add more details to SimpleTrap example

README.md

@@ -212,13 +212,13 @@ in the terminal. Remote execution on Berkeley HPC (Savio) requires running
 sbatch saviojob.sh
 ```
 
-The data will be saved as VTK files. The file named as ```<prefix>_<electrode name>.vtk``` stores potential, field (RF only), and field square (RF only). The file named as ```<prefix>_<electrode name>_mesh.vtk``` stores the charge distribution, and the final mesh after adaptive mesh during simulation.
+The data will be saved as VTK files. The file named as ```<prefix>_<electrode_name>.vtk``` stores potential, field (RF only), and field square (RF only). The file named as ```<prefix>_<electrode_name>_mesh.vtk``` stores the charge distribution, and the final mesh after adaptive mesh during simulation.
 
 ### 4. Result analysis <div id='id-6'/> 
 
 Lastly, after we get the results, we can visualize the result by simply calling 
 ```
-Result.view(prefix, '<electrode name>')
+Result.view(prefix, '<electrode_name>')
 ```
 For example, if we want to visualize the field square of the SimpleTrap's RF electrode, we can simply call ```Result.view(prefix, 'RF')``` in the same folder as the result VTK files. Here is the visualization example
 

bem/area_constraints.py

@@ -34,14 +34,12 @@ def __init__(self, start, end, radius, *a, **k):
 
     def lookup(self, x):
         # http://mathworld.wolfram.com/Point-LineDistance3-Dimensional.html
-        print((self.start-x).shape)
         d = np.linalg.norm(np.cross(self.start-x, self.end-x), axis=1)/np.linalg.norm(self.end-self.start)
         dmax = np.sqrt(np.linalg.norm(self.start-self.end)**2 + self.radius**2)
         dx1 = np.linalg.norm(self.start - x, axis=1)
         dx2 = np.linalg.norm(self.end - x, axis=1)
         # return np.where((d<self.radius), self.inside, self.outside)
         return np.where((d<self.radius)&(dx1<dmax)&(dx2<dmax), self.inside, self.outside)
-        # FIXME: cylinder has infinite length
 
 class Box(Constraint):
     def __init__(self, start=None, center=None, diagonal=None, end=None,