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Commit c5d0d2ba authored by Loic Hausammann's avatar Loic Hausammann
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Update code with changes in swift

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1 merge request!10Update SWIFT calls
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examples/cooling_box/plot_cooling.py
+ 1
− 1
View file @ c5d0d2ba
......@@ -131,7 +131,7 @@ if __name__ == "__main__":
overwrite = {
"GrackleCooling": {
"WithMetalCooling": with_metals,
"with_metal_cooling": with_metals,
}
}
with pyswiftsim.ParameterFile(overwrite) as filename:
......
examples/cooling_rate/plot_cooling.py
+ 111
− 52
View file @ c5d0d2ba
......@@ -20,6 +20,8 @@
from pyswiftsim.libcooling import coolingRate
import pyswiftsim
import matplotlib
from copy import deepcopy
import numpy as np
import matplotlib.pyplot as plt
......@@ -27,8 +29,20 @@ from astropy import units, constants
from time import strftime, gmtime
import sys
SMALL_SIZE = 13
MEDIUM_SIZE = 15
BIGGER_SIZE = 18
plt.rc('font', size=SMALL_SIZE) # controls default text sizes
plt.rc('axes', titlesize=SMALL_SIZE) # fontsize of the axes title
plt.rc('axes', labelsize=MEDIUM_SIZE) # fontsize of the x and y labels
plt.rc('xtick', labelsize=SMALL_SIZE) # fontsize of the tick labels
plt.rc('ytick', labelsize=SMALL_SIZE) # fontsize of the tick labels
plt.rc('legend', fontsize=SMALL_SIZE) # legend fontsize
plt.rc('figure', titlesize=BIGGER_SIZE) # fontsize of the figure title
plt.rc('text', usetex=True)
pyswiftsim.downloadCoolingTable()
# PARAMETERS
......@@ -40,6 +54,12 @@ with_cosmo = False
# include metals?
with_metals = 1
metallicity = 0.02041
# cooling table
cooling_tables = [
"./CloudyData_UVB=HM2012.h5",
]
# hydrogen mass fraction
h_mass_frac = 0.76
......@@ -50,6 +70,7 @@ if N_rho == 1:
density = np.array([1.])
else:
density = np.logspace(-6, 4, N_rho)
plot_cooling_length = False
# temperature in K
N_T = 1000
......@@ -113,7 +134,7 @@ def generate_initial_condition(us):
return d
def plot_solution(rate, data, us):
def plot_solution(rates, data, us):
print("Plotting solution")
energy = data["energy"]
rho = data["density"]
......@@ -131,55 +152,82 @@ def plot_solution(rate, data, us):
energy *= u_v**2
rate *= u_v**2 / u_t
rates = [rate * u_v**2 / u_t for rate in rates]
# lambda cooling
lam = rate * rho
lambdas = [rate * rho for rate in rates]
# do plot
if N_rho == 1:
# plot Lambda vs T
plt.figure()
plt.loglog(T, np.abs(lam),
label="SWIFT")
for i, lam in enumerate(lambdas):
plt.loglog(T, np.abs(lam),
label="Table %i" % i)
plt.xlabel("Temperature [K]")
plt.ylabel("$\\Lambda$ [erg s$^{-1}$ cm$^{3}$]")
plt.legend()
else:
m_p = constants.m_p.to("g") / units.g
rho /= m_p
shape = [N_rho, N_T]
cooling_time = energy / rate
cooling_length = np.sqrt(gamma * (gamma-1.) * energy) * cooling_time
cooling_length = np.log10(np.abs(cooling_length) / units.kpc.to('cm'))
# reshape
rho = rho.reshape(shape)
T = T.reshape(shape)
energy = energy.reshape(shape)
cooling_length = cooling_length.reshape(shape)
_min = -7
_max = 7
N_levels = 100
levels = np.linspace(_min, _max, N_levels)
plt.figure()
plt.contourf(rho, T, cooling_length, levels,
cmap=plt.get_cmap(colormap))
plt.xlabel("Density [atom/cm3]")
plt.ylabel("Temperature [K]")
ax = plt.gca()
ax.set_xscale("log")
ax.set_yscale("log")
cbar = plt.colorbar()
tc = np.arange(_min, _max, 1.5)
cbar.set_ticks(tc)
cbar.set_ticklabels(tc)
cbar.ax.set_ylabel("Log( Cooling Length / kpc )")
r = []
for rate in rates:
shape = [N_rho, N_T]
energy = np.reshape(energy, shape)
rate = np.reshape(rate, shape)
cooling_time = energy / rate
cooling_length = np.sqrt(gamma * (gamma-1.) * energy)
cooling_length *= cooling_time
cooling_length = np.log10(
