def make_continue_sub(simdir='.', paramname='snapshot.param', \
newparam='continue.param', t=None, t_extra=None, oldsub='subber.sh', \
newsub='cont_subber.sh'):
"""
Makes a submission script for continuing a simulation from a previous output.
Also makes a .param file for the continued simulation. The simulation
will be continued in the same directory, with snapshot numbering scheme
for outputs being the same.
Parameters for the original simulation cannot be altered (except the number
of steps you want to continue the simulation by). PBS runtime parameters
also cannot be changed (number of nodes, walltime, etc...)
Any checkpoints will be deleted.
Requires a submission script be present for the original simulation
NOTE: if nSteps, nSteps_extra are not set, the total number of steps
to simulate is not changed.
**ARGUMENTS**
simdir : str
The simulation directory
paramname : str
Filename of the .param file for the simulation
newparam : str
filename for the .param file for the continued simulation
t : float or SimArray
Total simulation time to run.
If no units are specified, it is in simulation units
t_extra : float or SimArray
Extra simulation time to run
If no units are specified, it is in simulation units
OVERIDES t!!!
oldsub : str
Filename for the original submission script
newsub : str
Filename for the new submission script
**RETURNS**
sub_path : str
Full path to the PBS submission script
"""
# Lazy man's way of dealing with files in another directory
cwd = os.getcwd()
os.chdir(simdir)
# Load param file
param = isaac.configparser(paramname, 'param')
fprefix = param['achOutName']
# Find all the outputs. They should be of the format fprefix.000000
search_exp = '^' + fprefix + '.(?:(?<!\d)\d{6}(?!\d))$'
flist = []
for fname in glob.glob(fprefix + '*'):
if re.search(search_exp, fname) is not None:
flist.append(fname)
# Find the number of the last output (the last 6 chars should be an int)
flist.sort()
iStartStep = int(flist[-1][-6:])
param['iStartStep'] = iStartStep
param['achInFile'] = flist[-1]
dDelta = param['dDelta']
# Set the number of steps to run
if t_extra is not None:
# Convert to simulation units if needed
if pynbody.units.has_units(t_extra):
t_unit = isaac.units_from_param(param)['t_unit']
t_extra.convert_units(t_unit)
# Assign output
param['nSteps'] = iStartStep + int(round(t_extra / dDelta))
elif t is not None:
# Convert to simulation units if needed
if pynbody.units.has_units(t):
t_unit = isaac.units_from_param(param)['t_unit']
t.convert_units(t_unit)
# Assign output
param['nSteps'] = int(round(t / dDelta))
# Save new param file
isaac.configsave(param, newparam, ftype='param')
# Delete old checkpoints
for checkpoint in glob.glob(fprefix + '.chk*'):
print 'removing ' + checkpoint
os.system('rm -rf ' + checkpoint)
if os.path.exists('lastcheckpoint'):
print 'removing lastcheckpoint'
os.remove('lastcheckpoint')
# Create a submission script for the simulation continuation
oldsubfile = open(oldsub, 'r')
newsubfile = open(newsub, 'w')
for line in oldsubfile:
newsubfile.write(line.replace(paramname, newparam))
oldsubfile.close()
newsubfile.close()
# Make the submission script executable
os.chmod(newsub, 0777)
sub_path = os.path.abspath(newsub)
# Change back to original working directory
os.chdir(cwd)
return sub_path
def find_clumps(f, n_smooth=32, param=None, arg_string=None, seed=None, verbose=True):
"""
Uses skid (https://github.com/N-BodyShop/skid) to find clumps in a gaseous
protoplanetary disk.
The linking length used is equal to the gravitational softening length of
the gas particles.
The density cut-off comes from the criterion that there are n_smooth particles
within the Hill sphere of a particle. This is formulated mathematically as:
rho_min = 3*n_smooth*Mstar/R^3
where R is the distance from the star. The trick used here is to multiply
all particle masses by R^3 before running skid so the density cut-off is:
rho_min = 3*n_smooth*Mstar
**ARGUMENTS**
*f* : TipsySnap, or str
A tipsy snapshot loaded/created by pynbody -OR- a filename pointing to a
snapshot.
