Refactor: remove `LCAO_Matrix` from several class #7002

Job	Run time
Build with GNU toolchain	7m 8s
Build with Intel toolchain	6m 5s
Build extra components with GNU toolchain	12m 58s
Build extra components with Intel toolchain	10m 10s
Build with CUDA support	14m 51s
Build without LCAO	4m 46s
Build without ELPA	7m 7s
Build without LCAO and MPI	3m 38s
	1h 6m 43s

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