Fix: make box smaller for no pbc structure

[anyangml]

This PR aims to solve the issue mentioned in #82. When running inference on no-pbc structures, an artificial box is created and the no-pbc structure is converted to pbc structure. However, the original design gives an unnecessarily large box, which leads to data loading bottleneck due to find_points_in_spheres function. The GPU usage is almost zero. I provided a fix by using a smaller box. The test results are mentioned in #82 .

[yanghan234]

Hi @anyangml, thanks for the contribution and sorry for the delay. Would you please apply the patch that I suggested in the comment above? I reproduced the problem that you raised in #82. It seems that we need a better way to handle isolated systems instead of using the extremely large cell. But, your fix is good enough for the moment. Thank you!

[anyangml]

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[yanghan234]

Merged! Thanks for your interest in MatterSim and your contribution!