def Chempy_gross(a):
from infall import PRIMORDIAL_INFALL
from time_integration import ABUNDANCE_MATRIX
from making_abundances import mass_fraction_to_abundances
from numpy.lib.recfunctions import append_fields
basic_solar, basic_sfr, basic_infall = initialise_stuff(a)
elements_to_trace = a.elements_to_trace
basic_primordial = PRIMORDIAL_INFALL(list(elements_to_trace),
np.copy(basic_solar.table))
basic_primordial.primordial(0)
cube = ABUNDANCE_MATRIX(np.copy(basic_sfr.t), np.copy(basic_sfr.sfr),
np.copy(basic_infall.infall),
list(elements_to_trace),
list(basic_primordial.symbols),
list(basic_primordial.fractions),
float(a.gas_at_start),
list(basic_primordial.symbols),
list(basic_primordial.fractions),
float(a.gas_reservoir_mass_factor),
float(a.outflow_feedback_fraction),
bool(a.check_processes),
float(a.starformation_efficiency),
float(a.gas_power),
float(a.sfr_factor_for_cosmic_accretion),
list(basic_primordial.symbols),
list(basic_primordial.fractions))
basic_ssp = SSP_wrap(a)
for i in range(len(basic_sfr.t) - 1):
j = len(basic_sfr.t) - i
metallicity = float(cube.cube['Z'][i])
solar_scaled_material = PRIMORDIAL_INFALL(list(elements_to_trace),
np.copy(basic_solar.table))
solar_scaled_material.solar(np.log10(metallicity / basic_solar.z))
element_fractions = list(solar_scaled_material.fractions)
for item in elements_to_trace:
element_fractions.append(
float(
np.copy(cube.cube[item][max(i - 1, 0)] /
cube.cube['gas'][max(i - 1, 0)]))
) ## gas element fractions from one time step before
time_steps = np.copy(basic_sfr.t[:j])
basic_ssp.calculate_feedback(float(metallicity),
list(elements_to_trace),
list(element_fractions),
np.copy(time_steps))
cube.advance_one_step(i + 1, np.copy(basic_ssp.table),
np.copy(basic_ssp.sn2_table),
np.copy(basic_ssp.agb_table),
np.copy(basic_ssp.sn1a_table))
abundances, elements, numbers = mass_fraction_to_abundances(
np.copy(cube.cube), np.copy(basic_solar.table))
weights = cube.cube['sfr']
abundances = append_fields(abundances, 'weights', weights)
abundances = np.array(abundances)
return cube, abundances
def Chempy(a):
'''
Chemical evolution run with the default parameters using the net yields.
INPUT:
a = ModelParameters() from parameter.py
OUTPUT:
cube = The ISM evolution class
abundances = The abundances of the ISM
'''
from .infall import PRIMORDIAL_INFALL
from .time_integration import ABUNDANCE_MATRIX
from .making_abundances import mass_fraction_to_abundances
from numpy.lib.recfunctions import append_fields
basic_solar, basic_sfr, basic_infall = initialise_stuff(a)
elements_to_trace = a.elements_to_trace
basic_primordial = PRIMORDIAL_INFALL(list(elements_to_trace),np.copy(basic_solar.table))
basic_primordial.primordial()
cube = ABUNDANCE_MATRIX(np.copy(basic_sfr.t),np.copy(basic_sfr.sfr),np.copy(basic_infall.infall),list(elements_to_trace),list(basic_primordial.symbols),list(basic_primordial.fractions),float(a.gas_at_start),list(basic_primordial.symbols),list(basic_primordial.fractions),float(a.gas_reservoir_mass_factor),float(a.outflow_feedback_fraction),bool(a.check_processes),float(a.starformation_efficiency),float(a.gas_power), float(a.sfr_factor_for_cosmic_accretion), list(basic_primordial.symbols), list(basic_primordial.fractions))
basic_ssp = SSP_wrap(a)
for i in range(len(basic_sfr.t)-1):
j = len(basic_sfr.t)-i
element_fractions = []
for item in elements_to_trace:
element_fractions.append(float(np.copy(cube.cube[item][max(i-1,0)]/cube.cube['gas'][max(i-1,0)])))## gas element fractions from one time step before
metallicity = float(cube.cube['Z'][i])
time_steps = np.copy(basic_sfr.t[:j])
basic_ssp.calculate_feedback(float(metallicity), list(elements_to_trace), list(element_fractions), np.copy(time_steps))
cube.advance_one_step(i+1,np.copy(basic_ssp.table),np.copy(basic_ssp.sn2_table),np.copy(basic_ssp.agb_table),np.copy(basic_ssp.sn1a_table),np.copy(basic_ssp.bh_table))
if cube.cube['gas'][i] < 0:
print(i, basic_sfr.t[i])
print('gas became negative. returning -inf')
return -np.inf, [0]
if cube.gas_reservoir['gas'][i] < 0:
print('gas_reservoir became negative. returning -inf')
return -np.inf, [0]
abundances,elements,numbers = mass_fraction_to_abundances(np.copy(cube.cube),np.copy(basic_solar.table))
weights = cube.cube['sfr']
abundances = append_fields(abundances,'weights',weights)
abundances = append_fields(abundances,'time', cube.cube['time'])
abundances = np.array(abundances)
return cube, abundances
def Chempy_all_times(a):
'''
Chemical evolution run with the default parameters using the net yields.
