Commit 52223171 authored by lhausamm's avatar lhausamm
Browse files

Test reproduce grackle graph (fig. 8 in Grackle: a Chemistry and Cooling Library for Astrophysics)

parent 39ee16db
......@@ -11,14 +11,22 @@ cdef extern from "parser.h":
cdef extern from "units.h":
struct unit_system:
double UnitMass_in_cgs;
double UnitLength_in_cgs;
double UnitTime_in_cgs;
double UnitCurrent_in_cgs;
double UnitTemperature_in_cgs;
void units_init(unit_system* us, const swift_params* params,
const char* category)
void units_print_backend(const unit_system *us)
cdef extern from "adiabatic_index.h":
float hydro_gamma
cdef extern from "physical_constants.h":
struct phys_const:
double const_boltzmann_k
double const_proton_mass
void phys_const_init(unit_system* us, phys_const* internal_const);
......@@ -9,6 +9,7 @@ from pyswiftsim.part_def cimport hydro_space
from pyswiftsim cimport equation_of_state
from pyswiftsim.equation_of_state cimport gas_entropy_from_internal_energy
from pyswiftsim.equation_of_state cimport gas_soundspeed_from_internal_energy
from libc.stdlib cimport malloc, free
from libc.math cimport M_PI
......@@ -17,6 +18,9 @@ import numpy as np
ctypedef np.float_t DTYPE_t
_hydro_gamma = hydro_gamma
def read_params(str filename):
# transform python to C
tmp = filename.encode(u"ascii")
......@@ -27,18 +31,18 @@ def read_params(str filename):
# init params
cdef swift_params *params = <swift_params*> malloc(sizeof(swift_params));
parser_read_file(cfilename, params)
return pointer_create(
def init_units(Pointer p_params):
# deal with inputs
pointer_check(p_params, pointer.swift_params)
pointer_check(p_params, pointer.type_swift_params)
cdef swift_params *params = <swift_params*> p_params._data
# init units
......@@ -46,7 +50,7 @@ def init_units(Pointer p_params):
cdef const char* category = "InternalUnitSystem"
units_init(units, params, category)
# init constants
cdef phys_const *constants = <phys_const*> malloc(sizeof(phys_const));
......@@ -54,33 +58,33 @@ def init_units(Pointer p_params):
# return
d = {}
d["constants"] = pointer_create(constants, pointer.phys_const)
d["units"] = pointer_create(units, pointer.unit_system)
d["constants"] = pointer_create(constants, pointer.type_phys_const)
d["units"] = pointer_create(units, pointer.type_unit_system)
return d
def pycooling_init(Pointer p_params,
Pointer p_units,
Pointer p_constants):
# deal with inputs
pointer_check(p_params, pointer.swift_params)
pointer_check(p_params, pointer.type_swift_params)
cdef swift_params *params = <swift_params*> p_params._data
pointer_check(p_units, pointer.unit_system)
pointer_check(p_units, pointer.type_unit_system)
cdef unit_system *units = <unit_system*> p_units._data
pointer_check(p_constants, pointer.phys_const)
pointer_check(p_constants, pointer.type_phys_const)
cdef phys_const *constants = <phys_const*> p_constants._data
# init cooling
cdef cooling_function_data *cooling = <cooling_function_data*> malloc(sizeof(cooling_function_data));
cooling_init(params, units, constants, cooling)
# print results
# store and return results
return pointer_create(cooling, pointer.cooling_function_data)
return pointer_create(cooling, pointer.type_cooling_function_data)
def pycooling_rate(Pointer p_units,
......@@ -97,15 +101,15 @@ def pycooling_rate(Pointer p_units,
# deal with inputs
# p_units
pointer_check(p_units, pointer.unit_system)
pointer_check(p_units, pointer.type_unit_system)
cdef unit_system *units = <unit_system*> p_units._data
# p_cooling
pointer_check(p_cooling, pointer.cooling_function_data)
pointer_check(p_cooling, pointer.type_cooling_function_data)
cdef cooling_function_data *cooling = <cooling_function_data*> p_cooling._data
# p_constants
pointer_check(p_constants, pointer.phys_const)
pointer_check(p_constants, pointer.type_phys_const)
cdef phys_const *constants = <phys_const*> p_constants._data
# initialize particles
......@@ -133,3 +137,19 @@ def pycooling_rate(Pointer p_units,
return rate
def soundspeed_from_internal_energy(np.ndarray [DTYPE_t, ndim=1] rho,
np.ndarray [DTYPE_t, ndim=1] u):
if rho.shape[0] != u.shape[0]:
raise Exception("Rho and u should be of the same size!")
