def gas_alpha(sim=False, t_range=[0, -1], OVERWRITE=False):
"""This calculates the global alpha-value from ts object via
alphah=(2./3.)*(ts3.uxuym)/(ts3.rhom*ts3.csm**2)
for the lastNentries of the time series.
Input:
t_range use this time range of the timeseries
OVERWRITE overwrite alpha file in sim.pc_datadir/alpha_<lastNentries>
return:
alpha dictionary
"""
from pencil import get_sim
from pencil.sim import sim
from pencil import io
from os.path import exists, join
import numpy as np
def empirical_std_deviation(x):
"""
(Geschaetzte) Streuung der Messwerte x um den (unbekannten) wahren Wert
(estimated) stray of the measurments x around the (unknown) true value
s(x) = SQRT( 1./(M-1) * SUM( (x-<x>)**2 ) )"""
import numpy as np
x = np.array(x)
M = np.size(x)
xm = np.mean(x)
# return np.sqrt(1./(M-1.)*np.sum((x-xm)**2))
return np.sqrt(M / (M - 1.0) * ((1.0 / M * np.sum(x**2)) - xm**2))
def std_deviation_of_mean_value(x):
"""
Messunsicherheit des Mittelwertes <x>
Empirical standarddeviation of the arithmetical mean value
s(<x>) = s(x)/SQRT( M ) = SQRT( 1./(M-1) * SUM( (x-<x>)**2 ) ) / SQRT( M )"""
import numpy as np
x = np.array(x)
M = np.size(x)
if M == 1:
return 0
return empirical_std_deviation(x) / np.sqrt(M)
if type(sim) == sim.__Simulation__:
SIM = sim
else:
SIM = get_sim()
filename = "alpha_" + str(t_range[0]) + "_" + str(t_range[1])
## skip if nothing is new
if not OVERWRITE and io.exists(name=filename, sim=SIM):
print('~ Alpha for "' + SIM.name + '" already exists. Loading file...')
return io.load(name=filename, sim=SIM)
print('~ Calculating alpha for "' + SIM.name + '" in "' + SIM.path + '"')
## import time series object
try:
print("~ reading time series..")
ts = SIM.get_ts()
except:
print("! ERROR: Couldnt read time series!")
return False
## correct if csm quantity is not correctly exported
try:
csm = ts.csm
if csm[0] == 0:
csm = 1.0
except:
print(
"? WARNING: Couldnt find >csm< in time series, set it to csm = 1. This may be incorrect!"
)
csm = 1.0
if t_range[1] == -1:
t_range[1] = ts.t[-1]
id_min = np.argmin(np.abs(ts.t - t_range[0]))
id_max = np.argmin(np.abs(ts.t - t_range[1]))
alpha_dict = {}
## calculate alpha
print("~ calculating alpha, its mean value and standard deviation for " +
str(t_range))
alpha_dict["alpha"] = -(2.0 / 3.0) * (ts.uxuym) / (ts.rhom * csm**2)
alpha_dict["alpha_mean"] = np.mean(alpha_dict["alpha"][id_min:id_max])
alpha_dict["alpha_stddev"] = std_deviation_of_mean_value(
alpha_dict["alpha"][id_min:id_max])
print("~ alpha_mean = " + str(alpha_dict["alpha_mean"]) +
" and alpha_stddev = " + str(alpha_dict["alpha_stddev"]))
## calculate alpha minus mean_flux
print(
"~ calculating alpha minus mean_flux (alpha_mmf), its mean value and standard deviation"
)
alpha_dict["alpha_mmf"] = (-(2.0 / 3.0) * (ts.uxuym - ts.uxm * ts.uym) /
(ts.rhom * csm**2))
alpha_dict["alpha_mmf_mean"] = np.mean(
alpha_dict["alpha_mmf"][id_min:id_max])
alpha_dict["alpha_mmf_stddev"] = std_deviation_of_mean_value(
alpha_dict["alpha_mmf"][id_min:id_max])
print("~ alpha_mmf_mean = " + str(alpha_dict["alpha_mmf_mean"]) +
" and alpha_mmf_stddev = " + str(alpha_dict["alpha_mmf_stddev"]))
import math
for v in alpha_dict.values():
if type(v) == type(1.1) and math.isnan(v):
io.debug_breakpoint()
## save alpha in plk
print("~ saving alpha values in " + SIM.pc_datadir + "/" + filename)
io.save(alpha_dict, filename, folder=SIM.pc_datadir)
return alpha_dict
def copy(
self,
path_root=".",
name=False,
start_optionals=False,
optionals=True,
quiet=True,
rename_submit_script=False,
OVERWRITE=False,
):
"""
This method does a copy of the simulation object by creating a new
directory 'name' in 'path_root' and copy all simulation components and
optiona)
ls to its directory.
