def loadData(field, extension):
global data
# check if data has already been loaded
if (field + extension in data.loaded) == False:
data.slices[field + extension], data.t = pc.read_slices(
datadir='data', field=field, extension=extension, proc=-1)
data.dim[field + extension] = pc.read_dim() # system dimensions
data.param[field + extension] = pc.read_param(
quiet=True) # system parameters
data.loaded.add(field + extension)
def slices2vtk(variables=['rho'],
extensions=['xy', 'xy2', 'xz', 'yz'],
datadir='data/',
destination='slices',
proc=-1,
format='native'):
"""
Convert slices from PencilCode format to vtk.
call signature::
slices2vtk(variables = ['rho'], extensions = ['xy', 'xy2', 'xz', 'yz'],
datadir = 'data/', destination = 'slices', proc = -1,
format = 'native'):
Read slice files specified by *variables* and convert
them into vtk format for the specified extensions.
Write the result in *destination*.
NB: You need to have called src/read_videofiles.x before using this script.
Keyword arguments:
*variables*:
All allowed fields which can be written as slice files, e.g. b2, uu1, lnrho, ...
See the pencil code manual for more (chapter: "List of parameters for `video.in'").
*extensions*:
List of slice positions.
*datadir*:
Directory where the data is stored.
*destination*:
Destination files.
*proc*:
Processor which should be read. Set to -1 for all processors.
*format*:
Endian, one of little, big, or native (default)
"""
# this should correct for the case the user types only one variable
if (len(variables) > 0):
if (len(variables[0]) == 1):
variables = [variables]
# this should correct for the case the user types only one extension
if (len(extensions) > 0):
if (len(extensions[0]) == 1):
extensions = [extensions]
# read the grid dimensions
grid = pc.read_grid(datadir=datadir, proc=proc, trim=True, quiet=True)
# read the user given parameters for the slice positions
params = pc.read_param(param2=True, quiet=True)
# run through all specified variables
for field in variables:
# run through all specified extensions
for ext in extensions:
print("read " + field + ' ' + ext)
slices, t = pc.read_slices(field=field,
datadir=datadir,
proc=proc,
extension=ext,
format=format)
dim_p = slices.shape[2]
dim_q = slices.shape[1]
if ext[0] == 'x':
d_p = (np.max(grid.x) - np.min(grid.x)) / (dim_p)
else:
d_p = (np.max(grid.y) - np.min(grid.y)) / (dim_p)
if ext[1] == 'y':
d_q = (np.max(grid.y) - np.min(grid.y)) / (dim_q)
else:
d_q = (np.max(grid.z) - np.min(grid.z)) / (dim_q)
if params.ix != -1:
x0 = grid.x[params.ix]
elif params.slice_position == 'm':
x0 = grid.x[int(len(grid.x) / 2)]
if params.iy != -1:
y0 = grid.y[params.iy]
elif params.slice_position == 'm':
y0 = grid.y[int(len(grid.y) / 2)]
if params.iz != -1:
z0 = grid.z[params.iz]
elif params.slice_position == 'm':
z0 = grid.z[int(len(grid.z) / 2)]
for i in range(slices.shape[0]):
# open the destination file for writing
fd = open(
destination + '_' + field + '_' + ext + '_' + str(i) +
'.vtk', 'wb')
# write the header
fd.write('# vtk DataFile Version 2.0\n')
fd.write(field + '_' + ext + '\n')
fd.write('BINARY\n')
fd.write('DATASET STRUCTURED_POINTS\n')
if ext[0:2] == 'xy':
x0 = grid.x[0]
y0 = grid.y[0]
fd.write('DIMENSIONS {0:9} {1:9} {2:9}\n'.format(
dim_p, dim_q, 1))
fd.write('ORIGIN {0:8.12} {1:8.12} {2:8.12}\n'.format(
x0, y0, z0))
fd.write('SPACING {0:8.12} {1:8.12} {2:8.12}\n'.format(
grid.dx, grid.dy, 1.))
