[drroe]

Version 7.12.5. Note that this revision increase also takes into account missing revision bumps from previous PRs:
7.12.4 : TIMatch #1193
7.12.3 : Inline common distance routines #1197
7.12.2 : Optimize two-mask radial calculation for orthogonal cells #1196
7.12.1 : Optimize radial calculation for orthogonal cells #1195

Inspired by the previous pull requests which have improved the speed of the radial command with orthogonal shells, I have refactored some of the distance calculations to further improve speed in radial for non-orthogonal cells and for other commands using imaged distance calculations in general.

Most benchmarks have remained at the previous performance (0.98x - 1.00x speedup). However, several benchmarks have improved from this PR:

#Benchmark                                              Old      New  SpeedUp   Change
nativecontacts_benchmark.                            2.9833   2.3967     1.24    19.66
SPAM_benchmark.                                      3.0800   2.4933     1.24    19.05
Hbond_nonortho_benchmark.                            2.7067   2.1333     1.27    21.18
LIE_benchmark.                                       1.5467   1.1433     1.35    26.08
Radial_solvent-solvent_by_site_benchmark.           22.1433  16.1467     1.37    27.08
Watershell_ortho_benchmark.                          3.1800   2.3033     1.38    27.57
Radial_solvent-solute,_center2_benchmark.            2.9900   2.0900     1.43    30.10
Radial_solvent-solvent_benchmark.                    9.9533   6.4033     1.55    35.67
Radial_solvent-solvent,_nointramol_benchmark.       20.1367  12.8767     1.56    36.05
Radial_solvent_to_solute_benchmark.                  5.4833   3.3433     1.64    39.03
Radial_solvent-solute_benchmark.                     4.4967   2.2800     1.97    49.30

In particular the non-orthogonal imaging in the radial command has been sped up almost 2x.

A new class Dcalc has been created which is intended to be used when multiple distances will be calculated in a single frame. Currently it is only used by radial but probably should be put anywhere multiple distances are being calculated. For non-orthogonal images, it uses the same logic employed in Dist_Imaged.cpp to cut down the number of images that need to be checked.

The DIST2_ImageNonOrtho() functions now just call the improved distance routine for non-orthogonal cells from Dist_Imaged.cpp (Cpptraj::Dist2_Imaged_Cart()). The results are identical.

This PR also adds a check for duplicate atom names in residues when topologies are loaded/created since this can lead to unexpected behavior (e.g. typically one expects the mask :1@CA to select a single atom.