Implement estimateVelocities in Molecule class

[harikrishna-au]

Feature: Estimate Velocities from Coordinates

I have implemented a new method estimateVelocities() in the Molecule class to calculate atomic velocities based on the differences in coordinate positions over time.

Changes:

• avogadro/core/molecule.h:

  • Added m_velocities to store velocity vectors for each time step.
  • Added estimateVelocities() method declaration.
  • Added velocities(int index) and setVelocities(...) accessors.

• avogadro/core/molecule.cpp:

  • Implemented estimateVelocities() using finite differences:
    • Forward Difference for the first frame ($t=0$): $v_0 = (r_1 - r_0) / \Delta t$
    • Backward Difference for subsequent frames ($t>0$): $v_i = (r_i - r_{i-1}) / \Delta t$
  • The implementation correctly handles the timestep $\Delta t$ derived from m_timesteps.

• tests/core/moleculetest.cpp:

  • Added a unit test estimateVelocities to verify the correctness of the velocity calculation for a known trajectory.

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