git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10423 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -481,8 +481,9 @@ potentials.  Click on the style itself for a full description:
 <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_mie.html">mie/cut</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_coul.html">tip4p/cut</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_mod.html">tersoff/mod</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/long</A></TD><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> 
+<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/cut</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long</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_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

@@ -781,6 +781,7 @@ potentials.  Click on the style itself for a full description:
 "sw"_pair_sw.html,
 "table"_pair_table.html,
 "tersoff"_pair_tersoff.html,
+"tersoff/mod"_pair_tersoff_mod.html,
 "tersoff/zbl"_pair_tersoff_zbl.html,
 "tip4p/cut"_pair_coul.html,
 "tip4p/long"_pair_coul.html,

doc/pair_tersoff_mod.html

@@ -11,8 +11,6 @@
 
 <H3>pair_style tersoff/mod command 
 </H3>
-<H3>pair_style tersoff/mod/omp 
-</H3>
 <P><B>Syntax:</B>
 </P>
 <PRE>pair_style tersoff/mod 
@@ -20,30 +18,32 @@
 <P><B>Examples:</B>
 </P>
 <PRE>pair_style tersoff/mod
-pair_coeff * * Si.tersoff_mod Si Si 
+pair_coeff * * Si.tersoff.mod Si Si 
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>The <I>tersoff/mod</I> style computes a bond-order type interatomic potential
+<P>The <I>tersoff/mod</I> style computes a bond-order type interatomic
-<A HREF = "#Kumagai">(Kumagai)</A> based on a 3-body Tersoff potential <A HREF = "#Tersoff_1">(Tersoff_1)</A>,
+potential <A HREF = "#Kumagai">(Kumagai)</A> based on a 3-body Tersoff potential
-<A HREF = "#Tersoff_2">(Tersoff_2)</A> with modified cutoff function and angular-dependent
+<A HREF = "#Tersoff_1">(Tersoff_1)</A>, <A HREF = "#Tersoff_2">(Tersoff_2)</A> with modified
-term, giving the energy E of a system of atoms as
+cutoff function and angular-dependent term, giving the energy E of a
+system of atoms as
 </P>
 <CENTER><IMG SRC = "Eqs/pair_tersoff_mod.jpg">
 </CENTER>
 <P>where f_R is a two-body term and f_A includes three-body interactions.
 The summations in the formula are over all neighbors J and K of atom I
-within a cutoff distance = R + D. 
+within a cutoff distance = R + D.
 </P>
-<P>The modified cutoff function f_C proposed by <A HREF = "#Murty">(Murty)</A> and having a
+<P>The modified cutoff function f_C proposed by <A HREF = "#Murty">(Murty)</A> and
-continuous second-order differential is employed. The angular-dependent
+having a continuous second-order differential is employed. The
-term g(theta) was modified to increase the flexibility of the potential.
+angular-dependent term g(theta) was modified to increase the
+flexibility of the potential.
 </P>
-<P>The <I>tersoff/mod</I> potential is fitted to both the elastic constants and
+<P>The <I>tersoff/mod</I> potential is fitted to both the elastic constants
-melting point by employing the modified Tersoff potential function form
+and melting point by employing the modified Tersoff potential function
-in which the angular-dependent term is improved. The model performs extremely
+form in which the angular-dependent term is improved. The model
-well in describing the crystalline, liquid, and amorphous phases
+performs extremely well in describing the crystalline, liquid, and
-<A HREF = "#Schelling">(Schelling)</A>.
+amorphous phases <A HREF = "#Schelling">(Schelling)</A>.
 </P>
 <P>Only a single pair_coeff command is used with the <I>tersoff/mod</I> style
 which specifies a Tersoff/MOD potential file with parameters for all
@@ -63,15 +63,16 @@ pair_coeff command:
 <P>The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
 in the Tersoff/MOD file. If a mapping value is specified as NULL, the
-mapping is not performed.  This can be used when a <I>tersoff/mod</I> potential
+mapping is not performed.  This can be used when a <I>tersoff/mod</I>
-is used as part of the <I>hybrid</I> pair style. The NULL values are
+potential is used as part of the <I>hybrid</I> pair style. The NULL values
-placeholders for atom types that will be used with other potentials.
+are placeholders for atom types that will be used with other
+potentials.
 </P>
-<P>Tersoff/MOD file in the <I>potentials</I> directory of the LAMMPS distribution
+<P>Tersoff/MOD file in the <I>potentials</I> directory of the LAMMPS
-have a ".tersoff_mod" suffix.  Lines that are not blank or comments
+distribution have a ".tersoff.mod" suffix.  Lines that are not blank
-(starting with #) define parameters for a triplet of elements.  The
+or comments (starting with #) define parameters for a triplet of
-parameters in a single entry correspond to coefficients in the formula
+elements.  The parameters in a single entry correspond to coefficients
-above:
+in the formula above:
 </P>
 <UL><LI>element 1 (the center atom in a 3-body interaction)
 <LI>element 2 (the atom bonded to the center atom)
@@ -113,28 +114,6 @@ for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
 </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_7">-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>This pair style does not support the <A HREF = "pair_modify.html">pair_modify</A>
@@ -176,7 +155,8 @@ appropriate units if your simulation doesn't use "metal" units.
 
