def gas_velo_at_particle_pos(
varfiles="last4", sim=False, scheme="tsc", use_IDL=False, OVERWRITE=False
):
"""This script calulates the gas velocity at the particle position and stores this together
with particle position, containing grid cell idicies, particle velocities, and particle index
in a gas_velo_at_particle_pos file.
Args:
varfiles: specifiy varfiles for calculation, e.g. 'last', 'first',
'all', 'VAR###', 'last4', 'first3'
scheme: possible are:
- ngp: nearest grid point
- cic: cloud in cell
- tsc: triangular shaped cloud
OVERWRITE: set to True to overwrite already calculated results
"""
from pencil import get_sim
from pencil import read
from pencil import diag
from pencil.io import mkdir
from os import listdir
from os.path import exists, join, dirname
import numpy as np
GAS_VELO_TAG = "gas_velo_at_particle_pos"
if sim == False:
sim = get_sim()
if sim == False:
print("! ERROR: Specify simulation object!")
return False
SIM = sim
if use_IDL:
print(
"? WARNING: IDL VERSION OF THIS SCRIPT BY JOHANSEN, not recommended for 2D data"
)
from ...backpack import pidly
print("## starting IDL engine..")
IDL = pidly.IDL(long_delay=0.05) # start IDL engine
## skip if nothing is new
if (
(not OVERWRITE)
and (exists(join(SIM.pc_datadir, "sigma.pkl")))
and (exists(join(SIM.pc_datadir, "zeta.pkl")))
):
print(
"~ "
+ SIM.name
+ " is already calculated and up-to-date! -> skipping it!"
)
else:
## start calculations
print(
'~ Calculating gas_velo_at_particle_pos for "'
+ SIM.name
+ '" in "'
+ SIM.path
+ '"'
)
IDL(
".COMPILE "
+ str(
join(
dirname(diag.particle.__file__), "gas_velo_at_particle_pos.pro"
)
)
)
IDL.pro(
"gas_velo_at_particle_pos",
datadir=SIM.datadir,
destination=GAS_VELO_TAG,
doforthelastNvar=varfiles[4:],
)
files = [
i.split("_")[-1].split(".sav")[0]
for i in listdir(join(SIM.pc_datadir, GAS_VELO_TAG))
if i.startswith(GAS_VELO_TAG)
and i.endswith(".sav")
or i.endswith(".pkl")
]
if files == []:
print(
"!! ERROR: No calc_gas_speed_at_particle_position-files found for "
+ SIM.name
+ "! Use idl script to produce them first!"
)
IDL.close()
return True
else:
print(
'~ Calculating gas_velo_at_particle_pos for "'
+ SIM.name
+ '" in "'
+ SIM.path
+ '"'
)
save_destination = join(SIM.pc_datadir, GAS_VELO_TAG)
mkdir(save_destination)
varlist = SIM.get_varlist(pos=varfiles, particle=False)
pvarlist = SIM.get_varlist(pos=varfiles, particle=True)
for f, p in zip(varlist, pvarlist):
save_filename = GAS_VELO_TAG + "_" + scheme + "_" + f[3:]
if not OVERWRITE and exists(save_filename, folder=save_destination):
continue
print("## Reading " + f + " ...")
ff = read.var(datadir=SIM.datadir, varfile=f, quiet=True, trimall=False)
pp = read.pvar(datadir=SIM.datadir, varfile=p)
## remove ghost zones from grid, call the reduced grid the "real grid"
realgridx = ff.x[ff.l1 : ff.l2]
realgridy = ff.y[ff.m1 : ff.m2]
realgridz = ff.z[ff.n1 : ff.n2]
nx = ff.l2 - ff.l1
ny = ff.m2 - ff.m1
nz = ff.n2 - ff.n1
## prepare list for all quantities
l_ipars = pp.ipars # particle number KNOWN
l_px = pp.xp
l_py = pp.yp
l_pz = pp.zp # particle absolut position KNOWN
l_vx = pp.vpx
l_vy = pp.vpy
l_vz = pp.vpz # particle velocity KNOWN
l_rix = []
l_riy = []
l_riz = (
[]
) # particle untrimmed realgrid index (grid index = l/m/n + readgrid index ???)
l_ix = []
l_iy = []
l_iz = [] # particle grid index (in untrimmed grid)
l_ux = []
l_uy = []
l_uz = [] # underlying gas velocity at position of particle
## get index of realgrid cell for each particle
for i in range(len(l_ipars)):
l_rix.append(np.abs(realgridx - l_px[i]).argmin())
l_riy.append(np.abs(realgridy - l_py[i]).argmin())
l_riz.append(np.abs(realgridz - l_pz[i]).argmin())
## convert into untrimmed grid
l_ix = np.array(l_rix) + ff.l1
l_iy = np.array(l_riy) + ff.m1
l_iz = np.array(l_riz) + ff.n1
## NGP
if scheme == "ngp" or scheme == "NGP":
print("## Calculating gas velocities via " + scheme)
l_ux = ff.ux[l_iz, l_iy, l_ix]
l_uy = ff.uy[l_iz, l_iy, l_ix]
l_uz = ff.uz[l_iz, l_iy, l_ix]
## CIC
if scheme == "cic" or scheme == "CIC":
print("## Calculating gas velocities via " + scheme)
for ix0, iy0, iz0, px, py, pz in zip(
l_ix, l_iy, l_iz, l_px, l_py, l_pz
): # for each particle
if ff.x[ix0] > px:
ix0 = ix0 - 1 # ix0 must be left to particle
if ff.y[iy0] > py:
iy0 = iy0 - 1 # iy0 must be below the particle
if ff.z[iz0] > pz:
iz0 = iz0 - 1 # iz0 must be under particle
ix1 = ix0
iy1 = iy0
iz1 = iz0 # if a dim. is zero, this is default, else:
if nx > 1:
ix1 = ix0 + 1
dx_1 = (
1.0 / ff.dx
) # if a dim is non-zero, ajust ix1 to right cell
if ny > 1:
iy1 = iy0 + 1
dy_1 = (
1.0 / ff.dy
) # if a dim is non-zero, ajust iy1 to above cell
if nz > 1:
iz1 = iz0 + 1
dz_1 = (
1.0 / ff.dz
) # if a dim is non-zero, ajust iz1 to above cell
ux = 0.0
uy = 0.0
uz = 0.0
for ix in [ix0, ix1]:
for iy in [iy0, iy1]:
for iz in [iz0, iz1]:
weight = 1.0
if nx > 1:
weight = weight * (1.0 - abs(px - ff.x[ix]) * dx_1)
if ny > 1:
weight = weight * (1.0 - abs(py - ff.y[iy]) * dy_1)
if nz > 1:
weight = weight * (1.0 - abs(pz - ff.z[iz]) * dz_1)
ux = ux + weight * ff.ux[iz, iy, ix]
uy = uy + weight * ff.uy[iz, iy, ix]
uz = uz + weight * ff.uz[iz, iy, ix]
if iz0 == iz1:
break # beware of degeneracy:
if iy0 == iy1:
break # beware of degeneracy:
if ix0 == ix1:
break # beware of degeneracy:
l_ux.append(ux)
l_uy.append(uy)
l_uz.append(uz)
## TSC
if scheme == "tsc" or scheme == "TSC":
for ix0, iy0, iz0, px, py, pz in zip(
l_ix, l_iy, l_iz, l_px, l_py, l_pz
): # for each particle
ixx0 = ix0
ixx1 = ix0 # beware of degeneracy
iyy0 = iy0
iyy1 = iy0
izz0 = iz0
izz1 = iz0
if nx > 1:
ixx0 = ix0 - 1
ixx1 = ix0 + 1
dx_1 = 1.0 / ff.dx
dx_2 = 1.0 / ff.dx ** 2
if ny > 1:
iyy0 = iy0 - 1
iyy1 = iy0 + 1
dy_1 = 1.0 / ff.dy
dy_2 = 1.0 / ff.dy ** 2
if nz > 1:
izz0 = iz0 - 1
izz1 = iz0 + 1
dz_1 = 1.0 / ff.dz
dz_2 = 1.0 / ff.dz ** 2
ux = 0.0
uy = 0.0
uz = 0.0
for ix in [ix0, ixx0, ixx1]:
weight_x = 0.0
if ix - ix0 == -1 or ix - ix0 == 1:
weight_x = (
1.125
- 1.5 * abs(px - ff.x[ix]) * dx_1
+ 0.5 * abs(px - ff.x[ix]) ** 2 * dx_2
)
elif nx != 1:
weight_x = 0.75 - (px - ff.x[ix]) ** 2 * dx_2
for iy in [iy0, iyy0, iyy1]:
