def add(self, *args):
"""Add simulation(s) to simulations object.
Args:
- simulation object
- list of simulation objects
- iterable of simulation objects
- simulations object
"""
from ..math import is_iterable
from .simulation import __Simulation__
from .simulation import simulation
import numpy as np
from pencilnew.io import debug_breakpoint
from pencilnew import get_sim
for arg in args:
if isinstance(arg, __Simulation__):
#print('\n self.add: __Simulation__')
#print(arg.path)
self.sims.append(arg)
return True
elif isinstance(arg, str):
#print('\n self.add: string')
self.sims.append(get_sim(arg))
return True
elif is_iterable(arg):
#print('\n self.add: iterable: '+str(args))
for ar in arg:
#print('n self.add: iterable add: '+str(a))
self.add(ar)
return True
else:
print('!! ERROR: Couldnt add to simulations object: ' +
str(args))
for kw, arg in kwargs:
print('!! ERROR: Not prepared for kwargs yet!!')
print(kw + ': ' + str(arg))
return False
def add(self, *args):
"""Add simulation(s) to simulations object.
Args:
- simulation object
- list of simulation objects
- iterable of simulation objects
- simulations object
"""
from ..math import is_iterable
from .simulation import __Simulation__
from .simulation import simulation
import numpy as np
from pencilnew.io import debug_breakpoint
from pencilnew import get_sim
for arg in args:
if isinstance(arg, __Simulation__):
#print('\n self.add: __Simulation__')
#print(arg.path)
self.sims.append(arg)
return True
elif isinstance(arg, str):
#print('\n self.add: string')
self.sims.append(get_sim(arg))
return True
elif is_iterable(arg):
#print('\n self.add: iterable: '+str(args))
for ar in arg:
#print('n self.add: iterable add: '+str(a))
self.add(ar)
return True
else:
print('!! ERROR: Couldnt add to simulations object: '+str(args))
for kw, arg in kwargs:
print('!! ERROR: Not prepared for kwargs yet!!')
print(kw+': '+str(arg))
return False
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 quanittiy to bin, set ti 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 pencilnew.get_sim() internally to get the extent
"""
import numpy as np
from pencilnew import get_sim
from pencilnew.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 extent == False:
grid = sim.grid
if 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 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])
ygrid = np.linspace(extent[1][0], extent[1][1], num=Nbins[1])
if 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[1][0], extent[1][1], num=Nbins[1])
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 zp == False:
return arr, xgrid, ygrid
else:
return arr, xgrid, ygrid, zgrid
def copy(self,
path_root,
name=False,
optionals=True,
quiet=True,
rename_submit_sripts=True,
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 optionals to his directory.
This method neither links/compiles the simulation, nor creates data dir nor does overwrite anything.
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!
Args:
path_root: Dir to create new sim.-folder(sim.-name) inside. This folder will be created if not existing!
name: 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: Add list of further files to be copied. Wildcasts allowed according to glob module! Set True to use self.optionals.
quiet: Set True to suppress output.
rename_submit_sripts: Set False if no renames shall be performed in subnmit* files
OVERWRITE: Set True to overwrite no matter what happens!
"""
from os.path import exists, join, abspath
from shutil import copyfile
from glob import glob
from pencilnew.io import mkdir
from pencilnew.sim import is_sim_dir
from pencilnew import get_sim
# 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
if name == False:
name = self.name + '_copy'
print(
'? Warning: No name specified, will alter old simulation name to '
+ name)
path_newsim = join(path_root, name) # simulation abspath
path_newsim_src = join(path_newsim, 'src')
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!')
