correct the description of how the F dot r contributions are computed

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Axel Kohlmeyer
2021-04-08 08:44:18 -04:00
parent 1ca38db9df
commit ac5bd8a4f7

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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, -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 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 :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 dot indicates a dot product. This is computed in parallel for each
used, N' necessarily includes periodic image (ghost) atoms outside the sub-domain and then summed over all parallel processes. Thus N'
central box, and the position and force vectors of ghost atoms are thus necessarily includes atoms from neighboring sub-domains (so-called ghost
included in the summation. When periodic boundary conditions are not atoms) and the position and force vectors of ghost atoms are thus
used, N' = N = the number of atoms in the system. :doc:`Fixes <fix>` included in the summation. Only when running in serial and without
that impose constraints (e.g. the :doc:`fix shake <fix_shake>` command) periodic boundary conditions is N' = N = the number of atoms in the
also contribute to the virial term. 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 A symmetric pressure tensor, stored as a 6-element vector, is also
calculated by this compute. The 6 components of the vector are calculated by this compute. The 6 components of the vector are