Merge pull request #100 from brittonsmith/realias

Remove p0 alias fallback.
trident-project · Sep 25, 2019 · faf8da0 · faf8da0
2 parents d6bbf44 + 7c2b6ee
commit faf8da0
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Showing 3 changed files with 34 additions and 55 deletions.
diff --git a/tests/test_absorption_spectrum.py b/tests/test_absorption_spectrum.py
@@ -60,13 +60,13 @@ def test_absorption_spectrum_cosmo(self):
         lr = LightRay(COSMO_PLUS, 'Enzo', 0.0, 0.03)
 
         lr.make_light_ray(seed=1234567,
-                          fields=['temperature', 'density', 'H_number_density'],
+                          fields=['temperature', 'density', 'H_p0_number_density'],
                           data_filename='lightray.h5')
 
         sp = AbsorptionSpectrum(900.0, 1800.0, 10000)
 
         my_label = 'HI Lya'
-        field = 'H_number_density'
+        field = 'H_p0_number_density'
         wavelength = 1215.6700  # Angstromss
         f_value = 4.164E-01
         gamma = 6.265e+08
@@ -76,7 +76,7 @@ def test_absorption_spectrum_cosmo(self):
                     gamma, mass, label_threshold=1.e10)
 
         my_label = 'HI Lya'
-        field = 'H_number_density'
+        field = 'H_p0_number_density'
         wavelength = 912.323660  # Angstroms
         normalization = 1.6e17
         index = 3.0
@@ -102,13 +102,13 @@ def test_absorption_spectrum_non_cosmo(self):
         ray_start = [0,0,0]
         ray_end = [1,1,1]
         lr.make_light_ray(start_position=ray_start, end_position=ray_end,
-                          fields=['temperature', 'density', 'H_number_density'],
+                          fields=['temperature', 'density', 'H_p0_number_density'],
                           data_filename='lightray.h5')
 
         sp = AbsorptionSpectrum(1200.0, 1300.0, 10001)
 
         my_label = 'HI Lya'
-        field = 'H_number_density'
+        field = 'H_p0_number_density'
         wavelength = 1215.6700  # Angstromss
         f_value = 4.164E-01
         gamma = 6.265e+08
@@ -136,13 +136,13 @@ def test_absorption_spectrum_non_cosmo_novpec(self):
         ray_start = [0,0,0]
         ray_end = [1,1,1]
         lr.make_light_ray(start_position=ray_start, end_position=ray_end,
-                          fields=['temperature', 'density', 'H_number_density'],
+                          fields=['temperature', 'density', 'H_p0_number_density'],
                           data_filename='lightray.h5', use_peculiar_velocity=False)
 
         sp = AbsorptionSpectrum(1200.0, 1300.0, 10001)
 
         my_label = 'HI Lya'
-        field = 'H_number_density'
+        field = 'H_p0_number_density'
         wavelength = 1215.6700  # Angstromss
         f_value = 4.164E-01
         gamma = 6.265e+08
@@ -170,11 +170,11 @@ def test_equivalent_width_conserved(self):
         ray_start = [0,0,0]
         ray_end = [1,1,1]
         lr.make_light_ray(start_position=ray_start, end_position=ray_end,
-                          fields=['temperature', 'density', 'H_number_density'],
+                          fields=['temperature', 'density', 'H_p0_number_density'],
                           data_filename='lightray.h5')
 
         my_label = 'HI Lya'
-        field = 'H_number_density'
+        field = 'H_p0_number_density'
         wave = 1215.6700  # Angstromss
         f_value = 4.164E-01
         gamma = 6.265e+08
@@ -207,13 +207,13 @@ def test_absorption_spectrum_fits(self):
         ray_start = [0,0,0]
         ray_end = [1,1,1]
         lr.make_light_ray(start_position=ray_start, end_position=ray_end,
-                          fields=['temperature', 'density', 'H_number_density'],
+                          fields=['temperature', 'density', 'H_p0_number_density'],
                           data_filename='lightray.h5')
 
         sp = AbsorptionSpectrum(900.0, 1800.0, 10000)
 
         my_label = 'HI Lya'
-        field = 'H_number_density'
+        field = 'H_p0_number_density'
         wavelength = 1215.6700  # Angstromss
         f_value = 4.164E-01
         gamma = 6.265e+08
@@ -223,7 +223,7 @@ def test_absorption_spectrum_fits(self):
                     gamma, mass, label_threshold=1.e10)
 
         my_label = 'HI Lya'
-        field = 'H_number_density'
+        field = 'H_p0_number_density'
         wavelength = 912.323660  # Angstroms
         normalization = 1.6e17
         index = 3.0
@@ -246,13 +246,13 @@ def test_absorption_spectrum_cosmo_sph(self):
 
         lr.make_light_ray(seed=1234567,
                           fields=[('gas', 'temperature'),
-                                  ('gas', 'H_number_density')],
+                                  ('gas', 'H_p0_number_density')],
                           data_filename='lightray.h5')
 
         sp = AbsorptionSpectrum(900.0, 1800.0, 10000)
 
         my_label = 'HI Lya'
-        field = ('gas', 'H_number_density')
+        field = ('gas', 'H_p0_number_density')
         wavelength = 1215.6700  # Angstromss
         f_value = 4.164E-01
         gamma = 6.265e+08
@@ -262,7 +262,7 @@ def test_absorption_spectrum_cosmo_sph(self):
                     gamma, mass, label_threshold=1.e10)
 
         my_label = 'HI Lya'
-        field = ('gas', 'H_number_density')
+        field = ('gas', 'H_p0_number_density')
         wavelength = 912.323660  # Angstroms
         normalization = 1.6e17
         index = 3.0
@@ -289,13 +289,13 @@ def test_absorption_spectrum_non_cosmo_sph(self):
         ray_end = ds.domain_right_edge
         lr.make_light_ray(start_position=ray_start, end_position=ray_end,
                           fields=[('gas', 'temperature'),
-                                  ('gas', 'H_number_density')],
+                                  ('gas', 'H_p0_number_density')],
                           data_filename='lightray.h5')
 
         sp = AbsorptionSpectrum(1200.0, 1300.0, 10001)
 
         my_label = 'HI Lya'
-        field = ('gas', 'H_number_density')
+        field = ('gas', 'H_p0_number_density')
         wavelength = 1215.6700  # Angstromss
         f_value = 4.164E-01
         gamma = 6.265e+08
@@ -324,13 +324,13 @@ def test_absorption_spectrum_with_continuum(self):
         ray_start = ds.domain_left_edge
         ray_end = ds.domain_right_edge
         lr.make_light_ray(start_position=ray_start, end_position=ray_end,
-                          fields=['temperature', 'density', 'H_number_density'],
+                          fields=['temperature', 'density', 'H_p0_number_density'],
                           data_filename='lightray.h5')
 
         sp = AbsorptionSpectrum(800.0, 1300.0, 5001)
 
         my_label = 'HI Lya'
-        field = 'H_number_density'
+        field = 'H_p0_number_density'
         wavelength = 1215.6700  # Angstromss
         f_value = 4.164E-01
         gamma = 6.265e+08
@@ -340,7 +340,7 @@ def test_absorption_spectrum_with_continuum(self):
                     gamma, mass, label_threshold=1.e10)
 
         my_label = 'Ly C'
-        field = 'H_number_density'
+        field = 'H_p0_number_density'
         wavelength = 912.323660  # Angstroms
         normalization = 1.6e17
         index = 3.0
@@ -372,7 +372,7 @@ def test_absorption_spectrum_with_zero_field(self):
 