INPUT:
a = ModelParameters() from parameter.py
OUTPUT:
cube = The ISM evolution class
abundances = The abundances of the ISM
'''
from .infall import PRIMORDIAL_INFALL
from .time_integration import ABUNDANCE_MATRIX
from .making_abundances import mass_fraction_to_abundances
from numpy.lib.recfunctions import append_fields
basic_solar, basic_sfr, basic_infall = initialise_stuff(a)
elements_to_trace = a.elements_to_trace
basic_primordial = PRIMORDIAL_INFALL(list(elements_to_trace),
np.copy(basic_solar.table))
basic_primordial.primordial()
gas_reservoir_mass_factor = a.gas_reservoir_mass_factor / a.shortened_sfr_rescaling
gas_at_start = a.gas_at_start / a.shortened_sfr_rescaling # unlikely to be needed unless a.gas_at_start is non-zero
cube = ABUNDANCE_MATRIX(np.copy(basic_sfr.t), np.copy(basic_sfr.sfr),
np.copy(basic_infall.infall),
list(elements_to_trace),
list(basic_primordial.symbols),
list(basic_primordial.fractions),
float(gas_at_start),
list(basic_primordial.symbols),
list(basic_primordial.fractions),
float(gas_reservoir_mass_factor),
float(a.outflow_feedback_fraction),
bool(a.check_processes),
float(a.starformation_efficiency),
float(a.gas_power),
float(a.sfr_factor_for_cosmic_accretion),
list(basic_primordial.symbols),
list(basic_primordial.fractions))
basic_ssp = SSP_wrap(a)
for i in range(len(basic_sfr.t) - 1):
j = len(basic_sfr.t) - i
element_fractions = []
for item in elements_to_trace:
element_fractions.append(
float(
np.copy(cube.cube[item][max(i - 1, 0)] /
cube.cube['gas'][max(i - 1, 0)]))
) ## gas element fractions from one time step before
if element_fractions[-1] < 0:
print('-ve Error')
#raise Exception('-ve Error')
metallicity = float(cube.cube['Z'][i])
#print(metallicity)
time_steps = np.copy(basic_sfr.t[:j])
basic_ssp.calculate_feedback(float(metallicity),
list(elements_to_trace),
list(element_fractions),
np.copy(time_steps))
cube.advance_one_step(i + 1, np.copy(basic_ssp.table),
np.copy(basic_ssp.sn2_table),
np.copy(basic_ssp.agb_table),
np.copy(basic_ssp.sn1a_table),
np.copy(basic_ssp.bh_table))
for item in elements_to_trace:
if cube.cube[item][i] < 0:
print(i, item)
print('element %s became negative. returning -inf' % item)
return -np.inf, [0]
if cube.cube['gas'][i] < 0:
print(i, basic_sfr.t[i])
print('gas became negative. returning -inf')
return -np.inf, [0]
if cube.gas_reservoir['gas'][i] < 0:
print('gas_reservoir became negative. returning -inf')
return -np.inf, [0]
abundances, elements, numbers = mass_fraction_to_abundances(
np.copy(cube.cube), np.copy(basic_solar.table))
weights = cube.cube['sfr']
abundances = append_fields(abundances, 'weights', weights)
abundances = append_fields(abundances, 'time', cube.cube['time'])
abundances = np.array(abundances)
for element in elements:
if element != 'Fe':
filt = np.where(np.logical_not(np.isfinite(abundances['Fe'])))
abundances[element][filt] = np.inf
filt2 = np.where(np.isfinite(abundances['Fe']))
abundances[element][filt2] -= abundances['Fe'][filt2]
#TEST output
#print('Chempy output')
#print(abundances[:][-1])
return cube, abundances