Merge branch 'master' into pair-hybrid-scaled

This commit is contained in:
Axel Kohlmeyer
2021-04-09 22:21:16 -04:00
30 changed files with 335 additions and 347 deletions

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@ -46,13 +46,14 @@ system volume (or area in 2d). The second term is the virial, equal to
-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
many-body, and long-range interactions, where :math:`r_i` and
:math:`f_i` are the position and force vector of atom *i*, and the black
dot indicates a dot product. When periodic boundary conditions are
used, N' necessarily includes periodic image (ghost) atoms outside the
central box, and the position and force vectors of ghost atoms are thus
included in the summation. When periodic boundary conditions are not
used, N' = N = the number of atoms in the system. :doc:`Fixes <fix>`
that impose constraints (e.g. the :doc:`fix shake <fix_shake>` command)
also contribute to the virial term.
dot indicates a dot product. This is computed in parallel for each
sub-domain and then summed over all parallel processes. Thus N'
necessarily includes atoms from neighboring sub-domains (so-called ghost
atoms) and the position and force vectors of ghost atoms are thus
included in the summation. Only when running in serial and without
periodic boundary conditions is N' = N = the number of atoms in the
system. :doc:`Fixes <fix>` that impose constraints (e.g. the :doc:`fix
shake <fix_shake>` command) may also contribute to the virial term.
A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The 6 components of the vector are