def anim(x,y,z): f = mlab.gcf() plt = mlab.points3d(x,y,z, colormap="copper", scale_factor=.25) while(True): # TODO: Paralelize md.evolve(25) x,y,z = md.get_positions() stats = md.system_stats() print('Temp',stats[-1]) plt.mlab_source.set(x=x, y=y, z=z) f.scene.render() yield
ax.set_xlim([-2.,2]) ax.set_ylim([-2.,2]) ax.set_zlim([-2.,2]) ax.scatter(x, y, z, c='grey', marker='o') ax.scatter(x_to_compare, y_to_compare, z_to_compare, c='grey', marker='^') #plt.show() plt.savefig('initial_positions.pdf') print() print('testing get positions') x2,y2,z2 = md.get_positions() print('x max diff.:',np.max(np.abs(x - x2))) print('y max diff.:',np.max(np.abs(y - y2))) print('z max diff.:',np.max(np.abs(z - z2))) print() #print('forces for single step') #fx,fy,fz = md.get_forces() #print(np.dstack([fx,fy,fz])) #print('single step') #md.evolve(1) #x2,y2,z2 = md.get_positions() ##print(np.dstack([x2,y2,z2])) #print(np.sqrt(np.max(x2**2+y2**2+z2**2)))