def update_lines(OVN_dic=OVN_dic, MdB=None):
if MdB is None:
MdB = pc.MdB(OVN_dic=OVN_dic)
lines_tab = MdB.get_fields(OVN_dic['master_table'])
lines_temis = MdB.get_fields(OVN_dic['temis_table'])
for line in lines_list:
if line[0] not in lines_tab:
command = 'ALTER TABLE {0} ADD `{1}` double NOT NULL DEFAULT 0;'.format(
OVN_dic['master_table'], line[0])
MdB.exec_dB(command)
print('Adding line {0}'.format(line[0]))
if line[0] + '_rad' not in lines_tab:
command = 'ALTER TABLE {0} ADD `{1}_rad` double NOT NULL DEFAULT 0;'.format(
OVN_dic['master_table'], line[0])
MdB.exec_dB(command)
print('Adding line {0}_rad'.format(line[0]))
if 'T_{0}'.format(line[0]) not in lines_temis:
command = 'ALTER TABLE {0} ADD `T_{1}` double NOT NULL DEFAULT 0;'.format(
OVN_dic['temis_table'], line[0])
MdB.exec_dB(command)
lines_temis = MdB.get_fields(OVN_dic['temis_table'])
for line in lines_temis:
line_label = line[2:]
if line_label not in [l[0] for l in lines_list]:
print('Line to be removed: {0}'.format(line))
def init_tab(OVN_dic=OVN_dic, MdB=None, delete_before=False):
table = OVN_dic['master_table']
if MdB is None:
MdB = pc.MdB(OVN_dic=OVN_dic)
if delete_before:
command = 'DROP TABLE IF EXISTS {0};'.format(table)
MdB.exec_dB(command)
command = "CREATE TABLE IF NOT EXISTS {0} (".format(table)
command += fields1
for elem in elem_list:
command += '`{0}` double NOT NULL DEFAULT -40,'.format(elem[0])
for line in lines_list:
command += "`{0[0]}` double NOT NULL DEFAULT 0, ".format(line)
command += "`{0[0]}_rad` double NOT NULL DEFAULT 0, ".format(line)
command += fields2
command += """PRIMARY KEY (`N`),
KEY `ref` (`ref`),
KEY `user` (`user`),
KEY `atm_file` (`atm_file`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 AUTO_INCREMENT=1 ;
"""
MdB.exec_dB(command)
MdB.close_dB()
def init_pending(OVN_dic=OVN_dic, MdB=None, delete_before=False):
table = OVN_dic['pending_table']
if MdB is None:
MdB = pc.MdB(OVN_dic=OVN_dic)
if delete_before:
command = 'DROP TABLE IF EXISTS {0};'.format(table)
MdB.exec_dB(command)
command = "CREATE TABLE IF NOT EXISTS {0} (".format(table)
command += fields1
for elem in elem_list:
command += '`{0}` double NOT NULL DEFAULT -40,'.format(elem[0])
command += """`priority` int(11) DEFAULT 10,
`procID` bigint(20) DEFAULT -1,
`lock` int(11) DEFAULT 0,
PRIMARY KEY (`N`),
KEY `status` (`status`),
KEY `priority` (`priority`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 AUTO_INCREMENT=1 ;
"""
MdB.exec_dB(command)
MdB.close_dB()
def init_lines(OVN_dic=OVN_dic, MdB=None, delete_before=False):
table = OVN_dic['lines_table']
if MdB is None:
MdB = pc.MdB(OVN_dic=OVN_dic)
if delete_before:
command = 'DROP TABLE IF EXISTS {0};'.format(table)
MdB.exec_dB(command)
command = """CREATE TABLE IF NOT EXISTS {0} (
`Nl` bigint(20) NOT NULL AUTO_INCREMENT,
`label` varchar(15) DEFAULT NULL,
`id` varchar(20) DEFAULT NULL,
`lambda` double DEFAULT NULL,
`name` varchar(40) NOT NULL,
`used` int(2) DEFAULT 1,
PRIMARY KEY (`Nl`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 AUTO_INCREMENT=1;
""".format(table)
MdB.exec_dB(command)
command = 'INSERT INTO {0} (`label`, `id`, `lambda`, `name`) VALUES '.format(
table)
for line in lines_list:
command += "('{0[0]}', '{0[1]}', {0[2]}, '{0[3]}'), ".format(line)
command = command[:-2]
command += ';'
MdB.exec_dB(command)
MdB.close_dB()
def make_CALIFA_dB():
"""
Create the pending entries to run individual grids of models corresponding to the CALIFA ages and metallicities.