This method neither links/compiles the simulation.
If start_optionals it creates data dir.
It does not overwrite anything, unless OVERWRITE is True.
Submit Script Rename:
Name in submit scripts will be renamed if possible!
Submit scripts will be identified by submit* plus appearenace of old
simulation name inside, latter will be renamed!
Parameters
----------
path_root : string
Path to new sim.-folder(sim.-name). This folder will
be created if not existing! Relative paths are
thought to be relative to the python current workdir
name : string
Name of new simulation, will be used as folder name.
Rename will also happen in submit script if found.
Simulation folders is not allowed to preexist!
optionals : bool
Add list of further files to be copied. Wildcasts
allowed according to glob module!
Set True to use self.optionals.
start optionals :
Add list of further files to be copied.
Wildcasts allowed according to glob module!
Set True to use self.optionals.
quiet : bool
Set True to suppress output.
rename_submit_script : bool
Set False if no renames shall be performed in submit* files
OVERWRITE : bool
Set True to overwrite no matter what happens!
"""
from glob import glob
from numpy import size
from os import listdir, symlink
from shutil import copyfile
from pencil import get_sim
from pencil.io import (
mkdir,
get_systemid,
rename_in_submit_script,
debug_breakpoint,
)
from pencil import is_sim_dir
# set up paths
if path_root == False or type(path_root) != type("string"):
print("! ERROR: No path_root specified to copy the simulation to.")
return False
path_root = abspath(path_root) # simulation root dir
# name and folder of new simulation but keep name of old if sim with old
# name is NOT existing in NEW directory
if name == False:
name = self.name
if exists(join(path_root, name)) and OVERWRITE == False:
name = name + "_copy"
if exists(join(path_root, name)):
name = name + str(
size([f
for f in listdir(path_root) if f.startswith(name)]))
print(
"? Warning: No name specified and simulation with that name " +
"already found! New simulation name now " + name)
path_newsim = join(path_root, name) # simulation abspath
path_newsim_src = join(path_newsim, "src")
if islink(join(path_root, self.name, "data")):
link_data = True
oldtmp = os.path.realpath(join(path_root, self.name, "data"))
newtmp = join(str.strip(str.strip(oldtmp, "data"), self.name),
name, "data")
if exists(newtmp) and OVERWRITE == False:
raise ValueError(
"Data directory {0} already exists".format(newtmp))
else:
path_newsim_data = newtmp
path_newsim_data_link = join(path_newsim, "data")
else:
link_data = False
path_newsim_data = join(path_newsim, "data")
path_initial_condition = join(self.path, "initial_condition")
if exists(path_initial_condition):
has_initial_condition_dir = True
path_newsim_initcond = join(path_newsim, "initial_condition")
else:
has_initial_condition_dir = False
if type(optionals) == type(["list"]):
optionals = self.optionals + optionals # optional files to be copied
if optionals == True:
optionals = self.optionals
if type(optionals) == type("string"):
optionals = [optionals]
if type(optionals) != type(["list"]):
print("! ERROR: optionals must be of type list!")
tmp = []
for opt in optionals:
files = glob(join(self.path, opt))
for f in files:
tmp.append(basename(f))
optionals = tmp
# optional files to be copied
if type(start_optionals) == type(["list"]):
start_optionals = self.start_optionals + start_optionals
if start_optionals == False:
start_optionals = self.start_optionals
if type(start_optionals) == type("string"):
start_optionals = [start_optionals]
if type(start_optionals) != type(["list"]):
print("! ERROR: start_optionals must be of type list!")