np.abs(cooling_length) / units.kpc.to('cm'))
# reshape
rho = rho.reshape(shape)
T = T.reshape(shape)
energy = energy.reshape(shape)
cooling_length = cooling_length.reshape(shape)
levels = 500
if plot_cooling_length:
_min = -7
_max = 7
levels = np.linspace(_min, _max, levels)
z = cooling_length
else:
z = np.log10(np.abs(rate))
plt.figure()
r.append(rate)
plt.contourf(np.log10(rho), np.log10(T), z,
levels,
cmap=plt.get_cmap(colormap))
plt.xlabel("Log( Density [atom/cm3] )")
plt.ylabel("Log( Temperature [K] )")
cbar = plt.colorbar()
if plot_cooling_length:
tc = np.arange(_min, _max, 1.5)
cbar.set_ticks(tc)
cbar.set_ticklabels(tc)
cbar.ax.set_ylabel("Log( Cooling Length [kpc] )")
else:
cbar.ax.set_ylabel("Log( Rate [s / erg] )")
if len(r) == 2:
plt.figure()
plt.contourf(rho, T, np.log10(np.abs((r[1] - r[0]) / r[1])), 500,
cmap=plt.get_cmap(colormap))
plt.xlabel("Density [atom/cm3]")
plt.ylabel("Temperature [K]")
ax = plt.gca()
ax.set_xscale("log")
ax.set_yscale("log")
cbar = plt.colorbar()
date = strftime("%d %b %Y", gmtime())
plt.title("Date: {}".format(date))
......@@ -188,24 +236,35 @@ def plot_solution(rate, data, us):
if __name__ == "__main__":
overwrite = {
"GrackleCooling": {
"WithMetalCooling": with_metals,
rates = []
for cooling_table in cooling_tables:
overwrite = {
"GrackleCooling": {
"with_metal_cooling": with_metals,
"redshift": 0,
"cloudy_table": cooling_table,
},
"GEARChemistry": {
"initial_metallicity": metallicity,
},
}
}
with pyswiftsim.ParameterFile(overwrite) as filename:
parser = pyswiftsim.parseYamlFile(filename)
us = parser["InternalUnitSystem"]
with pyswiftsim.ParameterFile(overwrite) as filename:
parser = pyswiftsim.parseYamlFile(filename)
us = parser["InternalUnitSystem"]
d = generate_initial_condition(us)
d = generate_initial_condition(us)
# du / dt
print("Computing cooling...")
# du / dt
print("Computing cooling...")
rate = coolingRate(filename,
d["density"].astype(np.float32),
d["energy"].astype(np.float32),
with_cosmo, d["time_step"])
rate = coolingRate(filename,
d["density"].astype(np.float32),
d["energy"].astype(np.float32),
with_cosmo, d["time_step"])
rates.append(rate)
plot_solution(rate, d, us)
plot_solution(rates, d, us)
pyswiftsim/__init__.py
+ 16
− 15
View file @ c5d0d2ba
......@@ -159,26 +159,27 @@ class ParameterFile:
},
"GrackleCooling": {
"CloudyTable": "CloudyData_UVB=HM2012.h5",
"WithUVbackground": 1,
"Redshift": 0,
"WithMetalCooling": 1,
"ProvideVolumetricHeatingRates": 0,
"ProvideSpecificHeatingRates": 0,
"SelfShieldingMethod": 0,
"ConvergenceLimit": 1e-2,
"MaxSteps": 20000,
"Omega": 0.8,
"ThermalTime_Myr": 5,
"cloudy_table": "CloudyData_UVB=HM2012.h5",
"with_UV_background": 1,
"redshift": 0,
"with_metal_cooling": 1,
"provide_volumetric_heating_rates": 0,
"provide_specific_heating_rates": 0,
"self_shielding_method": 0,
"convergence_limit": 1e-2,
"max_steps": 20000,
"omega": 0.8,
"thermal_time_myr": 5,
},
"GearChemistry": {
"InitialMetallicity": 0.01295,
"GEARChemistry": {
"initial_metallicity": 0.01295,
},
"GEARFeedback": {
"SupernovaeEnergy_erg": 1e51,
"YieldsTable": "chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5",
"supernovae_energy_erg": 1e51,
"yields_table": "chemistry-AGB+OMgSFeZnSrYBaEu-16072013.h5",
"discrete_yields": 0
},
}
"""
......
scripts/pyswift_lifetime
+ 3
− 3
View file @ c5d0d2ba
......@@ -92,9 +92,9 @@ if __name__ == "__main__":
# transform into internal units
units = parser["InternalUnitSystem"]
unit_mass = units["UnitMass_in_cgs"]
unit_vel = units["UnitVelocity_in_cgs"]
unit_length = units["UnitLength_in_cgs"]
unit_mass = float(units["UnitMass_in_cgs"])
unit_vel = float(units["UnitVelocity_in_cgs"])
unit_length = float(units["UnitLength_in_cgs"])
unit_time = unit_length / unit_vel
mass *= solMass_in_cgs / unit_mass
......
