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Fix deprecation errors of NumPy 1.25.0

Yuji Ikeda requested to merge yuzie007/ase:fix_for_numpy_1.25.0 into master

NumPy 1.25.0, published in 2023-06-17, has introduced several deprecations, some of which affect ASE testing. This MR fixes (at least some of) these deprecation errors.

As a good side effect, this change seems to fix also some errors in SocketIO Calculators (see https://gitlab.com/yuzie007/ase/-/jobs/4579431854, where I tested my own Docker image on top of ase-full-monty with updating numpy==1.25.0 and gpaw==23.6.0. While there are GPAW originated errors due to deprecation of np.product in NumPy 1.25.0 (which is fixed in current GPAW master but not in the latest 23.6.0), there are no SocketIO-related errors anymore.)

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