def bash(self, command, verbose="last100", logfile=False):
"""Executes command in simulation directory.
This method will use your settings as defined in your .bashrc-file.
A log file will be produced within 'self.path/pc'-folder
Parameters
----------
command : string
Command to be executed, can be a list of commands.
verbose : bool
lastN = show last N lines of output afterwards
False = no output
True = all output
"""
import subprocess
from pencil import io
from os.path import join
timestamp = io.timestamp()
io.mkdir(self.pc_dir)
if not type(logfile) == type("string"):
logfile = join(self.pc_dir, "bash_log_" + timestamp)
commands = ["cd " + realpath(self.path)]
# commands.append('source ~/.bashrc')
# commands.append('shopt -s expand_aliases')
if type(command) == type(["list"]):
for c in command:
commands.append(c)
elif type(command) == type("string"):
commands.append(command)
else:
print("! ERROR: Couldnt understand the command parameter: " +
str(command))
with open(logfile, "w") as f:
rc = subprocess.call(["/bin/bash", "-i", "-c", ";".join(commands)],
stdout=f,
stderr=f)
if type(verbose) == type("string"):
outputlength = -int(verbose.split("last")[-1])
with open(logfile, "r") as f:
strList = f.read().split("\n")[outputlength:]
print("\n".join([s for s in strList if not s == ""]))
elif verbose == True:
with open(logfile, "r") as f:
print(f.read())
if rc == 0:
return True
else:
print("! ERROR: Execution ended with error code " + str(rc) +
"!\n! Please check log file in")
print("! " + logfile)
return rc
def bash(self, command, verbose='last100', logfile=False):
"""Executes command in simulation directory.
This method will use your settings as defined in your .bashrc-file.
A log file will be produced within 'self.path/pc'-folder
Args:
- command: command to be executed, can be a list of commands
- verbose: lastN = show last N lines of output afterwards
False = no output
True = all output
"""
import subprocess
from pencil import io
from os.path import join, realpath
timestamp = io.timestamp()
io.mkdir(self.pc_dir)
if not type(logfile) == type('string'):
logfile = join(self.pc_dir, 'bash_log_' + timestamp)
commands = ['cd ' + realpath(self.path)]
#commands.append('source ~/.bashrc')
#commands.append('shopt -s expand_aliases')
if type(command) == type(['list']):
for c in command:
commands.append(c)
elif type(command) == type('string'):
commands.append(command)
else:
print('! ERROR: Couldnt understand the command parameter: ' +
str(command))
with open(logfile, 'w') as f:
rc = subprocess.call(['/bin/bash', '-i', '-c', ';'.join(commands)],
stdout=f,
stderr=f)
if type(verbose) == type('string'):
outputlength = -int(verbose.split('last')[-1])
with open(logfile, 'r') as f:
strList = f.read().split('\n')[outputlength:]
print('\n'.join([s for s in strList if not s == '']))
elif verbose == True:
with open(logfile, 'r') as f:
print(f.read())
if rc == 0:
return True
else:
print('! ERROR: Execution ended with error code ' + str(rc) +
'!\n! Please check log file in')
print('! ' + logfile)
return rc
def open_h5(
filename,
status,
driver=None,
comm=None,
overwrite=False,
size=1,
rank=0,
lfs=False,
MB=1,
count=1,
):
"""This function opens hdf5 file in serial or parallel.
Keyword arguments:
filename: relative or absolute path string for name of hdf5 file.
status: open state of file 'w': write, 'r': read or 'a'/'r+': append.
driver: 'mpio' required for parallel: version but absent for serial.
comm: only present for parallel version of h5py.
overwrite: flag to replace existing file.
rank: processor rank with root = 0.
"""
if "/" in filename:
fname = filename.split("/")[-1]
path = filename.split(fname)[0]
else:
fname = filename
path = "./"
if not (".h5" == filename[-3:] or ".hdf5" == filename[-5:]):
if np.mod(rank, size) == 0:
print("Relabelling h5 " + fname + " to " +
str.strip(fname, ".dat") + ".h5 on path " + path)
fname = str.strip(fname, ".dat") + ".h5"
mkdir(path, rank=rank, lfs=lfs, MB=MB, count=count)
if status == "w" and exists(join(path, fname)):
if not overwrite:
try:
cmd = "mv " + join(path, fname) + " " + join(
path, fname + ".bak")
process = sub.Popen(cmd.split(), stdout=sub.PIPE)
output, error = process.communicate()
print(cmd, output, error)
except:
while exists(join(path, fname)):
pass
if comm:
if not driver:
driver = "mpio"
dset = h5py.File(join(path, fname), status, driver=driver, comm=comm)
else:
dset = h5py.File(join(path, fname), status)
return dset
def export_fig(fig,
filepath,
filename=False,
PNG=True,
PDF=False,
EPS=False,
DPI=300,
EXPORT_BBOX_INCES='tight',
transparent=True,
verbose=True,
timestamp=False):
"""Does a proper export of a figure handle to all kind of image files.
"""
import datetime as dt
from os.path import join, split
from pencil.io import exists_file as exists
from pencil.io import mkdir
######## parse filepath and filename
if not filename:
filepath = split(filepath)
filename = filepath[-1]
filepath = filepath[0]
if filepath == '': filepath = '.'
filename = filename.strip()
filepath = filepath.strip()
complete_filepath = join(filepath, filename)
mkdir(filepath)
######## generate timestamp if demanded
if timestamp == True:
timestamp = str(dt.datetime.now())[:-7]
timestamp = timestamp.replace(" ", "_").replace(":", "-")
complete_filepath = complete_filepath + '_' + timestamp
######## do the export
if PNG:
fig.savefig(complete_filepath + '.png',
bbox_inches=EXPORT_BBOX_INCES,
dpi=DPI,
transparent=transparent)
if verbose: print('~ .png saved')
if PDF:
fig.savefig(complete_filepath + '.pdf',
bbox_inches=EXPORT_BBOX_INCES,
dpi=DPI,
transparent=transparent)
if verbose: print('~ .pdf saved')
if EPS:
fig.savefig(complete_filepath + '.png',
bbox_inches=EXPORT_BBOX_INCES,
dpi=DPI,
transparent=transparent)
if verbose: print('~ .eps saved')
if not PNG and not EPS and not EPS:
if verbose: print('? WARNING: NO OUTPUT FILE HAS BEEN PRODUCED !!')
else:
if verbose: print('~ Plots saved to ' + complete_filepath)
return True
def resume_from_var(self, sim_source, varno, DEBUG=False):
"""
Copies everything to resume a run from an older state.
It uses VAR-file number >varno< as new VAR0 and var.dat.
Does copy PVAR as well if available.
Args:
sim_source: simulation from where to copy all the files
varno: var-file number # from which to copy (VAR#)
"""
from os import listdir
from os.path import exists, join, isdir
import glob
from pencil.math import is_int
from pencil.io import mkdir
def copyfile(src, dst, DEBUG=False):
from shutil import copy2
from os.path import exists
if not exists(src): return False
if DEBUG: print('< ' + src)
if DEBUG: print('> ' + dst)
copy2(src, dst)
src = sim_source.datadir
dst = self.datadir
if is_int(varno): varno = 'VAR' + str(int(varno))
if not exists(src):
print('! ERROR: Source data directory does not exits: ' + str(src))
return False
if not exists(dst):
print('! ERROR: Destination data directory does not exits: ' +
str(dst))
return False
if not varno in sim_source.get_varlist():
print('! ERROR: Could not find ' + varno +
' in procX folder of sim_source: ' + sim_source.name)
return False
data_folders = [p for p in listdir(src) if isdir(join(src, p))]
procX_folder = [p for p in data_folders if p.startswith('proc')]
for p in data_folders:
mkdir(join(dst, p))
# data/
files = [
'def_var.pro', 'dim.dat', 'index.pro', 'move-me.list',
'particles_stalker_header.dat', 'params.log', 'pc_constants.pro',
'pdim.dat', 'pencils.list', 'pvarname.dat', 'svnid.dat',
'var.general', 'variables.pro', 'varname.dat'
]
for f in files:
copyfile(join(src, f), dst, DEBUG=DEBUG)
# data/allprocs/
files = ['grid.dat']
for f in files:
copyfile(join(src, 'allprocs', f),
join(dst, 'allprocs/'),
DEBUG=DEBUG)
# data/procX
files = ['dim.dat', 'grid.dat', 'proc_bounds.dat']
for X in procX_folder:
for f in files:
copyfile(join(src, X, f), join(dst, X), DEBUG=DEBUG)
copyfile(join(src, X, varno), join(dst, X, 'VAR0'), DEBUG=DEBUG)
copyfile(join(src, X, 'P' + varno),
join(dst, X, 'PVAR0'),
DEBUG=DEBUG)
copyfile(join(src, X, varno), join(dst, X, 'var.dat'), DEBUG=DEBUG)
copyfile(join(src, X, 'P' + varno),
join(dst, X, 'pvar.dat'),
DEBUG=DEBUG)
print('? WARNING: KNOWN ERRORS:')
print(
'? RUN MIGHT NOT START BECAUSE data/param.nml can get damaged in' +
' a run that crashes. This is not fixed by this routine.')
print('? TRY AND START A SINGLE CORE RUN WITH THIS SETUP AND USE THE' +
' CREATED param.nml FOR YOUR PURPOSE INSTEAD.')
print('? SAME FOR: - tstalk.dat')
return True
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!
Args:
path_root: 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: 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.
start 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 submit* files
OVERWRITE: 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)
files_to_be_copied = []
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 __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)
def gas_velo_at_particle_pos(
varfiles="last4", sim=False, scheme="tsc", use_IDL=False, OVERWRITE=False
):
"""This script calulates the gas velocity at the particle position and stores this together
with particle position, containing grid cell idicies, particle velocities, and particle index
in a gas_velo_at_particle_pos file.
Args:
varfiles: specifiy varfiles for calculation, e.g. 'last', 'first',
'all', 'VAR###', 'last4', 'first3'
scheme: possible are:
- ngp: nearest grid point
- cic: cloud in cell
- tsc: triangular shaped cloud
OVERWRITE: set to True to overwrite already calculated results
"""
from pencil import get_sim
from pencil import read
from pencil import diag
from pencil.io import mkdir
from os import listdir
from os.path import exists, join, dirname
import numpy as np
GAS_VELO_TAG = "gas_velo_at_particle_pos"
if sim == False:
sim = get_sim()
if sim == False:
print("! ERROR: Specify simulation object!")
return False
SIM = sim
if use_IDL:
print(
"? WARNING: IDL VERSION OF THIS SCRIPT BY JOHANSEN, not recommended for 2D data"
)
from ...backpack import pidly
print("## starting IDL engine..")
IDL = pidly.IDL(long_delay=0.05) # start IDL engine
## skip if nothing is new
if (
(not OVERWRITE)
and (exists(join(SIM.pc_datadir, "sigma.pkl")))
and (exists(join(SIM.pc_datadir, "zeta.pkl")))
):
print(
"~ "
+ SIM.name
+ " is already calculated and up-to-date! -> skipping it!"
)
else:
## start calculations
print(
'~ Calculating gas_velo_at_particle_pos for "'
+ SIM.name
+ '" in "'
+ SIM.path
+ '"'
)
IDL(
".COMPILE "
+ str(
join(
dirname(diag.particle.__file__), "gas_velo_at_particle_pos.pro"
)
)
)
IDL.pro(
"gas_velo_at_particle_pos",
datadir=SIM.datadir,
destination=GAS_VELO_TAG,
doforthelastNvar=varfiles[4:],
)
files = [
i.split("_")[-1].split(".sav")[0]
for i in listdir(join(SIM.pc_datadir, GAS_VELO_TAG))
if i.startswith(GAS_VELO_TAG)
and i.endswith(".sav")
or i.endswith(".pkl")
]
if files == []:
print(
"!! ERROR: No calc_gas_speed_at_particle_position-files found for "
+ SIM.name
+ "! Use idl script to produce them first!"
)
IDL.close()
return True
else:
print(
'~ Calculating gas_velo_at_particle_pos for "'
+ SIM.name
+ '" in "'
+ SIM.path
+ '"'
)
save_destination = join(SIM.pc_datadir, GAS_VELO_TAG)
mkdir(save_destination)
varlist = SIM.get_varlist(pos=varfiles, particle=False)
pvarlist = SIM.get_varlist(pos=varfiles, particle=True)
for f, p in zip(varlist, pvarlist):
save_filename = GAS_VELO_TAG + "_" + scheme + "_" + f[3:]
if not OVERWRITE and exists(save_filename, folder=save_destination):
continue
print("## Reading " + f + " ...")
ff = read.var(datadir=SIM.datadir, varfile=f, quiet=True, trimall=False)
pp = read.pvar(datadir=SIM.datadir, varfile=p)
## remove ghost zones from grid, call the reduced grid the "real grid"
realgridx = ff.x[ff.l1 : ff.l2]
realgridy = ff.y[ff.m1 : ff.m2]
realgridz = ff.z[ff.n1 : ff.n2]
nx = ff.l2 - ff.l1
ny = ff.m2 - ff.m1
nz = ff.n2 - ff.n1
## prepare list for all quantities
l_ipars = pp.ipars # particle number KNOWN
l_px = pp.xp
l_py = pp.yp
l_pz = pp.zp # particle absolut position KNOWN
l_vx = pp.vpx
l_vy = pp.vpy
l_vz = pp.vpz # particle velocity KNOWN
l_rix = []
l_riy = []
l_riz = (
[]
) # particle untrimmed realgrid index (grid index = l/m/n + readgrid index ???)
l_ix = []
l_iy = []
l_iz = [] # particle grid index (in untrimmed grid)
l_ux = []
l_uy = []
l_uz = [] # underlying gas velocity at position of particle
## get index of realgrid cell for each particle
for i in range(len(l_ipars)):
l_rix.append(np.abs(realgridx - l_px[i]).argmin())
l_riy.append(np.abs(realgridy - l_py[i]).argmin())
l_riz.append(np.abs(realgridz - l_pz[i]).argmin())
## convert into untrimmed grid
l_ix = np.array(l_rix) + ff.l1
l_iy = np.array(l_riy) + ff.m1
l_iz = np.array(l_riz) + ff.n1
## NGP
if scheme == "ngp" or scheme == "NGP":
print("## Calculating gas velocities via " + scheme)
l_ux = ff.ux[l_iz, l_iy, l_ix]
l_uy = ff.uy[l_iz, l_iy, l_ix]
l_uz = ff.uz[l_iz, l_iy, l_ix]
## CIC
if scheme == "cic" or scheme == "CIC":
print("## Calculating gas velocities via " + scheme)
for ix0, iy0, iz0, px, py, pz in zip(
l_ix, l_iy, l_iz, l_px, l_py, l_pz
): # for each particle
if ff.x[ix0] > px:
ix0 = ix0 - 1 # ix0 must be left to particle
if ff.y[iy0] > py:
iy0 = iy0 - 1 # iy0 must be below the particle
if ff.z[iz0] > pz:
iz0 = iz0 - 1 # iz0 must be under particle
ix1 = ix0
iy1 = iy0
iz1 = iz0 # if a dim. is zero, this is default, else:
if nx > 1:
ix1 = ix0 + 1
dx_1 = (
1.0 / ff.dx
) # if a dim is non-zero, ajust ix1 to right cell
if ny > 1:
iy1 = iy0 + 1
dy_1 = (
1.0 / ff.dy
) # if a dim is non-zero, ajust iy1 to above cell
if nz > 1:
iz1 = iz0 + 1
dz_1 = (
1.0 / ff.dz
) # if a dim is non-zero, ajust iz1 to above cell
ux = 0.0
uy = 0.0
uz = 0.0
for ix in [ix0, ix1]:
for iy in [iy0, iy1]:
for iz in [iz0, iz1]:
weight = 1.0
if nx > 1:
weight = weight * (1.0 - abs(px - ff.x[ix]) * dx_1)
if ny > 1:
weight = weight * (1.0 - abs(py - ff.y[iy]) * dy_1)
if nz > 1:
weight = weight * (1.0 - abs(pz - ff.z[iz]) * dz_1)
ux = ux + weight * ff.ux[iz, iy, ix]
uy = uy + weight * ff.uy[iz, iy, ix]
uz = uz + weight * ff.uz[iz, iy, ix]
if iz0 == iz1:
break # beware of degeneracy:
if iy0 == iy1:
break # beware of degeneracy:
if ix0 == ix1:
break # beware of degeneracy:
l_ux.append(ux)
l_uy.append(uy)
l_uz.append(uz)
## TSC
if scheme == "tsc" or scheme == "TSC":
for ix0, iy0, iz0, px, py, pz in zip(
l_ix, l_iy, l_iz, l_px, l_py, l_pz
): # for each particle
ixx0 = ix0
ixx1 = ix0 # beware of degeneracy
iyy0 = iy0
iyy1 = iy0
izz0 = iz0
izz1 = iz0
if nx > 1:
ixx0 = ix0 - 1
ixx1 = ix0 + 1
dx_1 = 1.0 / ff.dx
dx_2 = 1.0 / ff.dx ** 2
if ny > 1:
iyy0 = iy0 - 1
iyy1 = iy0 + 1
dy_1 = 1.0 / ff.dy
dy_2 = 1.0 / ff.dy ** 2
if nz > 1:
izz0 = iz0 - 1
izz1 = iz0 + 1
dz_1 = 1.0 / ff.dz
dz_2 = 1.0 / ff.dz ** 2
ux = 0.0
uy = 0.0
uz = 0.0
for ix in [ix0, ixx0, ixx1]:
weight_x = 0.0
if ix - ix0 == -1 or ix - ix0 == 1:
weight_x = (
1.125
- 1.5 * abs(px - ff.x[ix]) * dx_1
+ 0.5 * abs(px - ff.x[ix]) ** 2 * dx_2
)
elif nx != 1:
weight_x = 0.75 - (px - ff.x[ix]) ** 2 * dx_2
for iy in [iy0, iyy0, iyy1]:
weight_y = 0.0
if iy - iy0 == -1 or iy - iy0 == 1:
weight_y = (
1.125
- 1.5 * abs(py - ff.y[iy]) * dy_1
+ 0.5 * abs(py - ff.y[iy]) ** 2 * dy_2
)
elif ny != 1:
weight_y = 0.75 - (py - ff.y[iy]) ** 2 * dy_2
for iz in [iz0, izz0, izz1]:
weight_z = 0.0
if iz - iz0 == -1 or iz - iz0 == 1:
weight_z = (
1.125
- 1.5 * abs(pz - ff.z[iz]) * dz_1
+ 0.5 * abs(pz - ff.z[iz]) ** 2 * dz_2
)
elif nz != 1:
weight_z = 0.75 - (pz - ff.z[iz]) ** 2 * dz_2
weight = 1.0
if nx > 1:
weight = weight * weight_x
if ny > 1:
weight = weight * weight_y
if nz > 1:
weight = weight * weight_z
ux = ux + weight * ff.ux[iz, iy, ix]
uy = uy + weight * ff.uy[iz, iy, ix]
uz = uz + weight * ff.uz[iz, iy, ix]
if izz0 == izz1:
break # beware of degeneracy:
if iyy0 == iyy1:
break # beware of degeneracy:
if ixx0 == ixx1:
break # beware of degeneracy:
l_ux.append(ux)
l_uy.append(uy)
l_uz.append(uz)
## Convert all information into a single record array
data_set = np.core.records.fromarrays(
[
l_ipars.astype("int"),
l_px,
l_py,
l_pz,
l_vx,
l_vy,
l_vz,
l_rix,
l_riy,
l_riz,
l_ix,
l_iy,
l_iz,
l_ux,
l_uy,
l_uz,
],
names="ipar, ipx, ipy, ipz, vx, vy, vz, rix, riy, riz, ix, iy, iz, ux, uy, uz",
formats="int, float, float, float, float, float, float, int, int, int, int, int, int, float, float, float",
)
gas_velo_at_particle_pos = np.sort(data_set, order=["ix", "iy", "iz"])
Nix = int(gas_velo_at_particle_pos["rix"].max() + 1)
Niy = int(gas_velo_at_particle_pos["riy"].max() + 1)
Niz = int(gas_velo_at_particle_pos["riz"].max() + 1)
Npar_arr = np.array(
[
gas_velo_at_particle_pos["rix"],
gas_velo_at_particle_pos["riy"],
gas_velo_at_particle_pos["riz"],
]
)
# rgrid_edges = (grid.x[1:]-(grid.x[1:]-grid.x[:-1])/2)[2:-2]
xrange = np.arange(0, float(gas_velo_at_particle_pos["rix"].max()) + 2)
xrange = xrange - 0.5
yrange = np.arange(0, float(gas_velo_at_particle_pos["riy"].max()) + 2)
zrange = np.arange(0, float(gas_velo_at_particle_pos["riz"].max()) + 2)
Npar_hist, edges = np.histogramdd(Npar_arr.T, bins=(xrange, yrange, zrange))
Npar_hist, edges = np.histogramdd(Npar_arr.T, bins=(Nix, Niy, Niz))
gas_velo_at_particle_pos = {
"time": ff.t,
"par_pos": np.array(
[
gas_velo_at_particle_pos["ipx"],
gas_velo_at_particle_pos["ipy"],
gas_velo_at_particle_pos["ipz"],
]
),
"par_velo": np.array(
[
gas_velo_at_particle_pos["vx"],
gas_velo_at_particle_pos["vy"],
gas_velo_at_particle_pos["vz"],
]
),
"par_idx": np.array(
[
gas_velo_at_particle_pos["rix"],
gas_velo_at_particle_pos["riy"],
gas_velo_at_particle_pos["riz"],
]
),
"npar": np.array(
Npar_hist[
gas_velo_at_particle_pos["rix"],
gas_velo_at_particle_pos["riy"],
gas_velo_at_particle_pos["riz"],
]
),
"gas_velo": np.array(
[
gas_velo_at_particle_pos["ux"],
gas_velo_at_particle_pos["uy"],
gas_velo_at_particle_pos["uz"],
]
),
}
print("## Saving dataset into " + save_destination + "...")
pkl_save(
{"gas_velo_at_particle_pos": gas_velo_at_particle_pos, "t": ff.t},
save_filename,
folder=save_destination,
)
print("## Done!")
def 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 ("run" in filename or "start" in filename
or ".local" in filename or "print" in filename):
if ("=" in quantity_match_tmp.
string[quantity_match_tmp.start() +
2:quantity_match_tmp.end()]):
if line_matches:
line_matches[0] = ii
else:
line_matches.append(ii)
quantity_match = quantity_match_tmp
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":
if type(change_quantity_to) == list:
tmp = ""
for a in change_quantity_to:
tmp += "'" + a + "',"
change_quantity_to = tmp[:-1]
elif type(change_quantity_to) == int:
change_quantity_to = str(change_quantity_to)
else:
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":
if type(change_quantity_to) == str:
change_quantity_to = float(change_quantity_to)
change_quantity_to = "%e" % change_quantity_to
elif q_type == "INT":
if type(change_quantity_to) == str:
change_quantity_to = int(change_quantity_to)
change_quantity_to = "%i" % 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
if sim:
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 os
from pencil import io
from pencil import read
from pencil import get_sim
from os.path import exists
import numpy as np
GAS_VELO_TAG = 'gas_velo_at_particle_pos'
if sim == False:
sim = get_sim()
if sim == False:
print('! ERROR: Specify simulation object!')
return False
SIM = sim
if use_IDL:
print(
'? WARNING: IDL VERSION OF THIS SCRIPT BY JOHANSEN, not recommended for 2D data'
)
from pencil.backpack import pidly
print('## starting IDL engine..')
IDL = pidly.IDL(long_delay=0.05) # start IDL engine
## skip if nothing is new
if (not OVERWRITE) and (exists(
os.path.join(SIM.pc_datadir, 'sigma.pkl'))) and (exists(
os.path.join(SIM.pc_datadir, 'zeta.pkl'))):
print('~ ' + SIM.name +
' is already calculated and up-to-date! -> skipping it!')
else:
## start calculations
print('~ Calculating gas_velo_at_particle_pos for "' + SIM.name +
'" in "' + SIM.path + '"')
IDL.pro('gas_velo_at_particle_pos',
datadir=SIM.datadir,
destination=GAS_VELO_TAG,
doforthelastNvar=varfiles[4:])
files = [
i.split('_')[-1].split('.sav')[0]
for i in os.listdir(os.path.join(SIM.pendatadir, GAS_VELO_TAG))
if i.startswith(GAS_VELO_TAG) and i.endswith('.sav')
or i.endswith('.pkl')
]
if files == []:
print(
'!! ERROR: No calc_gas_speed_at_particle_position-files found for '
+ SIM.name + '! Use idl script to produce them first!')
IDL.close()
return True
else:
print('~ Calculating gas_velo_at_particle_pos for "' + SIM.name +
'" in "' + SIM.path + '"')
save_destination = os.path.join(SIM.pc_datadir, GAS_VELO_TAG)
io.mkdir(save_destination)
varlist = SIM.get_varlist(pos=varfiles, particle=False)
pvarlist = SIM.get_varlist(pos=varfiles, particle=True)
for f, p in zip(varlist, pvarlist):
save_filename = GAS_VELO_TAG + '_' + scheme + '_' + f[3:]
if not OVERWRITE and exists(save_filename,
folder=save_destination):
continue
print('## Reading ' + f + ' ...')
ff = read.var(datadir=SIM.datadir,
varfile=f,
quiet=True,
trimall=False)
pp = read.pvar(datadir=SIM.datadir, varfile=p)
## remove ghost zones from grid, call the reduced grid the "real grid"
realgridx = ff.x[ff.l1:ff.l2]
realgridy = ff.y[ff.m1:ff.m2]
realgridz = ff.z[ff.n1:ff.n2]
nx = ff.l2 - ff.l1
ny = ff.m2 - ff.m1
nz = ff.n2 - ff.n1
## prepare list for all quantities
l_ipars = pp.ipars # particle number KNOWN
l_px = pp.xp
l_py = pp.yp
l_pz = pp.zp # particle absolut position KNOWN
l_vx = pp.vpx
l_vy = pp.vpy
l_vz = pp.vpz # particle velocity KNOWN
l_rix = []
l_riy = []
l_riz = [
] # particle untrimmed realgrid index (grid index = l/m/n + readgrid index ???)
l_ix = []
l_iy = []
l_iz = [] # particle grid index (in untrimmed grid)
l_ux = []
l_uy = []
l_uz = [] # underlying gas velocity at position of particle
## get index of realgrid cell for each particle
for i in range(len(l_ipars)):
l_rix.append(np.abs(realgridx - l_px[i]).argmin())
l_riy.append(np.abs(realgridy - l_py[i]).argmin())
l_riz.append(np.abs(realgridz - l_pz[i]).argmin())
## convert into untrimmed grid
l_ix = np.array(l_rix) + ff.l1
l_iy = np.array(l_riy) + ff.m1
l_iz = np.array(l_riz) + ff.n1
## NGP
if scheme == 'ngp' or scheme == 'NGP':
print('## Calculating gas velocities via ' + scheme)
l_ux = ff.ux[l_iz, l_iy, l_ix]
l_uy = ff.uy[l_iz, l_iy, l_ix]
l_uz = ff.uz[l_iz, l_iy, l_ix]
## CIC
if scheme == 'cic' or scheme == 'CIC':
print('## Calculating gas velocities via ' + scheme)
for ix0, iy0, iz0, px, py, pz in zip(
l_ix, l_iy, l_iz, l_px, l_py,
l_pz): # for each particle
if ff.x[ix0] > px:
ix0 = ix0 - 1 # ix0 must be left to particle
if ff.y[iy0] > py:
iy0 = iy0 - 1 # iy0 must be below the particle
if ff.z[iz0] > pz:
iz0 = iz0 - 1 # iz0 must be under particle
ix1 = ix0
iy1 = iy0
iz1 = iz0 # if a dim. is zero, this is default, else:
if nx > 1:
ix1 = ix0 + 1
dx_1 = 1. / ff.dx # if a dim is non-zero, ajust ix1 to right cell
if ny > 1:
iy1 = iy0 + 1
dy_1 = 1. / ff.dy # if a dim is non-zero, ajust iy1 to above cell
if nz > 1:
iz1 = iz0 + 1
dz_1 = 1. / ff.dz # if a dim is non-zero, ajust iz1 to above cell
ux = 0.
