ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5007 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2010-10-07 21:20:45 +00:00
parent 2296334f94
commit b14753aae8
14 changed files with 352 additions and 123 deletions
Download Patch File Download Diff File Expand all files Collapse all files

BIN
doc/Eqs/pair_gauss.jpg Normal file
View File

Binary file not shown.
Side by Side

After

Width:  |  Height:  |  Size: 1.8 KiB

9
doc/Eqs/pair_gauss.tex Normal file
View File

@ -0,0 +1,9 @@
\documentclass[12pt]{article}
\begin{document}
$$
E = A \exp(-B r^2) \qquad r < r_c
$$
\end{document}

31
doc/Section_commands.html
View File

@ -377,21 +377,22 @@ potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_airebo.html">airebo</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_comb.html">comb</A></TD><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD ><A HREF = "pair_coul.html">coul/debye</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_eim.html">eim</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><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_cut.html">lj96/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><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></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><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_born.html">born</A></TD><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_colloid.html">colloid</A></TD><TD ><A HREF = "pair_comb.html">comb</A></TD><TD ><A HREF = "pair_coul.html">coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/debye</A></TD><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD ><A HREF = "pair_dipole.html">dipole/cut</A></TD><TD ><A HREF = "pair_dpd.html">dpd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD></TR>
<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_charmm.html">lj/charmm/coul/long/opt</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><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/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</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><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj96_cut.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</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_morse.html">morse/opt</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_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_yukawa.html">yukawa</A></TD></TR>
<TR ALIGN="center"><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

2
doc/Section_commands.txt
View File

@ -549,6 +549,7 @@ potentials. Click on the style itself for a full description:
"hybrid"_pair_hybrid.html,
"hybrid/overlay"_pair_hybrid.html,
"airebo"_pair_airebo.html,
"born"_pair_born.html,
"born/coul/long"_pair_born.html,
"buck"_pair_buck.html,
"buck/coul/cut"_pair_buck.html,
@ -569,6 +570,7 @@ potentials. Click on the style itself for a full description:
"eam/fs"_pair_eam.html,
"eam/fs/opt"_pair_eam.html,
"eim"_pair_eim.html,
"gauss"_pair_gauss.html,
"gayberne"_pair_gayberne.html,
"gayberne/gpu"_pair_gayberne.html,
"gran/hertz/history"_pair_gran.html,

