[whahnsr]

Summary

Use the existing Cpptraj::Dcalc class in Action_PairDist
to avoid redundant calculations when evaluating atom-pair distances.

The change:

• Initializes Dcalc once per frame.
• Calls SetXYZ1() once per outer-loop atom.
• Uses Dist2() in the inner loop.
• Covers both single-mask and two-mask calculations.

This builds on the distance-calculation improvements
introduced in #1198.

Validation

• All four existing PairDist regression comparisons pass.
• Baseline and optimized versions produce byte-for-byte
  identical benchmark output.
• Both orthogonal and nonorthogonal imaging were tested.

Performance

Benchmarks were run on an Intel i5-6600, pinned to CPU 2,
using single-threaded execution and five repetitions
with perf stat.

Independent MDAnalysis adenylate kinase trajectory:
47,681 atoms, 4 million atom pairs per frame.

Imaging	Frames	Elapsed time reduction	CPU cycle reduction	Instruction reduction
Orthogonal	100	7.4%	8.2%	22.4%
Nonorthogonal	10	23.5%	17.7%	25.8%

The orthogonal benchmark repeats 10 distinct trajectory
frames ten times. Its box angles were changed to 90 degrees
for a controlled orthogonal imaging comparison.

A separate CPPTRAJ truncated-octahedral benchmark showed
a 32.8% reduction in elapsed time.

Maintainer note

Thank you for reviewing and merging our earlier related
optimizations. I particularly appreciate the subsequent
work on distance calculations in #1198, which provided
the basis for this change.

I hope this is a useful extension of that work. If it
overlaps with anything already underway or planned,
please feel entirely free to close the PR. I certainly
don't want to duplicate effort or interfere with your
development plans.

Thanks again for your time and for maintaining CPPTRAJ.