vdW-D4: Switch to smooth cutoff

[Growl1234]

In dftd4/dftd4#377 upstream has discussed about enabling smooth cutoff that was introduced since 4.2.0 by default in the future releases. This will be important for PBC calculations as the images close to the cutoff radius will be affected; in principle the result from smooth-cutoff path will be better as smooth cutoff resolves some gradient/virial issues.

Since v4.2.0 is already the minimum required version of dftd4 for ABACUS, it's rather straight-forward to change this calculation type. However, the value setting of d4_smooth_cutoff_width_2 and d4_smooth_cutoff_width_3 might not be clear. I may leave the related discussion upstream.

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[Growl1234]

The Integration Test workflow is expected to fail for now because I did not update the reference yet. I'd also set the PR to draft until the smooth width value is made clear upstream. [Edit: it's surprising that tests passed; looks like the change doesn't reach the threshold.]

[Growl1234]

From upstream response they are willing to treat the 0.05 Bohr as a reasonable default. So the next question would be how we treat the cutoff width: as an internal logic, or expose it to users to allow adjustment? (my wish would be the latter, the only concern is how we can explain it well in the documentation)

[Growl1234]

I will add two new input parameters, vdw_cutoff_smooth_width_2b and vdw_cutoff_smooth_width_3b, for smooth cutoff. They will be both 0.05 Bohr by default, and setting to 0 will perform the same result as traditional sharp cutoff. In the near future I might modify DFT-D3 code to make it also use smooth cutoff (see dftd3/simple-dftd3#199), and the parameters can be reused then.

[Growl1234]

Side note: s-dftd3 package has marked dftd3_set_model_realspace_cutoff as deprecated; appearently this will also happen on dftd4 side, which means dftd4_set_model_realspace_cutoff will be removed in v5.0.0 release, and only dftd4_set_model_realspace_cutoff_smooth will be left. Therefore, the API change in this PR will become mandatory.

[ZhouXY-PKU]

Nice job!