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12
doc/Section_commands.html
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@ -426,12 +426,12 @@ potentials. Click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if

1
doc/Section_commands.txt
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@ -664,6 +664,7 @@ potentials. Click on the style itself for a full description:
"lj/gromacs"_pair_gromacs.html,
"lj/gromacs/coul/gromacs"_pair_gromacs.html,
"lj/smooth"_pair_lj_smooth.html,
"lj/smooth/linear"_pair_lj_smooth_linear.html,
"lj96/cut"_pair_lj96.html,
"lubricate"_pair_lubricate.html,
"lubricate/poly"_pair_lubricate.html,

1
doc/pair_coeff.html
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@ -134,6 +134,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj_smooth_linear.html">pair_style lj/smooth/linear</A> - linear smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj96.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> - hydrodynamic lubrication forces
<LI><A HREF = "pair_lubricate.html">pair_style lubricate/poly</A> - hydrodynamic lubrication forces with polydispersity

1
doc/pair_coeff.txt
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@ -131,6 +131,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential
"pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
"pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
"pair_style lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity

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doc/pair_lj_cut_smooth.html Normal file
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@ -0,0 +1,111 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/cut/smooth command
</H3>
<H3>pair_style lj/cut/smooth/cuda command
</H3>
<H3>pair_style lj/cut/smooth/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/cut/smooth Rc
</PRE>
<UL><LI>Rc = cutoff for lj/cut/smooth interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/cut/smooth 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
pair_coeff 1 1 20.0 1.3 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>lj/cut/smooth</I> computes a LJ interaction that combines the standard
12/6 Lennard-Jones function and subtracts a linear term that includes a
cutoff distance Rc.
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_cut_smooth.jpg">
</CENTER>
<P>At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
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, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff (distance units)
</UL>
<P>If not specified, the global value for Rc 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">Section_accelerate</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>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_6">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients and
cutoff distance can be mixed. The default mix value is geometric.
See the "pair_modify" command for details.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<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>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -121,7 +121,8 @@ to be specified in an input script that reads a restart file.
</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_lj_smooth_linear.html">pair
lj/smooth/linear</A>
</P>
<P><B>Default:</B> none
</P>

3
doc/pair_lj_smooth.txt
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@ -116,6 +116,7 @@ This pair style can only be used via the {pair} keyword of the
[Related commands:]
"pair_coeff"_pair_coeff.html
"pair_coeff"_pair_coeff.html, "pair
lj/smooth/linear"_pair_lj_smooth_linear.html
[Default:] none

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doc/pair_lj_smooth_linear.html Normal file
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@ -0,0 +1,86 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style lj/smooth/linear command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style lj/smooth/linear Rc
</PRE>
<UL><LI>Rc = cutoff for lj/smooth/linear interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style lj/smooth/linear 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
pair_coeff 1 1 20.0 1.3 9.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>lj/smooth/linear</I> computes a LJ interaction that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term that
includes the cutoff distance Rc, as in this formula:
</P>
<CENTER><IMG SRC = "Eqs/pair_lj_cut_smooth.jpg">
</CENTER>
<P>At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
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, or by mixing as described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global value
for Rc is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed. The default mix value is geometric.
See the "pair_modify" command for details.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option for the energy of the pair interaction.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
</P>
<P>This pair style writes its information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>This pair style can only be used via the <I>pair</I> keyword of the
<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>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_lj_smooth.html">pair lj/smooth</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

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@ -0,0 +1,81 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style lj/smooth/linear command :h3
[Syntax:]
pair_style lj/smooth/linear Rc :pre
Rc = cutoff for lj/smooth/linear interactions (distance units) :ul
[Examples:]
pair_style lj/smooth/linear 5.456108274435118
pair_coeff * * 0.7242785984051078 2.598146797350056
pair_coeff 1 1 20.0 1.3 9.0 :pre
[Description:]
Style {lj/smooth/linear} computes a LJ interaction that combines the
standard 12/6 Lennard-Jones function and subtracts a linear term that
includes the cutoff distance Rc, as in this formula:
:c,image(Eqs/pair_lj_cut_smooth.jpg)
At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
epsilon (energy units)
sigma (distance units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global value
for Rc is used.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance can be mixed. The default mix value is geometric.
See the "pair_modify" command for details.
This pair style does not support the "pair_modify"_pair_modify.html
shift option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant for
this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure, since the energy of the pair interaction is smoothed to 0.0
at the cutoff.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair lj/smooth"_pair_lj_smooth.html
[Default:] none

1
doc/pair_style.html
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@ -136,6 +136,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj_smooth_linear.html">pair_style lj/smooth/linear</A> - linear smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj96.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> - hydrodynamic lubrication forces
<LI><A HREF = "pair_lubricate.html">pair_style lubricate/poly</A> - hydrodynamic lubrication forces with polydispersity

1
doc/pair_style.txt
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@ -133,6 +133,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential
"pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
"pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
"pair_style lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity