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Cleanup of the config_reader module. #623

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Cleanup of the config_reader module. #623

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d81baa8
io.config_reader: Remove unused functions.
ftsamis Jul 13, 2016
c6c69b8
io.config_reader: Remove the config.structure duplicate of config.mod…
ftsamis Jul 15, 2016
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14 changes: 7 additions & 7 deletions tardis/gui/widgets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -680,25 +680,25 @@ def plot_model(self):
self.graph.cb = self.graph.figure.colorbar(t_rad_color_map)
self.graph.cb.set_label('T (K)')
self.graph.normalizing_factor = 0.2 * (
self.model.tardis_config.structure.r_outer.value[-1] -
self.model.tardis_config.structure.r_inner.value[0]) / (
self.model.tardis_config.structure.r_inner.value[0])
self.model.tardis_config.model.structure.r_outer.value[-1] -
self.model.tardis_config.model.structure.r_inner.value[0]) / (
self.model.tardis_config.model.structure.r_inner.value[0])

#self.graph.normalizing_factor = 8e-16
for i, t_rad in enumerate(self.model.t_rads.value):
r_inner = (self.model.tardis_config.structure.r_inner.value[i] *
r_inner = (self.model.tardis_config.model.structure.r_inner.value[i] *
self.graph.normalizing_factor)
r_outer = (self.model.tardis_config.structure.r_outer.value[i] *
r_outer = (self.model.tardis_config.model.structure.r_outer.value[i] *
self.graph.normalizing_factor)
self.shells.append(Shell(i, (0,0), r_inner, r_outer,
facecolor=t_rad_color_map.to_rgba(t_rad),
picker=self.graph.shell_picker))
self.graph.ax2.add_patch(self.shells[i])
self.graph.ax2.set_xlim(0,
self.model.tardis_config.structure.r_outer.value[-1] *
self.model.tardis_config.model.structure.r_outer.value[-1] *
self.graph.normalizing_factor)
self.graph.ax2.set_ylim(0,
self.model.tardis_config.structure.r_outer.value[-1] *
self.model.tardis_config.model.structure.r_outer.value[-1] *
self.graph.normalizing_factor)
self.graph.figure.tight_layout()
self.graph.draw()
Expand Down
334 changes: 1 addition & 333 deletions tardis/io/config_reader.py
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50 changes: 25 additions & 25 deletions tardis/io/tests/test_config_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,15 +89,15 @@ def test_abundances(self):

def test_velocities(self):
assert_almost_equal(self.yaml_data['model']['structure']['velocity']['start'].cgs.value,
self.config.structure.v_inner[0].cgs.value)
self.config.model.structure.v_inner[0].cgs.value)
assert_almost_equal(self.yaml_data['model']['structure']['velocity']['stop'].cgs.value,
self.config.structure.v_outer[-1].cgs.value)
assert len(self.config.structure.v_outer) == (self.yaml_data['model']['structure']['velocity']['num'])
self.config.model.structure.v_outer[-1].cgs.value)
assert len(self.config.model.structure.v_outer) == (self.yaml_data['model']['structure']['velocity']['num'])

def test_densities(self):
assert_almost_equal(self.config['structure']['mean_densities'][0].cgs.value,
assert_almost_equal(self.config['model']['structure']['mean_densities'][0].cgs.value,
(7.542803599143591e-14 * u.Unit('g/cm^3')).value)
assert_almost_equal(self.config['structure']['mean_densities'][-1].cgs.value,
assert_almost_equal(self.config['model']['structure']['mean_densities'][-1].cgs.value,
(1.432259798833509e-15 * u.Unit('g/cm^3')).value)


Expand Down Expand Up @@ -150,8 +150,8 @@ def setup(self):


def test_velocities(self):
assert self.config.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.structure.v_inner[0].value, 1e4 * 1e5)
assert self.config.model.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.model.structure.v_inner[0].value, 1e4 * 1e5)

def test_abundances(self):
oxygen_abundance = self.yaml_data['model']['abundances']['O']
Expand All @@ -169,8 +169,8 @@ def setup(self):


def test_velocities(self):
assert self.config.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.structure.v_inner[0].value, 1.259375e+03 * 1e5)
assert self.config.model.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.model.structure.v_inner[0].value, 1.259375e+03 * 1e5)

def test_abundances(self):
oxygen_abundance = self.yaml_data['model']['abundances']['O']
Expand All @@ -196,8 +196,8 @@ def setup(self):


def test_velocities(self):
assert self.config.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.structure.v_inner[0].value, 1.259375e+03 * 1e5)
assert self.config.model.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.model.structure.v_inner[0].value, 1.259375e+03 * 1e5)