"""
ff = 1.0
c = pc.CST.CLIGHT
MdB = pc.MdB(OVN_dic)
wP = use3MdB.writePending(MdB, OVN_dic)
wP.set_ref("CALIFA")
wP.set_user("Christophe")
wP.set_file('CALIFA')
wP.set_dir('CALIFA')
wP.set_priority(4)
wP.set_cloudy_others(('no molecules', 'no level2 lines',
'no fine opacities', 'COSMIC RAY BACKGROUND'))
wP.set_iterate(1)
wP.set_N_Hb_cut(4)
wP.set_C_version('17.01')
wP.set_geometry('Sphere')
wP.set_stop(('temperature 200', 'pfrac 0.05'))
all_tabs = [(lU_mean, met, dNO, age, fr, NH) for lU_mean in tab_lU_mean
for met in uniq_mets for dNO in tab_dNO for age in uniq_ages
for fr in tab_fr for NH in tab_NH]
for lU_mean, met, dNO, age, fr, NH in all_tabs:
U_mean = 10**lU_mean
w = (1 + fr**3.)**(1. / 3) - fr
Q0 = 4. * np.pi * c**3 * U_mean**3 / (3. * NH * ff**2 * alpha_B**2 *
w**3)
R_str = (3. * Q0 / (4 * np.pi * NH**2 * alpha_B * ff))**(1. / 3)
R_in = fr * R_str
wP.set_radius(r_in=np.log10(R_in))
wP.set_cste_density(dens=np.log10(NH))
coeff_met = met / 0.019
abunds = selected_abunds.copy()
for elem in abunds:
if elem != 'He':
abunds[elem] += np.log10(coeff_met)
abunds['N'] += dNO
wP.set_abund(ab_dict=abunds)
xt = 7.96
x = 12 + abunds['O']
if x > xt:
y = 2.21 + 1.00 * (8.69 - x)
else:
y = 0.68 + 3.08 * (8.69 - x)
Draine_fact = 2. / 3. # Draine 2001,
wP.set_dust('ism {0}'.format(Draine_fact * 10**(2.21 - y)))
wP.set_comments(
('lU_mean = {0}'.format(lU_mean), 'fr = {0}'.format(fr),
'age = {0}'.format(age), 'met = {0}'.format(met),
'NO = {0}'.format(dNO), 'NH = {0}'.format(NH)))
wP.set_star('table stars \"sp_cha.mod\" ',
age * 1e9,
np.log10(met),
lumi_unit='q(H)',
lumi_value=np.log10(Q0))
wP.insert_model()
MdB.close_dB()
def set_grid():
MdB = pc.MdB(OVN_dic)
models_dir = 'TEST1/'
name = 'test_2'
options = (
'no molecules',
'no level2 lines',
'no fine opacities',
'COSMIC RAY BACKGROUND',
)
wP = use3MdB.writePending(MdB, OVN_dic)
wP.set_ref(name)
wP.set_user('Test')
wP.set_C_version('17.01')
wP.set_iterate(1)
wP.set_file(name)
wP.set_dir(models_dir)
wP.set_cloudy_others(options)
wP.set_N_Hb_cut(4)
wP.set_geometry('Sphere')
wP.set_stop(('temperature 20', 'pfrac 0.02', 'zone 10'))
