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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7257 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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doc/pair_gauss.html
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@ -13,9 +13,14 @@
</H3>
<H3>pair_style gauss/omp command
</H3>
<H3>pair_style gauss/cut command
</H3>
<H3>pair_style gauss/cut/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style gauss cutoff
<PRE>pair_style gauss cutoff
pair_style gauss/cut cutoff
</PRE>
<UL><LI>cutoff = global cutoff for Gauss interactions (distance units)
</UL>
@ -25,6 +30,9 @@
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0
</PRE>
<PRE>pair_style gauss/cut 3.5
pair_coeff 1 4 0.2805 1.45 0.112
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>gauss</I> computes a tethering potential of the form
@ -47,12 +55,38 @@ commands:
<P>The last coefficient is optional. If not specified, the global cutoff
is used.
</P>
<P>Style <I>gauss/cut</I> computes a generalized Gaussian interaction potential
between pairs of particles:
</P>
<CENTER><IMG SRC = "Eqs/pair_gauss_cut.jpg">
</CENTER>
<P>where H determines together with the standard deviation sigma_h the
peak height of the Gaussian function, and r_mh the peak position.
Examples of the use of the Gaussian potentials include implicit
solvent simulations of salt ions <A HREF = "#Lenart">(Lenart)</A> and of surfactants
<A HREF = "#Jusufi">(Jusufi)</A>. In these instances the Gaussian potential mimics
the hydration barrier between a pair of particles. The hydration
barrier is located at r_mh and has a width of sigma_h. The prefactor
determines the hight of the potential barrier.
</P>
<P>The following coefficients must be defined for each pair of atom types
via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the example above,
or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands:
</P>
<UL><LI>H (energy * distance units)
<LI>r_mh (distance units)
<LI>sigma_h (distance units)
</UL>
<P>The global cutoff (r_c) specified in the pair_style command is used.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
the same as the corresponding style without the suffix. They have
been optimized to run faster, depending on your available hardware,
as discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
the same as the corresponding style without the suffix. They have
been optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">this section</A> of the manual.
The accelerated styles take the same arguments and should produce the
same results, except for round-off and precision issues.
</P>
@ -73,13 +107,17 @@ instructions on how to use the accelerated styles effectively.
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair style does not support mixing. Thus, coefficients for all
<P>These pair style do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
<P>The <I>gauss</I> style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option. There is no effect due to the Gaussian well beyond the
cutoff; hence reasonable cutoffs need to be specified.
</P>
<P>The <I>gauss/cut</I> style supports the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the Gauss-potential portion of the pair
interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
relevant for this pair style.
</P>
@ -95,7 +133,7 @@ to be specified in an input script that reads a restart file.
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<P>This pair style tallies an "occupancy" count of how many Gaussian-well
<P>Thes <I>gauss</I> pair style tallies an "occupancy" count of how many Gaussian-well
sites have an atom within the distance at which the force is a maximum
= sqrt(0.5/b). This quantity can be accessed via the <A HREF = "compute_pair.html">compute
pair</A> command as a vector of values of length 1.
@ -109,11 +147,16 @@ thermo_style custom step temp epair v_occ
</PRE>
<HR>
<P><B>Restrictions:</B> none
<P><B>Restrictions:</B>
</P>
<P>The <I>gauss/cut</I> style is part of the "user-misc" package. It is only enabled
if LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of LAMMPS</A>
section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
<P><A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "pair_coul_diel.html">pair_style coul/diel</A>
</P>
<P><B>Default:</B> none
</P>