def test_abundances(self):
assert_almost_equal(self.config.abundances.ix[14, 54], 0.21864420000000001)
Expand All @@ -220,8 +220,8 @@ def setup(self):


def test_velocities(self):
assert self.config.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.structure.v_inner[0].to(
assert self.config.model.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.model.structure.v_inner[0].to(
u.km / u.s).value, 9000)

def test_abundances(self):
Expand All @@ -241,7 +241,7 @@ def setup(self):
config_dirname=data_path(''))

def test_density(self):
assert_array_almost_equal(self.config.structure.mean_densities.to(u.Unit('g / cm3')).value,
assert_array_almost_equal(self.config.model.structure.mean_densities.to(u.Unit('g / cm3')).value,
1.e-14)

class TestParseConfigTinner:
Expand Down Expand Up @@ -277,8 +277,8 @@ def setup(self):


def test_velocities(self):
assert self.config.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.structure.v_inner[0].to(
assert self.config.model.structure.v_inner.unit == u.Unit('cm/s')
assert_almost_equal(self.config.model.structure.v_inner[0].to(
u.km / u.s).value, 11000)

def test_abundances(self):
Expand All @@ -298,13 +298,13 @@ def test_abundances(self):
assert_almost_equal(self.config.abundances.ix[6, 6], 0.5)

def test_densities(self):
assert_almost_equal(self.config.structure.mean_densities[0].to(u.Unit('g/cm3')).value, 9.7656229e-11 / 13.0**3 )
assert_almost_equal(self.config.structure.mean_densities[1].to(u.Unit('g/cm3')).value, 4.8170911e-11/ 13.0**3 )
assert_almost_equal(self.config.structure.mean_densities[2].to(u.Unit('g/cm3')).value, 2.5600000e-11/ 13.0**3 )
assert_almost_equal(self.config.structure.mean_densities[3].to(u.Unit('g/cm3')).value, 1.4450533e-11/ 13.0**3 )
assert_almost_equal(self.config.structure.mean_densities[4].to(u.Unit('g/cm3')).value, 8.5733893e-11/ 13.0**3 )
assert_almost_equal(self.config.structure.mean_densities[5].to(u.Unit('g/cm3')).value, 5.3037103e-11/ 13.0**3 )
assert_almost_equal(self.config.structure.mean_densities[6].to(u.Unit('g/cm3')).value, 3.3999447e-11/ 13.0**3 )
assert_almost_equal(self.config.model.structure.mean_densities[0].to(u.Unit('g/cm3')).value, 9.7656229e-11 / 13.0**3 )
assert_almost_equal(self.config.model.structure.mean_densities[1].to(u.Unit('g/cm3')).value, 4.8170911e-11/ 13.0**3 )
assert_almost_equal(self.config.model.structure.mean_densities[2].to(u.Unit('g/cm3')).value, 2.5600000e-11/ 13.0**3 )
assert_almost_equal(self.config.model.structure.mean_densities[3].to(u.Unit('g/cm3')).value, 1.4450533e-11/ 13.0**3 )
assert_almost_equal(self.config.model.structure.mean_densities[4].to(u.Unit('g/cm3')).value, 8.5733893e-11/ 13.0**3 )
assert_almost_equal(self.config.model.structure.mean_densities[5].to(u.Unit('g/cm3')).value, 5.3037103e-11/ 13.0**3 )
assert_almost_equal(self.config.model.structure.mean_densities[6].to(u.Unit('g/cm3')).value, 3.3999447e-11/ 13.0**3 )


def test_ascii_reader_power_law():
Expand All @@ -320,7 +320,7 @@ def test_ascii_reader_power_law():
v_outer = yaml_data['model']['structure']['velocity']['stop']
my_conf = config_reader.Configuration.from_yaml(data_path('tardis_configv1_density_power_law_test.yml'),
test_parser=True)
structure = my_conf['structure']
structure = my_conf['model']['structure']

expected_densites = [3.29072513e-14, 2.70357804e-14, 2.23776573e-14,
1.86501954e-14, 1.56435277e-14, 1.32001689e-14, 1.12007560e-14,
Expand Down Expand Up @@ -348,7 +348,7 @@ def test_ascii_reader_exponential_law():
v_outer = yaml_data['model']['structure']['velocity']['stop']
my_conf = config_reader.Configuration.from_yaml(data_path('tardis_configv1_density_exponential_test.yml'),
test_parser=True)
structure = my_conf['structure']
structure = my_conf['model']['structure']

