def test_read_write_atm_ptqr(tmpdir):
atmfile = "WASP-00b.atm"
atm = "{}/{}".format(tmpdir, atmfile)
nlayers = 11
pressure = pa.pressure('1e-8 bar', '1e2 bar', nlayers)
temperature = pa.tmodels.Isothermal(nlayers)(1500.0)
species = ["H2", "He", "H2O", "CO", "CO2", "CH4"]
abundances = [0.8496, 0.15, 1e-4, 1e-4, 1e-8, 1e-4]
qprofiles = pa.uniform(pressure, temperature, species, abundances)
radius = pa.hydro_g(pressure, temperature, 2.3, 2479.0, pc.bar, pc.rjup)
io.write_atm(atm,
pressure,
temperature,
species,
qprofiles,
radius=radius,
punits='bar',
runits='km',
header='# Test write atm\n')
assert atmfile in os.listdir(str(tmpdir))
atm_input = io.read_atm(atm)
assert atm_input[0] == ('bar', 'kelvin', 'volume', 'km')
np.testing.assert_equal(atm_input[1], np.array(species))
np.testing.assert_allclose(atm_input[2], pressure / pc.bar)
np.testing.assert_allclose(atm_input[3], temperature)
np.testing.assert_allclose(atm_input[4], qprofiles)
np.testing.assert_allclose(atm_input[5], radius / pc.km, rtol=1e-5)
def test_transmission_input_radius_overwrite(tmp_path):
cfg = make_config(
tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
reset={'atmfile': f'{INPUTS}/atmosphere_uniform_radius.atm'})
pyrat = pb.run(cfg)
atm = io.read_atm('inputs/atmosphere_uniform_radius.atm')
np.testing.assert_raises(AssertionError, np.testing.assert_array_equal,
pyrat.atm.radius, atm[5] * pc.km)
def test_transmission_input_radius(tmp_path):
cfg = make_config(
tmp_path,
ROOT + 'tests/configs/spectrum_transmission_test.cfg',
reset={'atmfile': f'{INPUTS}atmosphere_uniform_radius.atm'},
remove=['radmodel'])
pyrat = pb.run(cfg)
atm = io.read_atm('inputs/atmosphere_uniform_radius.atm')
np.testing.assert_allclose(pyrat.atm.radius, atm[5] * pc.km, rtol=rtol)
def test_transmission_qmass_input():
# This is the gist of it, prepare a qmass atmospheric file:
atm = io.read_atm('inputs/atmosphere_uniform_test.atm')
units, species, press, temp, q = atm
symbol, mass, diam = io.read_molecs(pc.ROOT +
"pyratbay/data/molecules.dat")
mm = pa.mean_weight(q, species)
qmass = qprofiles * molmass / mm
io.write_atm(atmfile)
# Then run spectrum, results must be the same as qnumber run:
pyrat = pb.run(ROOT + 'tests/configs/spectrum_transmission_qmass_test.cfg')
np.testing.assert_allclose(pyrat.spec.spectrum, expected['all'], rtol=rtol)
def test_atmosphere_hydro_default_runits(tmp_path):
atmfile = str(tmp_path / 'test.atm')
cfg = make_config(tmp_path,
ROOT + 'tests/configs/atmosphere_hydro_test.cfg',
reset={
'atmfile': atmfile,
'gplanet': '2478.7504116251885'
},
remove=['rplanet'])
press, temp, abund, species, radius = pb.run(cfg)
np.testing.assert_allclose(radius, expected_radius, rtol=1e-7)
atmf = io.read_atm(atmfile)
assert atmf[0] == ('bar', 'kelvin', 'volume', 'rjup')
np.testing.assert_allclose(atmf[5] * pc.rjup, expected_radius, rtol=5e-5)
def test_read_write_atm_pt(tmpdir):
atmfile = "WASP-00b.atm"
atm = "{}/{}".format(tmpdir, atmfile)
nlayers = 11
pressure = pa.pressure('1e-8 bar', '1e2 bar', nlayers)
temperature = pa.tmodels.Isothermal(nlayers)(1500.0)
io.write_atm(atm, pressure, temperature, punits='bar')
assert atmfile in os.listdir(str(tmpdir))
atm_input = io.read_atm(atm)
assert atm_input[0] == ('bar', 'kelvin', None, None)
assert atm_input[1] is None
np.testing.assert_allclose(atm_input[2], pressure / pc.bar)
np.testing.assert_allclose(atm_input[3], temperature)
assert atm_input[4] is None
assert atm_input[5] is None
def test_molecule_not_in_molfile(tmp_path, capfd):
# Modify atm:
units, species, press, temp, q, rad = \
io.read_atm(ROOT+'tests/inputs/atmosphere_uniform_test.atm')
press = press * pb.tools.u(units[0])
species[-1] = 'X'
new_atm = str(tmp_path/'new_atmosphere_uniform_test.atm')
io.write_atm(new_atm, press, temp, species, q, punits=units[0])
cfg = make_config(tmp_path,
ROOT+'tests/configs/spectrum_transmission_test.cfg',
reset={'atmfile':new_atm})
pyrat = pb.run(cfg)
assert pyrat is None
captured = capfd.readouterr()
assert "Error in module: 'read_atm.py', function: 'get_constants'" \
in captured.out
assert "These species: ['X'] are not listed in the molecules info file" \
in captured.out
def test_atmosphere_tea(tmp_path):
atmfile = str(tmp_path / 'test.atm')
cfg = make_config(tmp_path,
ROOT + 'tests/configs/atmosphere_tea_test.cfg',
reset={'atmfile': atmfile})
press, temp, abund, species, radius = pb.run(cfg)
np.testing.assert_allclose(press, expected_pressure, rtol=1e-7)
np.testing.assert_allclose(temp, expected_temperature, atol=1e-7)
np.testing.assert_allclose(abund, expected_abundance, rtol=1e-7)
# Compare against the atmospheric file now:
atmf = io.read_atm(atmfile)
assert atmf[0] == ('bar', 'kelvin', 'volume', None)
np.testing.assert_equal(
atmf[1], np.array('H2 He Na K H2O CH4 CO CO2 NH3 HCN N2'.split()))
# File read-write loses precision:
np.testing.assert_allclose(atmf[2] * pc.bar, expected_pressure, rtol=3e-5)
np.testing.assert_allclose(atmf[3], expected_temperature, rtol=5e-6)
np.testing.assert_allclose(atmf[4], expected_abundance, rtol=1e-7)
def test_atmosphere_uniform(tmp_path):
atmfile = str(tmp_path / 'test.atm')
cfg = make_config(tmp_path,
ROOT + 'tests/configs/atmosphere_uniform_test.cfg',
reset={'atmfile': atmfile})
press, temp, abund, species, radius = pb.run(cfg)
np.testing.assert_allclose(press, expected_pressure, rtol=1e-7)
np.testing.assert_allclose(temp, expected_temperature, rtol=1e-7)
q = np.tile([0.85, 0.149, 3.0e-6, 4.0e-4, 1.0e-4, 5.0e-4, 1.0e-7], (81, 1))
np.testing.assert_equal(abund, q)
# Compare against the atmospheric file now:
atm = io.read_atm(atmfile)
assert atm[0] == ('bar', 'kelvin', 'volume', None)
np.testing.assert_equal(atm[1],
np.array('H2 He Na H2O CH4 CO CO2'.split()))
# File read-write loses precision:
np.testing.assert_allclose(atm[2] * pc.bar, expected_pressure, rtol=3e-5)
np.testing.assert_allclose(atm[3], expected_temperature, rtol=1e-6)
np.testing.assert_equal(atm[4], q)
def test_read_atm_no_temp():
match = "Atmospheric file does not have '@TEMPERATURE' header"
with pytest.raises(ValueError, match=match):
dummy = io.read_atm('inputs/uniform_notemp_test.atm')
import os
import numpy as np
import matplotlib.pyplot as plt
import pyratbay as pb
import pyratbay.atmosphere as pa
import pyratbay.io as io
import pyratbay.tools as pt
import mc3
# Indices for species in atmosphere:
units, specs, press, temp, q, rad = io.read_atm(
'run_setup/isothermal_1500K_uniform.atm')
iHe = np.where(specs == 'He')[0][0]
iH2 = np.where(specs == 'H2')[0][0]
iH = np.where(specs == 'H')[0][0]
iH2O = np.where(specs == 'H2O')[0][0]
iCH4 = np.where(specs == 'CH4')[0][0]
iHCN = np.where(specs == 'HCN')[0][0]
def ZX(params, pyrat):
Zsun = 0.0134 # Asplund et al. 2009
Xsun = 0.7381
q2 = pa.qscale(pyrat.atm.qbase,
pyrat.mol.name,
pyrat.atm.molmodel,
pyrat.atm.molfree,
params[pyrat.ret.imol],
pyrat.atm.bulk,