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fix typos and make output section more readable

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This commit is contained in:
Axel Kohlmeyer
2022-03-04 06:25:16 -05:00
parent 04dbf307d0
commit 98f83f9b3a
1 changed files with 34 additions and 26 deletions
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doc/src/compute_tally.rst
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@ -31,7 +31,7 @@ Syntax
compute ID group-ID style group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or * or *pe/tally* or *pe/mol/tally* or *stress/tally*
* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally*
* group2-ID = group ID of second (or same) group
Examples
@ -61,7 +61,7 @@ mechanism. Compute *pe/mol/tally* is one such style, that can
- through using this mechanism - separately tally intermolecular
and intramolecular energies. Something that would otherwise be
impossible without integrating this as a core functionality into
the based classes of LAMMPS.
the base classes of LAMMPS.
----------
@ -148,30 +148,38 @@ pairwise property computations.
Output info
"""""""""""
Compute *pe/tally* calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar). Compute *pe/mol/tally* calculates a global 4-element vector
containing (in this order): *evdwl* and *ecoul* for intramolecular pairs
and *evdwl* and *ecoul* for intermolecular pairs. Since molecules are
identified by their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or
different. Compute *force/tally* calculates a global scalar (the force
magnitude) and a per atom 3-element vector (force contribution from
each atom). Compute *stress/tally* calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom). As in :doc:`compute heat/flux <compute_heat_flux>`,
compute *heat/flux/tally* calculates a global vector of length 6,
where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
components of the full heat flow vector,
and the next 3 components are the corresponding components
of just the convective portion of the flow, i.e. the
first term in the equation for :math:`\mathbf{Q}`.
Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
and a per atom 3-element vector
(contribution to the force acting over atoms in the first group
from individual atoms in both groups).
- Compute *pe/tally* calculates a global scalar (the energy) and a per
atom scalar (the contributions of the single atom to the global
scalar).
- Compute *pe/mol/tally* calculates a global 4-element vector containing
(in this order): *evdwl* and *ecoul* for intramolecular pairs and
*evdwl* and *ecoul* for intermolecular pairs. Since molecules are
identified by their molecule IDs, the partitioning does not have to be
related to molecules, but the energies are tallied into the respective
slots depending on whether the molecule IDs of a pair are the same or
different.
- Compute *force/tally* calculates a global scalar (the force magnitude)
and a per atom 3-element vector (force contribution from each atom).
- Compute *stress/tally* calculates a global scalar
(average of the diagonal elements of the stress tensor) and a per atom
vector (the 6 elements of stress tensor contributions from the
individual atom).
- As in :doc:`compute heat/flux <compute_heat_flux>`,
compute *heat/flux/tally* calculates a global vector of length 6,
where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
components of the full heat flow vector,
and the next 3 components are the corresponding components
of just the convective portion of the flow, i.e. the
first term in the equation for :math:`\mathbf{Q}`.
- Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
and a per atom 3-element vector
(contribution to the force acting over atoms in the first group
from individual atoms in both groups).
Both the scalar and vector values calculated by this compute are
"extensive".