expected_densites = [5.18114795e-14, 4.45945537e-14, 3.83828881e-14, 3.30364579e-14, 2.84347428e-14, 2.44740100e-14, 2.10649756e-14, 1.81307925e-14, 1.56053177e-14, 1.34316215e-14, 1.15607037e-14, 9.95038990e-15, 8.56437996e-15, 7.37143014e-15, 6.34464872e-15, 5.46088976e-15, 4.70023138e-15, 4.04552664e-15, 3.48201705e-15, 2.99699985e-15]
expected_unit = 'g / (cm3)'
Expand Down
14 changes: 7 additions & 7 deletions tardis/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,13 +91,13 @@ def __init__(self, tardis_config):

self.t_inner = tardis_config.plasma.t_inner

self.v_inner = tardis_config.structure.v_inner
self.v_outer = tardis_config.structure.v_outer
self.v_inner = tardis_config.model.structure.v_inner
self.v_outer = tardis_config.model.structure.v_outer
self.v_middle = 0.5 * (self.v_inner + self.v_outer)

self.ws = self.calculate_geometric_w(
tardis_config.structure.r_middle,
tardis_config.structure.r_inner[0])
tardis_config.model.structure.r_middle,
tardis_config.model.structure.r_inner[0])

if tardis_config.plasma.t_rads is None:
self.t_rads = self._init_t_rad(
Expand Down Expand Up @@ -177,14 +177,14 @@ def t_inner(self, value):
self._t_inner = value
self.luminosity_inner = (
4 * np.pi * constants.sigma_sb.cgs *
self.tardis_config.structure.r_inner[0] ** 2
self.tardis_config.model.structure.r_inner[0] ** 2
* self.t_inner ** 4).to('erg/s')

self.time_of_simulation = (1.0 * u.erg / self.luminosity_inner)
self.j_blues_norm_factor = (
constants.c.cgs * self.tardis_config.supernova.time_explosion /
(4 * np.pi * self.time_of_simulation *
self.tardis_config.structure.volumes))
self.tardis_config.model.structure.volumes))



Expand Down Expand Up @@ -227,7 +227,7 @@ def calculate_j_blues(self, init_detailed_j_blues=False):
index=self.atom_data.lines.index,
columns=np.arange(len(self.t_rads)))

for i in xrange(self.tardis_config.structure.no_of_shells):
for i in xrange(self.tardis_config.model.structure.no_of_shells):
zero_j_blues = self.j_blues[i] == 0.0
self.j_blues[i][zero_j_blues] = (
w_epsilon * intensity_black_body(
Expand Down
4 changes: 2 additions & 2 deletions tardis/montecarlo/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,10 +123,10 @@ def run(self, model, no_of_packets, no_of_virtual_packets=0, nthreads=1,last_run
:return:
"""
self.time_of_simulation = model.time_of_simulation
self.volume = model.tardis_config.structure.volumes
self.volume = model.tardis_config.model.structure.volumes
self._initialize_estimator_arrays(self.volume.shape[0],
model.plasma.tau_sobolevs.shape)
self._initialize_geometry_arrays(model.tardis_config.structure)
self._initialize_geometry_arrays(model.tardis_config.model.structure)

self._initialize_packets(model.t_inner.value,
no_of_packets)
Expand Down
2 changes: 1 addition & 1 deletion tardis/simulation/base.py
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Expand Up @@ -93,7 +93,7 @@ def estimate_t_inner(self, input_t_inner, luminosity_requested,
def get_convergence_status(self, t_rad, w, t_inner, estimated_t_rad, estimated_w,
estimated_t_inner):
convergence_section = self.tardis_config.montecarlo.convergence_strategy
no_of_shells = self.tardis_config.structure.no_of_shells
no_of_shells = self.tardis_config.model.structure.no_of_shells

convergence_t_rad = (abs(t_rad - estimated_t_rad) /
estimated_t_rad).value
Expand Down
4 changes: 2 additions & 2 deletions tardis/util.py
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Expand Up @@ -211,9 +211,9 @@ def create_synpp_yaml(radial1d_mdl, fname, shell_no=0, lines_db=None):


#raise Exception("there's a problem here with units what units does synpp expect?")
yaml_reference['opacity']['v_ref'] = float((radial1d_mdl.tardis_config.structure.v_inner[0].to('km/s') /
yaml_reference['opacity']['v_ref'] = float((radial1d_mdl.tardis_config.model.structure.v_inner[0].to('km/s') /
(1000. * u.km / u.s)).value)
yaml_reference['grid']['v_outer_max'] = float((radial1d_mdl.tardis_config.structure.v_outer[-1].to('km/s') /
yaml_reference['grid']['v_outer_max'] = float((radial1d_mdl.tardis_config.model.structure.v_outer[-1].to('km/s') /
(1000. * u.km / u.s)).value)

#pdb.set_trace()
Expand Down