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Merge branch 'master' into collected-small-changes

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Axel Kohlmeyer
2021-07-20 16:02:46 -04:00
parent d8ca3e4b16 2a0c6ad979
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1
doc/src/Commands_compute.rst
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@ -72,6 +72,7 @@ KOKKOS, o = OPENMP, t = OPT.
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
* :doc:`heat/flux <compute_heat_flux>`
* :doc:`heat/flux/tally <compute_tally>`
* :doc:`heat/flux/virial/tally <compute_tally>`
* :doc:`hexorder/atom <compute_hexorder_atom>`
* :doc:`hma <compute_hma>`
* :doc:`improper <compute_improper>`

11
doc/src/compute.rst
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@ -208,7 +208,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`event/displace <compute_event_displace>` - detect event on atom displacement
* :doc:`fabric <compute_fabric>` - calculates fabric tensors from pair interactions
* :doc:`fep <compute_fep>` -
* :doc:`force/tally <compute_tally>` -
* :doc:`force/tally <compute_tally>` - force between two groups of atoms via the tally callback mechanism
* :doc:`fragment/atom <compute_cluster_atom>` - fragment ID for each atom
* :doc:`global/atom <compute_global_atom>` -
* :doc:`group/group <compute_group_group>` - energy/force between two groups of atoms
@ -217,7 +217,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`gyration/shape <compute_gyration_shape>` - shape parameters from gyration tensor
* :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>` - shape parameters from gyration tensor for each chunk
* :doc:`heat/flux <compute_heat_flux>` - heat flux through a group of atoms
* :doc:`heat/flux/tally <compute_tally>` -
* :doc:`heat/flux/tally <compute_tally>` - heat flux through a group of atoms via the tally callback mechanism
* :doc:`heat/flux/virial/tally <compute_tally>` - virial heat flux between two groups via the tally callback mechanism
* :doc:`hexorder/atom <compute_hexorder_atom>` - bond orientational order parameter q6
* :doc:`hma <compute_hma>` - harmonically mapped averaging for atomic crystals
* :doc:`improper <compute_improper>` - energy of each improper sub-style
@ -240,8 +241,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`pe <compute_pe>` - potential energy
* :doc:`pe/atom <compute_pe_atom>` - potential energy for each atom
* :doc:`mesont <compute_mesont>` - Nanotube bending,stretching, and intertube energies
* :doc:`pe/mol/tally <compute_tally>` -
* :doc:`pe/tally <compute_tally>` -
* :doc:`pe/mol/tally <compute_tally>` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
* :doc:`pressure <compute_pressure>` - total pressure and pressure tensor
* :doc:`pressure/cylinder <compute_pressure_cylinder>` - pressure tensor in cylindrical coordinates
@ -289,7 +290,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
* :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
* :doc:`stress/mop/profile <compute_stress_mop>` - profile of the normal components of the local stress tensor using the method of planes
* :doc:`stress/tally <compute_tally>` -
* :doc:`stress/tally <compute_tally>` - stress between two groups of atoms via the tally callback mechanism
* :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` - per-atom chemical concentration of a specified species for each tDPD particle
* :doc:`temp <compute_temp>` - temperature of group of atoms
* :doc:`temp/asphere <compute_temp_asphere>` - temperature of aspherical particles

96
doc/src/compute_tally.rst
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@ -1,5 +1,6 @@
.. index:: compute force/tally
.. index:: compute heat/flux/tally
.. index:: compute heat/flux/virial/tally
.. index:: compute pe/tally
.. index:: compute pe/mol/tally
.. index:: compute stress/tally
@ -10,6 +11,9 @@ compute force/tally command
compute heat/flux/tally command
===============================
compute heat/flux/virial/tally command
======================================
compute pe/tally command
========================
@ -27,7 +31,7 @@ Syntax
compute ID group-ID style group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* style = *force/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally*
* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or * or *pe/tally* or *pe/mol/tally* or *stress/tally*
* group2-ID = group ID of second (or same) group
Examples
@ -38,13 +42,17 @@ Examples
compute 1 lower force/tally upper
compute 1 left pe/tally right
compute 1 lower stress/tally lower
compute 1 subregion heat/flux/tally all
compute 1 liquid heat/flux/virial/tally solid
Description
"""""""""""
Define a computation that calculates properties between two groups of
atoms by accumulating them from pairwise non-bonded computations. The
two groups can be the same. This is similar to :doc:`compute group/group <compute_group_group>` only that the data is
atoms by accumulating them from pairwise non-bonded computations.
Except for *heat/flux/virial/tally*, the two groups can be the same.
This is similar to :doc:`compute group/group <compute_group_group>`
only that the data is
accumulated directly during the non-bonded force computation. The
computes *force/tally*\ , *pe/tally*\ , *stress/tally*\ , and
*heat/flux/tally* are primarily provided as example how to program
@ -57,6 +65,76 @@ the based classes of LAMMPS.
----------
Compute *heat/flux/tally* obtains the heat flux
(strictly speaking, heat flow) inside the first group,
which is the sum of the convective contribution
due to atoms in the first group and the virial contribution
due to interaction between the first and second groups:
.. math::
\mathbf{Q}= \sum_{i \in \text{group 1}} e_i \mathbf{v}_i + \frac{1}{2} \sum_{i \in \text{group 1}} \sum_{\substack{j \in \text{group 2} \\ j \neq i } } \left( \mathbf{F}_{ij} \cdot \mathbf{v}_j \right) \mathbf{r}_{ij}
When the second group in *heat/flux/tally* is set to "all",
the resulting values will be identical
to that obtained by :doc:`compute heat/flux <compute_heat_flux>`,
provided only pairwise interactions exist.
Compute *heat/flux/virial/tally* obtains the total virial heat flux
(strictly speaking, heat flow) into the first group due to interaction
with the second group, and is defined as:
.. math::
Q = \frac{1}{2} \sum_{i \in \text{group 1}} \sum_{j \in \text{group 2}} \mathbf{F}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right)
Although, the *heat/flux/virial/tally* compute
does not include the convective term,
it can be used to obtain the total heat flux over control surfaces,
when there are no particles crossing over,
such as is often in solid-solid and solid-liquid interfaces.
This would be identical to the method of planes method.
Note that the *heat/flux/virial/tally* compute is distinctly different
from the *heat/flux* and *heat/flux/tally* computes,
that are essentially volume averaging methods.
The following example demonstrates the difference:
.. code-block:: LAMMPS
# System with only pairwise interactions.
# Non-periodic boundaries in the x direction.
# Has LeftLiquid and RightWall groups along x direction.
# Heat flux over the solid-liquid interface
compute hflow_hfvt LeftLiquid heat/flux/virial/tally RightWall
variable hflux_hfvt equal c_hflow_hfvt/(ly*lz)
# x component of approximate heat flux vector inside the liquid region,
# two approaches.
#
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom NULL virial
compute hflow_hf LeftLiquid heat/flux myKE myPE myStress
variable hflux_hf equal c_hflow_hf[1]/${volLiq}
#
compute hflow_hft LeftLiquid heat/flux/tally all
variable hflux_hft equal c_hflow_hft[1]/${volLiq}
# Pressure over the solid-liquid interface, three approaches.
#
compute force_gg RightWall group/group LeftLiquid
variable press_gg equal c_force_gg[1]/(ly*lz)
#
compute force_ft RightWall force/tally LeftLiquid
compute rforce_ft RightWall reduce sum c_force_ft[1]
variable press_ft equal c_rforce_ft/(ly*lz)
#
compute rforce_hfvt all reduce sum c_hflow_hfvt[1]
variable press_hfvt equal -c_rforce_hfvt/(ly*lz)
----------
The pairwise contributions are computing via a callback that the
compute registers with the non-bonded pairwise force computation.
This limits the use to systems that have no bonds, no Kspace, and no
@ -83,7 +161,17 @@ 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).
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".