git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8122 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -423,16 +423,16 @@ potentials.  Click on the style itself for a full description:
 <TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eim.html">eim</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "pair_gauss.html">gauss</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne</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_hbond_dreiding.html">hbond/dreiding/lj</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj</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_lcbop.html">lcbop</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj</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></TR>
-<TR ALIGN="center"><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><TD ><A HREF = "pair_lj.html">lj/cut</A></TD></TR>
+<TR ALIGN="center"><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><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
-<TR ALIGN="center"><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><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/tip4p</A></TD></TR>
+<TR ALIGN="center"><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><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD></TR>
-<TR ALIGN="center"><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><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</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_linear.html">lj/smooth/linear</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD></TR>
+<TR ALIGN="center"><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><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD></TR>
-<TR ALIGN="center"><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><TD ><A HREF = "pair_morse.html">morse</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_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_airebo.html">rebo</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_resquared.html">resquared</A></TD><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></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_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><TD ><A HREF = "pair_yukawa.html">yukawa</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_colloid.html">yukawa/colloid</A> 
+<TR ALIGN="center"><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

doc/Section_commands.txt

@@ -653,6 +653,7 @@ potentials.  Click on the style itself for a full description:
 "hbond/dreiding/lj"_pair_hbond_dreiding.html,
 "hbond/dreiding/morse"_pair_hbond_dreiding.html,
 "kim"_pair_kim.html,
+"lcbop"_pair_lcbop.html,
 "line/lj"_pair_line_lj.html,
 "lj/charmm/coul/charmm"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit"_pair_charmm.html,

doc/pair_coeff.html

@@ -128,6 +128,7 @@ section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
 <LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
 <LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/lj</A> - DREIDING hydrogen bonding LJ potential
 <LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/morse</A> - DREIDING hydrogen bonding Morse potential
+<LI><A HREF = "pair_lcbop.html">pair_style lcbop</A> - long-range bond-order potential (LCBOP)
 <LI><A HREF = "pair_line_lj.html">pair_style line/lj</A> - LJ potential between line segments
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent

doc/pair_coeff.txt

@@ -125,6 +125,7 @@ section of "this page"_Section_commands.html#cmd_5.
 "pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
 "pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential
 "pair_style hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential
+"pair_style lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
 "pair_style line/lj"_pair_line_lj.html - LJ potential between line segments
 "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
 "pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent

doc/pair_lcbop.html

@@ -0,0 +1,100 @@
+<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 lcbop command 
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>pair_style lcbop 
+</PRE>
+<P><B>Examples:</B>
+</P>
+<PRE>pair_style lcbop
+pair_coeff * * ../potentials/C.lcbop C 
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>The <I>lcbop</I> pair style computes the long-range bond-order potential
+for carbon (LCBOP) of <A HREF = "#Los">(Los and Fasolino)</A>.  See section II in
+that paper for the analytic equations associated with the potential.
+</P>
+<P>Only a single pair_coeff command is used with the <I>lcbop</I> style which
+specifies an LCBOP potential file with parameters for specific
+elements.  These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+</P>
+<UL><LI>filename
+<LI>N element names = mapping of LCBOP elements to atom types 
+</UL>
+<P>As an example, if your LAMMPS simulation has 4 atom types and you want
+the 1st 3 to be C you would use the following pair_coeff command:
+</P>
+<PRE>pair_coeff * * C.lcbop C C C NULL 
+</PRE>
+<P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first C argument maps LAMMPS atom type 1 to the C element in the
+LCBOP file. If a mapping value is specified as NULL, the mapping is
+not performed.  This can be used when a <I>lcbop</I> potential is used as
+part of the <I>hybrid</I> pair style.  The NULL values are placeholders for
+atom types that will be used with other potentials.
+</P>
+<P>The parameters/coefficients for the LCBOP potential as applied to C
+are listed in the C.lcbop file to agree with the original <A HREF = "#Los">(Los and
+Fasolino)</A> paper.  Thus the parameters are specific to this
+potential and the way it was fit, so modifying the file should be done
+carefully.
+</P>
+<HR>
+
+<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
+</P>
+<P>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
+mix, shift, table, and tail options.
+</P>
+<P>This pair style does not write its information to <A HREF = "restart.html">binary restart
+files</A>, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands 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>
+<P><B>Restrictions:</B>
+</P>
+<P>This pair styles is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package (which it is by default).  See
+the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
+</P>
+<P>This pair potential requires the <A HREF = "newton.html">newton</A> setting to be
+"on" for pair interactions.
+</P>
+<P>The C.lcbop potential file provided with LAMMPS (see the potentials
+directory) is parameterized for metal <A HREF = "units.html">units</A>.  You can use
+the LCBOP potential with any LAMMPS units, but you would need to
+create your own LCBOP potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "pair_airebo.html">pair_airebo</A>, <A HREF = "pair_coeff.html">pair_coeff</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Los"></A>
+
+<P><B>(Los and Fasolino)</B> J. H. Los and A. Fasolino, Phys. Rev. B 68, 024107
+(2003).
+</P>
+</HTML>