*n_smooth* : int (optional)
Number of particles used in SPH calculations. Should be the same as used
in the simulation. Default = 32
*param* : str (optional)
filename for a .param file for the simulation
*arg_string* : str (optional)
Additional arguments to be passed to skid. Cannot use -tau, -d, -m, -s, -o
*seed* : int
An integer used to seed the random filename generation for temporary
files. Necessary for multiprocessing and should be unique for each
thread.
*verbose* : bool
Verbosity flag. Default is True
**RETURNS**
*clumps* : array, int-like
Array containing the group number each particle belongs to, with star
particles coming after gas particles. A zero means the particle belongs
to no groups
"""
# Parse areguments
if isinstance(f, str):
f = pynbody.load(f, paramfile=param)
if seed is not None:
np.random.seed(seed)
# Estimate the linking length as the gravitational softening length
tau = f.g['eps'][0]
# Calculate minimum density
rho_min = 3*n_smooth*f.s['mass'][0]
# Center on star. This is done because R used in hill-sphere calculations
# is relative to the star
star_pos = f.s['pos'].copy()
f['pos'] -= star_pos
# Scale mass by R^3
R = isaac.strip_units(f['rxy'])
m0 = f['mass'].copy()
f['mass'] *= (R+tau)**3
# Save temporary snapshot
f_prefix = str(np.random.randint(np.iinfo(int).max))
f_name = f_prefix + '.std'
# Save temporary .param file
if param is not None:
param_name = f_prefix + '.param'
param_dict = isaac.configparser(param, 'param')
isaac.configsave(param_dict, param_name)
f.write(filename=f_name, fmt=pynbody.tipsy.TipsySnap)
f['pos'] += star_pos
f['mass'] = m0
command = 'totipnat < {} | skid -tau {:.2e} -d {:.2e} -m {:d} -s {:d} -o {}'\
.format(f_name, tau, rho_min, n_smooth, n_smooth, f_prefix)
p = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
if verbose:
for line in iter(p.stdout.readline, ''):
print line,
p.wait()
# Load clumps
clumps = isaac.loadhalos(f_prefix + '.grp')
# Cleanup
for name in glob.glob(f_prefix + '*'):
os.remove(name)
return clumps
# Save Output
# -------------------------------------------------
# Save snapshot
snapshot.write(filename=snapshotName, fmt=pynbody.tipsy.TipsySnap)
print 'Tipsy snapshot saved to {0}'.format(snapshotName)
# Start saving log file
logFile = open(logFileName, 'w')
logFile.write('Generated from settings file: {0}\n'.format(
os.path.abspath(settings_file)))
m_amu = float((m * 0.992733 / pynbody.units.m_p).in_units('1'))
# Save director file
if paramName is not None:
try:
import isaac
defPar = os.path.join(ICgenDir, 'default.param')
pars = isaac.configparser(defPar, ftype='param')
pars['achInFile'] = snapshotName
pars['achOutName'] = os.path.splitext(snapshotName)[0]
# Convert molecular mass from mass of proton to amu
pars['dMeanMolWeight'] = m_amu
isaac.configsave(pars, paramName, ftype='param')
print 'ChaNGa parameter file saved to {0}'.format(paramName)
logFile.write(
'ChaNGa parameter file saved to {0}\n'.format(paramName))
except:
print 'Could not save .param file. Check that the module isaac\
was properly imported'
#Continue writing to log file
logFile.write('Tipsy snapshot saved to {0}\n'.format(snapshotName))
logFile.write('Surface density profile saved to {0}\n\
def make_continue_sub(simdir='.', paramname='snapshot.param', \
newparam='continue.param', t=None, t_extra=None, oldsub='subber.sh', \
newsub='cont_subber.sh'):
"""
Makes a submission script for continuing a simulation from a previous output.
Also makes a .param file for the continued simulation. The simulation
will be continued in the same directory, with snapshot numbering scheme
for outputs being the same.
Parameters for the original simulation cannot be altered (except the number
of steps you want to continue the simulation by). PBS runtime parameters
also cannot be changed (number of nodes, walltime, etc...)
Any checkpoints will be deleted.
Requires a submission script be present for the original simulation
NOTE: if nSteps, nSteps_extra are not set, the total number of steps
to simulate is not changed.
