Fix: make box smaller for no pbc structure #84
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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_spheresfunction. The GPU usage is almost zero. I provided a fix by using a smaller box. The test results are mentioned in #82 .