elif ext[0:2] == 'xz':
x0 = grid.x[0]
z0 = grid.z[0]
fd.write('DIMENSIONS {0:9} {1:9} {2:9}\n'.format(
dim_p, 1, dim_q))
fd.write('ORIGIN {0:8.12} {1:8.12} {2:8.12}\n'.format(
x0, y0, z0))
fd.write('SPACING {0:8.12} {1:8.12} {2:8.12}\n'.format(
grid.dx, 1., grid.dy))
elif ext[0:2] == 'yz':
y0 = grid.y[0]
z0 = grid.z[0]
fd.write('DIMENSIONS {0:9} {1:9} {2:9}\n'.format(
1, dim_p, dim_q))
fd.write('ORIGIN {0:8.12} {1:8.12} {2:8.12}\n'.format(
x0, y0, z0))
fd.write('SPACING {0:8.12} {1:8.12} {2:8.12}\n'.format(
1., grid.dy, grid.dy))
fd.write('POINT_DATA {0:9}\n'.format(dim_p * dim_q))
fd.write('SCALARS ' + field + '_' + ext + ' float\n')
fd.write('LOOKUP_TABLE default\n')
for j in range(dim_q):
for k in range(dim_p):
fd.write(struct.pack(">f", slices[i, j, k]))
fd.close()
def pc2vtk_vid(ti=0,
tf=1,
datadir='data/',
proc=-1,
variables=['rho', 'uu', 'bb'],
magic=[],
b_ext=False,
destination='animation',
quiet=True):
"""
Convert data from PencilCode format to vtk.
call signature::
pc2vtk(ti = 0, tf = 1, datadir = 'data/', proc = -1,
variables = ['rho','uu','bb'], magic = [],
destination = 'animation')
Read *varfile* and convert its content into vtk format. Write the result
in *destination*.
Keyword arguments:
*ti*:
Initial time.
*tf*:
Final time.
*datadir*:
Directory where the data is stored.
*proc*:
Processor which should be read. Set to -1 for all processors.
*variables* = [ 'rho' , 'lnrho' , 'uu' , 'bb', 'b_mag', 'jj', 'j_mag', 'aa', 'ab', 'TT', 'lnTT', 'cc', 'lncc', 'ss', 'vort' ]
Variables which should be written.
*magic*: [ 'vort' , 'bb' ]
Additional variables which should be written.
*b_ext*:
Add the external magnetic field.
*destination*:
Destination files without '.vtk' extension.
*quiet*:
Keep quiet when reading the var files.
"""
# this should correct for the case the user type only one variable
if (len(variables) > 0):
if (len(variables[0]) == 1):
variables = [variables]
# this should correct for the case the user type only one variable
if (len(magic) > 0):
if (len(magic[0]) == 1):
magic = [magic]
# make sure magic is set when writing 'vort' or 'bb'
try:
index = variables.index('vort')
magic.append('vort')
except:
pass
try:
index = variables.index('bb')
magic.append('bb')
except:
pass
try:
index = variables.index('b_mag')
magic.append('bb')
except:
pass
try:
index = variables.index('jj')
magic.append('jj')
except:
pass
try:
index = variables.index('j_mag')
magic.append('jj')
except:
pass
for i in range(ti, tf + 1):
varfile = 'VAR' + str(i)
# reading pc variables and setting dimensions
var = pc.read_var(varfile=varfile,
datadir=datadir,
proc=proc,
magic=magic,
trimall=True,
quiet=quiet)
grid = pc.read_grid(datadir=datadir, proc=proc, trim=True, quiet=True)
params = pc.read_param(param2=True, quiet=True)
B_ext = np.array(params.b_ext)
# add external magnetic field
if (b_ext == True):
var.bb[0, ...] += B_ext[0]
var.bb[1, ...] += B_ext[1]
var.bb[2, ...] += B_ext[2]
dimx = len(grid.x)
dimy = len(grid.y)
dimz = len(grid.z)
dim = dimx * dimy * dimz
dx = (np.max(grid.x) - np.min(grid.x)) / (dimx - 1)
dy = (np.max(grid.y) - np.min(grid.y)) / (dimy - 1)
dz = (np.max(grid.z) - np.min(grid.z)) / (dimz - 1)
#fd = open(destination + "{0:1.0f}".format(var.t*1e5) + '.vtk', 'wb')
fd = open(destination + str(i) + '.vtk', 'wb')
fd.write('# vtk DataFile Version 2.0\n'.encode('utf-8'))
fd.write('density + magnetic field\n'.encode('utf-8'))
fd.write('BINARY\n'.encode('utf-8'))
fd.write('DATASET STRUCTURED_POINTS\n'.encode('utf-8'))
fd.write('DIMENSIONS {0:9} {1:9} {2:9}\n'.format(dimx, dimy,
dimz).encode('utf-8'))
fd.write('ORIGIN {0:8.12} {1:8.12} {2:8.12}\n'.format(
grid.x[0], grid.y[0], grid.z[0]).encode('utf-8'))
fd.write('SPACING {0:8.12} {1:8.12} {2:8.12}\n'.format(
dx, dy, dz).encode('utf-8'))
fd.write('POINT_DATA {0:9}\n'.format(dim).encode('utf-8'))
try:
index = variables.index('rho')
print('writing rho')
fd.write('SCALARS rho float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.rho[k, j, i]))
