def load_lum(run, batch, source, basename='xrb', reload=False, save=True,
silent=True, check_monotonic=True):
"""Attempts to load pre-extracted luminosity data, or load raw binary.
Returns [time (s), luminosity (erg/s)]
"""
def load_save(load_filepath, save_filepath):
lum_loaded = extract_lcdata(filepath=load_filepath, silent=silent)
if save:
try:
save_ascii(lum=lum_loaded, filepath=save_filepath)
except FileNotFoundError:
print("Can't save preloaded luminosity file, path not found")
return lum_loaded
pyprint.print_dashes()
batch_str = grid_strings.get_batch_string(batch, source)
analysis_path = grid_strings.get_source_subdir(source, 'burst_analysis')
input_path = os.path.join(analysis_path, batch_str, 'input')
presaved_filepath = os.path.join(input_path, f'{batch_str}_{run}.txt')
run_str = grid_strings.get_run_string(run, basename)
model_path = grid_strings.get_model_path(run, batch, source, basename)
binary_filepath = os.path.join(model_path, f'{run_str}.lc')
print(binary_filepath)
if reload:
print('Deleting preloaded file, reloading binary file')
subprocess.run(['rm', '-f', presaved_filepath])
try:
lum = load_save(binary_filepath, presaved_filepath)
except FileNotFoundError:
print('XXXXXXX lumfile not found. Skipping XXXXXXXX')
return
else:
try:
lum = load_ascii(presaved_filepath)
except (FileNotFoundError, OSError):
print('No preloaded file found. Reloading binary')
try:
lum = load_save(binary_filepath, presaved_filepath)
except FileNotFoundError:
print('XXXXXXX lumfile not found. Skipping XXXXXXX')
return
if check_monotonic:
dt = np.diff(lum[:, 0])
if True in (dt < 0):
pyprint.print_warning('Lightcurve timesteps are not in order. '
+ 'Something has gone horribly wrong!', n=80)
raise RuntimeError('Lightcurve timesteps are not in order')
pyprint.print_dashes()
return lum
def print_summary(runs,
batches,
source,
basename='xrb',
skip=1,
redshift=1.259,
**kwargs):
"""
prints summary analyser output of model
"""
source = grid_strings.source_shorthand(source=source)
batches = grid_tools.expand_batches(batches, source)
path = kwargs.get('path', GRIDS_PATH)
analyser_path = os.path.join(path, 'analyser', source)
runs = grid_tools.expand_runs(runs)
for batch in batches:
batch_name = grid_strings.get_batch_string(batch, source)
output_str = f'{batch_name}{OUTPUT_SUFFIX}'
print_title(f'Batch {batch}')
summ_filepath = os.path.join(analyser_path, output_str, 'summ.csv')
summ = pd.read_csv(summ_filepath)
summ_names = np.genfromtxt(summ_filepath,
delimiter="'",
usecols=[1],
dtype='str')
for run in runs:
run_str = grid_strings.get_run_string(run, basename)
idx = np.where(
summ_names == run_str)[0][0] # index of row for this run
N = int(summ['num'][idx]) # Number of bursts
dt = summ['tDel'][idx] * redshift / 3600
u_dt = summ['uTDel'][idx] * redshift / 3600
# ===== Print info =====
print(basename + str(run))
print('Total bursts = {n}'.format(n=N))
print('Exluding first {skip} bursts'.format(skip=skip))
print('Using redshift (1+z)={:.3f}'.format(redshift))
print('Delta_t = {:.2f} (hr)'.format(dt))
print('u(Delta_t) = {:.2f} (hr)'.format(u_dt))
print_dashes()
return {'N': N, 'dt': dt, 'u_dt': u_dt}
def extract_lightcurves(runs, path_data, path_target, basename='xrb'):
"""========================================================
Loads Kepler .lum binaries and saves txt file of [time, luminosity, radius] for input to kepler_analyser
Returns No. of cycles for each run
========================================================
runs = [] : list of run numbers, eg. [324,325,340]
path_data = str : path to directory where kepler output folders are located (include trailing slash)
path_target = str : path to directory where output .txt files will be written (include trailing slash)
in_name = str : base filename of input, eg. 'run' for run324
out_name = str : base filename of output, eg. 'xrb' for xrb324
NOTE: kepler_analyser overwrites summ.csv and db.csv, should put path_target as new directory
========================================================"""
print_title()