uy = 0.
uz = 0.
for ix in [ix0, ix1]:
for iy in [iy0, iy1]:
for iz in [iz0, iz1]:
weight = 1.
if nx > 1:
weight = weight * (
1. - abs(px - ff.x[ix]) * dx_1)
if ny > 1:
weight = weight * (
1. - abs(py - ff.y[iy]) * dy_1)
if nz > 1:
weight = weight * (
1. - abs(pz - ff.z[iz]) * dz_1)
ux = ux + weight * ff.ux[iz, iy, ix]
uy = uy + weight * ff.uy[iz, iy, ix]
uz = uz + weight * ff.uz[iz, iy, ix]
if iz0 == iz1: break # beware of degeneracy:
if iy0 == iy1: break # beware of degeneracy:
if ix0 == ix1: break # beware of degeneracy:
l_ux.append(ux)
l_uy.append(uy)
l_uz.append(uz)
## TSC
if scheme == 'tsc' or scheme == 'TSC':
for ix0, iy0, iz0, px, py, pz in zip(
l_ix, l_iy, l_iz, l_px, l_py,
l_pz): # for each particle
ixx0 = ix0
ixx1 = ix0 # beware of degeneracy
iyy0 = iy0
iyy1 = iy0
izz0 = iz0
izz1 = iz0
if nx > 1:
ixx0 = ix0 - 1
ixx1 = ix0 + 1
dx_1 = 1. / ff.dx
dx_2 = 1. / ff.dx**2
if ny > 1:
iyy0 = iy0 - 1
iyy1 = iy0 + 1
dy_1 = 1. / ff.dy
dy_2 = 1. / ff.dy**2
if nz > 1:
izz0 = iz0 - 1
izz1 = iz0 + 1
dz_1 = 1. / ff.dz
dz_2 = 1. / ff.dz**2
ux = 0.
uy = 0.
uz = 0.
for ix in [ix0, ixx0, ixx1]:
weight_x = 0.
if ix - ix0 == -1 or ix - ix0 == 1:
weight_x = 1.125 - 1.5 * abs(
px - ff.x[ix]) * dx_1 + 0.5 * abs(
px - ff.x[ix])**2 * dx_2
elif nx != 1:
weight_x = 0.75 - (px - ff.x[ix])**2 * dx_2
for iy in [iy0, iyy0, iyy1]:
weight_y = 0.
if iy - iy0 == -1 or iy - iy0 == 1:
weight_y = 1.125 - 1.5 * abs(
py - ff.y[iy]) * dy_1 + 0.5 * abs(
py - ff.y[iy])**2 * dy_2
elif ny != 1:
weight_y = 0.75 - (py - ff.y[iy])**2 * dy_2
for iz in [iz0, izz0, izz1]:
weight_z = 0.
if iz - iz0 == -1 or iz - iz0 == 1:
weight_z = 1.125 - 1.5 * abs(
pz - ff.z[iz]) * dz_1 + 0.5 * abs(
pz - ff.z[iz])**2 * dz_2
elif nz != 1:
weight_z = 0.75 - (pz - ff.z[iz])**2 * dz_2
weight = 1.
if nx > 1: weight = weight * weight_x
if ny > 1: weight = weight * weight_y
if nz > 1: weight = weight * weight_z
ux = ux + weight * ff.ux[iz, iy, ix]
uy = uy + weight * ff.uy[iz, iy, ix]
uz = uz + weight * ff.uz[iz, iy, ix]
if izz0 == izz1: break # beware of degeneracy:
if iyy0 == iyy1: break # beware of degeneracy:
if ixx0 == ixx1: break # beware of degeneracy:
l_ux.append(ux)
l_uy.append(uy)
l_uz.append(uz)
## Convert all information into a single record array
data_set = np.core.records.fromarrays(
[
l_ipars.astype('int'), l_px, l_py, l_pz, l_vx, l_vy, l_vz,
l_rix, l_riy, l_riz, l_ix, l_iy, l_iz, l_ux, l_uy, l_uz
],
names=
'ipar, ipx, ipy, ipz, vx, vy, vz, rix, riy, riz, ix, iy, iz, ux, uy, uz',
formats=
'int, float, float, float, float, float, float, int, int, int, int, int, int, float, float, float'
)
gas_velo_at_particle_pos = np.sort(data_set,
order=['ix', 'iy', 'iz'])
Nix = int(gas_velo_at_particle_pos['rix'].max() + 1)
Niy = int(gas_velo_at_particle_pos['riy'].max() + 1)
Niz = int(gas_velo_at_particle_pos['riz'].max() + 1)
Npar_arr = np.array([
gas_velo_at_particle_pos['rix'],
gas_velo_at_particle_pos['riy'],
gas_velo_at_particle_pos['riz']
])
#rgrid_edges = (grid.x[1:]-(grid.x[1:]-grid.x[:-1])/2)[2:-2]
xrange = np.arange(
0,
float(gas_velo_at_particle_pos['rix'].max()) + 2)
xrange = xrange - 0.5
yrange = np.arange(
0,
float(gas_velo_at_particle_pos['riy'].max()) + 2)
zrange = np.arange(
0,
float(gas_velo_at_particle_pos['riz'].max()) + 2)
Npar_hist, edges = np.histogramdd(Npar_arr.T,
bins=(xrange, yrange, zrange))
Npar_hist, edges = np.histogramdd(Npar_arr.T, bins=(Nix, Niy, Niz))
gas_velo_at_particle_pos = {
'time':
ff.t,
'par_pos':
np.array([
gas_velo_at_particle_pos['ipx'],
gas_velo_at_particle_pos['ipy'],
gas_velo_at_particle_pos['ipz']
]),
'par_velo':
np.array([
gas_velo_at_particle_pos['vx'],
gas_velo_at_particle_pos['vy'],
gas_velo_at_particle_pos['vz']
]),
'par_idx':
np.array([
gas_velo_at_particle_pos['rix'],
gas_velo_at_particle_pos['riy'],
gas_velo_at_particle_pos['riz']
]),
'npar':
np.array(Npar_hist[gas_velo_at_particle_pos['rix'],
gas_velo_at_particle_pos['riy'],
gas_velo_at_particle_pos['riz']]),
'gas_velo':
np.array([
gas_velo_at_particle_pos['ux'],
gas_velo_at_particle_pos['uy'],
gas_velo_at_particle_pos['uz']
])
}
print('## Saving dataset into ' + save_destination + '...')