**ARGUMENTS**
simdir : str
The simulation directory
paramname : str
Filename of the .param file for the simulation
newparam : str
filename for the .param file for the continued simulation
t : float or SimArray
Total simulation time to run.
If no units are specified, it is in simulation units
t_extra : float or SimArray
Extra simulation time to run
If no units are specified, it is in simulation units
OVERIDES t!!!
oldsub : str
Filename for the original submission script
newsub : str
Filename for the new submission script
**RETURNS**
sub_path : str
Full path to the PBS submission script
"""
# Lazy man's way of dealing with files in another directory
cwd = os.getcwd()
os.chdir(simdir)
# Load param file
param = isaac.configparser(paramname, 'param')
fprefix = param['achOutName']
# Find all the outputs. They should be of the format fprefix.000000
search_exp = '^' + fprefix + '.(?:(?<!\d)\d{6}(?!\d))$'
flist = []
for fname in glob.glob(fprefix + '*'):
if re.search(search_exp, fname) is not None:
flist.append(fname)
# Find the number of the last output (the last 6 chars should be an int)
flist.sort()
iStartStep = int(flist[-1][-6:])
param['iStartStep'] = iStartStep
param['achInFile'] = flist[-1]
dDelta = param['dDelta']
# Set the number of steps to run
if t_extra is not None:
# Convert to simulation units if needed
if pynbody.units.has_units(t_extra):
t_unit = isaac.units_from_param(param)['t_unit']
t_extra.convert_units(t_unit)
# Assign output
param['nSteps'] = iStartStep + int(round(t_extra/dDelta))
elif t is not None:
# Convert to simulation units if needed
if pynbody.units.has_units(t):
t_unit = isaac.units_from_param(param)['t_unit']
t.convert_units(t_unit)
# Assign output
param['nSteps'] = int(round(t/dDelta))
# Save new param file
isaac.configsave(param, newparam, ftype='param')
# Delete old checkpoints
for checkpoint in glob.glob(fprefix + '.chk*'):
print 'removing ' + checkpoint
os.system('rm -rf ' + checkpoint)
if os.path.exists('lastcheckpoint'):
print 'removing lastcheckpoint'
os.remove('lastcheckpoint')
# Create a submission script for the simulation continuation
oldsubfile = open(oldsub, 'r')
newsubfile = open(newsub, 'w')
for line in oldsubfile:
newsubfile.write(line.replace(paramname, newparam))
oldsubfile.close()
newsubfile.close()
# Make the submission script executable
os.chmod(newsub, 0777)
sub_path = os.path.abspath(newsub)
# Change back to original working directory
os.chdir(cwd)
return sub_path
# Save Output
# -------------------------------------------------
# Save snapshot
snapshot.write(filename=snapshotName, fmt=pynbody.tipsy.TipsySnap)
print "Tipsy snapshot saved to {0}".format(snapshotName)
# Start saving log file
logFile = open(logFileName, "w")
logFile.write("Generated from settings file: {0}\n".format(os.path.abspath(settings_file)))
m_amu = float((m * 0.992733 / pynbody.units.m_p).in_units("1"))
# Save director file
if paramName is not None:
try:
import isaac
defPar = os.path.join(ICgenDir, "default.param")
pars = isaac.configparser(defPar, ftype="param")
pars["achInFile"] = snapshotName
pars["achOutName"] = os.path.splitext(snapshotName)[0]
# Convert molecular mass from mass of proton to amu
pars["dMeanMolWeight"] = m_amu
isaac.configsave(pars, paramName, ftype="param")
print "ChaNGa parameter file saved to {0}".format(paramName)
logFile.write("ChaNGa parameter file saved to {0}\n".format(paramName))
except:
print "Could not save .param file. Check that the module isaac\
was properly imported"
# Continue writing to log file
logFile.write("Tipsy snapshot saved to {0}\n".format(snapshotName))
logFile.write(
"Surface density profile saved to {0}\n\
rho(z,r) saved to {1}\n\
def find_clumps(f,
n_smooth=32,
param=None,
arg_string=None,
seed=None,
verbose=True):
"""
Uses skid (https://github.com/N-BodyShop/skid) to find clumps in a gaseous
protoplanetary disk.
