diff --git a/docs/RST/examples.rst b/docs/RST/examples.rst
index 0912efdbcafde647c6059e69b21fbedb34a6d76f..ef5fc94927e18969ac0b05d00edefa2c20675d1b 100644
--- a/docs/RST/examples.rst
+++ b/docs/RST/examples.rst
@@ -8,3 +8,4 @@ If you wish to generate them, you will need to first install PySWIFTsim and then
:maxdepth: 2
examples/cooling.rst
+ examples/stellar.rst
diff --git a/docs/RST/examples/cooling.rst b/docs/RST/examples/cooling.rst
index 3f06576eef49c6208d0ce74caaad27d8f3f8c122..f72b3f8287868a6c5780fe8f44fca7620ddcffd7 100644
--- a/docs/RST/examples/cooling.rst
+++ b/docs/RST/examples/cooling.rst
@@ -6,12 +6,12 @@ Cooling Rate
~~~~~~~~~~~~
This example is generated in ``examples/cooling_rate`` with the Grackle cooling.
-The plot are the same than in [Smith2016]_.
+The plot are the same than in [Smith2016]_ and uses a solar metallicity.
The code has two different modes 1D or 2D.
In the first mode, the code generates particles at different temperatures but same density and computes the cooling rate associated to theses conditions.
-.. image:: https://obswww.unige.ch/~lhausamm/PySWIFTsim/examples/cooling_rate.png
+.. image:: https://obswww.unige.ch/lastro/projects/Clastro/PySWIFTsim/examples/cooling_rate.png
In the second mode, the code generates a grid of particles at different density and temperatures and then computes the cooling.
I suppose that in [Smith2016]_, they use the non equilibrium mode of Grackle to generate this graph.
@@ -19,12 +19,12 @@ It requires a careful initialization of the element fractions which is not easy
For simplicity, only Grackle with the equilibrium mode is shown in this documentation.
-.. image:: https://obswww.unige.ch/~lhausamm/PySWIFTsim/examples/cooling_rate_2d.png
+.. image:: https://obswww.unige.ch/lastro/projects/Clastro/PySWIFTsim/examples/cooling_rate_2d.png
Cooling Box
~~~~~~~~~~~
-.. image:: https://obswww.unige.ch/~lhausamm/PySWIFTsim/examples/cooling_box.png
+.. image:: https://obswww.unige.ch/lastro/projects/Clastro/PySWIFTsim/examples/cooling_box.png
diff --git a/docs/RST/examples/stellar.rst b/docs/RST/examples/stellar.rst
new file mode 100644
index 0000000000000000000000000000000000000000..94e1ac8ee917b03ae0ee1fd50d3886c07f312707
--- /dev/null
+++ b/docs/RST/examples/stellar.rst
@@ -0,0 +1,25 @@
+Stellar Examples
+================
+
+
+Initial Mass Function
+~~~~~~~~~~~~~~~~~~~~~
+
+This example is generated in ``examples/initial_mass_function`` with GEAR's stellar model.
+The initial mass function used in GEAR follows [Kroupa2001]_.
+
+.. image:: https://obswww.unige.ch/lastro/projects/Clastro/PySWIFTsim/examples/initial_mass_function.png
+
+
+Lifetime
+~~~~~~~~
+
+This example is generated in ``examples/lifetime`` with GEAR's stellar model.
+The lifetime in GEAR is a quadratic in metallicity and mass (see equation 3.32 in [Poirier2004]_)
+
+
+.. image:: https://obswww.unige.ch/lastro/projects/Clastro/PySWIFTsim/examples/lifetime.png
+
+
+.. [Kroupa2001] `On the variation of the Initial Mass Function <https://arxiv.org/abs/astro-ph/0009005>`_
+.. [Poirier2004] `Étude de l'évolution chimique et dynamique d'objets proto-galactiques: Application à l'évolution des galaxies spirales <https://obswww.unige.ch/~revaz/PyChem/_downloads/ff03ba21204a3f36fa4ec885abd545ae/ThesePoirier.pdf>`_
diff --git a/docs/RST/libstellar.rst b/docs/RST/libstellar.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1a4950817b25d46c1aa53ab9bb12f8b8365669e8
--- /dev/null
+++ b/docs/RST/libstellar.rst
@@ -0,0 +1,11 @@
+Libstellar
+==========
+
+.. automodule:: pyswiftsim.libstellar
+ :members:
+ :undoc-members:
+ :private-members:
+ :special-members:
+ :show-inheritance:
+ :inherited-members:
+
diff --git a/docs/RST/pyswiftsim.rst b/docs/RST/pyswiftsim.rst
index 0e77bb58ed4a0765bdd419362edebdda15f60178..d4b10ad0820d4c377a87ea1537b938d325e8b92e 100644
--- a/docs/RST/pyswiftsim.rst
+++ b/docs/RST/pyswiftsim.rst
@@ -5,7 +5,4 @@ PySWIFTsim
:members:
:undoc-members:
:private-members:
- :special-members:
- :show-inheritance:
- :inherited-members:
diff --git a/docs/index.rst b/docs/index.rst
index d11523e49bcf892c03137a516830300e753817cc..a799ccce26e3c2226423ef2d296779ad3c3bdaf2 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -14,6 +14,7 @@ The aim is to provide a python tool that benefits from HPC code and allows to di
RST/pyswiftsim.rst
RST/libcooling.rst
+ RST/libstellar.rst
RST/examples.rst
diff --git a/examples/lifetime/plot_lifetime.py b/examples/lifetime/plot_lifetime.py
index a1e1e9f2fec9e23a1d8bef49cd95361046617a9d..7696311e3cfd048d2dd000bebbbfc4389d448125 100644
--- a/examples/lifetime/plot_lifetime.py
+++ b/examples/lifetime/plot_lifetime.py
@@ -47,11 +47,17 @@ if __name__ == "__main__":
print("Computing lifetime...")
