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black without mortimer

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This commit is contained in:
Noe Brucy
2022-11-28 18:01:18 +01:00
parent 7548ef7e0a
commit fa396178c6
14 changed files with 371 additions and 304 deletions
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studyprocessor.py
+68 -52
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@@ -38,12 +38,9 @@ class StudyProcessor(Aggregator, HDF5Container):
Creates the basic structures needed for the outputs
"""
# log id
self.log_id = "study({})".format(tag)
super(StudyProcessor, self).__init__(path, path_out, params, tag)
# Open outfile
@@ -60,7 +57,12 @@ class StudyProcessor(Aggregator, HDF5Container):
# Select runs
if selector is None:
selector = RunSelector(
path, runs, nums, self.params.input.nml_filename, unit_time=unit_time, **kwargs
path,
runs,
nums,
self.params.input.nml_filename,
unit_time=unit_time,
**kwargs,
)
# Save infos
@@ -68,7 +70,6 @@ class StudyProcessor(Aggregator, HDF5Container):
self.runs = selector.runs
self.nums = selector.nums
run0 = self.runs[0]
self.info = selector.info[run0][self.nums[run0][0]]
self.namelist = selector.namelist
@@ -90,8 +91,6 @@ class StudyProcessor(Aggregator, HDF5Container):
unit_time=unit_time,
)
# Save namelist and logs
if self.params.out.copy_info:
for run in self.runs:
@@ -158,7 +157,16 @@ class StudyProcessor(Aggregator, HDF5Container):
prop[run] = getter(run)
return np.array(list(prop.values()))
def time_avg(self, name, start=None, end=None, span=None, unit_time=U.Myr, group="/series", select=None):
def time_avg(
self,
name,
start=None,
end=None,
span=None,
unit_time=U.Myr,
group="/series",
select=None,
):
"""Do the time average and quantiles of a time series
Parameters
@@ -273,18 +281,16 @@ class StudyProcessor(Aggregator, HDF5Container):
return value
def get_nml(self, nml_key=None, run=None):
if run is not None:
if nml_key is not None:
return self.namelist[run][nml_key]
else:
return self.namelist[run]
else:
if nml_key is not None:
return {run : self.namelist[run][nml_key] for run in self.runs}
else:
return self.namelist
if run is not None:
if nml_key is not None:
return self.namelist[run][nml_key]
else:
return self.namelist[run]
else:
if nml_key is not None:
return {run: self.namelist[run][nml_key] for run in self.runs}
else:
return self.namelist
def get_pdf_slope(self, name, run, num):
snap = self.snaps[run][num]
@@ -295,7 +301,7 @@ class StudyProcessor(Aggregator, HDF5Container):
def _extract_sinks_from_log(self, series, log_filename, run):
cmd_grep = f"grep 'Number of sink' {log_filename} -A 2"
content = os.popen(cmd_grep).readlines()
block_err = [] # Block that will ill parsed
block_err = [] # Block that will ill parsed
for i in range(0, len(content), 4):
try:
nb_sink = np.int(content[i].split("=")[1])
@@ -311,11 +317,11 @@ class StudyProcessor(Aggregator, HDF5Container):
except (ValueError, IndexError):
block_err.append(i)
if len(block_err) > 0:
self.logger.warning(
f"Errors encountered in parsing {log_filename} (grepped blocks {block_err})"
)
f"Errors encountered in parsing {log_filename} (grepped blocks {block_err})"
)
return series
def _extract_stellar_from_log(self, stellar_objects, log_filename, run):
@@ -324,7 +330,7 @@ class StudyProcessor(Aggregator, HDF5Container):
nb_stellar = list(map(lambda s: int(s.split()[1]), content))
line_numbers = list(map(lambda s: int(s.split(":")[0]), content))
current_line = 0
block_err = [] # Block that will ill parsed
block_err = [] # Block that will ill parsed
logfile = open(log_filename)
for i in range(0, len(line_numbers)):
try:
@@ -334,7 +340,9 @@ class StudyProcessor(Aggregator, HDF5Container):
for j in range(nb_stellar[i]):
line_stellar = logfile.readline().split()
current_line += 1
while line_stellar[0] == "random": # random number outputs are ... random
while (
line_stellar[0] == "random"
): # random number outputs are ... random
line_stellar = logfile.readline().split()
current_line += 1
mass = float(line_stellar[3])
@@ -349,11 +357,11 @@ class StudyProcessor(Aggregator, HDF5Container):
except (ValueError, IndexError):
block_err.append(i)
if len(block_err) > 0:
self.logger.warning(
f"Errors encountered in parsing {log_filename} (grepped blocks {block_err})"
)
f"Errors encountered in parsing {log_filename} (grepped blocks {block_err})"
)
logfile.close()
return stellar_objects
@@ -370,7 +378,7 @@ class StudyProcessor(Aggregator, HDF5Container):
def _extract_fine_step_from_log(self, series, log_filename, run):