tmp = []
for opt in start_optionals:
files = glob(join(self.datadir, opt))
for f in files:
tmp.append(basename(f))
start_optionals = tmp
## check if the copy was already created
if is_sim_dir(path_newsim) and OVERWRITE == False:
if not quiet:
print("? WARNING: Simulation already exists." +
" Returning with existing simulation.")
return get_sim(path_newsim, quiet=quiet)
## expand list of optionals wildcasts
# check existence of path_root+name, a reason to stop and not overwrite
if OVERWRITE == False and exists(path_newsim):
print(
"! ERROR: Folder to copy simulation to already exists!\n! -> "
+ path_newsim)
return False
# check existance of self.components
for comp in self.components:
if not exists(join(self.path, comp)):
print("! ERROR: Couldnt find component " + comp +
" from simulation " + self.name + " at location " +
join(self.path, comp))
return False
# check existance of optionals
for opt in optionals:
if not exists(join(self.path, opt)):
print("! ERROR: Couldnt find optional component " + opt +
" from simulation " + self.name + " at location " +
join(self.path, opt))
return False
# check existance of self.start_components
for comp in self.start_components:
if not exists(join(self.datadir, comp)):
print("! ERROR: Couldnt find component " + comp +
" from simulation " + self.name + " at location " +
join(self.path, comp))
return False
# check existance of start_optionals
for opt in start_optionals:
if not exists(join(self.datadir, opt)):
print("! ERROR: Couldnt find optional component " + opt +
" from simulation " + self.name + " at location " +
join(self.datadir, opt))
return False
# create folders
if mkdir(path_newsim) == False and OVERWRITE == False:
print("! ERROR: Couldnt create new simulation directory " +
path_newsim + " !!")
return False
if mkdir(path_newsim_src) == False and OVERWRITE == False:
print("! ERROR: Couldnt create new simulation src directory " +
path_newsim_src + " !!")
return False
if mkdir(path_newsim_data) == False and OVERWRITE == False:
print("! ERROR: Couldnt create new simulation data directory " +
path_newsim_data + " !!")
return False
if link_data:
symlink(path_newsim_data, path_newsim_data_link)
# copy files
files_to_be_copied = []
for f in self.components + optionals:
f_path = abspath(join(self.path, f))
copy_to = abspath(join(path_newsim, f))
if f_path == copy_to:
print("!! ERROR: file path f_path equal to destination " +
"copy_to. Debug this line manually!")
debug_breakpoint()
copyfile(f_path, copy_to)
for f in self.start_components + start_optionals:
f_path = abspath(join(self.datadir, f))
copy_to = abspath(join(path_newsim_data, f))
if f_path == copy_to:
print("!! ERROR: file path f_path equal to destination " +
"copy_to. Debug this line manually!")
debug_breakpoint()
copyfile(f_path, copy_to)
# Organizes any personalized initial conditions
if has_initial_condition_dir:
if mkdir(path_newsim_initcond) == False and OVERWRITE == False:
print(
"! ERROR: Couldnt create new simulation initial_condition"
+ " directory " + path_newsim_initcond + " !!")
return False
for f in listdir(path_initial_condition):
f_path = abspath(join(path_initial_condition, f))
copy_to = abspath(join(path_newsim_initcond, f))
if f_path == copy_to:
print("!! ERROR: file path f_path equal to destination " +
"copy_to. Debug this line manually!")
debug_breakpoint()
copyfile(f_path, copy_to)
# modify name in submit script files
if rename_submit_script != False:
if type(rename_submit_script) == type("STRING"):
rename_in_submit_script(new_name=rename_submit_script,
sim=get_sim(path_newsim))
else:
print("!! ERROR: Could not understand rename_submit_script=" +
str(rename_submit_script))
# done
return get_sim(path_newsim)
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. / 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 + '...')
pkl_save(
{
'gas_velo_at_particle_pos': gas_velo_at_particle_pos,
't': ff.t
},
save_filename,
folder=save_destination)
print('## Done!')
# coding: utf-8
# In[1]:
import pencil as pc
# You may need to compile and run simlation object from below first!
# In[2]:
sim = pc.get_sim('../sample_simulations/2d_streaming_instability/')
# ## Reading simulation parameters the easy way
# Use typ what quantitiy you need, parser does the rest!
# In[3]:
sim.get_value('beta_glnrho_global')
# ## Getting an overview of VAR files and PVAR files
# In[4]:
sim = pc.get_sim('../sample_simulations/2d_streaming_instability/')
varlist = sim.get_varlist()
pvarlist = sim.get_varlist(particle=True)
print(varlist[-1])
print(pvarlist[-1])
# ## Get last 10 VAR files
# Also check out all abilities of get_varlist and come up with your own!
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 = (
1.0 / 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 + "...")
io.pkl_save(
{"gas_velo_at_particle_pos": gas_velo_at_particle_pos, "t": ff.t},
save_filename,
folder=save_destination,
)
print("## Done!")
def part_to_grid(
xp,
yp,
zp=False,
quantity=False,
Nbins=[1024, 1024, 1024],
sim=False,
extent=False,
fill_gaps=False,
):
"""Bins quantity based on position data xp and yp to 1024^2 bins like a histrogram.
This method is not using TSC.
Args:
- xp, yp: array of x and y positions
- zp: specify if 3D run, set False to have zp == 0
- quantity: array of same shape as xp and yp, but with quantity to bin, set it False to count number of occurrences/histrogram2d
- Nbins: number of histrogram bins for each direction. if 2d only the first two entries in Nbins are used
- sim: to extract extent from by loading ghostzone-free grid
- extent: [[xmin, xmax],[ymin, ymax]] or set false and instead give a sim
set extent manually e.g. if you want to include ghost zones
- fill_gaps interpolate empty grid cells
Returns: arr, xgrid, ygrid
- arr: 2d array with binned values
- x-/ygrid: linspace of used x/y grid
- zgrid: if zp != False
Example:
vpx = part_to_grid_2d(pvar.xp, pvar.yp, pvar.vpx), notice that this will execute pc.get_sim() internally to get the extent
"""
import numpy as np
from pencil import get_sim
from pencil.calc import fill_gaps_in_grid
if not xp.shape == yp.shape and yp.shape == xp.shape and yp.shape == zp.shape:
print("! ERROR: Shape of xp, yp, zp and quantity needs to be equal!")
if extent == False and sim == False:
sim = get_sim()
if quantity == False:
quantity = xp / xp
if extent == False:
grid = sim.grid
if type(zp) == type(False) and zp == False:
extent = [
[grid.x[0] - grid.dx / 2, grid.x[-1] + grid.dx / 2],
[grid.y[0] - grid.dy / 2, grid.y[-1] + grid.dy / 2],
]
else:
extent = [
[grid.x[0] - grid.dx / 2, grid.x[-1] + grid.dx / 2],
[grid.y[0] - grid.dy / 2, grid.y[-1] + grid.dy / 2],
[grid.z[0] - grid.dz / 2, grid.z[-1] + grid.dz / 2],
]
if type(zp) == type(False) and zp == False:
arr = np.zeros((2, Nbins[0], Nbins[1]))
else:
arr = np.zeros((3, Nbins[0], Nbins[1], Nbins[2]))
arr[:] = np.NAN
xgrid = (np.linspace(extent[0][0], extent[0][1], num=Nbins[0] + 1)[:-1] +
np.linspace(extent[0][0], extent[0][1], num=Nbins[0] + 1)[1:]) / 2
ygrid = (np.linspace(extent[1][0], extent[1][1], num=Nbins[1] + 1)[:-1] +
np.linspace(extent[1][0], extent[1][1], num=Nbins[1] + 1)[1:]) / 2
if type(zp) == type(False) and zp == False:
for x, y, q in zip(xp, yp, quantity):
idx = np.argmin(np.abs(x - xgrid))
idy = np.argmin(np.abs(y - ygrid))
if np.isnan(arr[0, idx, idy]):
arr[0, idx, idy] = 0
arr[1, idx, idy] = 0
arr[0, idx, idy] += q
arr[1, idx, idy] += 1
else:
zgrid = (
np.linspace(extent[2][0], extent[2][1], num=Nbins[2] + 1)[:-1] +
np.linspace(extent[2][0], extent[2][1], num=Nbins[2] + 1)[1:]) / 2
for x, y, z, q in zip(xp, yp, zp, quantity):
idx = np.argmin(np.abs(x - xgrid))
idy = np.argmin(np.abs(y - ygrid))
idz = np.argmin(np.abs(z - zgrid))
if np.isnan(arr[0, idx, idy, idz]):
arr[0, idx, idy, idz] = 0
arr[1, idx, idy, idz] = 0
arr[0, idx, idy, idz] += q
arr[1, idx, idy, idz] += 1
arr = arr[0] / arr[1]
if fill_gaps == True:
arr = fill_gaps_in_grid(arr, key=np.NAN)
if type(zp) == type(False) and zp == False:
return arr, xgrid, ygrid
else:
return arr, xgrid, ygrid, zgrid
def get_value_from_file(filename,
quantity,
change_quantity_to=None,
sim=False,
filepath=False,
DEBUG=False,
silent=False):
""" Use to read in a quantity from
- *.in
- *.local
- submit*, i.e. submit.sh, submit.csh, files, only works if computer is readily specified in pc.io.get_systemid
Please add further functionallity by yourself!
Args:
filename: can be "run.in", "start.in", "cparam.local", path to that file is extraced from filepath or sim object
quantity: variable to read in from file
sim: put simulation object here, file will be found by filename automatically
filepath: normally not needed, specify here where to find the file with filename, can be a list of paths if unshure
DEBUG: make dry run, tell me what you would do but dont change anything!
silent: suppress certain output by setting True
Return:
Returns None if not successful
"""
import os
import numpy as np
from os.path import join, abspath, exists, split, isfile
from pencil import get_sim
from pencil.math import is_number, is_float, is_int
from pencil.io import timestamp, debug_breakpoint, mkdir
import re
import copy
def string_to_tuple(s):
q = s.split(',')
if is_number(q[0]):
q = np.array([float(t) for t in q])
q_type = 'TUPLE_FLOAT'
return q, q_type
if q[0] == 'T' or q[0] == 'F':
q = np.array([bool(t == 'T') for t in q])
q_type = 'TUPLE_BOOL'
return q, q_type
if type(q[0]) == type('string'):
q = [t.replace('"', '').replace("'", '') for t in q]
q_type = 'TUPLE_STRING'
return q, q_type
print('! ERROR: Could not parse string ' + s + ' into a tuple!')
print(
'! DEBUG_BREAKPOINT AKTIVATED - check out the following variables: string s, tuple q, first entry in tuple q[0]'
)
debug_breakpoint()
return None, None
def tuple_to_string(t, q_type):
return ','.join([str(a) for a in t])
######## prepare filename and quantity
filename = filename.strip() # get rid of whitespaces
quantity = quantity.strip()
q_type = False # q_type will store the type of the quantity value once found and identified
split_filename = split(filename)
if sim == False and split_filename[0] != '' and filepath == False:
filepath = split_filename[0]
filename = split_filename[1]
######## find correct file
# prepare search_path list to search filename in
if filepath == False:
if sim == False:
sim = get_sim()
else:
filepath = sim.path
search_paths = [sim.path, join(sim.path,
'src')] # add other search paths here!!
elif type(filepath) == type('string'):
if filepath.endswith(filename):
filepath = filepath[:-len(
filename
)] # clean filepath if filename occures to be in there at the end
search_paths = [abspath(filepath.strip())] # correct path format
elif type(filepath) == type(['list']):
search_paths = filepath
else:
print('! ERROR: Filename ' + str(filename) +
' could not be interprated or found!')
return None
absolute_filepath = None
for search_path in search_paths:
tmp_path = join(search_path, filename)
if os.path.isfile(tmp_path):
absolute_filepath = tmp_path
break
# Traps the case of not being able to find the file
if absolute_filepath is None:
if DEBUG:
print('~ DEBUG: File {0} not found in {1}!'.format(
filename, search_paths))
return None
######## open file
# now having absolute filepath to file, lets check that file and find quantity inside!
if DEBUG:
print('~ DEBUG: Found file {0} in {1}'.format(filename, filepath))
with open(absolute_filepath, 'r') as f:
data_raw = f.readlines()
######## find line in file which quantity in
line_matches = []
# scan through file for differently for different files
if filename.endswith(
'.in') or 'cparam.local' or 'Makefile.local' in filename:
FILE_IS = 'IN_LOCAL'
SYM_COMMENT = '!'
SYM_ASSIGN = '='
SYM_SEPARATOR = ','
for ii, line in enumerate(data_raw):
if line.strip().startswith('&'):
continue # filter out lines with &something, e.g. &density_run_pars
quantity_match_tmp = re.search(
'[^0-9a-zA-Z_]*{0}[^0-9a-zA-Z_]'.format(quantity),
line.split(SYM_COMMENT)[0])
# Check if this substring occurs as a string.
if quantity_match_tmp:
quantity_match = quantity_match_tmp
if str.count(line[0:quantity_match.start()], "'") % 2 == 0 and \
str.count(line[0:quantity_match.start()], '"') % 2 == 0:
if line_matches:
line_matches[0] = ii
else:
line_matches.append(ii)
elif filename.startswith('submit') and filename.split('.')[-1] in [
'csh', 'sh'
]:
FILE_IS = 'SUBMIT'
SYM_COMMENT = False
SYM_ASSIGN = '='
SYM_SEPARATOR = ','
for ii, line in enumerate(data_raw):
if line.replace(' ', '').startswith('#@') and quantity in line:
quantity_match_tmp = re.search(
'[^0-9a-zA-Z_]*{0}[^0-9a-zA-Z_]'.format(quantity),
line.split(SYM_COMMENT)[0])
if quantity_match_tmp:
quantity_match = quantity_match_tmp
if line_matches:
line_matches[0] = ii
else:
line_matches.append(ii)
else:
print(
'! ERROR: Filename unknown! No parsing possible! Please enhance this function to work with '
+ filename)
if len(line_matches) > 1:
print('! ERROR: Found more than one line with keyword "' + quantity +
'" inside!')
return None
if len(line_matches) == 0:
if silent == False:
print('! ERROR: Found no line with keyword "' + quantity +
'" inside ' + join(filepath, filename) + '!')
return None
filename = os.path.basename(filename)
######## get line with quantity inside
line = data_raw[line_matches[0]]
######## do separation of quantity from rest of line, i.e. get rid of comments and other quantities defined in this line
comment = ''
if SYM_COMMENT:
tmp = line.partition(SYM_COMMENT) # strip away comment
line = tmp[0]
if tmp[-1] != '':
comment = SYM_COMMENT + tmp[-1] # and store for later
# line = line.replace(' ','').replace('\n', '') # do cleanup in this line
# Find the position where the quantity is stored.
pos_equal_sign_left = quantity_match.end() + str.find(
line[quantity_match.end() - 1:], '=')
# pos_equal_sign_right = pos_equal_sign_left + str.find(line[pos_equal_sign_left:], ', *[0-9a-zA-Z][0-9a-zA-Z]* *= *[0-9a-zA-Z][0-9a-zA-Z]*')
pos_equal_sign_right = pos_equal_sign_left + str.find(
line[pos_equal_sign_left:], '=')
if pos_equal_sign_right < pos_equal_sign_left:
pos_equal_sign_right = -1
pos_right_comma = -1
else:
pos_right_comma = str.rfind(line[:pos_equal_sign_right], ',')