The linking length used is equal to the gravitational softening length of
the gas particles.
The density cut-off comes from the criterion that there are n_smooth particles
within the Hill sphere of a particle. This is formulated mathematically as:
rho_min = 3*n_smooth*Mstar/R^3
where R is the distance from the star. The trick used here is to multiply
all particle masses by R^3 before running skid so the density cut-off is:
rho_min = 3*n_smooth*Mstar
**ARGUMENTS**
*f* : TipsySnap, or str
A tipsy snapshot loaded/created by pynbody -OR- a filename pointing to a
snapshot.
*n_smooth* : int (optional)
Number of particles used in SPH calculations. Should be the same as used
in the simulation. Default = 32
*param* : str (optional)
filename for a .param file for the simulation
*arg_string* : str (optional)
Additional arguments to be passed to skid. Cannot use -tau, -d, -m, -s, -o
*seed* : int
An integer used to seed the random filename generation for temporary
files. Necessary for multiprocessing and should be unique for each
thread.
*verbose* : bool
Verbosity flag. Default is True
**RETURNS**
*clumps* : array, int-like
Array containing the group number each particle belongs to, with star
particles coming after gas particles. A zero means the particle belongs
to no groups
"""
# Parse areguments
if isinstance(f, str):
f = pynbody.load(f, paramfile=param)
if seed is not None:
np.random.seed(seed)
# Estimate the linking length as the gravitational softening length
tau = f.g['eps'][0]
# Calculate minimum density
rho_min = 3 * n_smooth * f.s['mass'][0]
# Center on star. This is done because R used in hill-sphere calculations
# is relative to the star
star_pos = f.s['pos'].copy()
f['pos'] -= star_pos
# Scale mass by R^3
R = isaac.strip_units(f['rxy'])
m0 = f['mass'].copy()
f['mass'] *= (R + tau)**3
# Save temporary snapshot
f_prefix = str(np.random.randint(np.iinfo(int).max))
f_name = f_prefix + '.std'
# Save temporary .param file
if param is not None:
param_name = f_prefix + '.param'
param_dict = isaac.configparser(param, 'param')
isaac.configsave(param_dict, param_name)
f.write(filename=f_name, fmt=pynbody.tipsy.TipsySnap)
f['pos'] += star_pos
f['mass'] = m0
command = 'totipnat < {} | skid -tau {:.2e} -d {:.2e} -m {:d} -s {:d} -o {}'\
.format(f_name, tau, rho_min, n_smooth, n_smooth, f_prefix)
p = subprocess.Popen(command,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
if verbose:
for line in iter(p.stdout.readline, ''):
print line,
p.wait()
# Load clumps
clumps = isaac.loadhalos(f_prefix + '.grp')
# Cleanup
for name in glob.glob(f_prefix + '*'):
os.remove(name)
return clumps
# ICgen modules
import calc_rho_zr
import calc_rho
import pos_gen_grid as pos_gen
import calc_temp
import calc_sigma
import pos_class
import make_snapshot
import isaac
import ICgen_settings
import make_sigma
ICgenDir = os.path.dirname(os.path.realpath(__file__))
param_filepath = os.path.join(ICgenDir, 'default.param')
param_default = isaac.configparser(param_filepath, ftype='param')
class IC:
def __init__(self):
# Initialize
# Load up default settings
self.settings = ICgen_settings.settings()
# Add modules/attributes
self.T = calc_temp.T(self)
self.maker = maker(self)
self.add = add(self)
def saver(filename = None):
"""
# ICgen modules
import calc_rho_zr
import calc_rho
import pos_gen_grid as pos_gen
import calc_temp
import calc_sigma
import pos_class
import make_snapshot
import isaac
import ICgen_settings
import make_sigma
ICgenDir = os.path.dirname(os.path.realpath(__file__))
param_filepath = os.path.join(ICgenDir, 'default.param')
param_default = isaac.configparser(param_filepath, ftype='param')
class IC:
def __init__(self):
# Initialize
# Load up default settings
self.settings = ICgen_settings.settings()
# Add modules/attributes
self.T = calc_temp.T(self)
self.maker = maker(self)
self.add = add(self)
def saver(filename=None):
"""