src/cooling_wrapper.c
+ 11
− 13
View file @ c5d0d2ba
......@@ -19,11 +19,6 @@
#include "cooling_wrapper.h"
#include "pyswiftsim_tools.h"
/* TODO Remove this */
struct cooling_function_data cooling;
int initialized;
/**
* @brief Set the cooling element fractions
*
......@@ -79,7 +74,6 @@ void pycooling_set_fractions(struct xpart *xp, PyArrayObject* frac, const int id
*/
PyObject* pycooling_rate(PyObject* self, PyObject* args) {
import_array();
char *filename;
......@@ -125,7 +119,6 @@ PyObject* pycooling_rate(PyObject* self, PyObject* args) {
struct chemistry_global_data chemistry;
chemistry_init_backend(&params, &us, &pconst, &chemistry);
/* Init entropy floor */
struct entropy_floor_properties floor_props;
entropy_floor_init(&floor_props, &pconst, &us,
......@@ -135,7 +128,7 @@ PyObject* pycooling_rate(PyObject* self, PyObject* args) {
struct xpart xp;
hydro_first_init_part(&p, &xp);
/* return object */
PyArrayObject *rate = (PyArrayObject *)PyArray_SimpleNew(PyArray_NDIM(energy), PyArray_DIMS(energy), NPY_FLOAT);
......@@ -150,16 +143,20 @@ PyObject* pycooling_rate(PyObject* self, PyObject* args) {
chemistry_first_init_part(&pconst, &us, &cosmo, &chemistry, &p, &xp);
if (fractions != NULL)
pycooling_set_fractions(&xp, fractions, i);
pycooling_set_fractions(&xp, fractions, i);
else {
/* Need to set the mass in order to estimate the element fractions */
hydro_set_mass(&p, p.rho);
p.h = 1;
/* Need to set the mass in order to estimate the element fractions */
hydro_set_mass(&p, p.rho);
p.h = 1;
cooling_first_init_part(&pconst, &us, &cosmo, &cooling, &p, &xp);
cooling_first_init_part(&pconst, &us, &hydro_props, &cosmo, &cooling, &p, &xp);
}
hydro_set_physical_internal_energy_dt(&p, &cosmo, 0);
for(int j = 0; j < GEAR_CHEMISTRY_ELEMENT_COUNT; j++) {
p.chemistry_data.smoothed_metal_mass_fraction[j] = p.chemistry_data.metal_mass_fraction[j];
}
/* compute cooling rate */
cooling_cool_part(&pconst, &us, &cosmo, &hydro_props,
......@@ -171,6 +168,7 @@ PyObject* pycooling_rate(PyObject* self, PyObject* args) {
/* Cleanup */
cosmology_clean(&cosmo);
cooling_clean(&cooling);
return (PyObject *) rate;
......
src/cooling_wrapper.h
+ 4
− 18
View file @ c5d0d2ba
......@@ -21,26 +21,12 @@
#include "pyswiftsim_includes.h"
/* A few global variables */
extern struct cooling_function_data cooling;
extern int initialized;
PyObject* pycooling_rate(PyObject* self, PyObject* args);
#define PYSWIFTSIM_INIT_COOLING() \
\
/* init cooling */ \
if (initialized == 0) { \
/* struct cooling_function_data cooling; */ \
cooling_init_backend(&params, &us, &pconst, &cooling); \
initialized = 1; \
} \
else if (initialized == 1) { \
message("WARNING: not reinitializing the cooling, need to be fixed"); \
initialized = 2; \
} \
\
#define PYSWIFTSIM_INIT_COOLING() \
struct cooling_function_data cooling; \
cooling_init_backend(&params, &us, &pconst, &hydro_props, \
&cooling); \
#endif // __PYSWIFTSIM_COOLING_H__
......