cmd_grep = "grep 'Fine step' {} ".format(log_filename)
content = os.popen(cmd_grep).readlines()
block_err = [] # Block that will ill parsed
block_err = [] # Block that will ill parsed
for i in range(0, len(content)):
try:
data = content[i].replace("=", " ").split()
@@ -388,11 +396,11 @@ class StudyProcessor(Aggregator, HDF5Container):
series["mem_parts"][run].append(mempc2)
except (ValueError, IndexError):
block_err.append(i)
if len(block_err) > 0:
self.logger.warning(
f"Error encountered in parsing {log_filename} (grepped blocks {block_err})"
)
f"Error encountered in parsing {log_filename} (grepped blocks {block_err})"
)
return series
def _extract_coarse_step_from_log(self, series, log_filename, run):
@@ -462,20 +470,19 @@ class StudyProcessor(Aggregator, HDF5Container):
if content[i][1:5] == "Fine":
data = content[i].replace("=", " ").split()
time = np.float(data[4])
elif content[i][1:3] == "SN" :
elif content[i][1:3] == "SN":
series["time"][run].append(time)
series["SN_momentum"][run].append(np.float(content[i].split()[-1]))
else:
raise ValueError("Wrong start of line")
except (AssertionError, ValueError, IndexError):
block_err.append(i)
if len(block_err) > 0:
self.logger.warning(
f"Error encountered in parsing {log_filename} (grepped blocks {block_err})"
)
f"Error encountered in parsing {log_filename} (grepped blocks {block_err})"
)
return series
def get_logs(self, run):
glob_str = f"{self.path}/{run}/{self.params.input.log_prefix}*"
@@ -508,7 +515,7 @@ class StudyProcessor(Aggregator, HDF5Container):
# Always prefer data from last log, assuming they come in the right order
time = series["time"][run]
time_new = time[size]
ind_overlap = np.searchsorted(time[:size], time_new, side='right')
ind_overlap = np.searchsorted(time[:size], time_new, side="right")
for key in series:
del series[key][run][ind_overlap:size]
@@ -523,13 +530,13 @@ class StudyProcessor(Aggregator, HDF5Container):
return series
def get_coldens0(self, run):
mp = 1.4 * 1.66 * 10**(-24) * U.g
mp = 1.4 * 1.66 * 10 ** (-24) * U.g
try:
z0 = self.get_nml("galbox_params/height0", run) * U.pc
n0 = self.get_nml("galbox_params/dens0", run) * U.cm**(-3)
n0 = self.get_nml("galbox_params/dens0", run) * U.cm ** (-3)
except KeyError:
z0 = self.get_nml("cloud_params/height0", run) * U.pc
n0 = self.get_nml("cloud_params/dens0", run) * U.cm**(-3)
n0 = self.get_nml("cloud_params/dens0", run) * U.cm ** (-3)
return (np.sqrt(2 * np.pi) * mp * z0 * n0).express(U.coldens)
@@ -537,13 +544,13 @@ class StudyProcessor(Aggregator, HDF5Container):
"""
Sum of gas plus sink mass
"""
time_gas = self.get_value("/series/coarse_step_from_log/time")
time_gas = self.get_value("/series/coarse_step_from_log/time")
mass_gas = self.get_value("/series/coarse_step_from_log/mcons")
mass_sink = self.get_value("/series/sinks_from_log/mass_sink")
time_sink = self.get_value("/series/sinks_from_log/time")
time_sink = self.get_value("/series/sinks_from_log/time")
total_mass = dict()
total_mass = {}
for run in self.runs:
if time_sink[run][-1] > time_gas[run][-1]:
@@ -552,11 +559,13 @@ class StudyProcessor(Aggregator, HDF5Container):
# A bit specific ... needs to be generalized (TODO)
info = self.snaps[run][self.nums[run][0]].info
surface = (info["unit_length"].express(U.pc)) ** 2
m0 = self.get_coldens0(run) * surface # Initial mass in Msun
m0 = self.get_coldens0(run) * surface # Initial mass in Msun
offset = time_gas[run].size - time_sink[run].size
mass_gas[run] = m0 + m0*mass_gas[run] # convert in Msun
mass_gas[run] = m0 + m0 * mass_gas[run] # convert in Msun
total_mass[run] = mass_gas[run].copy()
total_mass[run][offset:] = mass_gas[run][offset:] + mass_sink[run] # re add sink_mass
total_mass[run][offset:] = (
mass_gas[run][offset:] + mass_sink[run]
) # re add sink_mass
return time_gas, total_mass, mass_gas
def _ssfr_from_mass_sink(self, avg_window=None):
@@ -841,9 +850,16 @@ class StudyProcessor(Aggregator, HDF5Container):
},
),
"SN_momentum_from_log": Rule(
partial(self._from_log, ["time", "SN_momentum"], self._extract_SN_Mom_from_log),
partial(
self._from_log,
["time", "SN_momentum"],
self._extract_SN_Mom_from_log,
),
group="/series",
unit={"time": "unit_time", "SN_momentum" : {"unit_mass" : 1, "unit_velocity" : 1}},
unit={
"time": "unit_time",
"SN_momentum": {"unit_mass": 1, "unit_velocity": 1},
},
description={
"time": "Time",
"SN_momentum": "Injected momentum",
@@ -934,7 +950,7 @@ class StudyProcessor(Aggregator, HDF5Container):
"turb_power",
"time_rho_prof",
"time_coldens_pdf",
"time_rho_pdf"
"time_rho_pdf",
]:
self._gen_rule_avg(name)