87
doc/pair_born.html
View File

@ -9,17 +9,29 @@
<HR>
<H3>pair_style born command
</H3>
<H3>pair_style born/coul/long command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style born/coul/long cutoff (cutoff2)
<PRE>pair_style style args
</PRE>
<UL><LI>cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
<LI>cutoff2 = global cutoff for Coulombic (optional) (distance units)
<UL><LI>style = <I>born</I> or <I>born/coul/long</I>
<LI>args = list of arguments for a particular style
</UL>
<PRE> <I>born</I> args = cutoff
cutoff = global cutoff for non-Coulombic interactions (distance units)
<I>born/coul/long</I> args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
</PRE>
<P><B>Examples:</B>
</P>
<PRE>pair_style born 10.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</PRE>
<PRE>pair_style born/coul/long 10.0
pair_style born/coul/long 10.0 8.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
@ -27,32 +39,29 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
</PRE>
<P><B>Description:</B>
</P>
<P>This pair style compute the Born-Mayer-Huggins potential described in
<A HREF = "#FumiTosi">(Fumi and Tosi)</A>, given by
<P>The <I>born</I> style computes the Born-Mayer-Huggins or Tosi/Fumi
potential described in <A HREF = "#FumiTosi">(Fumi and Tosi)</A>, given by
</P>
<CENTER><IMG SRC = "Eqs/pair_born.jpg">
</CENTER>
<P>where sigma is an interaction-dependent length parameter, rho is an
ionic-pair dependent length parameter, and the last term represents
the usual Coulombic pairwise interaction between atoms I and J. In
the Coulombic term, k is an energy-conversion constant, Qi and Qj are
the charges on the 2 atoms, and epsilon is the dielectric constant
which can be set by the <A HREF = "dielectric.html">dielectric</A> command.
ionic-pair dependent length parameter, and Rc is the cutoff.
</P>
<P>If one cutoff is specified in the pair_style command, it is used for
both the A,C,D and Coulombic terms. If two cutoffs are specified, the
first is used as the cutoff for the A,C,D terms, and the second is the
cutoff for the Coulombic term.
<P>The <I>born/coul/long</I> style adds a Coulombic term as described for the
<A HREF = "pair_lj.html">lj/cut</A> pair styles. An additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the <A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Note that this potential is identical to the <A HREF = "pair_buck.html">Buckingham
potential</A> when sigma = D = 0.
<P>If one cutoff is specified for the <I>born/coulk/long</I> style, it is used
for both the A,C,D and Coulombic terms. If two cutoffs are specified,
the first is used as the cutoff for the A,C,D terms, and the second is
the cutoff for the Coulombic term.
</P>
<P>An additional damping factor is applied to the Coulombic term so it
can be used in conjunction with the <A HREF = "kspace_style.html">kspace_style</A>
command and its <I>ewald</I> or <I>pppm</I> option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
<P>Note that these potentials are related to the <A HREF = "pair_born.html">Buckingham
potential</A>.
</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
@ -67,36 +76,40 @@ commands, or by mixing as described below:
<LI>D (energy units * distance units^8)
<LI>cutoff (distance units)
</UL>
<P>The second coefficient, rho, must be greater than zero.
</P>
<P>The last coefficient is optional. If not specified, the global A,C,D
cutoff specified in the pair_style command is used. Only the A,C,D
cutoff can be specified since a Coulombic cutoff cannot be specified
for an individual I,J type pair. All type pairs use the same global
cutoff specified in the pair_style command is used.
</P>
<P>For <I>buck/coul/long</I> no Coulombic cutoff can be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This style does not support mixing. Thus, coefficients for all
<P>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>This style supports the <A HREF = "pair_modify.html">pair_modify</A> shift option
<P>These styles support the <A HREF = "pair_modify.html">pair_modify</A> shift option
for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
interaction.
</P>
<P>This style does not support the <A HREF = "pair_modify.html">pair_modify</A>
table option since a tabulation capability has not yet been added to
this potential.
<P>The <I>born/coul/long</I> pair style does not support the
<A HREF = "pair_modify.html">pair_modify</A> table option since a tabulation
capability has not yet been added to this potential.
</P>
<P>This style does not support the pair_modify tail option for
adding long-range tail corrections to energy and pressure.
<P>These styles support the pair_modify tail option for adding long-range
tail corrections to energy and pressure.
</P>
<P>This style writes its information to binary
<A HREF = "restart.html">restart</A> files, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
<P>Thess styles writes thei information to binary <A HREF = "restart.html">restart</A>
files, 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 style only supports the <I>pair</I> keyword of run_style respa.
See the <A HREF = "run_style.html">run_style</A> command for details.
<P>These styles can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
respa</A> command. They do not support the <I>inner</I>,
<I>middle</I>, <I>outer</I> keywords.
</P>
<HR>

