fix(abacus): do not collect the unconverged structure for AIMD

[pxlxingliang]

No description provided.

[njzjz]

If 0 is used to indicate systems that do not coverage, how can we collect 0-energy systems?

[pxlxingliang]

0 is really not a good choice. May "None" is better. I will change it.

[njzjz]

Can ABACUS calculate a hydrogen ion?

[njzjz]

Note that None will make the NumPy array become an object array:

>>> import numpy as np
>>> np.array([1., None]).dtype
dtype('O')

Maybe you can use np.nan or np.inf instead.

>>> np.array([1., np.nan, np.inf]).dtype
float64

>>> x = np.array([1., np.nan, np.inf])
>>> np.isnan(x)
array([False,  True, False])

[pxlxingliang]

Can ABACUS calculate a hydrogen ion?

Yes. I see. The previous statement is indeed incorrect.

[pxlxingliang]

Note that None will make the NumPy array become an object array:

>>> import numpy as np
>>> np.array([1., None]).dtype
dtype('O')

Maybe you can use np.nan or np.inf instead.

>>> np.array([1., np.nan, np.inf]).dtype
float64

>>> x = np.array([1., np.nan, np.inf])
>>> np.isnan(x)
array([False,  True, False])

Thanks for your suggestion, I don't know about the object array before.
I will change to "np.nan"

[codecov-commenter]

Codecov Report

Base: 82.33% // Head: 82.21% // Decreases project coverage by -0.11% ⚠️

Coverage data is based on head (5bfd1d1) compared to base (e8a2fbe).
Patch coverage: 41.17% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #368      +/-   ##
==========================================
- Coverage   82.33%   82.21%   -0.12%     
==========================================
  Files          67       67              
  Lines        5892     5909      +17     
==========================================
+ Hits         4851     4858       +7     
- Misses       1041     1051      +10     

Impacted Files	Coverage Δ
dpdata/abacus/md.py	90.75% <41.17%> (-8.27%)	⬇️

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[njzjz]

Can you add an extra test?

[pxlxingliang]

Can you add an extra test?

Ok, I will add one.