pygauss.isosurface module

Created on Mon May 25 15:23:49 2015

@author: chris based on add_isosurface function from chemview

pygauss.isosurface.calc_normals(verts, faces)

from; https://sites.google.com/site/dlampetest/python/calculating-normals-of-a-triangle-mesh-using-numpy

pygauss.isosurface.get_isosurface(coordinates, function, isolevel=0.03, color=(255, 0, 0, 255), extents=(5, 5, 5), resolution=100)

Add an isosurface to the current scene.

Parameters:

• coordinates (numpy.array) – the coordinates of the system
• function (func) – A function that takes x, y, z coordinates as input and is broadcastable using numpy. Typically simple functions that involve standard arithmetic operations and functions such as x**2 + y**2 + z**2 or np.exp(x**2 + y**2 + z**2) will work. If not sure, you can first pass the function through numpy.vectorize. Example: mv.add_isosurface(np.vectorize(f))
• isolevel (float) – The value for which the function should be constant.
• color ((int, int, int, int)) – The color given in RGBA format
• extents ((float, float, float)) – +/- x,y,z to extend the molecule geometrty when constructing the surface
• resolution (int) – The number of grid point to use for the surface. An high value will give better quality but lower performance.

pygauss.isosurface.normalize_v3(arr)

Normalize a numpy array of 3 component vectors shape=(n,3)