diff --git a/doc/src/pair_lj_relres.rst b/doc/src/pair_lj_relres.rst index 4efd7901b8..c0d3ae0103 100644 --- a/doc/src/pair_lj_relres.rst +++ b/doc/src/pair_lj_relres.rst @@ -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.` -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) `. @@ -53,8 +53,8 @@ Details can be found in :ref:`(Chaimovich) `. Energy and force resulting from this methodology can be plotted via the :doc:`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 ` 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 ` table option is not relevant