_crd2frag: use OB native PBC implementation

[njzjz]

The previous PBC implementation is to create ghost atoms and pass them to the OpenBabel. Since OpenBabel has supported PBC condition in v3.1.0, the previous implementation is migrated to the native one in this PR.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 71.42857% with 2 lines in your changes missing coverage. Please review.

Project coverage is 39.42%. Comparing base (b666f15) to head (c4623b7).
Report is 215 commits behind head on devel.

Files with missing lines	Patch %	Lines
dpgen/generator/lib/gaussian.py	71.42%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##            devel    #1006      +/-   ##
==========================================
+ Coverage   38.84%   39.42%   +0.58%     
==========================================
  Files          99       99              
  Lines       17995    17979      -16     
==========================================
+ Hits         6990     7089      +99     
+ Misses      11005    10890     -115     

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[njzjz]

@AnguseZhang Please check why the following test fails when open babel is installed.

dpgen/tests/generator/test_gromacs_engine.py

Lines 100 to 105 in e431b40

	@unittest.skipIf(importlib.util.find_spec("openbabel") is None, "requires openbabel")
	def test_make_fp_gaussian(self):
	make_fp_gaussian(iter_index=0, jdata=self.jdata)
	candi = np.loadtxt(os.path.join(self.fp_path, "candidate.shuffled.000.out"), dtype=np.str)
	candi_ref = np.loadtxt(os.path.join(self.dirname, "outputs", "candidate.shuffled.000.out"), dtype=np.str)
	self.assertEqual(sorted([int(i) for i in candi[:,1]]), [0,10,20,30,50])

[AnguseZhang]

I've fixed the ut in this PR njzjz#108. Please check and merge in your PR.

@AnguseZhang Please check why the following test fails when open babel is installed.

dpgen/tests/generator/test_gromacs_engine.py

Lines 100 to 105 in e431b40

	@unittest.skipIf(importlib.util.find_spec("openbabel") is None, "requires openbabel")
	def test_make_fp_gaussian(self):
	make_fp_gaussian(iter_index=0, jdata=self.jdata)
	candi = np.loadtxt(os.path.join(self.fp_path, "candidate.shuffled.000.out"), dtype=np.str)
	candi_ref = np.loadtxt(os.path.join(self.dirname, "outputs", "candidate.shuffled.000.out"), dtype=np.str)
	self.assertEqual(sorted([int(i) for i in candi[:,1]]), [0,10,20,30,50])