weight_y = 0.0
if iy - iy0 == -1 or iy - iy0 == 1:
weight_y = (
1.125
- 1.5 * abs(py - ff.y[iy]) * dy_1
+ 0.5 * abs(py - ff.y[iy]) ** 2 * dy_2
)
elif ny != 1:
weight_y = 0.75 - (py - ff.y[iy]) ** 2 * dy_2
for iz in [iz0, izz0, izz1]:
weight_z = 0.0
if iz - iz0 == -1 or iz - iz0 == 1:
weight_z = (
1.125
- 1.5 * abs(pz - ff.z[iz]) * dz_1
+ 0.5 * abs(pz - ff.z[iz]) ** 2 * dz_2
)
elif nz != 1:
weight_z = 0.75 - (pz - ff.z[iz]) ** 2 * dz_2
weight = 1.0
if nx > 1:
weight = weight * weight_x
if ny > 1:
weight = weight * weight_y
if nz > 1:
weight = weight * weight_z
ux = ux + weight * ff.ux[iz, iy, ix]
uy = uy + weight * ff.uy[iz, iy, ix]
uz = uz + weight * ff.uz[iz, iy, ix]
if izz0 == izz1:
break # beware of degeneracy:
if iyy0 == iyy1:
break # beware of degeneracy:
if ixx0 == ixx1:
break # beware of degeneracy:
l_ux.append(ux)
l_uy.append(uy)
l_uz.append(uz)
## Convert all information into a single record array
data_set = np.core.records.fromarrays(
[
l_ipars.astype("int"),
l_px,
l_py,
l_pz,
l_vx,
l_vy,
l_vz,
l_rix,
l_riy,
l_riz,
l_ix,
l_iy,
l_iz,
l_ux,
l_uy,
l_uz,
],
names="ipar, ipx, ipy, ipz, vx, vy, vz, rix, riy, riz, ix, iy, iz, ux, uy, uz",
formats="int, float, float, float, float, float, float, int, int, int, int, int, int, float, float, float",
)
gas_velo_at_particle_pos = np.sort(data_set, order=["ix", "iy", "iz"])
Nix = int(gas_velo_at_particle_pos["rix"].max() + 1)
Niy = int(gas_velo_at_particle_pos["riy"].max() + 1)
Niz = int(gas_velo_at_particle_pos["riz"].max() + 1)
Npar_arr = np.array(
[
gas_velo_at_particle_pos["rix"],
gas_velo_at_particle_pos["riy"],
gas_velo_at_particle_pos["riz"],
]
)
# rgrid_edges = (grid.x[1:]-(grid.x[1:]-grid.x[:-1])/2)[2:-2]
xrange = np.arange(0, float(gas_velo_at_particle_pos["rix"].max()) + 2)
xrange = xrange - 0.5
yrange = np.arange(0, float(gas_velo_at_particle_pos["riy"].max()) + 2)
zrange = np.arange(0, float(gas_velo_at_particle_pos["riz"].max()) + 2)
Npar_hist, edges = np.histogramdd(Npar_arr.T, bins=(xrange, yrange, zrange))
Npar_hist, edges = np.histogramdd(Npar_arr.T, bins=(Nix, Niy, Niz))
gas_velo_at_particle_pos = {
"time": ff.t,
"par_pos": np.array(
[
gas_velo_at_particle_pos["ipx"],
gas_velo_at_particle_pos["ipy"],
gas_velo_at_particle_pos["ipz"],
]
),
"par_velo": np.array(
[
gas_velo_at_particle_pos["vx"],
gas_velo_at_particle_pos["vy"],
gas_velo_at_particle_pos["vz"],
]
),
"par_idx": np.array(
[
gas_velo_at_particle_pos["rix"],
gas_velo_at_particle_pos["riy"],
gas_velo_at_particle_pos["riz"],
]
),
"npar": np.array(
Npar_hist[
gas_velo_at_particle_pos["rix"],
gas_velo_at_particle_pos["riy"],
gas_velo_at_particle_pos["riz"],
]
),
"gas_velo": np.array(
[
gas_velo_at_particle_pos["ux"],
gas_velo_at_particle_pos["uy"],
gas_velo_at_particle_pos["uz"],
]
),
}
print("## Saving dataset into " + save_destination + "...")