# Change the quantity in the line string.
q = copy.copy(line[pos_equal_sign_left:pos_right_comma])
# qs = line.partition(quantity+SYM_ASSIGN)
# if SYM_ASSIGN in qs[-1]:
# qs = qs[:2]+qs[-1].partition(SYM_ASSIGN)
# #qs = qs[:2]+qs[-1].partition(SYM_ASSIGN)
# qs = qs[:2]+qs[2].rpartition(',')+qs[3:]
#
# qs = list(qs)
# q = qs[2]
while q.endswith('\t'):
q = q[:-1]
comment = '\t' + comment # take care of trailing tabulator
while q.endswith(','):
q = q[:-1] # remove trailing ,
######## do a cleanup of quantity value q and convert into string, float, int or array, also remember data type of q
if q.startswith("'") and q.endswith(
"'"): # quantity q is string in form of 'STRING'
q = q[1:-1]
q_type = 'STRING'
elif q.startswith('"') and q.endswith(
'"'): # quantity q is string in form of "STRING"
q = q[1:-1]
q_type = 'STRING'
elif not is_number(
q[0]): # quantity q is string in form of not beeing a number
q = q.strip().replace('"', '').replace("'", '')
q_type = 'STRING'
try:
float(q)
q_type = 'FLOAT'
if is_int(q):
q = int(q)
q_type = 'INT'
except:
if type(q) == type('string') and ',' in q:
q, q_type = string_to_tuple(q) # q is a TULPE_something
print('q = {0}, q_type = {1}'.format(q, q_type))
if type(q) == type('string') and q in ['F', 'f']: # q is BOOL
q = False
q_type = 'BOOL'
if type(q) == type('string') and q in ['T', 't']:
q = True
q_type = 'BOOL'
if type(q) == type('string'):
if is_number(q[0]):
q_type = 'STRING'
if q_type == False: # catch if type of q was not recognized
print(
'! ERROR: Couldnt identify the data type of the quantity value: ' +
str(q))
DEBUG = True
debug_breakpoint()
elif DEBUG:
print('~ DEBUG: q_type = ' + q_type)
if q_type == 'FLOAT':
q = float(q)
elif q_type == 'INT':
q = int(q)
######## if value of quantity has to be changed do:
if change_quantity_to != None:
####### prepare change_quantity_to for string injection
if q_type == 'STRING':
if not FILE_IS == 'SUBMIT':
change_quantity_to = "'" + change_quantity_to + "'"
elif q_type == 'BOOL':
change_quantity_to = bool(change_quantity_to in ['T', 't', True])
if change_quantity_to == True:
change_quantity_to = 'T'
elif change_quantity_to == False:
change_quantity_to = 'F'
else:
print(
'! ERROR: There is something deeply wrong here! change_quantity_to should be bool...'
)
debug_breakpoint()
return None
elif q_type == 'FLOAT':
change_quantity_to = '%e' % change_quantity_to
elif q_type.startswith('TUPLE'):
if q_type.endswith('BOOL'):
if type(change_quantity_to) == type(
['list', 'of', 'bool', 'or', 'strings']):
for ii, val in enumerate(change_quantity_to):
if val in ['T', 't', True]:
change_quantity_to[ii] = 'T'
elif val in ['F', 'f', False]:
change_quantity_to[ii] = 'F'
else:
print(
'! ERROR: There is something deeply wrong here! change_quantity_to['
+ str(ii) +
'] should be bool or string representation, but it is '
+ str(change_quantity_to[ii]))
debug_breakpoint()
return None
change_quantity_to = ','.join(
[str(t) for t in change_quantity_to])
if q_type.endswith('FLOAT'):
change_quantity_to = str(list(change_quantity_to))[1:-1]
if q_type.endswith('STRING'):
change_quantity_to = str(list(change_quantity_to))[1:-1]
if DEBUG:
print('~ DEBUG: Would change quantity ' + quantity + ' from ' +
str(q) + ' to ' + str(change_quantity_to))
q = str(change_quantity_to)
######## further formatting
new_line = line[:pos_equal_sign_left] + q + line[
pos_right_comma:] + '\t' + comment # create new line and add comment stripped away before
# new_line = ''.join(qs).replace(SYM_SEPARATOR, SYM_SEPARATOR+' ')+'\t'+comment # create new line and add comment stripped away before
new_line = new_line.rstrip(
) # clean empty spaces on the right, no one needs that...
if new_line[-1] != '\n': new_line = new_line + '\n'
if FILE_IS == 'SUBMIT':
new_line = new_line.replace('#@', '#@ ').replace(
'=', ' = ') # optimizing format of submit script
if DEBUG:
print('~ DEBUG: old line: ' + str(data_raw[line_matches[0]])[:-1])
print('~ DEBUG: new line: ' + str(new_line)[:-1])
if not DEBUG:
####### do backup of file before changing it
from shutil import copyfile
target = join(sim.path, 'pc/backups/' + timestamp())
mkdir(target)
target = join(target, filename)
copyfile(absolute_filepath, target)
# replace line in raw data
data_raw[line_matches[0]] = new_line
# save on drive
f.close()
with open(absolute_filepath, 'w') as f:
for l in data_raw:
f.write(l)
######## DONE!