src/stellar_evolution_wrapper.c
+ 13
− 10
View file @ c5d0d2ba
......@@ -72,6 +72,9 @@ PyObject* pyinitial_mass_function(PyObject* self, PyObject* args) {
}
*imf_i = initial_mass_function_get_imf(&fp.stellar_model.imf, m);
/* change from internal units to solar mass */
*imf_i /= pconst.const_solar_mass;
}
return (PyObject *) imf;
......@@ -280,7 +283,7 @@ PyObject* pysupernovae_ia_rate(PyObject* self, PyObject* args) {
m2 = pow(10, m2);
/* Need to reverse 1 and 2 due to the lifetime being a decreasing function */
*r = supernovae_ia_get_number(&fp.stellar_model.snia, m2, m1) / (t2 - t1);
*r = supernovae_ia_get_number_per_unit_mass(&fp.stellar_model.snia, m2, m1) / (t2 - t1);
/* change units 1 / (solMass Myr) -> internal units */
*r /= pconst.const_solar_mass * pconst.const_year * 1e6;
......@@ -360,7 +363,7 @@ PyObject* pysupernovae_ii_rate(PyObject* self, PyObject* args) {
m2 = pow(10, m2);
/* Need to reverse 1 and 2 due to the lifetime being a decreasing function */
*r = supernovae_ii_get_number(&fp.stellar_model.snii, m2, m1) / (t2 - t1);
*r = supernovae_ii_get_number_per_unit_mass(&fp.stellar_model.snii, m2, m1) / (t2 - t1);
/* change units 1 / (solMass Myr) -> internal units */
*r /= pconst.const_solar_mass * pconst.const_year * 1e6;
......@@ -421,11 +424,11 @@ PyObject* pysupernovae_ii_yields(PyObject* self, PyObject* args) {
/* return object */
const int ndims = 2;
npy_intp dims[2] = {N, CHEMISTRY_ELEMENT_COUNT};
npy_intp dims[2] = {N, GEAR_CHEMISTRY_ELEMENT_COUNT};
PyArrayObject *yields_out = (PyArrayObject *)PyArray_SimpleNew(ndims, dims, NPY_FLOAT);
for(size_t i = 0; i < N; i++) {
float yields[CHEMISTRY_ELEMENT_COUNT] = {0.};
float yields[GEAR_CHEMISTRY_ELEMENT_COUNT] = {0.};
const float m1 = *(float*) PyArray_GETPTR1(mass1, i) / pconst.const_solar_mass;
const float log_m1 = log10(m1);
const float m2 = *(float*) PyArray_GETPTR1(mass2, i) / pconst.const_solar_mass;
......@@ -434,7 +437,7 @@ PyObject* pysupernovae_ii_yields(PyObject* self, PyObject* args) {
/* Compute the yields */
supernovae_ii_get_yields(&fp.stellar_model.snii, log_m1, log_m2, yields);
for(int j = 0; j < CHEMISTRY_ELEMENT_COUNT; j++) {
for(int j = 0; j < GEAR_CHEMISTRY_ELEMENT_COUNT; j++) {
float *y = (float*) PyArray_GETPTR2(yields_out, i, j);
*y = yields[j];
}
......@@ -608,12 +611,12 @@ PyObject* pysupernovae_ia_yields(PyObject* self, PyObject* args) {
/* return object */
const int ndims = 1;
npy_intp dims[1] = {CHEMISTRY_ELEMENT_COUNT};
npy_intp dims[1] = {GEAR_CHEMISTRY_ELEMENT_COUNT};
PyArrayObject *yields_out = (PyArrayObject *)PyArray_SimpleNew(ndims, dims, NPY_FLOAT);
const float *yields = supernovae_ia_get_yields(&fp.stellar_model.snia);
for(size_t i = 0; i < CHEMISTRY_ELEMENT_COUNT; i++) {
for(size_t i = 0; i < GEAR_CHEMISTRY_ELEMENT_COUNT; i++) {
float *y = (float*) PyArray_GETPTR1(yields_out, i);
*y = yields[i] / fp.stellar_model.snia.mass_white_dwarf;
......@@ -658,7 +661,7 @@ PyObject* pysupernovae_ia_mass_ejected(PyObject* self, PyObject* args) {
float *y = (float*) PyArray_GETPTR1(mass_ejected, 0);
*y = supernovae_ia_get_ejected_mass_fraction_processed(&fp.stellar_model.snia) / fp.stellar_model.snia.mass_white_dwarf;
*y = supernovae_ia_get_ejected_mass_processed(&fp.stellar_model.snia) / fp.stellar_model.snia.mass_white_dwarf;
return (PyObject *) mass_ejected;
......@@ -693,9 +696,9 @@ PyObject* pystellar_get_elements(PyObject* self, PyObject* args) {
feedback_props_init(&fp, &pconst, &us, &params, &hydro_props, &cosmo);
/* Save the variables */
PyObject *t = PyList_New(CHEMISTRY_ELEMENT_COUNT);
PyObject *t = PyList_New(GEAR_CHEMISTRY_ELEMENT_COUNT);
for(int i = 0; i < CHEMISTRY_ELEMENT_COUNT; i++) {
for(int i = 0; i < GEAR_CHEMISTRY_ELEMENT_COUNT; i++) {
const char *name = stellar_evolution_get_element_name(&fp.stellar_model, i);
PyObject *string = PyUnicode_FromString(name);
int test = PyList_SetItem(t, i, string);
......
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