Add feature to enable overlaying the atoms to the generated AFM images. #976

Job	Run time
Test docker image on ubuntu-latest	1m 56s
test-package (3.11)	11m 20s
test-package (3.8)	13m 12s
test-package (3.9)	12m 42s
test-package (3.13)	11m 32s
test-package (3.10)	11m 55s
test-package (3.12)	11m 19s
	1h 13m 56s

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