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read_mist_models.py
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read_mist_models.py
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from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
class ISO:
"""
Reads in MIST isochrone files.
"""
def __init__(self, filename, verbose=True):
"""
Args:
filename: the name of .iso file.
Usage:
>> iso = read_mist_models.ISO('MIST_v1.0_feh_p0.00_afe_p0.0_vvcrit0.4.iso')
>> age_ind = iso.age_index(8.0)
>> logTeff = iso.isos[age_ind]['log_Teff']
>> logL = iso.isos[age_ind]['log_L']
>> plt.plot(logTeff, logL) #plot the HR diagram for logage = 8.0
Attributes:
version Dictionary containing the MIST and MESA version numbers.
abun Dictionary containing Yinit, Zinit, [Fe/H], and [a/Fe] values.
rot Rotation in units of surface v/v_crit.
ages List of ages.
num_ages Number of isochrones.
hdr_list List of column headers.
isos Data.
"""
self.filename = filename
if verbose:
print('Reading in: ' + self.filename)
self.version, self.abun, self.rot, self.ages, self.num_ages, self.hdr_list, self.isos = self.read_iso_file()
def read_iso_file(self):
"""
Reads in the isochrone file.
Args:
filename: the name of .iso file.
"""
#open file and read it in
with open(self.filename) as f:
content = [line.split() for line in f]
version = {'MIST': content[0][-1], 'MESA': content[1][-1]}
abun = {content[3][i]:float(content[4][i]) for i in range(1,5)}
rot = float(content[4][-1])
num_ages = int(content[6][-1])
#read one block for each isochrone
iso_set = []
ages = []
counter = 0
data = content[8:]
for i_age in range(num_ages):
#grab info for each isochrone
num_eeps = int(data[counter][-2])
num_cols = int(data[counter][-1])
hdr_list = data[counter+2][1:]
formats = tuple([np.int32]+[np.float64 for i in range(num_cols-1)])
iso = np.zeros((num_eeps),{'names':tuple(hdr_list),'formats':tuple(formats)})
#read through EEPs for each isochrone
for eep in range(num_eeps):
iso_chunk = data[3+counter+eep]
iso[eep]=tuple(iso_chunk)
iso_set.append(iso)
ages.append(iso[0][1])
counter+= 3+num_eeps+2
return version, abun, rot, ages, num_ages, hdr_list, iso_set
def age_index(self, age):
"""
Returns the index for the user-specified age.
Args:
age: the age of the isochrone.
"""
diff_arr = abs(np.array(self.ages) - age)
age_index = np.where(diff_arr == min(diff_arr))[0][0]
if ((age > max(self.ages)) | (age < min(self.ages))):
print('The requested age is outside the range. Try between ' + str(min(self.ages)) + ' and ' + str(max(self.ages)))
return age_index
class ISOCMD:
"""
Reads in MIST CMD files.
"""
def __init__(self, filename, verbose=True):
"""
Args:
filename: the name of .iso.cmd file.
Usage:
>> isocmd = read_mist_models.ISOCMD('MIST_v1.0_feh_p0.00_afe_p0.0_vvcrit0.4.iso.cmd')
>> age_ind = isocmd.age_index(7.0)
>> B = isocmd.isocmds[age_ind]['Bessell_B']
>> V = isocmd.isocmds[age_ind]['Bessell_V']
>> plt.plot(B-V, V) #plot the CMD for logage = 7.0
Attributes:
version Dictionary containing the MIST and MESA version numbers.
photo_sys Photometric system.
abun Dictionary containing Yinit, Zinit, [Fe/H], and [a/Fe] values.
Av_extinction Av for CCM89 extinction.
rot Rotation in units of surface v/v_crit.
ages List of ages.
num_ages Number of ages.
hdr_list List of column headers.
isocmds Data.
"""
self.filename = filename
if verbose:
print('Reading in: ' + self.filename)
self.version, self.photo_sys, self.abun, self.Av_extinction, self.rot, self.ages, self.num_ages, self.hdr_list, self.isocmds = self.read_isocmd_file()
def read_isocmd_file(self):
"""
Reads in the cmd file.
Args:
filename: the name of .iso.cmd file.