print(f'Loading binaries from {path_data}')
print(f'Writing txt files to {path_target}')
print_title()
cycles = np.zeros(len(runs), dtype=int)
for i, run in enumerate(runs):
rname = grid_strings.get_run_string(run, basename)
lcfile = f'{rname}.lc'
savefile = f'{rname}.data'
print(f'Loading kepler binary for {rname}')
lcpath = os.path.join(path_data, rname, lcfile)
data = lcdata.load(lcpath, graphical=False)
print('Writing txt file')
savepath = os.path.join(path_target, savefile)
data.write_lc_txt(savepath)
# --- Save number of cycles in model ---
cycles[i] = len(data.time)
print_dashes()
def gravity_summary(r, m):
"""Prints summary gravitational properties given R, M
"""
redshift = get_redshift(r=r, m=m)
phi_newton, phi_gr = get_potentials(r=r, m=m)
g_newton, g_gr = get_accelerations(r=r, m=m)
print_dashes()
print('R (km), M (Msun)')
print(f'{r:.2f}, {m:.2f}')
print_dashes()
print('g (Newtonian)')
print(f'{g_newton:.3e}')
print_dashes()
print('g (GR)')
print(f'{g_gr:.3e}')
print_dashes()
print('(1+z) (GR)')
print(f'{redshift:.3f}')
print_dashes()
print('potential (Newtonian, erg/g)')
print(f'{phi_newton:.3e}')
print_dashes()
print('potential (GR, erg/g)')
print(f'{phi_gr:.3e}')
return g_newton, g_gr, phi_newton, phi_gr
def check_finished(batches,
source,
efficiency=True,
show='all',
basename='xrb',
extension='z1',
**kwargs):
"""Checks which running models are finished
t_end = flt : end-time of the simulations
basename = str : prefix for individual model names
extension = str : suffix of kepler dump
efficiency = bool : print time per 1000 steps
all = str : which models to show, based on their progress,
one of (all, finished, not_finished, started, not_started)
(path = str : path to location of model directories)
Notes
-----
timeused gets reset when a model is resumed,
resulting in unreliable values in efficiency
"""
def progress_string(batch, basename, run, progress, elapsed, remaining,
eff_str, eff2_str):
string = [
f'{batch} {basename}{run:02} {progress:.0f}% ' +
f'{elapsed:.0f}hrs ~{remaining:.0f}hrs, ' +
f'{eff_str}, {eff2_str}'
]
return string
def shorthand(string):
map_ = {
'a': 'all',
'ns': 'not_started',
'nf': 'not_finished',
'f': 'finished'
}
if string not in map_:
if string not in map_.values():
raise ValueError("invalid 'show' parameter")
return string
else:
return map_[string]
source = grid_strings.source_shorthand(source=source)
show = shorthand(show)
batches = expand_batches(batches=batches, source=source)
print_strings = []
print_idx = {
'finished': [],
'not_finished': [],
'started': [],
'not_started': []
}
for batch in batches:
n_runs = get_nruns(batch=batch, source=source)
print_strings += [f'===== Batch {batch} =====']
for run in range(1, n_runs + 1):
run_str = grid_strings.get_run_string(run, basename)
run_path = grid_strings.get_model_path(run,
batch,
source,
basename=basename)
string_idx = len(print_strings)
filename = f'{run_str}{extension}'
filepath = os.path.join(run_path, filename)
# ===== get t_end from cmd file =====
cmd_file = f'{run_str}.cmd'
cmd_filepath = os.path.join(run_path, cmd_file)
t_end = None
try:
with open(cmd_filepath) as f:
lines = f.readlines()
marker = '@time>'
for line in lines[-10:]:
if marker in line:
t_end = float(line.strip('@time>').strip())
break
kmodel = kepdump.load(filepath)
progress = kmodel.time / t_end
timeused = kmodel.timeused[0][-1] # CPU time elapsed
ncyc = kmodel.ncyc # No. of time-steps
remaining = (timeused / 3600) * (1 - progress) / progress
if efficiency:
eff = (timeused / (ncyc / 1e4)) / 3600 # Time per 1e4 cyc
eff2 = timeused / kmodel.time
eff_str = f'{eff:.1f} hr/10Kcyc'
eff2_str = f'{eff2:.2f} walltime/modeltime'
else:
eff_str = ''
eff2_str = ''
# ===== Tracking model progress =====
print_idx['started'] += [string_idx]
if f'{remaining:.0f}' == '0':
print_idx['finished'] += [string_idx]
else:
print_idx['not_finished'] += [string_idx]
except:
progress = 0
timeused = 0
remaining = 0
eff_str = ''
eff2_str = ''
print_idx['not_started'] += [string_idx]
progress *= 100
elapsed = timeused / 3600
