Fix clang-tidy warnings

[Rombur]

I ran clang-tidy a couple of months ago and forgot to push the changes. There is nothing really important. Here is the clang-tidy options that I have used:

Checks: >
  -*,
  bugprone-too-small-loop-variable,
  bugprone-unchecked-optional-access,
  bugprone-use-after-move,
  bugprone-virtual-near-miss,
  cppcoreguidelines-init-variables,
  modernize-deprecated-headers,
  modernize-use-nullptr,
  modernize-use-override,
  modernize-use-using,
  mpi-*
  performance-*,
  -performance-inefficient-string-concatenation,
  -performance-avoid-endl