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Description of Problem

I would like to create an animation of 100,000 atoms with 10,000 frames from my molecular dynamics simulations. Currently I am using dupliverts with a single uv sphere for each atom type. This has worked great in creating a single frame using the python api. However, I am unsure on the correct way to specify the change in vertices at each frame in Blender. I have data that will give me the position of each atom at each timestep/frame.

Initial Atom Configuration 512 Atoms

What I have Tried

What would be the ideal way to animate this simulation? From reading I have seen that using shape keys would allow me to specify the change in the vertices from initial positions (Basis). However, this would mean that I would have to create 10,000 shape keys and change the value from 0 to 1 for each step but would allow me to take advantage of interpolation. The best example I can find showing how this can be done using the blender python api simple example of shape key python api. However, when I used this I was only able to create one shape key not the 10,000 that I would need.

edit: So I got the functionality that I need using this code. But it still does not answer are shape keys the correct way to handle 10,000 steps?

obj = bpy.context.object
shape_keys = ['step ' + str(i) for i in range(10000)]
for shape_key in shape_keys:
    obj.shape_key_add(name=shape_key, from_mix=False)

for shape_key in shape_keys:
    bm = bmesh.new() 
    bm.from_mesh(obj.data)
    shape = bm.verts..layers.shape[shape_key]
    for vert in bm.verts:
        vert[shape] = 'change vertex position here'
    bm.to_mesh(obj.data)

Probably very inefficient would be interested if there are better ways.

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It is possible to keyframe each vertex. While by default Blender does not provide a GUI way to do this, it does include the AnimAll addon that provides a way to visually keyframe various components and values like vertices and edge creases. A python script can also easily keyframe the vertices.

import bpy
from random import random

obj = bpy.context.object
for f in range(bpy.context.scene.frame_end):
    for v in obj.data.vertices:
        m = random() * 0.1
        if f%2:
            v.co.z += m
        else:
            v.co.z -= m
        # index of 2 means only the z-axis
        # -1 (x,y, and z change), 0 x-axis, 1 y-axis
        # you will get weird behavior if the index and 
        # axis changed do not match
        v.keyframe_insert('co', index=2, frame=f)

Once keyframed they show in the graph editor and dopesheet like any other animation, meaning modifiers can be added and interpolation types changed. You will find the fcurves in obj.data.animation_data.action.fcurves.

keyframed vertices

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  • $\begingroup$ Perfect I like how the code example just works and does not require any addons. As an added benefit it feels like it is the "correct" way to do it. What would the index be for changing x,y,and z? $\endgroup$ – costrouc Apr 22 '17 at 12:50
  • $\begingroup$ I edited the above answer to include info on what index to use. $\endgroup$ – costrouc Apr 22 '17 at 12:59

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