optionals = self.optionals + optionals # optional files to be copied
tmp = []
for opt in optionals:
files = glob(opt)
for f in files:
tmp.append(f)
optionals = tmp
## check if the copy was already created
if is_sim_dir(path_newsim):
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 existance of path_root+name, a reason to stop to not overwrite anything
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 optinal component ' + opt +
' from simulation ' + self.name + ' at location ' +
join(self.path, 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
# 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))
copyfile(f_path, copy_to)
# modify name in submit script files
if rename_submit_sripts:
for f in self.components + optionals:
if f.startswith('submit'):
system_name, raw_name, job_name_key, submit_scriptfile, submit_line = pencilnew.io.get_systemid(
)
# done
return get_sim(path_newsim)
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 pencilnew.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, pencilnew
import numpy as np
from os.path import join, abspath, exists, split, isfile
from pencilnew.math import is_number, is_float, is_int
from pencilnew.io import timestamp, debug_breakpoint, mkdir
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 = pencilnew.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' 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
if quantity in line.split(SYM_COMMENT)[0]: 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: 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
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
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 DEBUG: print('~ DEBUG: Would change quantity '+quantity+' from '+str(q)+' to '+str(change_quantity_to))
qs[2] = str(change_quantity_to)
######## further formatting
new_line = ''.join(qs).replace(SYM_SEPARATOR, SYM_SEPARATOR+' ')+'\t'+comment # create new line and add comment stripped away before
if not (FILE_IS == 'SUBMIT' or filename == 'cparam.local'): new_line = ' '+new_line
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 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 pencilnew as pcn
from os.path import exists
import numpy as np
GAS_VELO_TAG = 'gas_velo_at_particle_pos'
if sim == False:
sim = pcn.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')
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.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.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 = 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 = pcn.read.var(datadir=SIM.datadir, varfile=f, quiet=True, trimall=False)
pp = pc.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!')
def get_value_from_file(filename, quantity, change_quantity_to=False, 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 pencilnew.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
"""
import os, pencilnew
import numpy as np
from os.path import join, abspath, exists, split, isfile
from pencilnew.math import is_number, is_float, is_int
from pencilnew.io import timestamp, debug_breakpoint, mkdir
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 = pencilnew.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 False
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 suiting 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' 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
if quantity in line.split(SYM_COMMENT)[0]: 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: 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
######## 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
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'
elif is_float(q):
q = float(q)
q_type = 'FLOAT'
if is_int(q):
q = int(q)
q_type = 'INT'
if type(q) == type('string') and ',' in q:
q, q_type = string_to_tuple(q) # q is a TULPE_something
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 value of quantity has to be changed do:
if change_quantity_to != False:
####### 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 DEBUG: print('~ DEBUG: Would change quantity '+quantity+' from '+str(q)+' to '+str(change_quantity_to))
qs[2] = str(change_quantity_to)
######## further formatting
new_line = ''.join(qs).replace(SYM_SEPARATOR, SYM_SEPARATOR+' ')+'\t\t'+comment # create new line and add comment stripped away before
if not FILE_IS == 'SUBMIT': new_line = ' '+new_line
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(filepath, target)
# replace line in raw data
data_raw[line_matches[0]] = new_line
# save on drive
f.close()
with open(filename, 'w') as f:
for l in data_raw: f.write(l)
######## DONE!
return q
def copy(self,
path_root='.',
name=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 optionals to his directory.
This method neither links/compiles the simulation, nor creates data dir nor does overwrite anything.
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!
Args:
path_root: Dir to create new sim.-folder(sim.-name) inside. This folder will be created if not existing! Relative paths are thought to be relative to the python current workdir
name: 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: Add list of further files to be copied. Wildcasts allowed according to glob module! Set True to use self.optionals.
quiet: Set True to suppress output.
rename_submit_script: Set False if no renames shall be performed in subnmit* files
OVERWRITE: Set True to overwrite no matter what happens!
"""
from os import listdir
from os.path import exists, join, abspath, basename
from shutil import copyfile
from glob import glob
from numpy import size
from pencilnew.sim import is_sim_dir
from pencilnew import get_sim
from pencilnew.io import mkdir, get_systemid, rename_in_submit_script, debug_breakpoint
from pencilnew.sim 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')
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
## 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 existance of path_root+name, a reason to stop to not overwrite anything
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 optinal component ' + opt +
' from simulation ' + self.name + ' at location ' +
join(self.path, 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
# 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)
# 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 __init__(self, varfile='pvar.dat', npar_max=-1,
datadir=False, sim=False, proc=-1, swap_endian=False, quiet=False, DEBUG=False):
"""
Read PVAR 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
- varfile put 'PVARXYZ' or just number here, 'VAR' will be replaced by 'PVAR' autom.
- npar_max maximal number of particles to be read in
- proc read from single proc, set number here
- swap_endian change if needed to True, default False
- quiet verbosity, default False
"""
import numpy as np
import os
import pencilnew as pcn
from pencilnew.math import is_number
from sys import byteorder
try:
cwd = os.getcwd()
from idlpy import IDL
os.chdir(cwd)
except:
print('! ERROR: no idl<->python bridge found. Try whats written in pstalk-comment to fix that issue.')
print('! ')
print('! Use something like: (enshure 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('! ')
return False
####### interprate parameters
if datadir == False:
if sim == False:
sim = pcn.get_sim()
datadir = sim.datadir
if quiet == False:
quiet = '0'
else:
quiet = '1'
if swap_endian == False:
if byteorder == 'little': swap_endian = '0'
elif byteorder == 'big': swap_endian = '1'
else: print('? WARNING: Couldnt determine endianness!')
####### preparing IDL call
# cleanup of varfile string
if is_number(varfile): varfile = 'PVAR'+str(varfile)
varfile = str(varfile)
if varfile=='var.dat': varfile='pvar.dat'
if varfile[:3]=='VAR': varfile='P'+varfile
#
idl_call = ', '.join(['pc_read_pvar',
'obj=pvar',
'varfile="'+varfile+'"',
'datadir="'+datadir+'"',
'quiet='+quiet,
'swap_endian='+swap_endian,
'proc='+str(proc)
])
# reduce number of particles to be read in
if npar_max > 0: idl_call= idl_call+', npar_max='+str(npar_max)
####### show idl_call string if DEBUG
if DEBUG == True: print('~ DEBUG: idl_call: '+idl_call)
###### read in var file in IDL
print('~ reading '+varfile+' in IDL..')
IDL.run(idl_call)
####### parse to python
print('~ parsing PVAR from IDL to python..')
pvar = IDL.pvar
for key in pvar.keys():
setattr(self, key, pvar[key])
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 pencilnew.get_sim() internally to get the extent
"""
import numpy as np
from pencilnew import get_sim
from pencilnew.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 __init__(self,
datadir=False,
sim=False,
swap_endian=False,
quiet=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
"""
import numpy as np
import os
import pencilnew as pcn
try:
cwd = os.getcwd()
from idlpy import IDL
os.chdir(cwd)
except:
print(
'! ERROR: no idl<->python bridge found. Try whats written in pstalk-comment to fix that issue.'
)
print('! ')
print(
'! Use something like: (enshure 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('~ reading pstalk in IDL..')
if datadir == False:
if sim == False:
sim = pcn.get_sim()
datadir = sim.datadir
if quiet == False:
quiet = '0'
else:
quiet = '1'
if swap_endian == False:
swap_endian = '0'
else:
swap_endian = '1'
idl_call = ', '.join([
'pc_read_pstalk', 'obj=pstalk', 'datadir="' + datadir + '"',
'quiet=' + quiet, 'swap_endian=' + swap_endian
])
IDL.run(idl_call)
print('~ parsing pstalk from IDL to python..')
ps = IDL.pstalk
for key in ps.keys():
setattr(self, key, ps[key].T)
def __init__(self,
datadir=False,
sim=False,
noutmax='-1',
swap_endian=False,
quiet=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
"""
import numpy as np
import os
from os.path import join
import pencilnew as pcn
if datadir == False:
if sim == False:
sim = pcn.get_sim()
datadir = sim.datadir
if quiet == False:
quiet = '0'
else:
quiet = '1'
if swap_endian == False:
swap_endian = '0'
else:
swap_endian = '1'
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 + '"',
'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 ps.keys():
setattr(self, key, 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: (enshure 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 pencilnew.backpack import pidly
IDL = pidly.IDL(long_delay=0.05) # start IDL engine
from scipy.io.idl import readsav
from pencilnew.io import mkdir
## read tstalk file
print('## reading particle stalker file..')
IDL('pc_read_pstalk, object=pstalk, datadir="' + sim.datadir +
'"' + ', quiet=' + quiet + ', 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.sav') + '"')
ps = readsav(join(sim.pc_datadir, 'tmp', 'pstalk.sav'))('pstalk')
#from pencilnew.io import debug_breakpoint; debug_breakpoint()
for key in set(ps.dtype.fields.keys()):
key = key.lower()
setattr(self, key, ps[key][0].T)
def copy(self, path_root='.', name=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 optionals to his directory.
This method neither links/compiles the simulation, nor creates data dir nor does overwrite anything.
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!