"""
#open file and read it in
with open(self.filename) as f:
content = [line.split() for line in f]
version = {'MIST': content[0][-1], 'MESA': content[1][-1]}
photo_sys = ' '.join(content[2][4:])
abun = {content[4][i]:float(content[5][i]) for i in range(1,5)}
rot = float(content[5][-1])
num_ages = int(content[7][-1])
Av_extinction = float(content[8][-1])
#read one block for each isochrone
isocmd_set = []
ages = []
counter = 0
data = content[10:]
for i_age in range(num_ages):
#grab info for each isochrone
num_eeps = int(data[counter][-2])
num_cols = int(data[counter][-1])
hdr_list = data[counter+2][1:]
formats = tuple([np.int32]+[np.float64 for i in range(num_cols-1)])
isocmd = np.zeros((num_eeps),{'names':tuple(hdr_list),'formats':tuple(formats)})
#read through EEPs for each isochrone
for eep in range(num_eeps):
isocmd_chunk = data[3+counter+eep]
isocmd[eep]=tuple(isocmd_chunk)
isocmd_set.append(isocmd)
ages.append(isocmd[0][1])
counter+= 3+num_eeps+2
return version, photo_sys, abun, Av_extinction, rot, ages, num_ages, hdr_list, isocmd_set
def age_index(self, age):
"""
Returns the index for the user-specified age.
Args:
age: the age of the isochrone.
"""
diff_arr = abs(np.array(self.ages) - age)
age_index = np.where(diff_arr == min(diff_arr))[0][0]
if ((age > max(self.ages)) | (age < min(self.ages))):
print('The requested age is outside the range. Try between ' + str(min(self.ages)) + ' and ' + str(max(self.ages)))
return age_index
class EEP:
"""
Reads in and plots MESA EEP files.
"""
def __init__(self, filename, verbose=True):
"""
Args:
filename: the name of .track.eep file.
Usage:
>> eep = read_mist_models.EEP('00200M.track.eep')
>> logTeff, center_h1, mdot = eep.eeps['log_Teff'], eep['center_h1'], eep['star_mdot']
Attributes:
version Dictionary containing the MIST and MESA version numbers.
abun Dictionary containing Yinit, Zinit, [Fe/H], and [a/Fe] values.
rot Rotation in units of surface v/v_crit.
minit Initial mass in solar masses.
hdr_list List of column headers.
eeps Data.
"""
self.filename = filename
if verbose:
print('Reading in: ' + self.filename)
self.version, self.abun, self.rot, self.minit, self.hdr_list, self.eeps = self.read_eep_file()
def read_eep_file(self):
"""
Reads in the EEP file.
Args:
filename: the name of .track.eep file.
"""
eeps = np.genfromtxt(self.filename, skip_header=11, names=True)
with open(self.filename) as f:
content = [line.split() for line in f]
version = {'MIST': content[0][-1], 'MESA': content[1][-1]}
abun = {content[3][i]:float(content[4][i]) for i in range(1,5)}
rot = float(content[4][-1])
minit = float(content[7][1])
hdr_list = content[11][1:]
return version, abun, rot, minit, hdr_list, eeps
def plot_HR(self, fignum=0, phases=[], phasecolor=[], **kwargs):
"""
Plots the HR diagram.
Args:
None.
Keywords:
accepts matplotlib keywords: color, linestyle, linewidth, etc.
keyword: fignum, phase*, phasecolor
* Following the FSPS notation,
* PMS:-1 ; MS:0 ; SGB+RGB:2 ; CHeB:3 ; EAGB:4 ; TPAGB:5 ; post-AGB:6 ; WR:9
Usage:
>> eep.plot_HR(fignum=3)
>> eep.plot_HR(phase=[0, 2], phasecolor=['Gray', 'Blue']) #highlight the MS and RGB phases in gray and blue.
"""
x = self.eeps['log_Teff']
y = self.eeps['log_L']
fig = plt.figure(fignum)
plt.xlabel('log(Teff) [K]', fontsize=22)
plt.ylabel('log(L/Lsun)', fontsize=22)
ax = fig.add_subplot(111)
ax.plot(x, y, **kwargs)
ax.axis([max(x)+0.2, min(x)-0.2, min(y)-0.2, max(y)+0.2])
if len(phases) >= 0:
if len(phases) != len(phasecolor):
print('The length of the phase and phasecolor array must be identical.')
return
for i_p, phase in enumerate(phases):
p = self.eeps['phase']
p_ind = np.where(p == phase)
if len(p_ind) > 0:
if phasecolor == '':
ax.plot(x[p_ind], y[p_ind], linewidth=4.0, alpha=0.5)
else:
ax.plot(x[p_ind], y[p_ind], color=phasecolor[i_p], linewidth=4.0, alpha=0.5)
class EEPCMD:
"""
Reads in and plots MESA EEP CMD files.
