Density docs

docs/examples/densitycust.rst

@@ -42,6 +42,13 @@ The values in the example here define a density profile that is dropping off wit
     taken as the outer boundaries of grid cells and the density is
     assumed to be uniform with each cell.
 
+Inner Boundary
+==============
+
+The first velocity-density pair in a custom density file (given by index 0) specifies the velocity of the inner boundary approximation. The density associated with this velocity is the density within the inner boundary, which does not affect TARDIS spectra. Therefore, the first density (5.4869692e-10 in the example above) can be replaced by a placeholder value. The user can choose to both specify a custom density file AND specify v_inner_boundary or v_outer_boundary in the configuration YAML file for a TARDIS run. However, the YAML specified values must be within the velocity range specified in the custom density file, otherwise TARDIS will raise an error. When one of the YAML specified boundary velocities falls within the velocity range specified in the custom density file, then the boundary velocity is set equal to the number in the configuration YAML file. This has the effect of splitting a cell in the custom density file into two parts, a region within the boundary and a region outside the boundary.
+
+It is always a good idea to check the model velocities and abundances used in a TARDIS simulation after it has been successfully run.
+
 .. warning::
 
    The example given here is to show the format only. It is not a

tardis/io/schemas/model.yml

@@ -109,11 +109,11 @@ definitions:
           description: file type
         v_inner_boundary:
           type: quantity
-          default: 0 km/s
+          default: -1 km/s
           description: location of the inner boundary chosen from the model
         v_outer_boundary:
           type: quantity
-          default: inf km/s
+          default: -1 km/s
           description: location of the inner boundary chosen from the model
       required:
       - filename

tardis/model/base.py

@@ -220,20 +220,23 @@ def no_of_raw_shells(self):
     def v_boundary_inner(self):
         if self._v_boundary_inner is None:
             return self.raw_velocity[0]
+        if self._v_boundary_inner < 0:
+            return self.raw_velocity[0]
         return self._v_boundary_inner
 
     @v_boundary_inner.setter
     def v_boundary_inner(self, value):
         if value is not None:
-            value = u.Quantity(value, self.v_boundary_inner.unit)
-            if value > self.v_boundary_outer:
-                raise ValueError('v_boundary_inner must not be higher than '
-                                 'v_boundary_outer.')
-            if value > self.raw_velocity[-1]:
-                raise ValueError('v_boundary_inner is outside of '
-                                 'the model range.')
-            if value <= self.raw_velocity[0]:
-                value = None
+            if value > 0:
+                value = u.Quantity(value, self.v_boundary_inner.unit)
+                if value > self.v_boundary_outer:
+                    raise ValueError('v_boundary_inner must not be higher than '
+                                     'v_boundary_outer.')
+                if value > self.raw_velocity[-1]:
+                    raise ValueError('v_boundary_inner is outside of '
+                                     'the model range.')
+                if value < self.raw_velocity[0]:
+                    raise ValueError('v_boundary_inner is outside of the model range.')
         self._v_boundary_inner = value
         # Invalidate the cached cut-down velocity array
         self._velocity = None
@@ -242,20 +245,23 @@ def v_boundary_inner(self, value):
     def v_boundary_outer(self):
         if self._v_boundary_outer is None:
             return self.raw_velocity[-1]
+        if self._v_boundary_outer < 0:
+            return self.raw_velocity[-1]
         return self._v_boundary_outer
 
     @v_boundary_outer.setter
     def v_boundary_outer(self, value):
         if value is not None:
-            value = u.Quantity(value, self.v_boundary_outer.unit)
-            if value < self.v_boundary_inner:
-                raise ValueError('v_boundary_outer must not be smaller than '
-                                 'v_boundary_inner.')
-            if value < self.raw_velocity[0]:
-                raise ValueError('v_boundary_outer is outside of '
-                                 'the model range.')
-            if value >= self.raw_velocity[-1]:
-                value = None
+            if value > 0:
+                value = u.Quantity(value, self.v_boundary_outer.unit)
+                if value < self.v_boundary_inner:
+                    raise ValueError('v_boundary_outer must not be smaller than '
+                                     'v_boundary_inner.')
+                if value < self.raw_velocity[0]:
+                    raise ValueError('v_boundary_outer is outside of '
+                                     'the model range.')
+                if value > self.raw_velocity[-1]:
+                    raise ValueError('v_boundary_outer is outside of the model range.')
         self._v_boundary_outer = value
         # Invalidate the cached cut-down velocity array
         self._velocity = None