print_strings += progress_string(batch=batch,
basename=basename,
run=run,
progress=progress,
elapsed=elapsed,
remaining=remaining,
eff_str=eff_str,
eff2_str=eff2_str)
print_idx['all'] = np.arange(len(print_strings))
print_dashes()
print('Batch Model elapsed remaining')
for i, string in enumerate(print_strings):
if i in print_idx[show]:
print(string)
def create_batch(batch, dv, source,
params={'x': [0.6, 0.8], 'z': [0.01, 0.02],
'tshift': [0.0], 'accrate': [0.05],
'qb': [0.125], 'acc_mult': [1.0], 'qnuc': [5.0],
'qb_delay': [0.0], 'mass': [1.4],
'accmass': [1e16], 'accdepth': [1e20]},
lburn=1, t_end=1.3e5, exclude={}, basename='xrb',
walltime=96, qos='normal', nstop=10000000, nsdump=500,
auto_t_end=True, notes='No notes given', debug=False,
nbursts=20, parallel=False, ntasks=8, kgrid=None,
nuc_heat=True, setup_test=False, predict_qnuc=False,
grid_version=None, qnuc_source='heat', minzone=51,
zonermax=10, zonermin=-1, thickfac=0.001,
substrate='fe54', substrate_off=True, adapnet_filename=None,
bdat_filename=None, ibdatov=1, params_full=None):
"""Generates a grid of Kepler models, containing n models over the range x
Parameters
---------
batch : int
params : {}
specifiy model parameters. If variable: give range
dv : {}
stepsize in variables (if ==-1: keep param as is)
exclude : {}
specify any parameter values to exclude from grid
params : {}
mass of NS (in Msun). Only changes geemult (gravity multiplier)
qos : str
quality of service (slurm), one of ['general', 'medium', 'short']
auto_t_end : bool
auto-choose t_end based on predicted recurrence time
parallel : bool
utilise parallel independent kepler tasks
ntasks : int
no. of tasks in each parallel job (split up by this)
kgrid : Kgrid
pre-loaded Kgrid object, optional (avoids reloading)
"""
# TODO: WRITE ALL PARAM DESCRIPTIONS
# TODO: set default values for params
# TODO: Overhaul/tidy up
# TODO: use pd table instead of dicts of arrays
source = grid_strings.source_shorthand(source=source)
mass_ref = 1.4 # reference NS mass (Msun)
radius_ref = 10 # default NS radius (km)
print_batch(batch=batch, source=source)
if params_full is None:
params = dict(params)
params_expanded, var = expand_params(dv, params)
# ===== Cut out any excluded values =====
cut_params(params=params_expanded, exclude=exclude)
print_grid_params(params_expanded)
params_full = grid_tools.enumerate_params(params_expanded)
n_models = len(params_full['x'])
if parallel and (n_models % ntasks != 0):
raise ValueError(f'n_models ({n_models}) not divisible by ntasks ({ntasks})')
if kgrid is None:
print('No kgrid provided. Loading:')
kgrid = grid_analyser.Kgrid(load_lc=False, source=source)
params_full['y'] = 1 - params_full['x'] - params_full['z'] # helium-4 values
params_full['geemult'] = params_full['mass'] / mass_ref # Gravity multiplier
gravities = gravity.get_acceleration_newtonian(r=radius_ref,
m=params_full['mass']).value
params_full['radius'] = np.full(n_models, radius_ref)
params_full['gravity'] = gravities
# TODO: rewrite properly (use tables)
if predict_qnuc:
if len(params['qnuc']) > 1:
raise ValueError('Cannot provide multiple "qnuc" in params if predict_qnuc=True')
linr_qnuc = qnuc_tools.linregress_qnuc(qnuc_source, grid_version=grid_version)
for i in range(n_models):
params_qnuc = {}
for param in param_list:
params_qnuc[param] = params_full[param][i]
params_full['qnuc'][i] = qnuc_tools.predict_qnuc(params=params_qnuc,
source=qnuc_source,
linr_table=linr_qnuc)
# ===== Create top grid folder =====
batch_model_path = grid_strings.get_batch_models_path(batch, source)
grid_tools.try_mkdir(batch_model_path)
# Directory to keep MonARCH logs and sbatch files
logpath = grid_strings.get_source_subdir(batch_model_path, 'logs')
grid_tools.try_mkdir(logpath)
# ===== Write parameter table MODELS.txt and NOTES.txt=====
write_model_table(n=n_models, params=params_full, lburn=lburn, path=batch_model_path)
filepath = os.path.join(batch_model_path, 'NOTES.txt')
with open(filepath, 'w') as f:
f.write(notes)
job_runs = []
if parallel:
n_jobs = int(n_models / ntasks)
for i in range(n_jobs):
start = i * ntasks
job_runs += [[start + 1, start + ntasks]]
else:
job_runs += [[1, n_models]]
print_dashes()
for runs in job_runs:
for restart in [True, False]:
kepler_jobscripts.write_submission_script(run0=runs[0], run1=runs[1],
restart=restart, batch=batch,
source=source, basename=basename,
path=logpath, qos=qos,
walltime=walltime,
parallel=parallel, debug=debug,
adapnet_filename=adapnet_filename,
bdat_filename=bdat_filename)
# ===== Directories and templates for each model =====
for i in range(n_models):
# ==== Create directory tree ====
print_dashes()
model = i + 1
run_path = grid_strings.get_model_path(model, batch, source, basename=basename)
# ==== Create task directory ====
grid_tools.try_mkdir(run_path)
# ==== Write burn file, set initial composition ====
x0 = params_full['x'][i]
z0 = params_full['z'][i]
kepler_files.write_rpabg(x0, z0, run_path, substrate=substrate)
# ==== Create model generator file ====
accrate0 = params_full['accrate'][i]
if auto_t_end:
mdot = params_full['accrate'][i] * params_full['acc_mult'][i]
rate_params = {}
for param in ('x', 'z', 'qb', 'mass'):
rate_params[param] = params_full[param][i]
fudge = 0.5 # extra time to ensure complete final burst
tdel = kgrid.predict_recurrence(accrate=mdot, params=rate_params)
t_end = (nbursts + fudge) * tdel
print(f'Using predicted dt={tdel/3600:.1f} hr')
if t_end < 0:
print('WARN! negative dt predicted. Defaulting n * 1.5hr')
t_end =nbursts * 1.5 * 3600
run = i + 1
print(f'Writing genfile for xrb{run}')
header = f'This generator belongs to model: {source}_{batch}/{basename}{run}'
accdepth = params_full['accdepth'][i]
if (params_full['x'][i] > 0.0) and (accdepth > 1e20):
print(f"!!!WARNING!!!: accdepth of {accdepth:.0e} may be too deep for" +
" models accreting hydrogen")
print(f'Using accdepth = {accdepth:.1e}')
kepler_files.write_genfile(h1=params_full['x'][i], he4=params_full['y'][i],
n14=params_full['z'][i], qb=params_full['qb'][i],
acc_mult=params_full['acc_mult'][i], qnuc=params_full['qnuc'][i],
lburn=lburn, geemult=params_full['geemult'][i],
path=run_path, t_end=t_end, header=header,
accrate0=accrate0, accdepth=accdepth,
accmass=params_full['accmass'][i],
nsdump=nsdump, nstop=nstop,
nuc_heat=nuc_heat, setup_test=setup_test, cnv=0,
minzone=minzone, zonermax=zonermax, zonermin=zonermin,
thickfac=thickfac, substrate_off=substrate_off,
ibdatov=ibdatov)
def create_batch(batch,
source,
params,
dv,
t_end=1.3e5,
exclude=None,
basename='xrb',
walltime=96,
auto_t_end=True,
notes='No notes given',
nbursts=20,
kgrid=None,
nuc_heat=True,
setup_test=False,
auto_qnuc=False,
grid_version=None,
qnuc_source='heat',
substrate='fe54',
substrate_off=True,
adapnet_filename=None,
bdat_filename=None,
params_full=None,
numerical_params=None,
scratch_file_sys=False):
"""Generates a grid of Kepler models, containing n models over the range x
Parameters
---------
batch : int
source : str
params : {}
specifiy model parameters. If variable: give range
dv : {}
stepsize in variables (if ==-1: keep param as is)
exclude : {}
specify any parameter values to exclude from grid
params : {}
mass of NS (in Msun). Only changes geemult (gravity multiplier)
auto_t_end : bool
auto-choose t_end based on predicted recurrence time
kgrid : Kgrid
pre-loaded Kgrid object, optional (avoids reloading)
t_end : float (optional)
basename : str (optional)
walltime : int (optional)
notes : str (optional)
nbursts : int (optional)
auto_qnuc : bool (optional)
nuc_heat : bool (optional)
setup_test : bool (optional)
grid_version : int (optional)
qnuc_source : str (optional)
substrate : str (optional)
substrate_off : bool (optional)
adapnet_filename : str (optional)
bdat_filename : str (optional)
params_full : {} (optional)
numerical_params : {} (optional)
Overwrite default numerical kepler parameters (e.g. nsdump, zonermax, lburn,
For all parameters: see 'numerical_params' in config/default.ini
scratch_file_sys : bool (optional)
whether to use the scratch file system on ICER cluster