# Starting the main loop on the 4 parameters.
for age in 1e6 * (1 + np.arange(200) / 100):
wP.set_priority(5)
wP.set_radius(r_in=18)
wP.set_cste_density(dens=2)
ab_O = -3.5
abund = {
'He': -1,
'C': -4,
'N': ab_O - 1,
'O': ab_O,
'Ne': ab_O - 0.73,
'Mg': ab_O - 2.02,
'Si': ab_O - 2.02,
'S': ab_O - 1.66,
'Cl': ab_O - 3.54,
'Ar': ab_O - 2.32,
'Fe': ab_O - 1.83
}
wP.set_abund(ab_dict=abund)
wP.set_dust('ism 1')
wP.set_distance(1.0)
wP.set_star('table stars',
atm_file='sp_cha.mod',
atm1=age,
atm2=-2.4,
lumi_unit='q(H)',
lumi_value=50)
wP.insert_model()
def init_temis(OVN_dic=OVN_dic, MdB=None, delete_before=False):
table = OVN_dic['temis_table']
if MdB is None:
MdB = pc.MdB(OVN_dic = OVN_dic)
if delete_before:
command = 'DROP TABLE IF EXISTS {0};'.format(table)
MdB.exec_dB(command)
command = "CREATE TABLE IF NOT EXISTS {0} (`N` bigint(20) NOT NULL DEFAULT '0',".format(table)
command += "`ref` varchar(40) NOT NULL ,"
for line in lines_list:
command += "`T_{0[0]}` double NOT NULL DEFAULT 0, ".format(line)
command += "PRIMARY KEY (`N`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1;"
MdB.exec_dB(command)
MdB.close_dB()
def post_processing(OVN_dic=OVN_dic):
MdB = pc.MdB(OVN_dic)
ref = 'PNe_2020'
MdB.exec_dB(
"update tab_17 set com6 = '' where ref like '{0}' ".format(ref))
MdB.exec_dB(
"update tab_17 set com3 = 'R' where ref like '{0}' and MassFrac >= 0.95"
.format(ref))
MdB.exec_dB(
"update tab_17 set com3 = 'M80' where ref like '{0}' and MassFrac < 0.95 and MassFrac >= 0.7"
.format(ref))
MdB.exec_dB(
"update tab_17 set com3 = 'M60' where ref like '{0}' and MassFrac < 0.7 and MassFrac >= 0.5"
.format(ref))
MdB.exec_dB(
"update tab_17 set com3 = 'M40' where ref like '{0}' and MassFrac < 0.5 and MassFrac >= 0.3"
.format(ref))
MdB.exec_dB(
"update tab_17 set com3 = 'M20' where ref like '{0}' and MassFrac < 0.3"
.format(ref))
MdB.exec_dB(
"update tab_17 set cloudy5 = '1' where ref like '{0}' and lumi < 4.2 and (lumi > 3.4 or atm1 > 100000) and lumi > 1.5e-5*atm1-0.25"
.format(ref))
MdB.exec_dB(
"update tab_17 set cloudy6 = '1' where ref like '{0}' and H_mass < 1.0"
.format(ref))
MdB.exec_dB(
"update tab_17 join abion_17 on tab_17.N = abion_17.N set tab_17.cloudy7 = abion_17.A_HYDROGEN_vol_1 where tab_17.ref like '{0}'"
.format(ref))
MdB.exec_dB(
"update tab_17 set cloudy8 = '1' where ref like '{0}' and nH_mean * pow(10,rout*3) > 2e53 and nH_mean * pow(10, rout*3) < 3e56"
.format(ref))
MdB.exec_dB(
"update tab_17 set cloudy9 = '1' where ref like '{0}' and H__1_486133A/pow(4*3.1415967*pow(10,rout)*206265., 2) < 1e-11 and H__1_486133A/pow(4*3.1415967*pow(10,rout)*206265., 2) > 1e-15"
.format(ref))
MdB.exec_dB(
"update tab_17 set com6 = '1' where ref like '{0}' and cloudy5 = '1' and cloudy6 = '1' and cloudy8 = '1' and cloudy9 = '1' and MassFrac > 0.2"
.format(ref))
MdB.exec_dB(
"update tab_17 set com6 = '0' where ref like '{0}' and com6 != '1'".
