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RMSD: reformulate two loops so their omp simd pragmas can be honoured… #4

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Run time

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Job	Run time
conda / conda (macos-15)	13m 19s
docker / docker (fedora39)	29m 57s
conda / conda (macos-14)	12m 41s
codecheck / codecheck	1h 27m 34s
conda / conda (ubuntu-22.04)	20m 34s
docker / docker (rocky8)	34m 3s
python / linux-build-plumed	8m 43s
mac / macsimple (macos-latest)	9m 38s
mac / macsimple (macos-14)	7m 54s
linux / linux (-coverage-mpi-)	1h 1m 18s
linux / linux (-mpi-)	55m 14s
linux / linux (-intel-)	47m 30s
linux / linux (-pycv-mpi-)	17m 50s
linux / linux (-doc-mpi-)	39m 57s
linux / linux (-debug-mpi-)	39m 57s
linux / linux (-debug-)	34m 57s
linux / linux (-nvhpc-mpi-)	29m 55s
python / linux-test-python (3.10)	2m 16s
python / linux-test-python (3.9)	3m 56s
python / linux-test-python (3.13)	2m 14s
python / linux-test-python (3.11)	2m 2s
python / linux-test-python (3.12)	2m 14s
	9h 23m 43s