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Fixes from Fortitude linter #1108

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Run time

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Job	Run time
Code format check	12s
Basic build (7)	1m 1s
Intel build	1m 44s
Basic build (9)	58s
Debug build	1m 19s
Basic build (10)	57s
Optimized build (9)	56s
FFTW build	1m 45s
TCPB build	31s
Optimized build (12)	1m 2s
MPICH build (7, 3.4.3)	1m 21s
MPICH build (7, 4.0.2)	1m 23s
OpenMPI build	40s
MPICH build (10, 3.4.3)	1m 1s
PLUMED build (2.7.6)	1m 3s
MPICH build (10, 4.0.2)	1m 11s
PLUMED build (2.8.2)	1m 4s
	18m 8s