Args:
path_root: Dir to create new sim.-folder(sim.-name) inside. This folder will be created if not existing! Relative paths are thought to be relative to the python current workdir
name: 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: Add list of further files to be copied. Wildcasts allowed according to glob module! Set True to use self.optionals.
quiet: Set True to suppress output.
rename_submit_script: Set False if no renames shall be performed in subnmit* files
OVERWRITE: Set True to overwrite no matter what happens!
"""
from os import listdir
from os.path import exists, join, abspath, basename
from shutil import copyfile
from glob import glob
from numpy import size
from pencilnew.sim import is_sim_dir
from pencilnew import get_sim
from pencilnew.io import mkdir, get_systemid, rename_in_submit_script, debug_breakpoint
from pencilnew.sim 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')
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
## 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 existance of path_root+name, a reason to stop to not overwrite anything
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 optinal component '+opt+' from simulation '+self.name+' at location '+join(self.path, 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
# 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)
# 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 __init__(self, varfile='pvar.dat', npar_max=-1,
datadir=False, sim=False, proc=-1, swap_endian=False, quiet=False, DEBUG=False):
"""
Read PVAR 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
- varfile put 'PVARXYZ' or just number here, 'VAR' will be replaced by 'PVAR' autom.
- npar_max maximal number of particles to be read in
- proc read from single proc, set number here
- swap_endian change if needed to True, default False
- quiet verbosity, default False
"""
import numpy as np
import os
import pencilnew as pcn
from pencilnew.math import is_number
from sys import byteorder
try:
cwd = os.getcwd()
from idlpy import IDL
os.chdir(cwd)
except:
print('! ERROR: no idl<->python bridge found. Try whats written in pstalk-comment to fix that issue.')
print('! ')
print('! Use something like: (enshure 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('! ')
return None
####### interprate parameters
if datadir == False:
if sim == False:
sim = pcn.get_sim()
datadir = sim.datadir
if quiet == False:
quiet = '0'
else:
quiet = '1'
if swap_endian == False:
if byteorder == 'little': swap_endian = '0'
elif byteorder == 'big': swap_endian = '1'
else: print('? WARNING: Couldnt determine endianness!')
####### preparing IDL call
# cleanup of varfile string
if is_number(varfile): varfile = 'PVAR'+str(varfile)
varfile = str(varfile)
if varfile=='var.dat': varfile='pvar.dat'
if varfile[:3]=='VAR': varfile='P'+varfile
#
idl_call = ', '.join(['pc_read_pvar',
'obj=pvar',
'varfile="'+varfile+'"',
'datadir="'+datadir+'"',
'quiet='+quiet,
'swap_endian='+swap_endian,
'proc='+str(proc)
])
# reduce number of particles to be read in
if npar_max > 0: idl_call= idl_call+', npar_max='+str(npar_max)
####### show idl_call string if DEBUG
if DEBUG == True: print('~ DEBUG: idl_call: '+idl_call)
###### read in var file in IDL
print('~ reading '+varfile+' in IDL..')
IDL.run(idl_call)
####### parse to python
print('~ parsing PVAR from IDL to python..')
pvar = IDL.pvar
for key in pvar.keys():
setattr(self, key.lower(), pvar[key])
setattr(self, 'xp', pvar['XX'][0])
setattr(self, 'yp', pvar['XX'][1])
setattr(self, 'zp', pvar['XX'][2])
setattr(self, 'vpx', pvar['VV'][0])
setattr(self, 'vpy', pvar['VV'][1])
setattr(self, 'vpz', pvar['VV'][2])
def dispersion_and_drift(sim=False, OVERWRITE=False, GLOBAL=True, LOCAL=True, use_IDL=False, recalculate_gas_velo_at_particle_pos=False):
"""This calculates the dispersion (sigma) and drift (zeta) locally and globally
by using the gas_velo_at_particle_pos script and dataset for all particles.
With sigma = sqrt( 1/N_par * sum_i^N_par( (v_par(i) - <v_par>)^2 ) ) and
zeta = sqrt( 1/N_par * sum_i^N_par( (v_par(i) - u(xp_i))^2 ) )
Arg:
OVERWRITE: set to True to overwrite already calculated results
GLOBAL: Calculate drift and dispersion globally, i.e. whole simulation domain
LOCAL: Calculate drift and dispersion locally, i.e. grid cell wise
recalculate_gas_velo_at_particle_pos:
if the dataset shall be recalcualted
use_IDL: use backup solution of IDL script and sav files
returns True if successfull
"""
import pencilnew as pcn
import pencilnew.io.mkdir as mkdir
import pencilnew.diag.particle.gas_velo_at_particle_pos as gas_velo_at_particle_pos
from scipy.io import readsav
from os import listdir
from os.path import exists, join, dirname
import numpy as np
if sim == False:
sim = pcn.get_sim()
if sim == False:
print('! ERROR: Specify simulation object!')
return False
SIM = sim
## calculate gas speed at particle position dataset
gas_velo_at_particle_pos(OVERWRITE=recalculate_gas_velo_at_particle_pos, use_IDL=use_IDL, sim=sim)
print('\n##################### Starting the whole calculation process of DISPERSON and DRIFT for '+SIM.name+' #####################')
## default and setup
GASVELO_DESTINATION = 'gas_velo_at_particle_pos'
GASVELO_DIR = join(SIM.pc_datadir, GASVELO_DESTINATION)
## get list of available files
if use_IDL:
file_filetype = '.sav'
else:
file_filetype = '.pkl'
files = []
if exists(GASVELO_DIR):
files = [i for i in listdir(GASVELO_DIR) if i.startswith(GASVELO_DESTINATION) and i.endswith(file_filetype)]
if files == []: print('!! ERROR: No calc_gas_speed_at_particle_position-files found for '+SIM.name+'! Use idl script to produce them first!')
if use_IDL:
USE_PKL_FILES = False
files = [i.split('_')[-1].split(file_filetype)[0] for i in files]
scheme = ''
else:
USE_PKL_FILES = True
files = [i.split('_')[-1].split(file_filetype)[0] for i in files]
scheme = '_tsc'
## calculate global dispersion for all snapshot for which gas_velo_at_particle_pos files are found
for file_no in files:
print('## Starting the calculation for DISPERSON and DRIFT for ### VAR'+str(file_no)+' ###')
# check if files already exist
if (not OVERWRITE) and pcn.io.exists('sigma_'+file_no, folder=SIM.pc_datadir) and pcn.io.exists('zeta_'+file_no, folder=SIM.pc_datadir) and pcn.io.exists('sigma_l_'+file_no, folder=join(SIM.pc_datadir, 'sigma_l')) and pcn.io.exists('zeta_l_'+file_no, folder=join(SIM.pc_datadir, 'zeta_l')):
print('## Skipping calculations')
continue
## read sav and var file
print('## reading gas_velo_at_particle_pos file and VAR')
if USE_PKL_FILES:
sav_file = pcn.io.load(join(GASVELO_DIR, GASVELO_DESTINATION+scheme+'_'+file_no+'.pkl'))[GASVELO_DESTINATION]
else:
sav_file = readsav(join(GASVELO_DIR, GASVELO_DESTINATION+scheme+'_'+file_no+'.sav'))[GASVELO_DESTINATION]
var_file = pcn.read.var(varfile='VAR'+file_no, quiet=True, trimall=True, datadir=SIM.datadir)
## get everything ready
dim = SIM.dim
pdim = pcn.read.pdim(sim=SIM)
npar = pdim.npar
npar1 = 1./npar
## get first quantities and setup the DATA_SET
if use_IDL:
time = sav_file['time'][0]
DATA_SET = np.core.records.fromarrays(
[range(0,npar),
sav_file['par_idx'][0][0].astype('int'), sav_file['par_idx'][0][1].astype('int'), sav_file['par_idx'][0][2].astype('int'),
sav_file['par_pos'][0][0], sav_file['par_pos'][0][1], sav_file['par_pos'][0][2],
sav_file['par_velo'][0][0], sav_file['par_velo'][0][1], sav_file['par_velo'][0][2],
