def export_fig(fig,
filepath,
filename=False,
PNG=True,
PDF=False,
EPS=False,
DPI=300,
EXPORT_BBOX_INCES='tight',
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 pencilnew.io import exists, 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 (not timestamp):
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)
print('~ .png saved')
if PDF:
fig.savefig(complete_filepath + '.pdf',
bbox_inches=EXPORT_BBOX_INCES,
dpi=DPI)
print('~ .pdf saved')
if EPS:
fig.savefig(complete_filepath + '.png',
bbox_inches=EXPORT_BBOX_INCES,
dpi=DPI)
print('~ .eps saved')
if not PNG and not EPS and not EPS:
print('? WARNING: NO OUTPUT FILE HAS BEEN PRODUCED !!')
else:
print('~ Plots saved to ' + complete_filepath)
return fig
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 pencilnew.io import exists_file as exists
from pencilnew.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 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 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,
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 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: provide number # of which var-file VAR# should be copied from
"""
from os import listdir
from os.path import exists, join, isdir
import glob
from pencilnew.math import is_int
from pencilnew.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 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
import pencilnew.io.mkdir as 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 = 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 pencilnew.backpack.pidly as 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(pcn.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 = 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 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 pencilnew.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 pencilnew.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 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 pencilnew.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 pencilnew.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