         HI_parameters = {
             'name': 'HI',
-            'field': 'H_number_density',
+            'field': 'H_p0_number_density',
             'f': [.4164],
             'Gamma': [6.265E8],
             'wavelength': [1215.67],

diff --git a/tests/test_ion_balance.py b/tests/test_ion_balance.py
@@ -308,9 +308,7 @@ def test_to_not_overwrite_fields_for_grid():
     Test to not overwrite an existing ion field
     """
     ds = load(ISO_GALAXY)
-    # temporary fix until p0 fields are fixed in yt
-    # val_before = ds.r['H_p0_number_density'][0]
-    val_before = ds.r['H_number_density'][0]
+    val_before = ds.r['H_p0_number_density'][0]
     add_ion_fields(ds, ['H'], ftype='gas')
     val_after = ds.r['H_p0_number_density'][0]
     assert val_before == val_after

diff --git a/trident/ion_balance.py b/trident/ion_balance.py
@@ -480,21 +480,14 @@ def add_ion_number_density_field(atom, ion, ds, ftype="gas",
         if ion == 1:
             alias_field += "_%s" % ionization_table.split(os.sep)[-1].split(".h5")[0]
 
-    ### temporary fix until p0 fields are fixed in yt
-    if ion == 1 and ('gas', alias_field) in ds.derived_field_list:
-        mylog.info('("gas", "%s") already exists, aliasing ("gas", "%s") to that.' %
-                   (alias_field, field))
-        _alias_field(ds, ("gas", field), ("gas", alias_field))
-
     add_ion_fraction_field(atom, ion, ds, ftype, ionization_table,
                            field_suffix=field_suffix,
                            sampling_type=sampling_type)
 
-    if not (ion == 1 and ('gas', alias_field) in ds.derived_field_list):
-        _add_field(ds, ("gas", field),function=_ion_number_density,
-                   units="cm**-3", sampling_type=sampling_type)
-        if ion == 1: # add aliased field too
-            _alias_field(ds, ("gas", alias_field), ("gas", field))
+    _add_field(ds, ("gas", field),function=_ion_number_density,
+               units="cm**-3", sampling_type=sampling_type)
+    if ion == 1: # add aliased field too
+        _alias_field(ds, ("gas", alias_field), ("gas", field))
 
 def add_ion_density_field(atom, ion, ds, ftype="gas",
                           ionization_table=None,
@@ -588,16 +581,10 @@ def add_ion_density_field(atom, ion, ds, ftype="gas",
     add_ion_number_density_field(atom, ion, ds, ftype, ionization_table,
                                  sampling_type=sampling_type)
 
-    ### temporary fix until p0 fields are fixed in yt
-    if ion == 1 and ('gas', alias_field) in ds.derived_field_list:
-        mylog.info('("gas", "%s") already exists, aliasing ("gas", "%s") to that.' %
-                   (alias_field, field))
-        _alias_field(ds, ("gas", field), ("gas", alias_field))
-    else:
-        _add_field(ds, ("gas", field), function=_ion_density,
-                   units="g/cm**3", sampling_type=sampling_type)
-        if ion == 1: # add aliased field too
-            _alias_field(ds, ("gas", alias_field), ("gas", field))
+    _add_field(ds, ("gas", field), function=_ion_density,
+               units="g/cm**3", sampling_type=sampling_type)
+    if ion == 1: # add aliased field too
+        _alias_field(ds, ("gas", alias_field), ("gas", field))
 
 def add_ion_mass_field(atom, ion, ds, ftype="gas",
                        ionization_table=None,
@@ -693,16 +680,10 @@ def add_ion_mass_field(atom, ion, ds, ftype="gas",
                           field_suffix=field_suffix,
                           sampling_type=sampling_type)
 
-    ### temporary fix until p0 fields are fixed in yt
-    if ion == 1 and ('gas', alias_field) in ds.derived_field_list:
-        mylog.info('("gas", "%s") already exists, aliasing ("gas", "%s") to that.' %
-                   (alias_field, field))
-        _alias_field(ds, ("gas", field), ("gas", alias_field))
-    else:
-        _add_field(ds, ("gas", field), function=_ion_mass, units=r"g",
-                   sampling_type=sampling_type)
-        if ion == 1: # add aliased field too
-            _alias_field(ds, ("gas", alias_field), ("gas", field))
+    _add_field(ds, ("gas", field), function=_ion_mass, units=r"g",
+               sampling_type=sampling_type)
+    if ion == 1: # add aliased field too
+        _alias_field(ds, ("gas", alias_field), ("gas", field))
 
 def _ion_mass(field, data):
     """