Add filaments postproc, improve units detection, add automatic map rules, add selection
This commit is contained in:
Noe Brucy
+66
-41
@@ -88,47 +88,7 @@ class Comparator(Aggregator, HDF5Container):
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)
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return missing_nums
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def _get_units(self, unit, data=None):
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"""
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Get real units from info files
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unit is either:
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1. An instance of cst.Unit (pymses unit class)
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2. A string beginning by "unit_", referring to a code unit,
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available in self.info
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3. A dict {unit1 : exp1, unit2: exp2, ...} with unitX as 2.
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and expX a float, referring to the compound unit
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unit1**exp1 * unit2**exp2
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4. A dict {key: unit, ...} where key is a field name (eg. 'time', or 'mass')
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and unit the corresponding unit (on one on the above format)
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Returns:
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1-3. : a cst.Unit instance
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4. : a dict {key: unit, ...} with same key as input and unit being cst.Unit instances
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"""
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if isinstance(unit, cst.Unit):
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return unit
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if isinstance(unit, str) and unit[:5] == "unit_":
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res = self.info[unit]
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if unit == "unit_length":
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res = res / self.info["boxlen"]
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return res
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if list(unit)[0][:5] == "unit_":
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new_unit = cst.none
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for base_unit_str in unit:
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expo = unit[base_unit_str]
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base_unit = self._get_units(base_unit_str)
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new_unit = new_unit * base_unit ** expo
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return new_unit
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if (not data is None) and isinstance(data, dict) and list(unit)[0] in data:
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for key in unit:
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unit[key] = self._get_units(unit[key])
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return unit
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else:
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raise ValueError("Invalid unit")
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def _save_data(self, name_full, data, description, unit):
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unit = self._get_units(unit, data=data)
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super(Comparator, self)._save_data(name_full, data, description, unit)
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self.save.get_node(name_full)._v_attrs.nums = self.nums
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@@ -276,6 +236,24 @@ class Comparator(Aggregator, HDF5Container):
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series["sfr"][run].append(sfr)
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return series
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def _extract_cons_from_log(self, series, log_filename, run):
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cmd_grep = "grep 'Main step' {} -A 2".format(log_filename)
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content = os.popen(cmd_grep).readlines()
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for i in range(0, len(content), 4):
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series["time"][run].append(
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np.float(content[i + 2].split("=")[2].split()[0])
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)
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series["step"][run].append(np.int(content[i].split("=")[1].split()[0]))
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series["mcons"][run].append(np.float(content[i].split("=")[2].split()[0]))
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series["econs"][run].append(np.float(content[i].split("=")[3].split()[0]))
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series["epot"][run].append(np.float(content[i].split("=")[4].split()[0]))
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series["ekin"][run].append(np.float(content[i].split("=")[5].split()[0]))
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series["eint"][run].append(np.float(content[i].split("=")[6].split()[0]))
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series["emag"][run].append(
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np.float(content[i + 1].split("=")[1].split()[0])
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)
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return series
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def _extract_rms_from_log(self, series, log_filename, run):
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cmd_grep = "grep 'turbulent rms' {} -C 1".format(log_filename)
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content = os.popen(cmd_grep).readlines()
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@@ -334,7 +312,8 @@ class Comparator(Aggregator, HDF5Container):
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ssfr = {}
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for run in self.runs:
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# Surface of the box in pc^2
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surface = (self.info["unit_length"].express(cst.pc)) ** 2
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info = self.pp[run][self.nums[run][0]].info
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surface = (info["unit_length"].express(cst.pc)) ** 2
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# WARNING : We do not multiply by boxlen since already done in 'unit_length' (pymses)
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time = self.save.get_node("/series/sinks_from_log/time/" + run).read()
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@@ -360,6 +339,22 @@ class Comparator(Aggregator, HDF5Container):
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return ssfr, {"avg_window": avg_window}
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def _surfacic_sink_mass(self):
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mass_unit = self.save.get_node("/series/sinks_from_log/mass_sink")._v_attrs.unit
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ssm = {}
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for run in self.runs:
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# Surface of the box in pc^2
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info = self.pp[run][self.nums[run][0]].info
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surface = (info["unit_length"].express(cst.pc)) ** 2
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mass_sink = self.save.get_node(
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"/series/sinks_from_log/mass_sink/" + run
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).read()
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mass_sink = mass_sink * mass_unit.express(cst.Msun)
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ssm[run] = mass_sink / surface
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return ssm
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def _turb_power(self):
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turb_power = {}
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for run in self.runs:
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@@ -475,6 +470,14 @@ class Comparator(Aggregator, HDF5Container):
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description="Instantaneous surfacic star formation rate",
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dependencies=["sinks_from_log"],
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),
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"ssm": Rule(
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self,
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self._surfacic_sink_mass,
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group="/series/sinks_from_log",
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unit=cst.Msun / cst.pc ** 2,
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description="Surfacic sink mass",
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dependencies=["sinks_from_log"],
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),
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"sfr_from_log": Rule(
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self,
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partial(self._from_log, ["time", "sfr"], self._extract_sfr_from_log),
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@@ -510,6 +513,25 @@ class Comparator(Aggregator, HDF5Container):
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"turb_energy": "Injected turbulent energy",
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},
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),
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"cons_from_log": Rule(
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self,
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partial(
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self._from_log,
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["time", "step", "mcons", "econs", "epot", "ekin", "eint", "emag"],
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self._extract_cons_from_log,
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),
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group="/series",
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unit={
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"time": "unit_time",
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"step": cst.none,
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"mcons": cst.none,
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"econs": cst.none,
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"epot": cst.none, # TODO find unit
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"ekin": cst.none,
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"eint": cst.none,
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"emag": cst.none,
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},
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),
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"turb_power": Rule(
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self,
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self._turb_power,
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@@ -574,6 +596,9 @@ class Comparator(Aggregator, HDF5Container):
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self._gen_rule_time_global("mwa_sigma", "time_sigma", unit="unit_velocity")
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self._gen_rule_time_global("max_fluct_coldens")
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self._gen_rule_time_global(
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"mass", unit=self.info["unit_density"] * self.info["unit_length"] ** 3
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)
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self._gen_rule_time_global("mwa_B_int", unit="unit_mag")
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for name in [
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