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Merge branch 'collected-small-changes' into pair-zero-full

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Axel Kohlmeyer
2022-10-04 14:36:02 -04:00
parent ef3b01f340 7f90e43d0a
commit 8be7634b5f
8 changed files with 338 additions and 148 deletions
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69
doc/src/pair_list.rst
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@ -30,15 +30,17 @@ Description
"""""""""""
Style *list* computes interactions between explicitly listed pairs of
atoms with the option to select functional form and parameters for
each individual pair. Because the parameters are set in the list
file, the pair_coeff command has no parameters (but still needs to be
provided). The *check* and *nocheck* keywords enable/disable a test
that checks whether all listed bonds were present and computed.
atoms with the option to select functional form and parameters for each
individual pair. Because the parameters are set in the list file, the
pair_coeff command has no parameters (but still needs to be provided).
The *check* and *nocheck* keywords enable/disable tests that checks
whether all listed pairs of atom IDs were present and the interactions
computed. If *nocheck* is set and either atom ID is not present, the
interaction is skipped.
This pair style can be thought of as a hybrid between bonded,
non-bonded, and restraint interactions. It will typically be used as
an additional interaction within the *hybrid/overlay* pair style. It
non-bonded, and restraint interactions. It will typically be used as an
additional interaction within the *hybrid/overlay* pair style. It
currently supports three interaction styles: a 12-6 Lennard-Jones, a
Morse and a harmonic potential.
@ -55,10 +57,10 @@ The format of the list file is as follows:
ID2 = atom ID of second atom
style = style of interaction
coeffs = list of coeffs
cutoff = cutoff for interaction (optional)
cutoff = cutoff for interaction (optional, except for style *quartic*)
The cutoff parameter is optional. If not specified, the global cutoff
is used.
The cutoff parameter is optional for all but the *quartic* interactions.
If it is not specified, the global cutoff is used.
Here is an example file:
@ -69,6 +71,7 @@ Here is an example file:
15 259 lj126 1.0 1.0 50.0
15 603 morse 10.0 1.2 2.0 10.0 # and another comment
18 470 harmonic 50.0 1.2 5.0
19 332 quartic 5.0 -1.2 1.2 5.0
The style *lj126* computes pairwise interactions with the formula
@ -85,7 +88,7 @@ The style *morse* computes pairwise interactions with the formula
.. math::
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c
E = D_0 \left[ 1 - e^{-\alpha (r - r_0)} \right]^2 \qquad r < r_c
and the coefficients:
@ -106,6 +109,21 @@ and the coefficients:
Note that the usual 1/2 factor is included in :math:`K`.
The style *quartic* computes pairwise interactions with the formula
.. math::
E = K (r - r_c)^2 (r - r_c -b_1) (r - r_c - b_2) \qquad r < r_c
and the coefficients:
* :math:`K` (energy units)
* :math:`b_1` (distance units)
* :math:`b_2` (distance units)
* :math:`r_c` (distance units)
Note that the per list entry cutoff :math:`r_c` is **required** for *quartic* interactions.
----------
Mixing, shift, table, tail correction, restart, rRESPA info
@ -120,8 +138,9 @@ pair style.
The :doc:`pair_modify <pair_modify>` table and tail options are not
relevant for this pair style.
This pair style does not write its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need
to be specified in an input script that reads a restart file.
This pair style does not write its information to :doc:`binary restart
files <restart>`, so pair_style and pair_coeff commands need to be
specified in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
@ -133,17 +152,18 @@ Restrictions
""""""""""""
This pair style does not use a neighbor list and instead identifies
atoms by their IDs. This has two consequences: 1) The cutoff has to be
chosen sufficiently large, so that the second atom of a pair has to be
a ghost atom on the same node on which the first atom is local;
otherwise the interaction will be skipped. You can use the *check*
option to detect, if interactions are missing. 2) Unlike other pair
styles in LAMMPS, an atom I will not interact with multiple images of
atom J (assuming the images are within the cutoff distance), but only
with the nearest image.
atoms by their IDs. This has two consequences: 1) The cutoff has to be
chosen sufficiently large, so that the second atom of a pair has to be a
ghost atom on the same node on which the first atom is local; otherwise
the interaction will be skipped. You can use the *check* option to
detect, if interactions are missing. 2) Unlike other pair styles in
LAMMPS, an atom I will not interact with multiple images of atom J
(assuming the images are within the cutoff distance), but only with the
closest image.
This style is part of the MISC package. It is only enabled if
LAMMPS is build with that package. See the :doc:`Build package <Build_package>` page on for more info.
This style is part of the MISC package. It is only enabled if LAMMPS is
build with that package. See the :doc:`Build package <Build_package>`
page on for more info.
Related commands
""""""""""""""""
@ -151,8 +171,9 @@ Related commands
:doc:`pair_coeff <pair_coeff>`,
:doc:`pair_style hybrid/overlay <pair_hybrid>`,
:doc:`pair_style lj/cut <pair_lj>`,
:doc:`pair_style morse <pair_morse>`,
:doc:`bond_style morse <bond_morse>`,
:doc:`bond_style harmonic <bond_harmonic>`
:doc:`bond_style quartic <bond_quartic>`
Default
"""""""