doc/pair_lcbop.txt

@@ -0,0 +1,94 @@
+"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 lcbop command :h3
+
+[Syntax:]
+
+pair_style lcbop :pre
+
+[Examples:]
+
+pair_style lcbop
+pair_coeff * * ../potentials/C.lcbop C :pre
+
+[Description:]
+
+The {lcbop} pair style computes the long-range bond-order potential
+for carbon (LCBOP) of "(Los and Fasolino)"_#Los.  See section II in
+that paper for the analytic equations associated with the potential.
+
+Only a single pair_coeff command is used with the {lcbop} style which
+specifies an LCBOP potential file with parameters for specific
+elements.  These are mapped to LAMMPS atom types by specifying N
+additional arguments after the filename in the pair_coeff command,
+where N is the number of LAMMPS atom types:
+
+filename
+N element names = mapping of LCBOP elements to atom types :ul
+
+As an example, if your LAMMPS simulation has 4 atom types and you want
+the 1st 3 to be C you would use the following pair_coeff command:
+
+pair_coeff * * C.lcbop C C C NULL :pre
+
+The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
+The first C argument maps LAMMPS atom type 1 to the C element in the
+LCBOP file. If a mapping value is specified as NULL, the mapping is
+not performed.  This can be used when a {lcbop} potential is used as
+part of the {hybrid} pair style.  The NULL values are placeholders for
+atom types that will be used with other potentials.
+
+The parameters/coefficients for the LCBOP potential as applied to C
+are listed in the C.lcbop file to agree with the original "(Los and
+Fasolino)"_#Los paper.  Thus the parameters are specific to this
+potential and the way it was fit, so modifying the file should be done
+carefully.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair style does not support the "pair_modify"_pair_modify.html
+mix, shift, table, and tail options.
+
+This pair style does not write its information to "binary restart
+files"_restart.html, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands 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.
+
+[Restrictions:]
+
+This pair styles is part of the MANYBODY package.  It is only enabled
+if LAMMPS was built with that package (which it is by default).  See
+the "Making LAMMPS"_Section_start.html#start_3 section for more info.
+
+This pair potential requires the "newton"_newton.html setting to be
+"on" for pair interactions.
+
+The C.lcbop potential file provided with LAMMPS (see the potentials
+directory) is parameterized for metal "units"_units.html.  You can use
+the LCBOP potential with any LAMMPS units, but you would need to
+create your own LCBOP potential file with coefficients listed in the
+appropriate units if your simulation doesn't use "metal" units.
+
+[Related commands:]
+
+"pair_airebo"_pair_airebo.html, "pair_coeff"_pair_coeff.html
+
+[Default:] none
+
+:line
+
+:link(Los)
+[(Los and Fasolino)] J. H. Los and A. Fasolino, Phys. Rev. B 68, 024107
+(2003).

doc/pair_style.html

@@ -130,6 +130,7 @@ section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
 <LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
 <LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/lj</A> - DREIDING hydrogen bonding LJ potential
 <LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/morse</A> - DREIDING hydrogen bonding Morse potential
+<LI><A HREF = "pair_lcbop.html">pair_style lcbop</A> - long-range bond-order potential (LCBOP)
 <LI><A HREF = "pair_line_lj.html">pair_style line/lj</A> - LJ potential between line segments
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
 <LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent

doc/pair_style.txt

@@ -127,6 +127,7 @@ section of "this page"_Section_commands.html#cmd_5.
 "pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
 "pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential
 "pair_style hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential
+"pair_style lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
 "pair_style line/lj"_pair_line_lj.html - LJ potential between line segments
 "pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
 "pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent