refactoring: Create class for coordination number calculation

[Thomas3R]

Since some methods use different counting functions or parameters for coordination number calculations, I refactored the ncoord functionalities into a new base class, NCoordBase. This design allows for easy input of new parameters and the creation of derived classes with customized counting functions.

Additionally, cn and dcndr have been moved to be member variables of NCoordBase.

[marvinfriede]

The issue with different matrix orderings should be fixed first (to N, 3N). Otherwise, the object-oriented implementation does not make much sense, because we are duplicating the coordination number calculation again.

[Copilot]

Pull Request Overview

This PR refactors coordination number calculation functionality by introducing a new class hierarchy with NCoordBase as the base class. The design enables customization of counting functions and parameters for different coordination number calculation methods while centralizing common functionality.

• Creates NCoordBase class with virtual methods for counting functions and electronegativity factors
• Implements NCoordErf and NCoordErfD4 derived classes with specific counting behavior
• Moves cn and dcndr vectors to be member variables of the base class

Reviewed Changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
include/dftd_ncoord.h	Defines new class hierarchy with base and derived classes for coordination number calculations
src/dftd_ncoord.cpp	Implements the new class methods and refactors existing functions to use class-based approach
src/dftd_eeq.cpp	Updates EEQ charge calculation to use new NCoordErf class
src/dftd_dispersion.cpp	Updates dispersion calculation to use new NCoordErfD4 class
test/test_ncoord.cpp	Adds comprehensive numerical gradient tests for both coordination number classes
test/test_grad.cpp	Adds numerical gradient test for charge derivatives and fixes memory management
test/test_ghost.cpp	Updates ghost atom tests to use new class interface
include/dftd_cblas.h	Fixes matrix-vector multiplication logic for transposed operations

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