"""
# TODO:
# - WRITE ALL PARAM DESCRIPTIONS
# - Overhaul/tidy up
# - use pd table instead of dicts of arrays
print_batch(batch=batch)
source = grid_strings.source_shorthand(source=source)
mass_ref = 1.4 # reference NS mass (Msun)
radius_ref = 10 # default NS radius (km)
specified = {
'params': params,
'dv': dv,
'numerical_params': numerical_params
}
if specified['numerical_params'] is None:
specified['numerical_params'] = {}
config = grid_tools.setup_config(specified=specified, source=source)
# TODO: print numerical_params being used
if params_full is None:
params_expanded, var = expand_params(params=config['params'],
dv=config['dv'])
params_full = exclude_params(params_expanded=params_expanded,
exclude=exclude)
n_models = len(params_full['x'])
if kgrid is None:
print('No kgrid provided. Loading default:')
kgrid = grid_analyser.Kgrid(load_lc=False,
linregress_burst_rate=True,
source=source)
params_full['y'] = 1 - params_full['x'] - params_full[
'z'] # helium-4 values
params_full[
'geemult'] = params_full['mass'] / mass_ref # Gravity multiplier
gravities = gravity.get_acceleration_newtonian(r=radius_ref,
m=params_full['mass']).value
params_full['radius'] = np.full(n_models, radius_ref)
params_full['gravity'] = gravities
if auto_qnuc:
predict_qnuc(params_full=params_full,
qnuc_source=qnuc_source,
grid_version=grid_version)
# ===== Create top grid folder =====
batch_model_path = grid_strings.get_batch_models_path(batch, source)
grid_tools.try_mkdir(batch_model_path)
# Directory to keep MonARCH logs and sbatch files
logpath = grid_strings.get_source_subdir(batch_model_path, 'logs')
grid_tools.try_mkdir(logpath)
# ===== Write parameter table MODELS.txt and NOTES.txt=====
write_model_table(n=n_models, params=params_full, path=batch_model_path)
filepath = os.path.join(batch_model_path, 'NOTES.txt')
with open(filepath, 'w') as f:
f.write(notes)
# ===== Write jobscripts for submission on clusters =====
print_dashes()
kepler_jobs.write_both_jobscripts(run0=1,
run1=n_models,
batch=batch,
source=source,
basename=basename,
path=logpath,
walltime=walltime,
adapnet_filename=adapnet_filename,
bdat_filename=bdat_filename,
scratch_file_sys=scratch_file_sys)
# ===== Directories and templates for each model =====
for i in range(n_models):
# ==== Create directory tree ====
print_dashes()
model = i + 1
run_path = grid_strings.get_model_path(model,
batch,
source,
basename=basename)
# ==== Create task directory ====
grid_tools.try_mkdir(run_path)
# ==== Write burn file, set initial composition ====
x0 = params_full['x'][i]
z0 = params_full['z'][i]
kepler_files.write_rpabg(x0, z0, run_path, substrate=substrate)
# ==== Create model generator file ====
if auto_t_end:
mdot = params_full['accrate'][i] * params_full['acc_mult'][i]
rate_params = {}
for param in ('x', 'z', 'qb', 'mass'):
rate_params[param] = params_full[param][i]
fudge = 0.5 # extra time to ensure complete final burst
tdel = kgrid.predict_recurrence(accrate=mdot, params=rate_params)
t_end = (nbursts + fudge) * tdel
print(f'Using predicted dt={tdel/3600:.1f} hr')
if t_end < 0:
print('WARN! negative dt predicted. Defaulting n * 1.5hr')
t_end = nbursts * 1.5 * 3600
run = i + 1
print(f'Writing genfile for xrb{run}')
header = f'This generator belongs to model: {source}_{batch}/{basename}{run}'
accdepth = params_full['accdepth'][i]
if (params_full['x'][i] > 0.0) and (accdepth > 1e20):
print(
f"!!!WARNING!!!: accdepth of {accdepth:.0e} may be too deep for"
+ " models accreting hydrogen")
print(f'Using accdepth = {accdepth:.1e}')
kepler_files.write_genfile(h1=params_full['x'][i],
he4=params_full['y'][i],
n14=params_full['z'][i],
qb=params_full['qb'][i],
acc_mult=params_full['acc_mult'][i],
qnuc=params_full['qnuc'][i],
geemult=params_full['geemult'][i],
accrate0=params_full['accrate'][i],
accmass=params_full['accmass'][i],
accdepth=params_full['accdepth'][i],
path=run_path,
t_end=t_end,
header=header,
nuc_heat=nuc_heat,
setup_test=setup_test,
substrate_off=substrate_off,
numerical_params=config['numerical_params'])