lifetime = libstellar.lifetimeFromMass(filename, mass, Z)
+ mass_from_lifetime = libstellar.massFromLifetime(filename, lifetime, Z)
+
lifetime /= 1e6
- plt.loglog(mass, lifetime)
+ plt.loglog(mass, lifetime, label="Lifetime from mass")
+ plt.loglog(mass_from_lifetime, lifetime, "--",
+ label="Mass from lifetime")
plt.xlabel("Mass [Msun]")
plt.ylabel("Lifetime [Myr]")
+ plt.legend()
+
plt.show()
diff --git a/pyswiftsim/__init__.py b/pyswiftsim/__init__.py
index 002511420fac8e158ac031bd79c41fbeea6bf6ef..7852bc713c33d950db8883ca686b71f12e998b4f 100644
--- a/pyswiftsim/__init__.py
+++ b/pyswiftsim/__init__.py
@@ -23,6 +23,10 @@ import yaml
def downloadCoolingTable():
+ """
+ Download the cooling table if it does not already exist in the current
+ repository.
+ """
url = "http://virgodb.cosma.dur.ac.uk/"
url += "swift-webstorage/CoolingTables/CloudyData_UVB=HM2012.h5"
filename = "CloudyData_UVB=HM2012.h5"
@@ -32,17 +36,81 @@ def downloadCoolingTable():
urllib.request.urlretrieve(url, filename)
-def downloadChemistryTable():
- print("Not available")
+def downloadYieldsTable():
+ """
+ Download the yields table if it does not already exist in the current
+ repository.
+ """
+ url = "https://obswww.unige.ch/"
+ url += "lastro/projects/Clastro/PySWIFTsim/"
+ filename = "chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5"
+
+ if not os.path.isfile(filename):
+ # Download the file from `url` and save it locally under `file_name`:
+ urllib.request.urlretrieve(url, filename)
def parseYamlFile(filename):
+ """
+ Parse a yaml file and return it as a dictionaryw.
+
+ Parameters
+ ==========
+
+ filename: str
+ The filename of the yaml file
+
+ Returns
+ =======
+
+ yaml: dict
+ The parameters
+
+ Examples
+ ========
+
+ >>> yaml = parseYamlFile("swift.yml")
+ >>> us = yaml["InternalUnitSystem"]
+
+ Everything in the dictionary is a string, therefore you will need to
+ convert them manually.
+
+ >>> unit_mass = float(us["UnitMass_in_cgs"])
+ """
with open(filename, "r") as stream:
stream = yaml.load(stream)
return stream
class ParameterFile:
+ """
+ This structure generates a temporary parameter file that is automatically
+ removed. If the code crashes before the destruction of the parameter file,
+ the parameter file will not be removed, but it should be taken care
+ of by the operating system.
+
+ Parameters
+ ==========
+
+ overwrite: dict
+ Allow to overwrite some default parameters or to add new parameters.
+
+ existing: str
+ Filename of an existing parameter file.
+
+ Examples
+ ========
+
+ >>> overwrite = {"InternalUnitSystem": {"UnitMass_in_cgs": 1.}}
+ >>> with ParameterFile(overwrite=overwrite) as filename:
+ >>> params = parseYamlFile(filename)
+ >>> unit_mass = params["InternalUnitSystem"]["UnitMass_in_cgs"]
+ >>> print(unit_mass)
+ 1.
+
+
+ When leaving the ``with`` environment, the file is deleted.
+ """
default_parameters = {
"InternalUnitSystem": {
"UnitMass_in_cgs": 1.989e43, # 1e10 Msun
@@ -105,12 +173,44 @@ class ParameterFile:
"constant": [-261.365, 17.073, 9.8661],
}
}
+ """
+ Dictionnary containing all the default parameters to write in the
+ parameter file.
+ """
def _write(self, f, txt):
+ """
+ Encode and then write the string into a stream.
+
+ Parameters
+ ==========
+
+ f: stream (e.g. an opened file)
+ The stream where to write the information
+
+ txt: str
+ The text to write in the steam
+
+ """
txt = txt.encode()
f.write(txt)
def _writeParameters(self, f, d, overwrite):
+ """
+ Writes the parameters file.