85
doc/pair_born.txt
View File

@ -7,17 +7,27 @@
:line
pair_style born command :h3
pair_style born/coul/long command :h3
[Syntax:]
pair_style born/coul/long cutoff (cutoff2) :pre
pair_style style args :pre
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :ul
style = {born} or {born/coul/long}
args = list of arguments for a particular style :ul
{born} args = cutoff
cutoff = global cutoff for non-Coulombic interactions (distance units)
{born/coul/long} args = cutoff (cutoff2)
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
[Examples:]
pair_style born 10.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
pair_style born/coul/long 10.0
pair_style born/coul/long 10.0 8.0
pair_coeff * * 6.08 0.317 2.340 24.18 11.51
@ -25,32 +35,29 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
[Description:]
This pair style compute the Born-Mayer-Huggins potential described in
"(Fumi and Tosi)"_#FumiTosi, given by
The {born} style computes the Born-Mayer-Huggins or Tosi/Fumi
potential described in "(Fumi and Tosi)"_#FumiTosi, given by
:c,image(Eqs/pair_born.jpg)
where sigma is an interaction-dependent length parameter, rho is an
ionic-pair dependent length parameter, and the last term represents
the usual Coulombic pairwise interaction between atoms I and J. In
the Coulombic term, k is an energy-conversion constant, Qi and Qj are
the charges on the 2 atoms, and epsilon is the dielectric constant
which can be set by the "dielectric"_dielectric.html command.
ionic-pair dependent length parameter, and Rc is the cutoff.
If one cutoff is specified in the pair_style command, it is used for
both the A,C,D and Coulombic terms. If two cutoffs are specified, the
first is used as the cutoff for the A,C,D terms, and the second is the
cutoff for the Coulombic term.
The {born/coul/long} style adds a Coulombic term as described for the
"lj/cut"_pair_lj.html pair styles. An additional damping factor is
applied to the Coulombic term so it can be used in conjunction with
the "kspace_style"_kspace_style.html command and its {ewald} or {pppm}
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Note that this potential is identical to the "Buckingham
potential"_pair_buck.html when sigma = D = 0.
If one cutoff is specified for the {born/coulk/long} style, it is used
for both the A,C,D and Coulombic terms. If two cutoffs are specified,
the first is used as the cutoff for the A,C,D terms, and the second is
the cutoff for the Coulombic term.
An additional damping factor is applied to the Coulombic term so it
can be used in conjunction with the "kspace_style"_kspace_style.html
command and its {ewald} or {pppm} option. The Coulombic cutoff
specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
Note that these potentials are related to the "Buckingham
potential"_pair_born.html.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
@ -65,36 +72,40 @@ C (energy units * distance units^6)
D (energy units * distance units^8)
cutoff (distance units) :ul
The second coefficient, rho, must be greater than zero.
The last coefficient is optional. If not specified, the global A,C,D
cutoff specified in the pair_style command is used. Only the A,C,D
cutoff can be specified since a Coulombic cutoff cannot be specified
for an individual I,J type pair. All type pairs use the same global
cutoff specified in the pair_style command is used.
For {buck/coul/long} no Coulombic cutoff can be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This style does not support mixing. Thus, coefficients for all
These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This style supports the "pair_modify"_pair_modify.html shift option
These styles support the "pair_modify"_pair_modify.html shift option
for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
interaction.
This style does not support the "pair_modify"_pair_modify.html
table option since a tabulation capability has not yet been added to
this potential.
The {born/coul/long} pair style does not support the
"pair_modify"_pair_modify.html table option since a tabulation
capability has not yet been added to this potential.
This style does not support the pair_modify tail option for
adding long-range tail corrections to energy and pressure.
These styles support the pair_modify tail option for adding long-range
tail corrections to energy and pressure.
This style writes its information to binary
"restart"_restart.html files, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
Thess styles writes thei information to binary "restart"_restart.html
files, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.
This style only supports the {pair} keyword of run_style respa.
See the "run_style"_run_style.html command for details.
These styles can only be used via the {pair} keyword of the "run_style
respa"_run_style.html command. They do not support the {inner},
{middle}, {outer} keywords.
:line

45
doc/pair_buck.html
View File

@ -55,12 +55,25 @@ Lennard-Jones 12/6) given by
</P>
<CENTER><IMG SRC = "Eqs/pair_buck.jpg">
</CENTER>
<P>Rc is the cutoff.
<P>where rho is an ionic-pair dependent length parameter, and Rc is the
cutoff.
</P>
<P>The <I>buck/coul/cut</I> and <I>buck/coul/long</I> styles add a Coulombic term
as described for the <A HREF = "pair_lj.html">lj/cut</A> pair styles.
as described for the <A HREF = "pair_lj.html">lj/cut</A> pair styles. For
<I>buck/coul/long</I>, an additional damping factor is applied to the
Coulombic term so it can be used in conjunction with the
<A HREF = "kspace_style.html">kspace_style</A> command and its <I>ewald</I> or <I>pppm</I>
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
</P>
<P>Note that this potential is related to the <A HREF = "pair_born.html">Born-Mayer-Huggins
<P>If one cutoff is specified for the <I>born/coul/cut</I> and
<I>born/coulk/long</I> styles, it is used for both the A,C and Coulombic
terms. If two cutoffs are specified, the first is used as the cutoff
for the A,C terms, and the second is the cutoff for the Coulombic
term.
</P>
<P>Note that these potentials are related to the <A HREF = "pair_born.html">Born-Mayer-Huggins
potential</A>.
</P>
<P>The following coefficients must be defined for each pair of atoms
@ -93,28 +106,26 @@ pair_style command.
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>None of the Buckingham pair styles support mixing. Thus, coefficients
for all I,J pairs must be specified explicitly.
<P>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>All of the Buckingham pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
exp() and 1/r^6 portion of the pair interaction.
<P>These styles support the <A HREF = "pair_modify.html">pair_modify</A> shift option
for the energy of the exp() and 1/r^6 portion of the pair interaction.
</P>
<P>The <I>buck/coul/long</I> pair style does not support the
<A HREF = "pair_modify.html">pair_modify</A> table option since a tabulation
capability has not yet been added to this potential.
</P>
<P>None of the Buckingham pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
corrections to energy and pressure.
<P>These styles do not support the <A HREF = "pair_modify.html">pair_modify</A> tail
option for adding long-range tail corrections to energy and pressure.
</P>
<P>All of the Buckingham pair styles write their 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>These styles write their 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>All of the Buckingham pair styles can only be used via the <I>pair</I>
keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
<P>These styles can only be used via the <I>pair</I> keyword of the <A HREF = "run_style.html">run_style
respa</A> command. They do not support the <I>inner</I>,
<I>middle</I>, <I>outer</I> keywords.
</P>
<P><B>Restrictions:</B>
</P>