sav_file['npar'][0],
sav_file['gas_velo'][0][0], sav_file['gas_velo'][0][1], sav_file['gas_velo'][0][2],
var_file.rho[sav_file['par_idx'][0][2].astype('int'), sav_file['par_idx'][0][1].astype('int'), sav_file['par_idx'][0][0].astype('int')],
var_file.rhop[sav_file['par_idx'][0][2].astype('int'), sav_file['par_idx'][0][1].astype('int'), sav_file['par_idx'][0][0].astype('int')]
],
names = 'parid, idx, idy, idz, posx, posy, posz, vx, vy, vz, npar, gasv_x, gasv_y, gasv_z, rho, rhop',
formats = 'int, int,int,int, float,float,float, float,float,float, int, float,float,float, float, float')
else:
time = sav_file['time']
DATA_SET = np.core.records.fromarrays(
[range(0,npar),
sav_file['par_idx'][0].astype('int'), sav_file['par_idx'][1].astype('int'), sav_file['par_idx'][2].astype('int'),
sav_file['par_pos'][0], sav_file['par_pos'][1], sav_file['par_pos'][2],
sav_file['par_velo'][0], sav_file['par_velo'][1], sav_file['par_velo'][2],
sav_file['npar'],
sav_file['gas_velo'][0], sav_file['gas_velo'][1], sav_file['gas_velo'][2],
var_file.rho[sav_file['par_idx'][2].astype('int'), sav_file['par_idx'][1].astype('int'), sav_file['par_idx'][0].astype('int')],
var_file.rhop[sav_file['par_idx'][2].astype('int'), sav_file['par_idx'][1].astype('int'), sav_file['par_idx'][0].astype('int')]
],
names = 'parid, idx, idy, idz, posx, posy, posz, vx, vy, vz, npar, gasv_x, gasv_y, gasv_z, rho, rhop',
formats = 'int, int,int,int, float,float,float, float,float,float, int, float,float,float, float, float')
DATA_SET = np.sort(DATA_SET, order=['idx', 'idy', 'idz'])
# calculate GLOBAL DISPERSION in x, y and z direction, also the absolute magnitude
if GLOBAL:
print('## Calculating GLOBAL DISPERSION values in x,y,z direction and abs value')
mean_vx = np.mean(DATA_SET['vx']); mean_vy = np.mean(DATA_SET['vy']); mean_vz = np.mean(DATA_SET['vz'])
SIGMA = {'SIGMA_o_x': np.sqrt(npar1 * np.sum( (DATA_SET['vx'] - mean_vx)**2 ) ),
'SIGMA_o_y': np.sqrt(npar1 * np.sum( (DATA_SET['vy'] - mean_vy)**2 ) ),
'SIGMA_o_z': np.sqrt(npar1 * np.sum( (DATA_SET['vz'] - mean_vz)**2 ) ),
'SIGMA_o': np.sqrt(npar1 * np.sum( (DATA_SET['vx'] - mean_vx)**2 + (DATA_SET['vy'] - mean_vy)**2 + (DATA_SET['vz'] - mean_vz)**2 ) )}
# calculate GLOBAL DRIFT in x, y and z direction, also the absolute magnitude
print('## Calculating GLOBAL DRIFT values in x,y,z direction and abs value')
ZETA = {'ZETA_o_x': np.sqrt(npar1 * np.sum((DATA_SET['vx'] - DATA_SET['gasv_x'])**2)),
'ZETA_o_y': np.sqrt(npar1 * np.sum((DATA_SET['vy'] - DATA_SET['gasv_y'])**2)),
'ZETA_o_z': np.sqrt(npar1 * np.sum((DATA_SET['vz'] - DATA_SET['gasv_z'])**2)),
'ZETA_o': np.sqrt(npar1 * np.sum((DATA_SET['vx'] - DATA_SET['gasv_x'])**2 + (DATA_SET['vy'] - DATA_SET['gasv_y'])**2 + (DATA_SET['vz'] - DATA_SET['gasv_z'])**2))}
print('## saving calculated GLOBAL DISPERSION and DRIFT')
pcn.io.save(SIGMA, 'sigma_'+file_no, folder=SIM.pc_datadir)
pcn.io.save(ZETA, 'zeta_'+file_no, folder=SIM.pc_datadir)
# calculate LOCAL DISPERSION and DRIFT
if LOCAL:
print('## Calculating LOCAL DISPERSION and DRIFT values')
tmp_id = [DATA_SET[0]['idx'], DATA_SET[0]['idy'], DATA_SET[0]['idz']];
sigma_l = np.zeros((dim.nx,dim.ny,dim.nz))
zeta_l = np.zeros((dim.nx,dim.ny,dim.nz))
particles_l = []
for particle in DATA_SET:
if [particle['idx'],particle['idy'],particle['idz']] == tmp_id:
particles_l.append(particle)
else:
np_l = np.size(particles_l)