io.pkl_save(
{
'gas_velo_at_particle_pos': gas_velo_at_particle_pos,
't': ff.t
},
save_filename,
folder=save_destination)
print('## Done!')
def rename_in_submit_script(new_name,
submit_script_path=False,
sim=False,
old_name=False):
import os
from os.path import exists, join, abspath, dirname
from pencil.io import timestamp, get_systemid, mkdir
if submit_script_path != False:
path = dirname(abspath(submit_script_path))
filename = basename(abspath(submit_script_path))
# locate submit script file if not given
if submit_script_path == False:
# get path of simulation folder where submit script should be around
if sim == False:
path = "."
else:
path = sim.path
list_of_possible_submit_scripts = [
f for f in os.listdir(path)
if f.startswith("submit") and f.split(".")[-1] in ["sh", "csh"]
]
# only works if a single submit script could be identified, else prompt error and let the user do it manually
if len(list_of_possible_submit_scripts) == 0:
print("!! ERROR: Could not find a submit script in " + str(path))
return False
elif len(list_of_possible_submit_scripts) > 1:
print(
"!! ERROR: Could not identify submit script, please specify manually:"
+ str(list_of_possible_submit_scripts))
return False
else:
filename = list_of_possible_submit_scripts[0]
# path to submit script should now be clear, but better check its a string
if type(path) != type("STRING"):
print(
"!! ERROR: Could not identify submit script path, please check manually: "
+ str(path))
path_filename = join(path, filename)
# open submit script as f and read content into s
with open(path_filename) as f:
s = f.read()
# if the old name is known, we can simply replace that string with the new name
if old_name != False and type(old_name) == type("STRING"):
with open(path_filename) as f:
s = f.read()
if old_name in s:
s = s.replace(old_name, new_name)
else:
print("?? ERROR: Could not find old_name " + str(old_name) +
" in submit script " + str(path_filename))
return False
# else we need to look for specific identifiers, that differ from queue system and cluster
else:
# get submit name line identifier
identify = get_systemid()[2]
if identify == False:
print(
"!! ERROR: Could not identify an submit script name identifier, please update pc.io.get_systemid.py by adding your machine."
)
if identify in s:
if s.count(identify) > 1:
print(
"ERROR: Job name identifier has multiple appearences in submit script!"
)
return False
s = s.split("\n")
for ii, line in enumerate(s):
if identify in line:
break
s[ii] = identify + " " + new_name
s = "\n".join(s)
else:
print(
"!! ERROR: Could not find name identifier in submit script, identifier is "
+ str(identify))
# s should now be updated, we can save it in now in the file submit_script_path, but let us backup the old one
# backup
from shutil import copyfile
target_dir = join(path, "pc/backups/")
mkdir(target_dir)
copyfile(path_filename,
join(target_dir, filename + ".BAK" + str(timestamp())))
# save new submit script
with open(path_filename, "w") as f:
f.write(s)
# done
return True
def clone_sims_from_obj(simset,
simsdir="..",
template_sim=None,
specify_nml=True):
"""
clone_sims_from_obj(simset, simsdir="..", template_sim=None, specify_nml=True):
Create a set of simulation directories from a dictionary object, simset,
which contains the list of parameters to combine across set of clones.
This differs from the clone_sims function in that it is more configurable,
and uses the native Python way of copying the sim.
Parameters
----------
simset : dictionary
Parameters to combine across set of clones.
simsdir : string
Root directory for collection of clone simulations.
template_sim : obj
A pencil simulation object (returned by pc.get_sim).
If not specified, the simulation in the current directory will be used.
specify_nml : bool
Whether, for files like run.in, you also specify the namelist in simset.
If so, f90nml will be directly used to write the value. If not, the
change_value_in_file function will be used even for these files.
Returns
-------
Set of unexecuted simulation run directories with
parameters updated.
Example
--------
>>> template_sim = pc.get_sim("simulation_to_clone")
>>> template_sim.optionals.append("job.pbs") #A job submission script which
... #one wants to copy along with the other simulation files.
>>> params = pc.pipelines.parameter_table("example_filename.txt")
>>> simset = pc.pipelines.make_sims_dict(params)
>>> pc.pipelines.clone_sims_from_obj(simset, template_sim=template_sim, simsdir=".")
"""
if not template_sim:
template_sim = get_sim()
if not os.path.isdir(simsdir):
if os.path.exists(simsdir):
raise RuntimeError(
"simsdir ({}) exists but is not a directory!".format(simsdir))
else:
mkdir(simsdir)
# For each set of simulation parameters create new simulation subdirectory
for sim in simset:
newdir = join(simsdir, sim)
out = template_sim.copy(path_root=simsdir, name=sim)
if out is False:
raise RuntimeError("Copying sim failed")
for filename in simset[sim]:
if filename == "compile":
if simset[sim]["compile"]:
print(
"Warning: clone_sims_from_obj: compilation not implemented yet, so not compiling."