cdef int N = rho.shape[0]
cdef np.ndarray[DTYPE_t, ndim=1] cs = np.empty_like(rho)
for i in range(N):
cs[i] = gas_soundspeed_from_internal_energy(rho[i], u[i])
return cs
cdef extern from "equation_of_state.h":
cdef float gas_entropy_from_internal_energy(float density, float u)
cdef float gas_soundspeed_from_entropy(float density, float entropy)
cdef float gas_soundspeed_from_internal_energy(float density, float u)
......@@ -3,11 +3,11 @@ cdef extern from "clocks.h":
cdef enum pointer_type:
cdef const char **pointer_name
from libc.stdlib cimport free
from cooling cimport unit_system, phys_const
clocks_set_cpufreq(0); # estimate automatically cpufreq and init time
......@@ -27,6 +28,15 @@ cdef class Pointer:
def __del__(self):
def __getattr__(self, value):
data_type = self._data_type
if data_type == type_unit_system:
return pointer_unit_system_getattr(self, value)
if data_type == type_phys_const:
return pointer_phys_const_getattr(self, value)
raise Exception("Data type not implemented")
# method to call when creating a pointer
cdef pointer_create(void *params, int data_type):
......@@ -43,3 +53,30 @@ cdef pointer_check(Pointer ptr, int data_type):
raise Exception("Value not set for pointer type %s" % data_name)
cdef pointer_unit_system_getattr(Pointer ptr, str attr):
pointer_check(ptr, type_unit_system)
cdef unit_system us = (<unit_system*> ptr._data)[0]
if attr == "UnitMass_in_cgs":
return us.UnitMass_in_cgs
elif attr == "UnitLength_in_cgs":
return us.UnitLength_in_cgs
elif attr == "UnitTime_in_cgs":
return us.UnitTime_in_cgs
elif attr == "UnitCurrent_in_cgs":
return us.UnitCurrent_in_cgs
elif attr == "UnitTemperature_in_cgs":
return us.UnitTemperature_in_cgs
raise Exception("unit_system does not contain %s" % attr)
cdef pointer_phys_const_getattr(Pointer ptr, str attr):
pointer_check(ptr, type_phys_const)
cdef phys_const consts = (<phys_const*> ptr._data)[0]
if attr == "const_boltzmann_k":
return consts.const_boltzmann_k
if attr == "const_proton_mass":
return consts.const_proton_mass
raise Exception("phys_const does not contain %s" % attr)
#!/usr/bin/env python3
from pyswiftsim import pointer
from pyswiftsim import cooling
import astropy.units
import matplotlib.pyplot as plt
import numpy as np
# number of particles
N = 100
# params file
params = "/home/loikki/swift_test/cooling_box/coolingBox.yml"
# read params
params = cooling.read_params(params)
# init units
d = cooling.init_units(params)
units = d["units"]
consts = d["constants"]
# init cooling
cooling_data = cooling.pycooling_init(params, units, consts)
# Init variables
rho = np.logspace(-6, 4, N).astype(np.float) # in cm-3
rho *= consts.const_proton_mass * units.UnitLength_in_cgs**3
T = np.logspace(1,9, N).astype(np.float) # in K
rho, T = np.meshgrid(rho, T)
shape = rho.shape
rho = rho.reshape(
T = T.reshape(
# u = k_b T / (gamma - 1) mu m_p
mu = 2
u = consts.const_boltzmann_k * T / ((cooling._hydro_gamma - 1.) * mu * consts.const_proton_mass)
# compute cooling
rate = cooling.pycooling_rate(units, cooling_data, consts, rho, u)
cs = cooling.soundspeed_from_internal_energy(rho, u)
rho = rho.reshape(shape) / (units.UnitLength_in_cgs**3 * consts.const_proton_mass)
T = T.reshape(shape)
# du / dt [e / s] = [kg m2 / s3]
rate = rate.reshape(shape) * units.UnitMass_in_cgs * units.UnitLength_in_cgs**2 / units.UnitTime_in_cgs**3
cs = cs.reshape(shape) * units.UnitLength_in_cgs / units.UnitTime_in_cgs
L_cool = -rate * cs /"cm")
plt.title("Cooling Length")
plt.contourf(rho, T, np.log(L_cool))
plt.xlabel("Density [$cm^{-3}$]")
plt.ylabel("Temperature [K]")
ax = plt.gca()
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