format(ref))
def init_teion(OVN_dic=OVN_dic, MdB=None, delete_before=False):
table = OVN_dic['teion_table']
if MdB is None:
MdB = pc.MdB(OVN_dic = OVN_dic)
if delete_before:
command = 'DROP TABLE IF EXISTS {0};'.format(table)
MdB.exec_dB(command)
command = "CREATE TABLE IF NOT EXISTS {0} (`N` bigint(20) NOT NULL DEFAULT '0',".format(table)
command += "`ref` varchar(40) NOT NULL ,"
for elem in elem_list:
for i in range(elem[1]+1):
command += "`T_{0}_vol_{1}` double NOT NULL DEFAULT '-40',".format(elem[0], i)
command += "`T_{0}_rad_{1}` double NOT NULL DEFAULT '-40',".format(elem[0], i)
command += "PRIMARY KEY (`N`) ) ENGINE=MyISAM DEFAULT CHARSET=latin1;"
MdB.exec_dB(command)
MdB.close_dB()
def init_procIDs(OVN_dic=OVN_dic, MdB=None, delete_before=False):
table = OVN_dic['procIDs_table']
if MdB is None:
MdB = pc.MdB(OVN_dic=OVN_dic)
if delete_before:
command = 'DROP TABLE IF EXISTS {0};'.format(table)
MdB.exec_dB(command)
command = """CREATE TABLE IF NOT EXISTS {0} (
`ID` bigint(20) NOT NULL AUTO_INCREMENT,
`proc_name` varchar(80) NOT NULL,
`datetime` datetime NOT NULL DEFAULT 0,
`user` varchar(80) NOT NULL,
`host` varchar(80) NOT NULL,
PRIMARY KEY (`ID`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 AUTO_INCREMENT=3 ;
""".format(table)
MdB.exec_dB(command)
MdB.close_dB()
def init_SEDs(OVN_dic=OVN_dic, MdB=None, delete_before=False):
table = OVN_dic['seds_table']
if MdB is None:
MdB = pc.MdB(OVN_dic=OVN_dic)
if delete_before:
command = 'DROP TABLE IF EXISTS {0};'.format(table)
MdB.exec_dB(command)
command = """CREATE TABLE IF NOT EXISTS {0} (
`N` bigint(20) NOT NULL AUTO_INCREMENT,
`ref` varchar(40) NOT NULL DEFAULT '',
`sed_name` varchar(40) NOT NULL DEFAULT '',
`atm_cmd` varchar(60) NOT NULL DEFAULT '',
`atm_file` varchar(40) NOT NULL DEFAULT '',
`atm1` double DEFAULT NULL,
`atm2` double DEFAULT NULL,
`atm3` double DEFAULT NULL,
`lumi_unit` varchar(40) NOT NULL DEFAULT '',
`lumi` double DEFAULT NULL,
PRIMARY KEY (`N`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 AUTO_INCREMENT=1;
""".format(table)
MdB.exec_dB(command)
def init_tab(OVN_dic=OVN_dic, MdB=None, delete_before=False):
table = OVN_dic['master_table']
if MdB is None:
MdB = pc.MdB(OVN_dic=OVN_dic)
if delete_before:
command = 'DROP TABLE IF EXISTS {0};'.format(table)
MdB.exec_dB(command)
command = "CREATE TABLE IF NOT EXISTS {0} (".format(table)
command += fields1
for elem in elem_list:
command += '`{0}` double NOT NULL DEFAULT -40,'.format(elem[0])
for line in lines_list:
command += "`{0[0]}` double NOT NULL DEFAULT 0, ".format(line)
command += "`{0[0]}_rad` double NOT NULL DEFAULT 0, ".format(line)
command += """`DepthFrac` double NOT NULL DEFAULT 1,
`MassFrac` double NOT NULL DEFAULT 1,
`HbFrac` double NOT NULL DEFAULT 1,
`rout` double NOT NULL DEFAULT 0,
`thickness` double NOT NULL DEFAULT 0,
`N_zones` int(11) NOT NULL DEFAULT '0',
`CloudyEnds` varchar(180) NOT NULL DEFAULT '',
`FirstZone` varchar(180) NOT NULL DEFAULT '',
`LastZone` varchar(180) NOT NULL DEFAULT '',
`CalculStop` varchar(180) NOT NULL DEFAULT '',
`logQ` float NOT NULL DEFAULT 0,
`logQ0` float NOT NULL DEFAULT 0,
`logQ1` float NOT NULL DEFAULT 0,
`logQ2` float NOT NULL DEFAULT 0,
`logQ3` float NOT NULL DEFAULT 0,
`logPhi` float NOT NULL DEFAULT 0,
`logPhi0` float NOT NULL DEFAULT 0,
`logPhi1` float NOT NULL DEFAULT 0,
`logPhi2` float NOT NULL DEFAULT 0,
`logPhi3` float NOT NULL DEFAULT 0,
`logU_in` float NOT NULL DEFAULT '0',
`logU_out` float NOT NULL DEFAULT '0',
`logU_mean` float NOT NULL DEFAULT 0,
`t2_H1` float NOT NULL DEFAULT 0,
`t2_O1` float NOT NULL DEFAULT 0,
`t2_O2` float NOT NULL DEFAULT 0,
`t2_O3` float NOT NULL DEFAULT 0,
`ne_H1` float NOT NULL DEFAULT 0,
`ne_O1` float NOT NULL DEFAULT 0,
`ne_O2` float NOT NULL DEFAULT 0,
`ne_O3` float NOT NULL DEFAULT 0,
`H_mass` float NOT NULL DEFAULT 0,
`H1_mass` float NOT NULL DEFAULT 0,
`nH_mean` float NOT NULL DEFAULT 0,
`nH_in` float NOT NULL DEFAULT 0,
`nH_out` float NOT NULL DEFAULT 0,
`Hb_SB` float NOT NULL DEFAULT 0,
`Hb_EW` float NOT NULL DEFAULT 0,
`Ha_EW` float NOT NULL DEFAULT 0,
`Cloudy_version` varchar(20) NOT NULL DEFAULT 0,
`bad` int(11) NOT NULL DEFAULT '0',
`abion` tinyint(1) NOT NULL DEFAULT '0',
`teion` tinyint(1) NOT NULL DEFAULT '0',
`temis` tinyint(1) NOT NULL DEFAULT '0',
`interpol` int(11) NOT NULL DEFAULT '0',
`datetime` datetime NOT NULL DEFAULT 0,
`N_pending` bigint(20) NOT NULL DEFAULT 0,
`N1` bigint(20) NOT NULL DEFAULT -1,
`N2` bigint(20) NOT NULL DEFAULT -1,
`W1` float NOT NULL DEFAULT 1,
PRIMARY KEY (`N`),
KEY `ref` (`ref`),
KEY `user` (`user`),
KEY `atm_file` (`atm_file`)
) ENGINE=MyISAM DEFAULT CHARSET=utf8 AUTO_INCREMENT=1 ;
"""
MdB.exec_dB(command)
MdB.close_dB()
from pyCloudy.db import use3MdB
OVN_dic = {'host' : 'nefeles',
'user_name' : 'OVN_admin',
'user_passwd' : 'getenv',
'base_name' : '3MdB_17',
'pending_table' : '`pending_17`',
'master_table' : '`tab_17`',
'teion_table' : '`teion_17`',
'abion_table' : '`abion_17`',
'temis_table' : '`temis_17`',
'lines_table' : '`lines_17`',
'procIDs_table' : '`procIDs`'
}
MdB = pc.MdB(OVN_dic)
models_dir = 'BOND/'
name = 'BOND'
alpha_B = 2.6e-13
options = ('no molecules',
'no level2 lines',
'no fine opacities',
'COSMIC RAY BACKGROUND',
)
NH = 1e2
ff = 1.0
def make_inputs_MdB(SED='BB', dens_law='C', dust=True, ab_O=-2.76):
name = '{0}_{1}'.format(SED, dens_law)
all_tabs = [(T, R, dens, L) for T in tabs_T[SED] for R in tab_R
for dens in tab_dens for L in tab_L]
ab_NO = -0.39
MdB = pc.MdB(OVN_dic)
pc.log_.level = 3
wP = use3MdB.writePending(MdB, OVN_dic)
wP.set_ref("PNe_2020")
wP.set_user('Gloria')
wP.set_C_version('17.01')
wP.set_iterate(1)
wP.set_file(name)
wP.set_priority(10)
wP.set_cloudy_others(('no molecules', 'no level2 lines',
'no fine opacities', 'COSMIC RAY BACKGROUND'))
wP.set_N_Mass_cut(4)
wP.set_dir('PNe_2020/')
for T, R, dens, L in all_tabs:
Q0 = L + Q02Lum[SED][T]
wP.set_comments(dic_O[ab_O], i_com=3)
wP.set_radius(R)
if dens_law == 'C':
wP.set_cste_density(dens)
elif dens_law == 'G1':
thickness = S_thickness(Q0, 10.**dens, 10.**R)
wP.set_dlaw((3, 0., 10.**dens, 0.0, np.log10(thickness) + 0.05, 0.,
17., 17.))