)
## KG: I am not sure if the following works as intended; it just hangs for me.
# new_sim = get_sim(join(simsdir, newdir))
# new_sim.compile()
elif specify_nml and ("run.in" in filename
or "start.in" in filename):
# Use f90nml for these files
pars = f90nml.read(filename)
newpars = pars.copy()
for group in simset[sim][filename]:
for item in simset[sim][filename][group]:
newpars[group][item] = simset[sim][filename][group][
item]
newpars.write(join(newdir, filename), force=True)
else:
file_path = newdir
if "local" in filename:
file_path = join(file_path, "src")
for item in simset[sim][filename]:
change_value_in_file(
filename,
item,
simset[sim][filename][item],
filepath=file_path,
)
def clone_sims(simset, simsdir=None):
"""
clone_sims(simset, simsdir=None)
Create a set of simulation directories from a dictionary object, simset,
which contains the list of parameters to combine across set of clones.
Parameters
----------
simset : dictionary
Parameters to combine across set of clones.
simsdir : string
Root directory for collection of clone simulations.
Returns
-------
Set of uncompiled and unexecuted simulation run directories with
parameters updated.
Notes
-----
It is assumed that the user is working in the compiled source directory.
Examples
--------
>>> simsdir = '/path/to/set_of_clones'
>>> params = pencil.pipelines.parameter_table('example_filename.txt')
>>> params = user_own_trim_table(params)#See pc.pipelines.trim_table
>>> simset = pencil.pipelines.make_sims_dict(params)
>>> clone_sims(simset,simsdir=simsdir)
"""
# If user provides no clone path
if not simsdir:
simsdir = os.getcwd().strip(os.getcwd().split("/")[-1])
mkdir(simsdir)
# For each set of simulation parameters create new simulation subdirectory
sourced = False
for sim in simset:
newdir = join(simsdir, sim)
cmd = ["pc_newrun", "-s", newdir]
# Only compile if makefile.local or cparam.local change
if "compile" in simset[sim].keys():
if not sourced:
moduleinfo = "src/.moduleinfo"
cmd = ["source " + moduleinfo]
process = subprocess.Popen(cmd,
shell=True,
stdout=subprocess.PIPE)
try:
outs, errs = process.communicate()
except TimeoutExpired:
process.kill()
outs, errs = process.communicate()
if simset[sim]["compile"]:
cmd = ["pc_newrun", newdir]
process = subprocess.Popen(cmd, stdout=subprocess.PIPE)
process.communicate()
for filename in simset[sim]:
#'compile' flag only used above
if not filename == "compile":
# Files which are f90nml-compatible
if "run.in" in filename or "start.in" in filename:
pars = f90nml.read(filename)
newpars = pars.copy()
for group in simset[sim][filename]:
for item in simset[sim][filename][group]:
newpars[group][item] = simset[sim][filename][
group][item]
newpars.write(join(newdir, filename), force=True)
else:
file_path = newdir
if "local" in filename:
file_path = join(file_path, "src")
for item in simset[sim][filename]:
change_value_in_file(
filename,
item,
simset[sim][filename][item],
filepath=file_path,
)
def resume_from_var(self, sim_source, varno, DEBUG=False):
"""
Copies everything to resume a run from an older state.
It uses VAR-file number >varno< as new VAR0 and var.dat.
Does copy PVAR as well if available.
Parameters
----------
sim_source : string
Simulation from where to copy all the files.
varno : int
var-file number # from which to copy (VAR#).
"""
from os import listdir
from os.path import exists, join, isdir
from pencil.math import is_int
from pencil.io import mkdir
def copyfile(src, dst, DEBUG=False):
from shutil import copy2
from os.path import exists
if not exists(src):
return False
if DEBUG:
print("< " + src)
if DEBUG:
print("> " + dst)
copy2(src, dst)
src = sim_source.datadir
dst = self.datadir
if is_int(varno):
varno = "VAR" + str(int(varno))
if not exists(src):
print("! ERROR: Source data directory does not exist: " + str(src))
return False
if not exists(dst):
print("! ERROR: Destination data directory does not exist: " +
str(dst))
return False
if not varno in sim_source.get_varlist():
print("! ERROR: Could not find " + varno +
" in procX folder of sim_source: " + sim_source.name)
return False
data_folders = [p for p in listdir(src) if isdir(join(src, p))]
procX_folder = [p for p in data_folders if p.startswith("proc")]
for p in data_folders:
mkdir(join(dst, p))
# data/
files = [
"def_var.pro",
"dim.dat",
"index.pro",
"move-me.list",
"particles_stalker_header.dat",
"params.log",
"pc_constants.pro",
"pdim.dat",
"pencils.list",
"pvarname.dat",
"svnid.dat",
"var.general",
"variables.pro",
"varname.dat",
]
for f in files:
copyfile(join(src, f), dst, DEBUG=DEBUG)
# data/allprocs/
files = ["grid.dat"]
for f in files:
copyfile(join(src, "allprocs", f),
join(dst, "allprocs/"),
DEBUG=DEBUG)
# data/procX
files = ["dim.dat", "grid.dat", "proc_bounds.dat"]
for X in procX_folder:
for f in files:
copyfile(join(src, X, f), join(dst, X), DEBUG=DEBUG)
copyfile(join(src, X, varno), join(dst, X, "VAR0"), DEBUG=DEBUG)
copyfile(join(src, X, "P" + varno),
join(dst, X, "PVAR0"),
DEBUG=DEBUG)
copyfile(join(src, X, varno), join(dst, X, "var.dat"), DEBUG=DEBUG)
copyfile(join(src, X, "P" + varno),
join(dst, X, "pvar.dat"),
DEBUG=DEBUG)
print("? WARNING: KNOWN ERRORS:")
print(
"? RUN MIGHT NOT START BECAUSE data/param.nml can get damaged in" +
" a run that crashes. This is not fixed by this routine.")
print("? TRY AND START A SINGLE CORE RUN WITH THIS SETUP AND USE THE" +
" CREATED param.nml FOR YOUR PURPOSE INSTEAD.")
print("? SAME FOR: - tstalk.dat")
return True