pkl_save(
{"gas_velo_at_particle_pos": gas_velo_at_particle_pos, "t": ff.t},
save_filename,
folder=save_destination,
)
print("## Done!")
def particles_to_vtk(
var_file="pvar.dat",
datadir="data",
proc=-1,
destination="particles.vtk",
ti=-1,
tf=-1,
binary=True,
):
"""
Read the pVAR files from Pencil Code and write them as vtk files.
call signature:
particles_to_vtk(var_file='pvar.dat', datadir='data', proc=-1,
destination='particles.vtk', ti=-1, tf=-1, binary=True)
Keyword arguments:
*var_file*:
Name of the PVAR file.
*datadir*:
Directory where the data is stored.
*proc*:
Processor to be read. If -1 read all and assemble to one array.
*destination*:
Destination file (only if ti, tf > 0).
*ti*:
Initial time index for animation.
*tf*:
Final time index for animation.
*binary*:
Determines if binary or clear text data for the vtk files.
"""
from pencil import read
# Read the particle data and save it in a list.
pvar_list = []
if (ti >= 0) and (tf >= 0):
for tidx in range(ti, tf):
var_file = "PVAR{0}".format(tidx)
pvar = read.pvar(varfile=var_file, datadir=datadir, proc=proc)
pvar_list.append(pvar)
else:
pvar = read.pvar(varfile=var_file, datadir=datadir, proc=proc)
pvar_list.append(pvar)
# Convert the data into vtk.
particles_vtk_tmp = ParticlesVtk()
particles_vtk_tmp.convert_to_vtk(pvar_list)
# Define some constants.
particles_vtk_tmp.ti = ti
particles_vtk_tmp.tf = tf
particles_vtk_tmp.binary = binary
particles_vtk_tmp.destination = destination
# Write the data inot vtk files.
particles_vtk_tmp.write_to_vtk()
return particles_vtk_tmp
def gas_velo_at_particle_pos(varfiles='last4',
sim=False,
scheme='tsc',
use_IDL=False,
OVERWRITE=False):
"""This script calulates the gas velocity at the particle position and stores this together
with particle position, containing grid cell idicies, particle velocities, and particle index
in a gas_velo_at_particle_pos file.
Args:
varfiles: specifiy varfiles for calculation, e.g. 'last', 'first',
'all', 'VAR###', 'last4', 'first3'
scheme: possible are:
- ngp: nearest grid point
- cic: cloud in cell
- tsc: triangular shaped cloud
OVERWRITE: set to True to overwrite already calculated results
"""
import os
from pencil import io
from pencil import read
from pencil import get_sim
from os.path import exists
import numpy as np
GAS_VELO_TAG = 'gas_velo_at_particle_pos'
if sim == False:
sim = get_sim()
if sim == False:
print('! ERROR: Specify simulation object!')
return False
SIM = sim
if use_IDL:
print(
'? WARNING: IDL VERSION OF THIS SCRIPT BY JOHANSEN, not recommended for 2D data'
)
from pencil.backpack import pidly
print('## starting IDL engine..')
