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use the diameter for sigma in lj/sphere. update docs

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This commit is contained in:
Axel Kohlmeyer
2023-03-30 14:14:30 -04:00
parent 664a022c46
commit 8439c0e0c6
4 changed files with 15 additions and 11 deletions
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11
doc/src/pair_lepton.rst
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@ -54,7 +54,7 @@ Examples
pair_style lepton/sphere 2.5
pair_coeff 1 * "k*((r-r0)^2*step(r0-r)); k=200; r0=radi+radj"
pair_coeff 2 2 "4.0*eps*((sig/r)^12 - (sig/r)^6); eps=1.0; sig=sqrt(radi*radj)"
pair_coeff 2 2 "4.0*eps*((sig/r)^12 - (sig/r)^6); eps=1.0; sig=2.0*sqrt(radi*radj)"
Description
"""""""""""
@ -72,9 +72,12 @@ using "r" as the distance variable. With pair style *lepton/coul* one
may additionally reference the charges of the two atoms of the pair with
"qi" and "qj", respectively. With pair style *lepton/coul* one may
instead reference the radii of the two atoms of the pair with "radi" and
"radj", respectively. Note that further constants in the expression can
be defined in the same string as additional expressions separated by
semi-colons as shown in the examples above.
"radj", respectively; this is half of the diameter that can be set in
:doc:`data files <read_data>` or the :doc:`set command <set>`.
Note that further constants in the expressions can be defined in the
same string as additional expressions separated by semi-colons as shown
in the examples above.
The expression `"200.0*(r-1.5)^2"` represents a harmonic potential
around the pairwise distance :math:`r_0` of 1.5 distance units and a

9
doc/src/pair_lj_sphere.rst
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@ -47,10 +47,11 @@ given by
This is the same potential function as used by the :doc:`lj/cut
<pair_lj>` pair style, but the :math:`\sigma_{ij}` parameter is not set
as a per-type parameter via the :doc:`pair_coeff command <pair_coeff>`,
but taken from the per-atom radius attribute of :doc:`atom_style sphere
<atom_style>`. The individual value of :math:`\sigma_{ij}` is computed
using the mixing rule for pair coefficients as set by the
:doc:`pair_modify mix <pair_modify>` command.
but taken from the per-atom diameter attribute of :doc:`atom_style
sphere <atom_style>`. The individual value of :math:`\sigma_{ij}` is
computed from the diameters of the two atoms using the mixing rule for
pair coefficients as set by the :doc:`pair_modify mix <pair_modify>`
command (defaults to geometric mixing).
Note that :math:`\sigma_{ij}` is defined in the LJ formula above as the
zero-crossing distance for the potential, *not* as the energy minimum which

4
src/EXTRA-PAIR/pair_lj_sphere.cpp
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@ -101,7 +101,7 @@ void PairLJSphere::compute(int eflag, int vflag)
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
sigma6 = powint(mix_distance(rtmp, radius[j]), 6);
sigma6 = powint(2.0 * mix_distance(rtmp, radius[j]), 6);
forcelj = r6inv * 24.0 * epsilon[itype][jtype] * (2.0 * sigma6 * sigma6 * r6inv - sigma6);
fpair = factor_lj * forcelj * r2inv;
@ -330,7 +330,7 @@ double PairLJSphere::single(int i, int j, int itype, int jtype, double rsq, doub
{
double r2inv, r6inv, sigma6, forcelj, philj;
sigma6 = powint(mix_distance(atom->radius[i], atom->radius[j]), 6);
sigma6 = powint(2.0 * mix_distance(atom->radius[i], atom->radius[j]), 6);
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
forcelj = r6inv * 24.0 * epsilon[itype][jtype] * (sigma6 * sigma6 * r6inv - sigma6);

2
src/OPENMP/pair_lj_sphere_omp.cpp
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@ -127,7 +127,7 @@ void PairLJSphereOMP::eval(int iifrom, int iito, ThrData *const thr)
r2inv = 1.0 / rsq;
r6inv = r2inv * r2inv * r2inv;
sigma6 = powint(mix_distance(rtmp, radius[j]), 6);
sigma6 = powint(2.0 * mix_distance(rtmp, radius[j]), 6);
forcelj = r6inv * 24.0 * epsiloni[jtype] * (2.0 * sigma6 * sigma6 * r6inv - sigma6);
fpair = factor_lj * forcelj * r2inv;