"""
def __init__(self, filename, verbose=True):
"""
Args:
filename: the name of .track.eep.cmd file.
Usage:
>> eepcmd = read_mist_models.EEPCMD('00200M.track.eep.cmd')
>> B, V, mdot = eepcmd.eepcmds['Bessell_B'], eep['Bessell_V'], eep['star_mdot']
Attributes:
version Dictionary containing the MIST and MESA version numbers.
photo_sys Photometric system.
abun Dictionary containing Yinit, Zinit, [Fe/H], and [a/Fe] values.
rot Rotation in units of surface v/v_crit.
minit Initial mass in solar masses.
hdr_list List of column headers.
Av_extinction Av for CCM89 extinction.
eepcmds Data.
"""
self.filename = filename
if verbose:
print('Reading in: ' + self.filename)
self.version, self.photo_sys, self.abun, self.rot, self.minit, self.Av_extinction, self.hdr_list, self.eepcmds = self.read_eepcmd_file()
def read_eepcmd_file(self):
"""
Reads in the EEP CMD file.
Args:
filename: the name of .eep.cmd file.
"""
eepcmds = np.genfromtxt(self.filename, skip_header=14, names=True)
with open(self.filename) as f:
content = [line.split() for line in f]
version = {'MIST': content[0][-1], 'MESA': content[1][-1]}
photo_sys = ' '.join(content[2][4:])
abun = {content[4][i]:float(content[5][i]) for i in range(1,5)}
rot = float(content[5][-1])
minit = float(content[8][1])
Av_extinction = float(content[11][-1])
hdr_list = content[14][1:]
return version, photo_sys, abun, rot, minit, Av_extinction, hdr_list, eepcmds
def plot_CMD(self, filters, fignum=0, phases=[], phasecolor=[], **kwargs):
"""
Plots the CMD diagram.
Args:
filters: a list of three filters, ['filter1', 'filter2', 'filter3']. x-axis: 'filter1'-'filter2', y-axis: 'filter3'
Keywords:
accepts matplotlib keywords: color, linestyle, linewidth, etc.
keyword: fignum, phase*, phasecolor
* Following the FSPS notation,
* PMS:-1 ; MS:0 ; SGB+RGB:2 ; CHeB:3 ; EAGB:4 ; TPAGB:5 ; post-AGB:6 ; WR:9
Usage:
>> eepcmd.plot_CMD(['Bessell_B', 'Bessell_V', 'Bessell_V'], fignum=3)
"""
try:
x1 = self.eepcmds[filters[0]]
except:
print(filters[0]) + ' does not appear in this file.'
return
try:
x2 = self.eepcmds[filters[1]]
except:
print(filters[1]) + ' does not appear in this file.'
return
try:
y = self.eepcmds[filters[2]]
except:
print(filters[2]) + ' does not appear in this file.'
return
fig = plt.figure(fignum)
plt.xlabel(' '.join(filters[0].split('_')) + '-' + ' '.join(filters[1].split('_')), fontsize=22)
plt.ylabel(' '.join(filters[2].split('_')), fontsize=22)
ax = fig.add_subplot(111)
ax.plot(x1-x2, y, **kwargs)
ax.axis([min(x1-x2)-0.2, max(x1-x2)+0.2, max(y)+0.2, min(y)-0.2])
if len(phases) >= 0:
if len(phases) != len(phasecolor):
print('The length of the phase and phasecolor array must be identical.')
return
for i_p, phase in enumerate(phases):
p = self.eepcmds['phase']
p_ind = np.where(p == phase)
if len(p_ind) > 0:
if phasecolor == '':
ax.plot(x1[p_ind]-x2[p_ind], y[p_ind], linewidth=4.0, alpha=0.5)
else:
ax.plot(x1[p_ind]-x2[p_ind], y[p_ind], color=phasecolor[i_p], linewidth=4.0, alpha=0.5)