IDL = pidly.IDL(long_delay=0.05) # start IDL engine
## skip if nothing is new
if (not OVERWRITE) and (exists(
os.path.join(SIM.pc_datadir, 'sigma.pkl'))) and (exists(
os.path.join(SIM.pc_datadir, 'zeta.pkl'))):
print('~ ' + SIM.name +
' is already calculated and up-to-date! -> skipping it!')
else:
## start calculations
print('~ Calculating gas_velo_at_particle_pos for "' + SIM.name +
'" in "' + SIM.path + '"')
IDL.pro('gas_velo_at_particle_pos',
datadir=SIM.datadir,
destination=GAS_VELO_TAG,
doforthelastNvar=varfiles[4:])
files = [
i.split('_')[-1].split('.sav')[0]
for i in os.listdir(os.path.join(SIM.pendatadir, GAS_VELO_TAG))
if i.startswith(GAS_VELO_TAG) and i.endswith('.sav')
or i.endswith('.pkl')
]
if files == []:
print(
'!! ERROR: No calc_gas_speed_at_particle_position-files found for '
+ SIM.name + '! Use idl script to produce them first!')
IDL.close()
return True
else:
print('~ Calculating gas_velo_at_particle_pos for "' + SIM.name +
'" in "' + SIM.path + '"')
save_destination = os.path.join(SIM.pc_datadir, GAS_VELO_TAG)
io.mkdir(save_destination)
varlist = SIM.get_varlist(pos=varfiles, particle=False)
pvarlist = SIM.get_varlist(pos=varfiles, particle=True)
for f, p in zip(varlist, pvarlist):
save_filename = GAS_VELO_TAG + '_' + scheme + '_' + f[3:]
if not OVERWRITE and exists(save_filename,
folder=save_destination):
continue
print('## Reading ' + f + ' ...')
ff = read.var(datadir=SIM.datadir,
varfile=f,
quiet=True,
trimall=False)
pp = read.pvar(datadir=SIM.datadir, varfile=p)
## remove ghost zones from grid, call the reduced grid the "real grid"
realgridx = ff.x[ff.l1:ff.l2]
realgridy = ff.y[ff.m1:ff.m2]
realgridz = ff.z[ff.n1:ff.n2]
nx = ff.l2 - ff.l1
ny = ff.m2 - ff.m1
nz = ff.n2 - ff.n1
## prepare list for all quantities
l_ipars = pp.ipars # particle number KNOWN
l_px = pp.xp
l_py = pp.yp
l_pz = pp.zp # particle absolut position KNOWN
l_vx = pp.vpx
l_vy = pp.vpy
l_vz = pp.vpz # particle velocity KNOWN
l_rix = []
l_riy = []
l_riz = [
] # particle untrimmed realgrid index (grid index = l/m/n + readgrid index ???)
