Merge pull request #93 from brittonsmith/pr92pick

backport PR 92 to master

trident/light_ray.py

@@ -416,6 +416,13 @@ def make_light_ray(self, seed=None, periodic=True,
             the dataset redshift for a cosmological dataset.
             Default: None.
 
+        :field_parameters: optional, dict
+            Used to set field parameters in light rays. For example,
+            if the 'bulk_velocity' field parameter is set, the relative
+            velocities used to calculate peculiar velocity will be adjusted
+            accordingly.
+            Default: None.
+
         :njobs: optional, int
 
             The number of parallel jobs over which the segments will
@@ -514,10 +521,11 @@ def make_light_ray(self, seed=None, periodic=True,
         all_fields.extend(['x', 'y', 'z', 'dx', 'dy', 'dz'])
         data_fields.extend(['x', 'y', 'z', 'dx', 'dy', 'dz'])
         if use_peculiar_velocity:
-            all_fields.extend(['velocity_x', 'velocity_y', 'velocity_z',
+            all_fields.extend(['relative_velocity_x', 'relative_velocity_y',
+                               'relative_velocity_z',
                                'velocity_los', 'redshift_eff',
                                'redshift_dopp'])
-            data_fields.extend(['velocity_x', 'velocity_y', 'velocity_z'])
+            data_fields.extend(['relative_velocity_x', 'relative_velocity_y', 'relative_velocity_z'])
 
         all_ray_storage = {}
         for my_storage, my_segment in parallel_objects(self.light_ray_solution,
@@ -604,9 +612,9 @@ def make_light_ray(self, seed=None, periodic=True,
                 if use_peculiar_velocity:
                     line_of_sight = sub_segment[0] - sub_segment[1]
                     line_of_sight /= ((line_of_sight**2).sum())**0.5
-                    sub_vel = ds.arr([sub_ray['velocity_x'],
-                                      sub_ray['velocity_y'],
-                                      sub_ray['velocity_z']])
+                    sub_vel = ds.arr([sub_ray['relative_velocity_x'],
+                                      sub_ray['relative_velocity_y'],
+                                      sub_ray['relative_velocity_z']])
                     # Line of sight velocity = vel_los
                     sub_vel_los = (np.rollaxis(sub_vel, 1) * \
                                    line_of_sight).sum(axis=1)

trident/ray_generator.py

@@ -36,7 +36,7 @@
 def make_simple_ray(dataset_file, start_position, end_position,
                     lines=None, ftype="gas", fields=None,
                     solution_filename=None, data_filename=None,
-                    trajectory=None, redshift=None,
+                    trajectory=None, redshift=None, field_parameters=None,
                     setup_function=None, load_kwargs=None,
                     line_database=None, ionization_table=None):
     """
@@ -157,6 +157,13 @@ def make_simple_ray(dataset_file, start_position, end_position,
         it will use a redshift of 0.
         Default: None
 
+    :field_parameters: optional, dict
+        Used to set field parameters in light rays. For example,
+        if the 'bulk_velocity' field parameter is set, the relative
+        velocities used to calculate peculiar velocity will be adjusted
+        accordingly.
+        Default: None.
+
     :setup_function: function, optional
 
         A function that will be called on the dataset as it is loaded but
@@ -263,6 +270,7 @@ def make_simple_ray(dataset_file, start_position, end_position,
                              setup_function=setup_function,
                              solution_filename=solution_filename,
                              data_filename=data_filename,
+                             field_parameters=field_parameters,
                              redshift=redshift)
 
 def make_compound_ray(parameter_filename, simulation_type,
@@ -272,7 +280,8 @@ def make_compound_ray(parameter_filename, simulation_type,
                       use_minimum_datasets=True, max_box_fraction=1.0,
                       deltaz_min=0.0, minimum_coherent_box_fraction=0.0,
                       seed=None, setup_function=None, load_kwargs=None,
-                      line_database=None, ionization_table=None):
+                      line_database=None, ionization_table=None,
+                      field_parameters = None):
     """
     Create a yt LightRay object for multiple consecutive datasets (eg IGM).
     This is a wrapper function around yt's LightRay interface to reduce some
@@ -473,6 +482,13 @@ def make_compound_ray(parameter_filename, simulation_type,
         it uses the table specified in ~/.trident/config
         Default: None
 
+    :field_parameters: optional, dict
+        Used to set field parameters in light rays. For example,
+        if the 'bulk_velocity' field parameter is set, the relative
+        velocities used to calculate peculiar velocity will be adjusted
+        accordingly.
+        Default: None.
+
     **Example**
 
     Generate a compound ray passing from the redshift 0 to redshift 0.05
@@ -581,7 +597,8 @@ def setup_ds(ds):
                              setup_function=setup_ds,
                              solution_filename=solution_filename,
                              data_filename=data_filename,
-                             redshift=None, njobs=-1)
+                             redshift=None, njobs=-1,
+                             field_parameters = field_parameters)
 
 def _determine_ions_from_lines(line_database, lines):
     """