except:
pass
try:
index = variables.index('lnrho')
print('writing lnrho')
fd.write('SCALARS lnrho float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.lnrho[k, j, i]))
except:
pass
try:
index = variables.index('uu')
print('writing uu')
fd.write('VECTORS vfield float\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.uu[0, k, j, i]))
fd.write(struct.pack(">f", var.uu[1, k, j, i]))
fd.write(struct.pack(">f", var.uu[2, k, j, i]))
except:
pass
try:
index = variables.index('bb')
print('writing bb')
fd.write('VECTORS bfield float\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.bb[0, k, j, i]))
fd.write(struct.pack(">f", var.bb[1, k, j, i]))
fd.write(struct.pack(">f", var.bb[2, k, j, i]))
except:
pass
try:
index = variables.index('b_mag')
b_mag = np.sqrt(pc.dot2(var.bb))
print('writing b_mag')
fd.write('SCALARS b_mag float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", b_mag[k, j, i]))
except:
pass
try:
index = variables.index('jj')
print('writing jj')
fd.write('VECTORS jfield float\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.jj[0, k, j, i]))
fd.write(struct.pack(">f", var.jj[1, k, j, i]))
fd.write(struct.pack(">f", var.jj[2, k, j, i]))
except:
pass
try:
index = variables.index('j_mag')
j_mag = np.sqrt(pc.dot2(var.jj))
print('writing j_mag')
fd.write('SCALARS j_mag float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", j_mag[k, j, i]))
except:
pass
try:
index = variables.index('aa')
print('writing aa')
fd.write('VECTORS afield float\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.aa[0, k, j, i]))
fd.write(struct.pack(">f", var.aa[1, k, j, i]))
fd.write(struct.pack(">f", var.aa[2, k, j, i]))
except:
pass
try:
index = variables.index('ab')
ab = pc.dot(var.aa, var.bb)
print('writing ab')
fd.write('SCALARS ab float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", ab[k, j, i]))
except:
pass
try:
index = variables.index('TT')
print('writing TT')
fd.write('SCALARS TT float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.TT[k, j, i]))
except:
pass
try:
index = variables.index('lnTT')
print('writing lnTT')
fd.write('SCALARS lnTT float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.lnTT[k, j, i]))
except:
pass
try:
index = variables.index('cc')
print('writing cc')
fd.write('SCALARS cc float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.cc[k, j, i]))
except:
pass
try:
index = variables.index('lncc')
print('writing lncc')
fd.write('SCALARS lncc float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.lncc[k, j, i]))
except:
pass
try:
index = variables.index('ss')
print('writing ss')
fd.write('SCALARS ss float\n'.encode('utf-8'))
fd.write('LOOKUP_TABLE default\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.ss[k, j, i]))
except:
pass
try:
index = variables.index('vort')
print('writing vort')
fd.write('VECTORS vorticity float\n'.encode('utf-8'))
for k in range(dimz):
for j in range(dimy):
for i in range(dimx):
fd.write(struct.pack(">f", var.vort[0, k, j, i]))
fd.write(struct.pack(">f", var.vort[1, k, j, i]))
fd.write(struct.pack(">f", var.vort[2, k, j, i]))
except:
pass
del (var)
fd.close()
N = 50
tmax = t.max()
ux = ts.ux2m
uy = ts.uy2m
rhomax = ts.rhomax
rhomin = ts.rhomin
# quick set up for intervals of time
# use Orbit_Len to properly get the length of the interval
# for Orbits from the time series
# ======================================
# pc.read_pararm()
# ======================================
par = pc.read_param()
h = par.cs0
if (par.iprimary == 1):
q = par.pmass[1]
else:
q = par.pmass[0]
par1 = par.pmass[1]
par2 = par.pmass[0]
gamma = par.gamma
Gamma0 = (q / h)**2
alpha = par.density_power_law
beta = par.temperature_power_law
kernel = np.ones((N, )) / N
time = np.convolve(t, kernel, mode='valid')
torqint = np.convolve(ts.torqint_2, kernel, mode='valid')
def get_params():
# return all params needed for this script
par = pc.read_param()
h = par.cs0
cs = par.cs0 # sound speed
return cs