l_ix = []
l_iy = []
l_iz = [] # particle grid index (in untrimmed grid)
l_ux = []
l_uy = []
l_uz = [] # underlying gas velocity at position of particle
## get index of realgrid cell for each particle
for i in range(len(l_ipars)):
l_rix.append(np.abs(realgridx - l_px[i]).argmin())
l_riy.append(np.abs(realgridy - l_py[i]).argmin())
l_riz.append(np.abs(realgridz - l_pz[i]).argmin())
## convert into untrimmed grid
l_ix = np.array(l_rix) + ff.l1
l_iy = np.array(l_riy) + ff.m1
l_iz = np.array(l_riz) + ff.n1
## NGP
if scheme == 'ngp' or scheme == 'NGP':
print('## Calculating gas velocities via ' + scheme)
l_ux = ff.ux[l_iz, l_iy, l_ix]
l_uy = ff.uy[l_iz, l_iy, l_ix]
l_uz = ff.uz[l_iz, l_iy, l_ix]
## CIC
if scheme == 'cic' or scheme == 'CIC':
print('## Calculating gas velocities via ' + scheme)
for ix0, iy0, iz0, px, py, pz in zip(
l_ix, l_iy, l_iz, l_px, l_py,
l_pz): # for each particle
if ff.x[ix0] > px:
ix0 = ix0 - 1 # ix0 must be left to particle
if ff.y[iy0] > py:
iy0 = iy0 - 1 # iy0 must be below the particle
if ff.z[iz0] > pz:
iz0 = iz0 - 1 # iz0 must be under particle
ix1 = ix0
iy1 = iy0
iz1 = iz0 # if a dim. is zero, this is default, else:
if nx > 1:
ix1 = ix0 + 1
dx_1 = 1. / ff.dx # if a dim is non-zero, ajust ix1 to right cell
if ny > 1:
iy1 = iy0 + 1
dy_1 = 1. / ff.dy # if a dim is non-zero, ajust iy1 to above cell
if nz > 1:
iz1 = iz0 + 1
dz_1 = 1. / ff.dz # if a dim is non-zero, ajust iz1 to above cell
ux = 0.
uy = 0.
uz = 0.
for ix in [ix0, ix1]:
for iy in [iy0, iy1]:
for iz in [iz0, iz1]:
weight = 1.
if nx > 1:
weight = weight * (
1. - abs(px - ff.x[ix]) * dx_1)
if ny > 1:
weight = weight * (
1. - abs(py - ff.y[iy]) * dy_1)
if nz > 1:
weight = weight * (
1. - abs(pz - ff.z[iz]) * dz_1)
ux = ux + weight * ff.ux[iz, iy, ix]
uy = uy + weight * ff.uy[iz, iy, ix]
uz = uz + weight * ff.uz[iz, iy, ix]
if iz0 == iz1: break # beware of degeneracy:
if iy0 == iy1: break # beware of degeneracy:
if ix0 == ix1: break # beware of degeneracy:
l_ux.append(ux)
l_uy.append(uy)
l_uz.append(uz)
## TSC
if scheme == 'tsc' or scheme == 'TSC':
for ix0, iy0, iz0, px, py, pz in zip(
l_ix, l_iy, l_iz, l_px, l_py,
l_pz): # for each particle
ixx0 = ix0
ixx1 = ix0 # beware of degeneracy
iyy0 = iy0
iyy1 = iy0
izz0 = iz0
izz1 = iz0
if nx > 1:
ixx0 = ix0 - 1
ixx1 = ix0 + 1
dx_1 = 1. / ff.dx
dx_2 = 1. / ff.dx**2
if ny > 1:
iyy0 = iy0 - 1
iyy1 = iy0 + 1
dy_1 = 1. / ff.dy
dy_2 = 1. / ff.dy**2
if nz > 1:
izz0 = iz0 - 1
izz1 = iz0 + 1
dz_1 = 1. / ff.dz
dz_2 = 1. / ff.dz**2
ux = 0.
uy = 0.
uz = 0.
for ix in [ix0, ixx0, ixx1]:
weight_x = 0.
if ix - ix0 == -1 or ix - ix0 == 1:
weight_x = 1.125 - 1.5 * abs(
px - ff.x[ix]) * dx_1 + 0.5 * abs(
px - ff.x[ix])**2 * dx_2
elif nx != 1:
weight_x = 0.75 - (px - ff.x[ix])**2 * dx_2
for iy in [iy0, iyy0, iyy1]:
weight_y = 0.
if iy - iy0 == -1 or iy - iy0 == 1:
weight_y = 1.125 - 1.5 * abs(
py - ff.y[iy]) * dy_1 + 0.5 * abs(
py - ff.y[iy])**2 * dy_2
elif ny != 1:
weight_y = 0.75 - (py - ff.y[iy])**2 * dy_2
for iz in [iz0, izz0, izz1]:
weight_z = 0.