45
doc/pair_buck.txt
View File

@ -49,12 +49,25 @@ Lennard-Jones 12/6) given by
:c,image(Eqs/pair_buck.jpg)
Rc is the cutoff.
where rho is an ionic-pair dependent length parameter, and Rc is the
cutoff.
The {buck/coul/cut} and {buck/coul/long} styles add a Coulombic term
as described for the "lj/cut"_pair_lj.html pair styles.
as described for the "lj/cut"_pair_lj.html pair styles. For
{buck/coul/long}, an additional damping factor is applied to the
Coulombic term so it can be used in conjunction with the
"kspace_style"_kspace_style.html command and its {ewald} or {pppm}
option. The Coulombic cutoff specified for this style means that
pairwise interactions within this distance are computed directly;
interactions outside that distance are computed in reciprocal space.
Note that this potential is related to the "Born-Mayer-Huggins
If one cutoff is specified for the {born/coul/cut} and
{born/coulk/long} styles, it is used for both the A,C and Coulombic
terms. If two cutoffs are specified, the first is used as the cutoff
for the A,C terms, and the second is the cutoff for the Coulombic
term.
Note that these potentials are related to the "Born-Mayer-Huggins
potential"_pair_born.html.
The following coefficients must be defined for each pair of atoms
@ -87,28 +100,26 @@ pair_style command.
[Mixing, shift, table, tail correction, restart, rRESPA info]:
None of the Buckingham pair styles support mixing. Thus, coefficients
for all I,J pairs must be specified explicitly.
These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
All of the Buckingham pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
exp() and 1/r^6 portion of the pair interaction.
These styles support the "pair_modify"_pair_modify.html shift option
for the energy of the exp() and 1/r^6 portion of the pair interaction.
The {buck/coul/long} pair style does not support the
"pair_modify"_pair_modify.html table option since a tabulation
capability has not yet been added to this potential.
None of the Buckingham pair styles support the
"pair_modify"_pair_modify.html tail option for adding long-range tail
corrections to energy and pressure.
These styles do not support the "pair_modify"_pair_modify.html tail
option for adding long-range tail corrections to energy and pressure.
All of the Buckingham pair styles write their 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.
These styles write their 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.
All of the Buckingham pair styles can only be used via the {pair}
keyword of the "run_style respa"_run_style.html command. They do not
support the {inner}, {middle}, {outer} keywords.
These styles can only be used via the {pair} keyword of the "run_style
respa"_run_style.html command. They do not support the {inner},
{middle}, {outer} keywords.
[Restrictions:]

2
doc/pair_coeff.html
View File

@ -88,6 +88,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> - multiple styles of superposed pairwise interactions
</UL>
<UL><LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AI-REBO potential
<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckingham with cutoff Coulomb
@ -107,6 +108,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM
<LI><A HREF = "pair_eim.html">pair_style eim</A> - embedded ion method (EIM)
<LI><A HREF = "pair_gauss.html">pair_style gauss</A> - Gaussian potential
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
<LI><A HREF = "pair_gayberne.html">pair_style gayberne/gpu</A> - GPU-enabled Gay-Berne ellipsoidal potential
<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions

2
doc/pair_coeff.txt
View File

@ -85,6 +85,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions :ul
"pair_style airebo"_pair_airebo.html - AI-REBO potential
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulomb
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb
@ -104,6 +105,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
"pair_style eim"_pair_eim.html - embedded ion method (EIM)
"pair_style gauss"_pair_gauss.html - Gaussian potential
"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"pair_style gayberne/gpu"_pair_gayberne.html - GPU-enabled Gay-Berne ellipsoidal potential
"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions

84
doc/pair_gauss.html Normal file
View File

@ -0,0 +1,84 @@
<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 gauss command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style gauss cutoff
</PRE>
<UL><LI>cutoff = global cutoff for Gauss interactions (distance units)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style gauss 12.0
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>gauss</I> computes a tethering potential of the form
</P>
<CENTER><IMG SRC = "Eqs/pair_gauss.jpg">
</CENTER>
<P>between an atom and its corresponding tether site which will typically
be a frozen atom in the simulation. Rc is the cutoff.
</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 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:
</P>
<UL><LI>A (energy units)
<LI>B (1/distance^2 units)
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global cutoff
is used.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>This pair style does 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>
shift option. There is no effect due to the Gaussian well beyond the
cutoff; hence reasonable cutoffs need to be specified.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
relevant for this pair style.
</P>
<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
table option, since a tabulation capability does not exist for this
potential.
</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 = "fix_adapt.html">fix adapt</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

79
doc/pair_gauss.txt Normal file
View File

@ -0,0 +1,79 @@
"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 gauss command :h3
[Syntax:]
pair_style gauss cutoff :pre
cutoff = global cutoff for Gauss interactions (distance units) :ul
[Examples:]
pair_style gauss 12.0
pair_coeff * * 1.0 0.9
pair_coeff 1 4 1.0 0.9 10.0 :pre
[Description:]
Style {gauss} computes a tethering potential of the form
:c,image(Eqs/pair_gauss.jpg)
between an atom and its corresponding tether site which will typically
be a frozen atom in the simulation. Rc is the cutoff.
The following coefficients must be defined for each pair of atom 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:
A (energy units)
B (1/distance^2 units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global cutoff
is used.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
This pair style does not support the "pair_modify"_pair_modify.html
shift option. There is no effect due to the Gaussian well beyond the
cutoff; hence reasonable cutoffs need to be specified.
The "pair_modify"_pair_modify.html table and tail options are not
relevant for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
table option, since a tabulation capability does not exist for this
potential.
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, "fix adapt"_fix_adapt.html
[Default:] none

2
doc/pair_style.html
View File

@ -90,6 +90,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> - multiple styles of superposed pairwise interactions
</UL>
<UL><LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AI-REBO potential
<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckingham with cutoff Coulomb
@ -109,6 +110,7 @@ the pair_style command, and coefficients specified by the associated
<LI><A HREF = "pair_eam.html">pair_style eam/fs</A> - Finnis-Sinclair EAM
<LI><A HREF = "pair_eam.html">pair_style eam/fs/opt</A> - optimized version of Finnis-Sinclair EAM
<LI><A HREF = "pair_eim.html">pair_style eim</A> - embedded ion method (EIM)
<LI><A HREF = "pair_gauss.html">pair_style gauss</A> - Gaussian potential
<LI><A HREF = "pair_gayberne.html">pair_style gayberne</A> - Gay-Berne ellipsoidal potential
<LI><A HREF = "pair_gayberne.html">pair_style gayberne/gpu</A> - GPU-enabled Gay-Berne ellipsoidal potential
<LI><A HREF = "pair_gran.html">pair_style gran/hertz/history</A> - granular potential with Hertzian interactions

2
doc/pair_style.txt
View File

@ -87,6 +87,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions :ul
"pair_style airebo"_pair_airebo.html - AI-REBO potential
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulomb
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb
@ -106,6 +107,7 @@ the pair_style command, and coefficients specified by the associated
"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
"pair_style eam/fs/opt"_pair_eam.html - optimized version of Finnis-Sinclair EAM
"pair_style eim"_pair_eim.html - embedded ion method (EIM)
"pair_style gauss"_pair_gauss.html - Gaussian potential
"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
"pair_style gayberne/gpu"_pair_gayberne.html - GPU-enabled Gay-Berne ellipsoidal potential
"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions