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Update to use cutoff term

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This commit is contained in:
Mark Chaimovich
2021-03-02 20:55:37 -05:00
parent 3ab5b5f63a
commit d17daf150b
1 changed files with 18 additions and 17 deletions
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doc/src/pair_lj_relres.rst
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@ -13,8 +13,8 @@ Syntax
pair_style lj/relres Rsi Rso Rci Rco pair_style lj/relres Rsi Rso Rci Rco
* Rsi = inner switching distance between the fine-grained and coarse-grained potentials (distance units) * Rsi = inner switching cutoff between the fine-grained and coarse-grained potentials (distance units)
* Rso = outer switching distance between the fine-grained and coarse-grained potentials (distance units) * Rso = outer switching cutoff between the fine-grained and coarse-grained potentials (distance units)
* Rci = inner cutoff beyond which the force smoothing for all interactions is applied (distance units) * Rci = inner cutoff beyond which the force smoothing for all interactions is applied (distance units)
* Rco = outer cutoff for all interactions (distance units) * Rco = outer cutoff for all interactions (distance units)
@ -48,14 +48,14 @@ a reference system :ref:`(Chaimovich2) <Chaimovich2>`.
0, & \quad\mathrm{if}\quad r\geq r_{co}.\end{array}\right. 0, & \quad\mathrm{if}\quad r\geq r_{co}.\end{array}\right.
The FG parameters of the LJ potential (:math:`\epsilon^{FG}` and The FG parameters of the LJ potential (:math:`\epsilon^{FG}` and
:math:`\sigma^{FG}`) are applied up to the inner switching distance, :math:`\sigma^{FG}`) are applied up to the inner switching cutoff,
:math:`r_{si}`, while the CG parameters of the LJ potential :math:`r_{si}`, while the CG parameters of the LJ potential
(:math:`\epsilon^{CG}` and :math:`\sigma^{CG}`) are applied beyond the (:math:`\epsilon^{CG}` and :math:`\sigma^{CG}`) are applied beyond the
outer switching distance, :math:`r_{so}`. Between :math:`r_{si}` and outer switching cutoff, :math:`r_{so}`. Between :math:`r_{si}` and
:math:`r_{so}` a polynomial smoothing function is applied so that the :math:`r_{so}` a polynomial smoothing function is applied so that the
force and its derivative are continuous between the FG and CG force and its derivative are continuous between the FG and CG
potentials. An analogous smoothing function is applied between the potentials. An analogous smoothing function is applied between the
inner and outer cutoff distances (:math:`r_{ci}` and :math:`r_{co}`). inner and outer cutoffs (:math:`r_{ci}` and :math:`r_{co}`).
The offsets :math:`\Gamma_{si}`, :math:`\Gamma_{so}` and The offsets :math:`\Gamma_{si}`, :math:`\Gamma_{so}` and
:math:`\Gamma_{c}` ensure the continuity of the energy over the entire :math:`\Gamma_{c}` ensure the continuity of the energy over the entire
domain. The corresponding polynomial coefficients :math:`\gamma_{sm}` domain. The corresponding polynomial coefficients :math:`\gamma_{sm}`
@ -147,16 +147,17 @@ case, Ref. :ref:`(Chaimovich2) <Chaimovich2>` discusses the alternative
formula, and in such a situation, the pair_coeff command should be explicitly formula, and in such a situation, the pair_coeff command should be explicitly
used for all combinations of atom types :math:`I\;!=J`. used for all combinations of atom types :math:`I\;!=J`.
The switching distance is another crucial parameter in RelRes: The switching distance (the midpoint between inner and outer switching
decreasing it improves the computational efficiency, yet if it is too cutoffs) is another crucial factor in RelRes: decreasing it improves the
small, the molecular simulations may not capture the system behavior computational efficiency, yet if it is too small, the molecular simulations
correctly. As a rule of thumb, the switching distance should be may not capture the system behavior correctly. As a rule of thumb,
approximately :math:`\,\sim\! 1.5\sigma` :ref:`(Chaimovich1) <Chaimovich1>`; the switching distance should be approximately :math:`\,\sim\! 1.5\sigma`
recommendations can be found in Ref. :ref:`(Chaimovich2) <Chaimovich2>`. :ref:`(Chaimovich1) <Chaimovich1>`; recommendations can be found in
Regarding the smoothing zone itself, :math:`\,\sim\!0.1\sigma` is Ref. :ref:`(Chaimovich2) <Chaimovich2>`.
Regarding the switching smoothing zone, :math:`\,\sim\!0.1\sigma` is
recommended; if desired, smoothing can be eliminated by setting recommended; if desired, smoothing can be eliminated by setting
the inner switching distance, :math:`r_{si}`, equal to the outer the inner switching cutoff, :math:`r_{si}`, equal to the outer
switching distance, :math:`r_{so}` (the same is true for the cutoffs switching cutoff, :math:`r_{so}` (the same is true for the other cutoffs
:math:`r_{ci}` and :math:`r_{co}`). :math:`r_{ci}` and :math:`r_{co}`).
---------- ----------
@ -176,7 +177,7 @@ the following commands should be used:
In a more complex situation, there may be two distinct clusters in a system In a more complex situation, there may be two distinct clusters in a system
(these two clusters may be on same molecule or on different molecules), (these two clusters may be on same molecule or on different molecules),
each with its own switching distance. If there are still two atom types each with its own switching cutoffs. If there are still two atom types
in each cluster as in the earlier example, the commands should be: in each cluster as in the earlier example, the commands should be:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -188,7 +189,7 @@ in each cluster as in the earlier example, the commands should be:
pair_coeff 4 4 epsilon_FG4 sigma_FG4 0.0 0.0 pair_coeff 4 4 epsilon_FG4 sigma_FG4 0.0 0.0
pair_modify shift yes pair_modify shift yes
In this example, the switching distance for the first cluster (atom types 1 In this example, the switching cutoffs for the first cluster (atom types 1
and 2) is defined explicitly in the pair_coeff command which overrides the and 2) is defined explicitly in the pair_coeff command which overrides the
global values, while the second cluster (atom types 3 and 4) uses the global global values, while the second cluster (atom types 3 and 4) uses the global
definition from the pair_style command. The emphasis here is that the atom definition from the pair_style command. The emphasis here is that the atom
@ -214,7 +215,7 @@ system from the previous example, we recommend using the following commands:
pair_modify shift yes pair_modify shift yes
Notice that the CG parameters are mixed only for interactions between atom Notice that the CG parameters are mixed only for interactions between atom
types associated with hybrid sites, and that the switching distances are types associated with hybrid sites, and that the cutoffs are
mixed on the cluster basis. mixed on the cluster basis.
More examples can be found in the *examples/relres* folder. More examples can be found in the *examples/relres* folder.