 <A NAME = "Kumagai"></A>
 
-<P><B>(Kumagai)</B> T. Kumagai, S. Izumi, S. Hara, S. Sakai, Comp. Mat. Science, 39, 457 (2007).
+<P><B>(Kumagai)</B> T. Kumagai, S. Izumi, S. Hara, S. Sakai,
+Comp. Mat. Science, 39, 457 (2007).
 </P>
 <A NAME = "Tersoff_1"></A>
 

doc/pair_tersoff_mod.txt

@@ -7,7 +7,6 @@
 :line
 
 pair_style tersoff/mod command :h3
-pair_style tersoff/mod/omp :h3
 
 [Syntax:]
 
@@ -16,30 +15,32 @@ pair_style tersoff/mod :pre
 [Examples:]
 
 pair_style tersoff/mod
-pair_coeff * * Si.tersoff_mod Si Si :pre
+pair_coeff * * Si.tersoff.mod Si Si :pre
 
 [Description:]
 
-The {tersoff/mod} style computes a bond-order type interatomic potential
+The {tersoff/mod} style computes a bond-order type interatomic
-"(Kumagai)"_#Kumagai based on a 3-body Tersoff potential "(Tersoff_1)"_#Tersoff_1,
+potential "(Kumagai)"_#Kumagai based on a 3-body Tersoff potential
-"(Tersoff_2)"_#Tersoff_2 with modified cutoff function and angular-dependent
+"(Tersoff_1)"_#Tersoff_1, "(Tersoff_2)"_#Tersoff_2 with modified
-term, giving the energy E of a system of atoms as
+cutoff function and angular-dependent term, giving the energy E of a
+system of atoms as
 
 :c,image(Eqs/pair_tersoff_mod.jpg)
 
 where f_R is a two-body term and f_A includes three-body interactions.
 The summations in the formula are over all neighbors J and K of atom I
-within a cutoff distance = R + D. 
+within a cutoff distance = R + D.
 
-The modified cutoff function f_C proposed by "(Murty)"_#Murty and having a
+The modified cutoff function f_C proposed by "(Murty)"_#Murty and
-continuous second-order differential is employed. The angular-dependent
+having a continuous second-order differential is employed. The
-term g(theta) was modified to increase the flexibility of the potential.
+angular-dependent term g(theta) was modified to increase the
+flexibility of the potential.
 
-The {tersoff/mod} potential is fitted to both the elastic constants and
+The {tersoff/mod} potential is fitted to both the elastic constants
-melting point by employing the modified Tersoff potential function form
+and melting point by employing the modified Tersoff potential function
-in which the angular-dependent term is improved. The model performs extremely
+form in which the angular-dependent term is improved. The model
-well in describing the crystalline, liquid, and amorphous phases
+performs extremely well in describing the crystalline, liquid, and
-"(Schelling)"_#Schelling.
+amorphous phases "(Schelling)"_#Schelling.
 
 Only a single pair_coeff command is used with the {tersoff/mod} style
 which specifies a Tersoff/MOD potential file with parameters for all
@@ -59,15 +60,16 @@ pair_coeff * * Si.tersoff_mod Si Si Si :pre
 The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
 The three Si arguments map LAMMPS atom types 1,2,3 to the Si element
 in the Tersoff/MOD file. If a mapping value is specified as NULL, the
-mapping is not performed.  This can be used when a {tersoff/mod} potential
+mapping is not performed.  This can be used when a {tersoff/mod}
-is used as part of the {hybrid} pair style. The NULL values are
+potential is used as part of the {hybrid} pair style. The NULL values
-placeholders for atom types that will be used with other potentials.
+are placeholders for atom types that will be used with other
+potentials.
 
-Tersoff/MOD file in the {potentials} directory of the LAMMPS distribution
+Tersoff/MOD file in the {potentials} directory of the LAMMPS
-have a ".tersoff_mod" suffix.  Lines that are not blank or comments
+distribution have a ".tersoff.mod" suffix.  Lines that are not blank
-(starting with #) define parameters for a triplet of elements.  The
+or comments (starting with #) define parameters for a triplet of
-parameters in a single entry correspond to coefficients in the formula
+elements.  The parameters in a single entry correspond to coefficients
-above:
+in the formula above:
 
 element 1 (the center atom in a 3-body interaction)
 element 2 (the atom bonded to the center atom)
@@ -109,28 +111,6 @@ for SiSiSi means Si bonded to a Si with another Si atom influencing the bond.
 
 :line
 
-Styles with a {cuda}, {gpu}, {omp}, or {opt} 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 "Section_accelerate"_Section_accelerate.html of the
-manual.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-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 "Making LAMMPS"_Section_start.html#start_3
-section for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
-use the "suffix"_suffix.html command in your input script.
-
-See "Section_accelerate"_Section_accelerate.html of the manual for
-more instructions on how to use the accelerated styles effectively.
-
-:line
-
 [Mixing, shift, table, tail correction, restart, rRESPA info]:
 
 This pair style does not support the "pair_modify"_pair_modify.html
@@ -171,7 +151,8 @@ appropriate units if your simulation doesn't use "metal" units.
 :line
 
 :link(Kumagai)
-[(Kumagai)] T. Kumagai, S. Izumi, S. Hara, S. Sakai, Comp. Mat. Science, 39, 457 (2007).
+[(Kumagai)] T. Kumagai, S. Izumi, S. Hara, S. Sakai,
+Comp. Mat. Science, 39, 457 (2007).
 
 :link(Tersoff_1)
 [(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988).