consolidate pair-wise vs pairwise spelling

This commit is contained in:
Axel Kohlmeyer
2022-01-21 10:48:35 -05:00
parent 3a6bd2e698
commit 3311b1344c
13 changed files with 15 additions and 15 deletions

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@ -225,7 +225,7 @@ follows:
commands in an input script.
- The Force class computes various forces between atoms. The Pair
parent class is for non-bonded or pair-wise forces, which in LAMMPS
parent class is for non-bonded or pairwise forces, which in LAMMPS
also includes many-body forces such as the Tersoff 3-body potential if
those are computed by walking pairwise neighbor lists. The Bond,
Angle, Dihedral, Improper parent classes are styles for bonded

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@ -416,7 +416,7 @@ This will most likely cause errors in kinetic fluctuations.
not defined for the specified atom style.
*Molecule has bond topology but no special bond settings*
This means the bonded atoms will not be excluded in pair-wise
This means the bonded atoms will not be excluded in pairwise
interactions.
*Molecule template for create_atoms has multiple molecules*

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@ -106,7 +106,7 @@ individual ranks. Here is an example output for this section:
----------
The third section above lists the number of owned atoms (Nlocal),
ghost atoms (Nghost), and pair-wise neighbors stored per processor.
ghost atoms (Nghost), and pairwise neighbors stored per processor.
The max and min values give the spread of these values across
processors with a 10-bin histogram showing the distribution. The total
number of histogram counts is equal to the number of processors.
@ -114,7 +114,7 @@ number of histogram counts is equal to the number of processors.
----------
The last section gives aggregate statistics (across all processors)
for pair-wise neighbors and special neighbors that LAMMPS keeps track
for pairwise neighbors and special neighbors that LAMMPS keeps track
of (see the :doc:`special_bonds <special_bonds>` command). The number
of times neighbor lists were rebuilt is tallied, as is the number of
potentially *dangerous* rebuilds. If atom movement triggered neighbor

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@ -214,7 +214,7 @@ threads/task as Nt. The product of these two values should be N, i.e.
The default for the :doc:`package kokkos <package>` command when
running on KNL is to use "half" neighbor lists and set the Newton flag
to "on" for both pairwise and bonded interactions. This will typically
be best for many-body potentials. For simpler pair-wise potentials, it
be best for many-body potentials. For simpler pairwise potentials, it
may be faster to use a "full" neighbor list with Newton flag to "off".
Use the "-pk kokkos" :doc:`command-line switch <Run_options>` to change
the default :doc:`package kokkos <package>` options. See its page for

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@ -383,7 +383,7 @@ multiple groups, its weight is the product of the weight factors.
This weight style is useful in combination with pair style
:doc:`hybrid <pair_hybrid>`, e.g. when combining a more costly many-body
potential with a fast pair-wise potential. It is also useful when
potential with a fast pairwise potential. It is also useful when
using :doc:`run_style respa <run_style>` where some portions of the
system have many bonded interactions and others none. It assumes that
the computational cost for each group remains constant over time.

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@ -61,7 +61,7 @@ Restrictions
This compute currently calculates the pressure tensor contributions
for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
and in the presence of bonded interactions, the result will be incorrect
due to exclusions for special bonds) and requires pair-wise force
due to exclusions for special bonds) and requires pairwise force
calculations not available for most many-body pair styles. K-space
calculations are also excluded. Note that this pressure compute outputs
the configurational terms only; the kinetic contribution is not included

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@ -460,7 +460,7 @@ using *neigh/thread* *on*, a full neighbor list must also be used. Using
is turned on by default only when there are 16K atoms or less owned by
an MPI rank and when using a full neighbor list. Not all KOKKOS-enabled
potentials support this keyword yet, and only thread over atoms. Many
simple pair-wise potentials such as Lennard-Jones do support threading
simple pairwise potentials such as Lennard-Jones do support threading
over both atoms and neighbors.
The *newton* keyword sets the Newton flags for pairwise and bonded

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@ -119,7 +119,7 @@ name are the older, original LAMMPS implementations. They compute the
LJ and Coulombic interactions with an energy switching function (esw,
shown in the formula below as S(r)), which ramps the energy smoothly
to zero between the inner and outer cutoff. This can cause
irregularities in pair-wise forces (due to the discontinuous second
irregularities in pairwise forces (due to the discontinuous second
derivative of energy at the boundaries of the switching region), which
in some cases can result in detectable artifacts in an MD simulation.

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@ -50,7 +50,7 @@ Style *dpd* computes a force field for dissipative particle dynamics
Style *dpd/tstat* invokes a DPD thermostat on pairwise interactions,
which is equivalent to the non-conservative portion of the DPD force
field. This pair-wise thermostat can be used in conjunction with any
field. This pairwise thermostat can be used in conjunction with any
:doc:`pair style <pair_style>`, and in leiu of per-particle thermostats
like :doc:`fix langevin <fix_langevin>` or ensemble thermostats like
Nose Hoover as implemented by :doc:`fix nvt <fix_nh>`. To use

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@ -164,7 +164,7 @@ Following the *LJCutMelt* example, here are the two functions:
.. note::
The evaluation of scripted python code will slow down the
computation pair-wise interactions quite significantly. However, this
computation pairwise interactions quite significantly. However, this
can be largely worked around through using the python pair style not
for the actual simulation, but to generate tabulated potentials on the
fly using the :doc:`pair_write <pair_write>` command. Please see below

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@ -154,10 +154,10 @@ accelerated styles exist.
* :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
* :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
* :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pair-wise DPD thermostatting with generalized force field
* :doc:`dpd/ext/tstat <pair_dpd_ext>` - pairwise DPD thermostatting with generalized force field
* :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
* :doc:`dpd/fdt/energy <pair_dpd_fdt>` - DPD for constant energy and enthalpy
* :doc:`dpd/tstat <pair_dpd>` - pair-wise DPD thermostatting
* :doc:`dpd/tstat <pair_dpd>` - pairwise DPD thermostatting
* :doc:`dsmc <pair_dsmc>` - Direct Simulation Monte Carlo (DSMC)
* :doc:`e3b <pair_e3b>` - Explicit-three body (E3B) water model
* :doc:`drip <pair_drip>` - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)

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@ -202,7 +202,7 @@ elements are the same. Thus the two-body parameters for Si
interacting with C, comes from the SiCC entry. The three-body
parameters can in principle be specific to the three elements of the
configuration. In the literature, however, the three-body parameters
are usually defined by simple formulas involving two sets of pair-wise
are usually defined by simple formulas involving two sets of pairwise
parameters, corresponding to the ij and ik pairs, where i is the
center atom. The user must ensure that the correct combining rule is
used to calculate the values of the three-body parameters for

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@ -89,7 +89,7 @@ in its 3d FFTs. In this scenario, splitting your P total processors
into 2 subsets of processors, P1 in the first partition and P2 in the
second partition, can enable your simulation to run faster. This is
because the long-range forces in PPPM can be calculated at the same
time as pair-wise and bonded forces are being calculated, and the FFTs
time as pairwise and bonded forces are being calculated, and the FFTs
can actually speed up when running on fewer processors.
To use this style, you must define 2 partitions where P1 is a multiple