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Axel Kohlmeyer
2021-02-09 08:27:29 -05:00
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doc/src/pair_lj_relres.rst
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@ -11,7 +11,7 @@ Syntax
pair_style lj/relres Rsi Rso Rci Rco
* Rsi = inner switching distance - boundary up to which LJ potential of fine-grained model is applied (distance units)
* Rso = outer switching distance - boundary beyond which LJ potential of coarse-grained model is applied (distance units)
* Rso = outer switching distance - boundary beyond which LJ potential of coarse-grained model is applied (distance units)
* Rci = inner cutoff beyond which force smoothing is applied (distance units)
* Rco = outer cutoff for lj/relres interactions (distance units)
@ -28,8 +28,8 @@ Description
"""""""""""
Style *lj/relres* computes a LJ interaction with RelRes methodology developed by :ref:`Chaimovich at al.<Chaimovich1>`
This methodology applies fine-grained model between near neighbors (up to :math:`r_{si}` boundary) and a simplified coarse-grained model
for far neighbors (beyond :math:`r_{so}` boundary) allowing significant improvement in computational efficiency while preserving correctness
This methodology applies fine-grained model between near neighbors (up to :math:`r_{si}` boundary) and a simplified coarse-grained model
for far neighbors (beyond :math:`r_{so}` boundary) allowing significant improvement in computational efficiency while preserving correctness
of simulation results.
.. math::
@ -41,10 +41,10 @@ of simulation results.
\sum_{m=0}^{4} C_{cm}\left(r-r_{ci}\right)^m -G_c, & r_{ci}\leq r< r_{co} \\
0, & r\geq r_{co}\end{array}\right.
Between :math:`r_{si}` and :math:`r_{so}` the polynomial smoothing is applied in a way that the force and its 1st derivative are not discontinued
at switching between fine- and coarse-grained potentials (between :math:`r_{si}` and :math:`r_{so}`) and at cutoff (between :math:`r_{ci}` and :math:`r_{co}`).
The corresponding polynomial coefficients :math:`C_{sm}` and :math:`C_{cm}` and shifting constants :math:`G_{si}`, :math:`G_{so}` and :math:`G_{c}` are computed by LAMMPS accordingly.
To avoid smoothing, the inner switching distance :math:`r_{si}` parameter should be set equal to the outer switching distance :math:`r_{so}` parameter
Between :math:`r_{si}` and :math:`r_{so}` the polynomial smoothing is applied in a way that the force and its 1st derivative are not discontinued
at switching between fine- and coarse-grained potentials (between :math:`r_{si}` and :math:`r_{so}`) and at cutoff (between :math:`r_{ci}` and :math:`r_{co}`).
The corresponding polynomial coefficients :math:`C_{sm}` and :math:`C_{cm}` and shifting constants :math:`G_{si}`, :math:`G_{so}` and :math:`G_{c}` are computed by LAMMPS accordingly.
To avoid smoothing, the inner switching distance :math:`r_{si}` parameter should be set equal to the outer switching distance :math:`r_{so}` parameter
(:math:`r_{si}=r_{so}`). Similarly, to avoid smoothing at cutoff, inner and outer cutoff parameters should be set equal (:math:`r_{ci}=r_{co}`).
Details can be found in :ref:`(Chaimovich) <Chaimovich2>`.
@ -53,8 +53,8 @@ Details can be found in :ref:`(Chaimovich) <Chaimovich2>`.
Energy and force resulting from this methodology can be plotted via the
:doc:`pair_write <pair_write>` command to see the effect.
In implementation of *lj/relres* style, atoms are grouped in the way that one of the atoms in the group plays the role of a coarse-grained site for the calculation
of interactions beyond :math:`r_{so}` distance while continuing to play the role of a fine-grained site for shorter distances.
In implementation of *lj/relres* style, atoms are grouped in the way that one of the atoms in the group plays the role of a coarse-grained site for the calculation
of interactions beyond :math:`r_{so}` distance while continuing to play the role of a fine-grained site for shorter distances.
This atom must be defined as a different atom type. Other atoms in the group participate in the fine-grained interactions only.
The following coefficients must be defined for each pair of atom
@ -68,7 +68,7 @@ commands, or by mixing as will be described below:
* :math:`\epsilon^{CG}` (energy units)
* :math:`\sigma^{CG}` (distance units)
For atom types that are used as fine-grained sites only, :math:`\epsilon^{CG}` must be set to 0 (zero).
For atom types that are used as fine-grained sites only, :math:`\epsilon^{CG}` must be set to 0 (zero).
For atom types that are used as coarse-grained sites only (if any), :math:`\epsilon^{FG}` must be set to 0 (zero).
Additional parameters can be defined to specify different :math:`r_{si}`, :math:`r_{so}`, :math:`r_{ci}`, :math:`r_{co}` for a particular set of atom types:
@ -78,7 +78,7 @@ Additional parameters can be defined to specify different :math:`r_{si}`, :math:
* :math:`r_{ci}` (distance units)
* :math:`r_{co}` (distance units)
These parameters are optional and they are used to override global values defined in the pair_style command.
These parameters are optional and they are used to override global values defined in the pair_style command.
If this override option is used, all four values must be specified. If not specified, the global values for :math:`r_{si}`, :math:`r_{so}`, :math:`r_{ci}`, and :math:`r_{co}` are used.
Mixing, shift, table, tail correction, restart, rRESPA info
@ -87,11 +87,11 @@ Mixing, shift, table, tail correction, restart, rRESPA info
For atom type pairs I,J with I != J, the :math:`\epsilon^{FG}`, :math:`\sigma^{FG}`, :math:`\epsilon^{CG}`, :math:`\sigma^{CG}`, :math:`r_{si}`, :math:`r_{so}`, :math:`r_{ci}`, and :math:`r_{co}`
parameters for this pair style can be mixed, if not defined explicitly.
All parameters are mixed according to the pair_modify mix option. The
default mix value is *geometric*\ , and it is recommended to use with this *lj/relres* style.
See the "pair_modify" command for details.
default mix value is *geometric*\ , and it is recommended to use with this *lj/relres* style.
See the "pair_modify" command for details.
This pair style supports the :doc:`pair_modify <pair_modify>` shift
option for the energy of the pair interaction. It is recommended to set this option to *yes*\ .
option for the energy of the pair interaction. It is recommended to set this option to *yes*\ .
Otherwise, the shifting constant :math:`G_{c}` is set to zero. Constants :math:`G_{si}` and :math:`G_{so}` are not impacted by this option.
The :doc:`pair_modify <pair_modify>` table option is not relevant