From d17daf150bd576e957aab39a6f965cfa80c00d1e Mon Sep 17 00:00:00 2001 From: Mark Chaimovich Date: Tue, 2 Mar 2021 20:55:37 -0500 Subject: [PATCH] Update to use cutoff term --- doc/src/pair_lj_relres.rst | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/doc/src/pair_lj_relres.rst b/doc/src/pair_lj_relres.rst index 703586e1e0..a19a3912ac 100644 --- a/doc/src/pair_lj_relres.rst +++ b/doc/src/pair_lj_relres.rst @@ -13,8 +13,8 @@ Syntax pair_style lj/relres Rsi Rso Rci Rco -* Rsi = inner switching distance between the fine-grained and coarse-grained potentials (distance units) -* Rso = outer 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 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) * Rco = outer cutoff for all interactions (distance units) @@ -48,14 +48,14 @@ a reference system :ref:`(Chaimovich2) `. 0, & \quad\mathrm{if}\quad r\geq r_{co}.\end{array}\right. 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:`\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 force and its derivative are continuous between the FG and CG 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 :math:`\Gamma_{c}` ensure the continuity of the energy over the entire domain. The corresponding polynomial coefficients :math:`\gamma_{sm}` @@ -147,16 +147,17 @@ case, Ref. :ref:`(Chaimovich2) ` discusses the alternative formula, and in such a situation, the pair_coeff command should be explicitly used for all combinations of atom types :math:`I\;!=J`. -The switching distance is another crucial parameter in RelRes: -decreasing it improves the computational efficiency, yet if it is too -small, the molecular simulations may not capture the system behavior -correctly. As a rule of thumb, the switching distance should be -approximately :math:`\,\sim\! 1.5\sigma` :ref:`(Chaimovich1) `; -recommendations can be found in Ref. :ref:`(Chaimovich2) `. -Regarding the smoothing zone itself, :math:`\,\sim\!0.1\sigma` is +The switching distance (the midpoint between inner and outer switching +cutoffs) is another crucial factor in RelRes: decreasing it improves the +computational efficiency, yet if it is too small, the molecular simulations +may not capture the system behavior correctly. As a rule of thumb, +the switching distance should be approximately :math:`\,\sim\! 1.5\sigma` +:ref:`(Chaimovich1) `; recommendations can be found in +Ref. :ref:`(Chaimovich2) `. +Regarding the switching smoothing zone, :math:`\,\sim\!0.1\sigma` is recommended; if desired, smoothing can be eliminated by setting -the inner switching distance, :math:`r_{si}`, equal to the outer -switching distance, :math:`r_{so}` (the same is true for the cutoffs +the inner switching cutoff, :math:`r_{si}`, equal to the outer +switching cutoff, :math:`r_{so}` (the same is true for the other cutoffs :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 (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: .. 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_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 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 @@ -214,7 +215,7 @@ system from the previous example, we recommend using the following commands: pair_modify shift yes 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. More examples can be found in the *examples/relres* folder.