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change wording to be more in line with LAMMPS terminology and current state of implementation

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Donatas Surblys
2019-11-13 22:19:34 +09:00
parent 85e96bf31c
commit 28269c4a21
2 changed files with 22 additions and 15 deletions
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9
doc/src/compute_heat_flux.rst
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@ -54,7 +54,7 @@ third calculates per-atom stress (\ *stress-ID*\ ).
(or any group whose atoms are superset of the atoms in this compute's
group). LAMMPS does not check for this.
In case of pairwise interactions the heat flux is defined as:
In case of two-body interactions, the heat flux is defined as:
.. math::
\mathbf{J} &= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i - \sum_{i} \mathbf{S}_{i} \mathbf{v}_i \right] \\
@ -69,10 +69,10 @@ per-atom stress tensor calculated by the compute *stress-ID*.
See :doc:`compute stress/atom <compute_stress_atom>`
and :doc:`compute centroid/stress/atom <compute_stress_atom>`
for possible definitions of atomic stress :math:`\mathbf{S}_i`
in the case of thee-body and larger many-body interactions.
in the case of bonded and many-body interactions.
The tensor multiplies :math:`\mathbf{v}_i` as a 3x3 matrix-vector multiply
to yield a vector.
Note that as discussed below, the :math:`\frac{1}{V}` scaling factor in the
Note that as discussed below, the 1/:math:`{V}` scaling factor in the
equation for :math:`\mathbf{J}` is NOT included in the calculation performed by
these computes; you need to add it for a volume appropriate to the atoms
included in the calculation.
@ -92,8 +92,7 @@ included in the calculation.
.. warning::
The compute *heat/flux* has been reported to produce unphysical
values for three and larger many-body interactions such
as angles, dihedrals and torsions,
values for angle, dihedral and improper contributions
when used with :doc:`compute stress/atom <compute_stress_atom>`,
as discussed in :ref:`(Surblys) <Surblys2>` and :ref:`(Boone) <Boone>`.
You are strongly advised to

28
doc/src/compute_stress_atom.rst
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@ -112,8 +112,7 @@ The sixth and seventh terms, Kspace and :doc:`fix <fix>` contribution
respectively, are computed identical to compute *stress/atom*.
Although the total system virial is the same as compute *stress/atom*,
compute *centroid/stress/atom* is know to result in more consistent
heat flux values for three and larger many-body interactions
such as angles, dihedrals and impropers,
heat flux values for angle, dihedras and improper contributions
when computed via :doc:`compute heat/flux <compute_heat_flux>`.
If no extra keywords are listed, the kinetic contribution
@ -138,16 +137,20 @@ the interaction, with the :math:`r` vectors unwrapped by periodic boundaries
so that the cluster of atoms is close together. The total
contribution for the cluster interaction is divided evenly among those
atoms. Details of how compute *centroid/stress/atom* obtains
the virial for individual atoms for many-body potentials
the virial for individual atoms
is given in :ref:`(Surblys) <Surblys1>`,
where the idea is that the virial of the atom :math:`I`
is the result of only the force :math:`\mathbf{F}_I` on the atom due
to the many-body interaction
to the interaction
and its positional vector :math:`\mathbf{r}_{I0}`,
relative to the geometric center of the
interacting atoms. The periodic boundary treatment is identical to
interacting atoms, regardless of the number of participating atoms.
The periodic boundary treatment is identical to
that of compute *stress/atom*, and both of them reduce to identical
expressions for pairwise interactions.
expressions for two-body interactions,
i.e. computed values for contributions from bonds and two-body pair styles,
such as :doc:`Lennard-Jones <pair_lj>`, will be the same,
while contributions from angles, dihedrals and impropers will be different.
The :doc:`dihedral\_style charmm <dihedral_charmm>` style calculates
pairwise interactions between 1-4 atoms. The virial contribution of
@ -225,10 +228,15 @@ The per-atom array values will be in pressure\*volume
Restrictions
""""""""""""
Pair styles with three and larger many-body interactions,
such as Tersoff do not currently support
compute *centroid/stress/atom* and LAMMPS will generate an error
in such cases.
Currently, compute *centroid/stress/atom* does not support
pair styles with many-body interactions,
such as :doc:`Tersoff <pair_tersoff>`,
and LAMMPS will generate an error in such cases.
In principal, equivalent formulation
to that of angle, dihedral and improper contributions
in the virial :math:`W_{ab}` formula
can also be applied to the many-body pair styles,
and is planned in the future.
Related commands
""""""""""""""""