elif dens_law == 'G2':
thickness = S_thickness(Q0, 10.**dens, 10.**R)
wP.set_dlaw((310, 10.**dens / 0.37 / 5., 10.**dens / 0.37,
np.log10(thickness) + 0.05,
np.log10(thickness) + 0.05, 0., 17., 17.))
else:
pc.log_.error('unknown dens_law {0}'.format(dens_law))
wP.set_comments(dens_law, i_com=1)
if dust:
wP.set_dust('ism', 1.)
wP.set_comments('D', i_com=4)
else:
wP.set_dust()
wP.set_comments('N', i_com=4)
if SED == 'BB':
wP.set_star('Blackbody',
atm1=T,
lumi_unit='luminosity total solar',
lumi_value=L)
wP.set_comments('BB', i_com=0)
elif SED == 'BB2':
wP.set_star('Blackbody',
atm1=T,
lumi_unit='luminosity total solar',
lumi_value=L)
wP.set_comments('BB', i_com=0)
elif SED == 'TR':
wP.set_star('table star \"{0}\"'.format(dic_SEDs[SED]),
atm1=T,
atm2=6,
atm3=0,
lumi_unit='luminosity total solar',
lumi_value=L)
wP.set_comments('TR', i_com=0)
elif SED == 'TL':
wP.set_star('table star \"{0}\"'.format(dic_SEDs[SED]),
atm1=T,
atm2=4,
atm3=0,
lumi_unit='luminosity total solar',
lumi_value=L)
wP.set_comments('TL', i_com=0)
elif SED == 'WM':
wP.set_star('table star \"{0}\"'.format(dic_SEDs[SED]),
atm1=T,
atm2=4,
atm3=0,
lumi_unit='luminosity total solar',
lumi_value=L)
wP.set_comments('WM', i_com=0)
else:
pc.log_.error('unknown SED {0}'.format(SED))
ab_dict = {
'He': -1.00,
'Li': -8.69,
'Be': -10.67,
'B': -9.21,
'C': ab_O + 0.25,
'N': ab_O + ab_NO,
'O': ab_O,
'F': -6.5,
'Ne': ab_O - 0.60,
'Na': -5.7,
'Mg': -5.8,
'Al': -6.57,
'Si': -5.0,
'P': -6.7,
'S': ab_O - 1.64,
'Cl': ab_O - 3.41,
'Ar': ab_O - 2.21,
'K': -6.9,
'Ca': -7.9,
'Sc': -8.83,
'Ti': -6.98,
'V': -8.0,
'Cr': -6.33,
'Mn': -6.54,
'Fe': -6.30,
'Co': -7.08,
'Ni': -5.75,
'Cu': -7.79,
'Zn': -7.4
}
wP.set_abund(ab_dict=ab_dict)
wP.set_stop(
('eden {0}'.format(dens - 3), 'temperature off', 'pfrac 0.02'))
wP.insert_model()
