
gdf.write_field(gdf_file, dummy*u.Unit('T'),
'mag_field_y_pert',
'y Component of Pertubation Magnetic Field'
)
gdf.write_field(gdf_file, Bz,
'mag_field_z_bg',
'z Component of Background Magnetic Field'
)
gdf.write_field(gdf_file, dummy*u.Unit('T'),
'mag_field_z_pert',
'z Component of Pertubation Magnetic Field'
)
gdf.write_field(gdf_file, dummy*u.Unit('m/s'),
'velocity_x',
'x Component of Velocity'
)
gdf.write_field(gdf_file, dummy*u.Unit('m/s'),
'velocity_y',
'y Component of Velocity'
)
gdf.write_field(gdf_file, dummy*u.Unit('m/s'),
'velocity_z',
'z Component of Velocity'
)
gdf_file.close()
def save_SACsources(
sourcesfile,
Fx,
Fy,
option_pars,
physical_constants,
coords,
Nxyz
):
""" Save the balancing forces for a SAC model with multiple flux tubes in
hdf5 (gdf default) format after collating the data from mpi sub processes
if necessary.
"""
rank = 0
if option_pars['l_mpi']:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
gather_vars = [
Fx,Fy
]
concat_vars = []
for var in gather_vars:
concat_vars.append(comm.gather(var, root=0))
if rank == 0:
out_vars = []
for cvar in concat_vars:
out_vars.append(np.concatenate(cvar, axis=0))
Fx,Fy = out_vars
if rank == 0:
print'writing',sourcesfile
print'SAC background source terms'
grid_dimensions = [Nxyz[0], Nxyz[1], Nxyz[2]]
left_edge = u.Quantity([coords['xmin'],
coords['ymin'],
coords['zmin']]).to(u.m)
right_edge = u.Quantity([coords['xmax'],
coords['ymax'],
coords['zmax']]).to(u.m)
g0 = physical_constants['gravity']
simulation_parameters = gdf.SimulationParameters([
['boundary_conditions', np.zeros(6) + 2],
['cosmological_simulation', 0 ],
['current_iteration', 0 ],
['current_time', 0.0 ],
['dimensionality', 3 ],
['domain_dimensions', grid_dimensions ],
['domain_left_edge', left_edge ],
['domain_right_edge', right_edge ],
['eta', 0.0 ],
['field_ordering', 0 ],
['gamma', physical_constants['gamma'] ],
['gravity0', 0.0 ],
['gravity1', 0.0 ],
['gravity2', physical_constants['gravity']],
['nu', 0.0 ],
['num_ghost_zones', 0 ],
['refine_by', 0 ],
['unique_identifier', 'sacgdf2014' ]
])
gdf_file = gdf.create_file(h5py.File(sourcesfile,'w'), simulation_parameters, grid_dimensions)
gdf.write_field(gdf_file,
Fx,
'balancing_force_x_bg',
'x Component of Background Balancing Force'
)
gdf.write_field(gdf_file,
Fy,
'balancing_force_y_bg',
'y Component of Background Balancing Force'
)
gdf_file.close()