if np_l != 0:
np1_l = 1./np_l
mean_vx_l = 0; mean_vy_l = 0; mean_vz_l = 0
sum_s_l = 0; sum_z_l = 0
for entry in particles_l:
mean_vx_l = mean_vx_l + np1_l*entry['vx']
mean_vy_l = mean_vy_l + np1_l*entry['vy']
mean_vz_l = mean_vz_l + np1_l*entry['vz']
for entry in particles_l:
sum_s_l = sum_s_l + (entry['vx'] - mean_vx_l)**2 + (entry['vy'] - mean_vy_l)**2 + (entry['vz'] - mean_vz_l)**2
sum_z_l = sum_z_l + (entry['vx'] - entry['gasv_x'])**2 + (entry['vy'] - entry['gasv_y'])**2 + (entry['vz'] - entry['gasv_z'])**2
sigma_l[tmp_id[0]][tmp_id[1]][tmp_id[2]] = np.sqrt(np1_l * sum_s_l)
zeta_l[tmp_id[0]][tmp_id[1]][tmp_id[2]] = np.sqrt(np1_l * sum_z_l)
# reset all local variables and lists to the new state (ie towards the newst particle)
tmp_id = [particle['idx'],particle['idy'],particle['idz']]
particles_l = []
particles_l.append(particle)
# do this local calculations a last time for the last grid cell
np_l = np.size(particles_l)
np1_l = 1./np_l
mean_vx_l = 0; mean_vy_l = 0; mean_vz_l = 0
sum_s_l = 0; sum_z_l = 0
for entry in particles_l:
mean_vx_l = mean_vx_l + np1_l*entry['vx']
mean_vy_l = mean_vy_l + np1_l*entry['vy']
mean_vz_l = mean_vz_l + np1_l*entry['vz']
for entry in particles_l:
sum_s_l = sum_s_l + (entry['vx'] - mean_vx_l)**2 + (entry['vy'] - mean_vy_l)**2 + (entry['vz'] - mean_vz_l)**2
sum_z_l = sum_z_l + (entry['vx'] - entry['gasv_x'])**2 + (entry['vy'] - entry['gasv_y'])**2 + (entry['vz'] - entry['gasv_z'])**2
sigma_l[tmp_id[0]][tmp_id[1]][tmp_id[2]] = np.sqrt(np1_l * sum_s_l)
zeta_l[tmp_id[0]][tmp_id[1]][tmp_id[2]] = np.sqrt(np1_l * sum_z_l)
# save sigma, zeta locally and globally to SIM.pc_datadir
print('## saving calculated LOCAL DISPERSION and DRIFT')
pcn.io.save(sigma_l, 'sigma_l_'+file_no, folder=join(SIM.pc_datadir, 'sigma_l'))
pcn.io.save(zeta_l, 'zeta_l_'+file_no, folder=join(SIM.pc_datadir, 'zeta_l'))
## Please keep this lines as a reminder on how to add columns to an record array!
# add colums to DATA_SET fror local zeta and sigma for the individuel particle
#DATA_SET = add_column_to_record_array(DATA_SET, 'zeta_l', zeta_l[DATA_SET['idx'],DATA_SET['idy'],DATA_SET['idz']], dtypes='float', usemask=False, asrecarray=True)
#DATA_SET = add_column_to_record_array(DATA_SET, 'sigma_l', sigma_l[DATA_SET['idx'],DATA_SET['idy'],DATA_SET['idz']], dtypes='float', usemask=False, asrecarray=True)
return True
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
"""
import pencilnew as pcn
from pencilnew.io import save
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.) * ( (1./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) == pcn.sim.__Simulation__:
SIM = sim
else:
SIM = pcn.get_sim()
filename = 'alpha_'+str(t_range[0])+'_'+str(t_range[1])
## skip if nothing is new
if not OVERWRITE and pcn.io.exists(name=filename, sim=SIM):
print('~ Alpha for "'+SIM.name+'" already exists. Loading file...')
return pcn.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.
except:
print('? WARNING: Couldnt find >csm< in time series, set it to csm = 1. This may be incorrect!')
csm = 1.
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./3.)*(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./3.)*(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):
pencilnew.io,debug_breakpoint()
## save alpha in plk
print('~ saving alpha values in '+SIM.pc_datadir+'/'+filename)
pcn.io.save(alpha_dict, filename, folder=SIM.pc_datadir)
return alpha_dict
