Deprecated keywords

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An annoying thing about Tonto is the regular keyword changes.

Keyword changes occur because the program is developing all the time!

Errors are being corrected!

To make keyword changes less annoying, we list here keywords that are deprecated or changed.

And we give notice of correction of errors and bugs.


Deprecations and changes due for 2012


  • pos= becomes position=
  • thermal_tensor= becomes ADP= ; u_tensor= and ADP_tesnor= are also acceptable
  • thermal_axis_system= becomes ADP_axis_system=


  • ex= becomes exponent= ; deprecated immediately
  • pos= becomes position= ; deprecated immediately


  • force_thermal_symmetry is deprecated immediately
  • optimise_thermals= is deprecated immediately


  • cc= becomes contractions= ; deprecated immediately
  • ex= becomes exponents= ; deprecated immediately
  • pos= becomes position= ; deprecated immediately


  • cc= becomes contractions= ; deprecated immediately
  • ex= becomes exponents= ; deprecated immediately
  • pos= becomes position= ; deprecated immediately


The following commands were used to hack dispersion or other experimental corrections into Tonto, and should no longer be needed.

  • add_to_f_calc=; deprecated immediately
  • add_to_f_exp=; deprecated immediately
  • add_to_f_pred=; deprecated immediately
  • add_to_i_exp=; deprecated immediately
  • add_to_i_pred=; deprecated immediately
  • add_to_i_sigma=; deprecated immediately

Change in behaviour: all quantities referring to F2 should now use I instead. That is because the intensity I is now identified with F2, whereas previously the intensity included LP and angular velocity corrections. It assumed that such corrections are removed from the experimental intensity data.

  • F2_exp=; deprecated immediately, use I_exp=
  • F2_pred=; deprecated immediately, use I_pred=
  • F2_sigma=; deprecated immediately, use I_sigma=. Note also that the algorithm for calculating sigma's in F from sigmas in I has changed, so previous results may not be exactly reproducible. It is recommended to use the new default, refining all models relative top experimental intensities rather than experimental structure factors. In this way the artificial and unnecessary manipulations in the sigmas can be avoided, and one can retain negative values for the experimental intensities.


  • prune_weak_reflections; an error was corrected in the pruning of weak reflections which were entered as F2 (intensity) values. The error was that rather than using F2_exp/F2_sigma to reject weak reflections, F_exp/F_sigma was used. Since the latter is usually smaller than the former, more reflections would have been rejected than expected according to the correct criteria.mme
  • F2_sigma_cutoff=; deprecated immediately; please use I_sigma_cutoff= instead.
  • prune_bad_reflections; deprecated immediately; please use prune_bad_F_reflections instead. Also consider using the new keyword prune_bad_I_reflections which rejects on intensities rather than structure factors.
  • prune_negative_I_exp; new keyword, functions like prune_negative_F_exp to remove negative intensity values from the data set.