return q
def __init__(self,
datadir=False,
sim=False,
tmin=0,
tmax=-1,
noutmax='-1',
swap_endian=False,
quiet=False,
use_existing_pstalk_sav=False):
"""
Read PSTALK files from Pencil Code using IDL.
Uses IDL<->Python Bridge, this must be activated manually!
Args:
- datadir specify datadir, default False
- sim specify simulation from which you want to read
- swap_endian change if needed to True, default False
- quiet verbosity, default False
- use_existing_pstalk_sav
use existing <sim.datadir>/data/pc/tmp/pstalk.sav for speed up
"""
import numpy as np
import os
from os.path import join
from pencil import get_sim
if datadir == False:
if sim == False:
sim = get_sim()
datadir = sim.datadir
if quiet == False:
quiet = '0'
else:
quiet = '1'
if swap_endian == False:
swap_endian = '0'
else:
swap_endian = '1'
if use_existing_pstalk_sav == True:
from scipy.io.idl import readsav
print('~ reading existing pstalk..')
ps = readsav(join(sim.pc_datadir, 'tmp', 'pstalk.sav'))('pstalk')
for key in set(ps.dtype.fields.keys()):
if hasattr(self, key.lower()): continue
setattr(self, key.lower(), ps[key][0].T)
else:
try:
cwd = os.getcwd()
from idlpy import IDL
os.chdir(cwd)
print('~ reading pstalk in IDL..')
idl_call = ', '.join([
'pc_read_pstalk', 'obj=pstalk',
'datadir="' + datadir + '"', 'it0=' + str(tmin),
'it1=' + str(tmax), 'quiet=' + quiet,
'swap_endian=' + swap_endian, 'noutmax=' + str(noutmax)
])
IDL.run(idl_call)
print('~ parsing pstalk from IDL to python..')
ps = IDL.pstalk
for key in set(ps.keys()):
if hasattr(self, key.lower()): continue
setattr(self, key.lower(), ps[key].T)
except:
print(
'! ERROR: no idl<->python bridge found. Try whats written in pstalk-comment to fix that issue.'
)
print('! ')
print(
'! Use something like: (ensure you have IDL 8.5.1 or larger)'
)
print(
'! export PYTHONPATH=$PYTHONPATH:$IDL_HOME/lib/bridges:$IDL_HOME/bin/bin.linux.x86_64'
)
print(
'! export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64:$IDL_HOME/bin/bin.linux.x86_64'
)
print('! in your .bashrc')
print('! ')
print(
'! If you have it already installed, try: from idlpy import IDL and check for errors'
)
print('! ')
print(
'~ BACKUP SOLUTION: reading pstalk via pidly, starting IDL..'
)
from pencil.backpack import pidly
IDL = pidly.IDL(long_delay=0.05) # start IDL engine
from scipy.io.idl import readsav
from pencil.io import mkdir
## read tstalk file
print('## reading particle stalker file..')
IDL('pc_read_pstalk, object=pstalk, datadir="' + sim.datadir +
'"' + ', quiet=' + quiet + ', it0=' + str(tmin) +
', it1=' + str(tmax) + ', swap_endian=' + swap_endian)
print('## transfering pstalk file from IDL to python..')
mkdir(join(sim.pc_datadir, 'tmp'))
IDL('save, pstalk, filename="' +
join(sim.pc_datadir, 'tmp', 'pstalk_' + str(tmin) + '_' +
str(tmax) + '.sav') + '"')
ps = readsav(join(sim.pc_datadir, 'tmp',
'pstalk.sav'))('pstalk')
#from pc.io import debug_breakpoint; debug_breakpoint()
for key in set(ps.dtype.fields.keys()):
if hasattr(self, key.lower()): continue
setattr(self, key.lower(), ps[key][0].T)