if iz - iz0 == -1 or iz - iz0 == 1:
weight_z = 1.125 - 1.5 * abs(
pz - ff.z[iz]) * dz_1 + 0.5 * abs(
pz - ff.z[iz])**2 * dz_2
elif nz != 1:
weight_z = 0.75 - (pz - ff.z[iz])**2 * dz_2
weight = 1.
if nx > 1: weight = weight * weight_x
if ny > 1: weight = weight * weight_y
if nz > 1: weight = weight * weight_z
ux = ux + weight * ff.ux[iz, iy, ix]
uy = uy + weight * ff.uy[iz, iy, ix]
uz = uz + weight * ff.uz[iz, iy, ix]
if izz0 == izz1: break # beware of degeneracy:
if iyy0 == iyy1: break # beware of degeneracy:
if ixx0 == ixx1: break # beware of degeneracy:
l_ux.append(ux)
l_uy.append(uy)
l_uz.append(uz)
## Convert all information into a single record array
data_set = np.core.records.fromarrays(
[
l_ipars.astype('int'), l_px, l_py, l_pz, l_vx, l_vy, l_vz,
l_rix, l_riy, l_riz, l_ix, l_iy, l_iz, l_ux, l_uy, l_uz
],
names=
'ipar, ipx, ipy, ipz, vx, vy, vz, rix, riy, riz, ix, iy, iz, ux, uy, uz',
formats=
'int, float, float, float, float, float, float, int, int, int, int, int, int, float, float, float'
)
gas_velo_at_particle_pos = np.sort(data_set,
order=['ix', 'iy', 'iz'])
Nix = int(gas_velo_at_particle_pos['rix'].max() + 1)
Niy = int(gas_velo_at_particle_pos['riy'].max() + 1)
Niz = int(gas_velo_at_particle_pos['riz'].max() + 1)
Npar_arr = np.array([
gas_velo_at_particle_pos['rix'],
gas_velo_at_particle_pos['riy'],
gas_velo_at_particle_pos['riz']
])
#rgrid_edges = (grid.x[1:]-(grid.x[1:]-grid.x[:-1])/2)[2:-2]
xrange = np.arange(
0,
float(gas_velo_at_particle_pos['rix'].max()) + 2)
xrange = xrange - 0.5
yrange = np.arange(
0,
float(gas_velo_at_particle_pos['riy'].max()) + 2)
zrange = np.arange(
0,
float(gas_velo_at_particle_pos['riz'].max()) + 2)
Npar_hist, edges = np.histogramdd(Npar_arr.T,
bins=(xrange, yrange, zrange))
Npar_hist, edges = np.histogramdd(Npar_arr.T, bins=(Nix, Niy, Niz))
gas_velo_at_particle_pos = {
'time':
ff.t,
'par_pos':
np.array([
gas_velo_at_particle_pos['ipx'],
gas_velo_at_particle_pos['ipy'],
gas_velo_at_particle_pos['ipz']
]),
'par_velo':
np.array([
gas_velo_at_particle_pos['vx'],
gas_velo_at_particle_pos['vy'],
gas_velo_at_particle_pos['vz']
]),
'par_idx':
np.array([
gas_velo_at_particle_pos['rix'],
gas_velo_at_particle_pos['riy'],
gas_velo_at_particle_pos['riz']
]),
'npar':
np.array(Npar_hist[gas_velo_at_particle_pos['rix'],
gas_velo_at_particle_pos['riy'],
gas_velo_at_particle_pos['riz']]),
'gas_velo':
np.array([
gas_velo_at_particle_pos['ux'],
gas_velo_at_particle_pos['uy'],
gas_velo_at_particle_pos['uz']
])
}
print('## Saving dataset into ' + save_destination + '...')
io.pkl_save(
{
'gas_velo_at_particle_pos': gas_velo_at_particle_pos,
't': ff.t
},
save_filename,
folder=save_destination)
print('## Done!')