+
+ Parameters
+ ==========
+
+ f: stream (e.g. opened file)
+ The stream where to write the parameter file.
+
+ d: dict
+ The dictionary containing the default parameters to write.
+
+ overwrite: dict
+ The dictionary containing the parameters to overwrite.
+ """
_format = " {}: {}\n"
for sec in d.keys():
p = d[sec]
@@ -167,6 +267,19 @@ class ParameterFile:
print()
def __init__(self, overwrite=None, existing=None):
+ """
+ This function Initializes the structure, but does not create the file.
+
+ Parameters
+ ==========
+
+ overwrite: dict
+ Allow to overwrite some default parameters or to add new parameters.
+
+ existing: str
+ Filename of an existing parameter file.
+
+ """
if overwrite is not None and existing is not None:
raise Exception("Cannot overwrite default parameters and"
" use existing parameter file")
@@ -175,6 +288,15 @@ class ParameterFile:
self.existing = existing
def __enter__(self):
+ """
+ Create the parameter file.
+
+ Returns
+ =======
+
+ filename: str
+ The filename of the parameter file.
+ """
if self.existing is not None:
return self.existing
@@ -187,5 +309,8 @@ class ParameterFile:
return self.filename
def __exit__(self, *args):
+ """
+ Remove the temporary file.
+ """
if self.existing is None:
os.remove(self.filename)
diff --git a/src/libstellar.c b/src/libstellar.c
index 579ec51c5902d425f5481f1df6e4930a53099809..fcd1cb304d5207fd409eb9461337e0bac03ac60e 100644
--- a/src/libstellar.c
+++ b/src/libstellar.c
@@ -33,27 +33,67 @@ static PyMethodDef libstellar_methods[] = {
"filename: str\n"
"\t Parameter file\n"
"mass: array\n"
- "\t Mass of the stars in internal units\n"
+ "\t Mass of the stars in internal units.\n"
"\n"
"Returns\n"
"-------\n"
"imf: array\n"
- "\t The initial mass function\n"
+ "\t The initial mass function.\n"
"\n"
"Examples\n"
"--------\n"
">>> mass = np.array([1, 10])\n"
">>> filename = 'params.yml'\n"
- ">>> imf = initialMassFunction(filename, mass)\n"
+ ">>> imf = libstellar.initialMassFunction(filename, mass)\n"
},
{"lifetimeFromMass", pylifetime_from_mass, METH_VARARGS,
- "TODO\n"
+ "Compute the lifetime of a star from its mass and metallicity.\n\n"
+ "Parameters\n"
+ "----------\n\n"
+ "filename: str\n"
+ "\t Parameter file\n"
+ "mass: array\n"
+ "\t Mass of the stars in internal units.\n"
+ "metallicity: array\n"
+ "\t Metallicity of the stars.\n"
+ "\n"
+ "Returns\n"
+ "-------\n"
+ "tau: array\n"
+ "\t The lifetime of the stars.\n"
+ "\n"
+ "Examples\n"
+ "--------\n"
+ ">>> mass = np.array([1, 10])\n"
+ ">>> Z = np.array([0.02, 0.01])\n"
+ ">>> filename = 'params.yml'\n"
+ ">>> tau = libstellar.lifetimeFromMass(filename, mass, Z)\n"
},
{"massFromLifetime", pymass_from_lifetime, METH_VARARGS,
- "TODO\n"
+ "Compute the mass of a star from its lifetime and metallicity.\n\n"
+ "Parameters\n"
+ "----------\n\n"
+ "filename: str\n"
+ "\t Parameter file\n"
+ "lifetime: array\n"
+ "\t Lifetime of the stars in internal units.\n"
+ "metallicity: array\n"
+ "\t Metallicity of the stars.\n"
+ "\n"
+ "Returns\n"
+ "-------\n"
+ "mass: array\n"
+ "\t The mass of the stars.\n"
+ "\n"
+ "Examples\n"
+ "--------\n"
+ ">>> lifetime = np.array([1e7, 1e9])\n"
+ ">>> Z = np.array([0.02, 0.01])\n"
+ ">>> filename = 'params.yml'\n"
+ ">>> mass = libstellar.massFromLifetime(filename, lifetime, Z)\n"
},
diff --git a/tests/test_lifetime.py b/tests/test_lifetime.py
index 6fb9f092a99d17c0a937fec8a424ee8df2187c11..9a1816e22438b5a857a9945e571961af280cccbc 100644
--- a/tests/test_lifetime.py
+++ b/tests/test_lifetime.py
@@ -47,5 +47,11 @@ if __name__ == "__main__":
print("Computing lifetime...")
lifetime = libstellar.lifetimeFromMass(filename, mass, Z)
+ mass_from_lifetime = libstellar.massFromLifetime(filename, lifetime, Z)
+
+ print("Mass used: {}".format(mass))
print("Lifetime obtained: {}".format(lifetime))
+
+ print("Relative error on the mass from the lifetime: {}".format(
+ (mass_from_lifetime - mass) / mass))