lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity

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

This commit is contained in:
sjplimp 2013-07-26 16:36:26 +00:00
parent 6563ff8b74
commit efa18fbd01
4 changed files with 58 additions and 95 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
doc/Section_commands.html
View File

@ -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_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_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/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

1
doc/Section_commands.txt
View File

@ -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,

74
doc/pair_tersoff_mod.html
View File

@ -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
<A HREF = "#Kumagai">(Kumagai)</A> based on a 3-body Tersoff potential <A HREF = "#Tersoff_1">(Tersoff_1)</A>,
<A HREF = "#Tersoff_2">(Tersoff_2)</A> with modified cutoff function and angular-dependent
term, giving the energy E of a system of atoms as
<P>The <I>tersoff/mod</I> style computes a bond-order type interatomic
potential <A HREF = "#Kumagai">(Kumagai)</A> based on a 3-body Tersoff potential
<A HREF = "#Tersoff_1">(Tersoff_1)</A>, <A HREF = "#Tersoff_2">(Tersoff_2)</A> with modified
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
continuous second-order differential is employed. The angular-dependent
term g(theta) was modified to increase the flexibility of the potential.
<P>The modified cutoff function f_C proposed by <A HREF = "#Murty">(Murty)</A> and
having a continuous second-order differential is employed. The
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
melting point by employing the modified Tersoff potential function form
in which the angular-dependent term is improved. The model performs extremely
well in describing the crystalline, liquid, and amorphous phases
<A HREF = "#Schelling">(Schelling)</A>.
<P>The <I>tersoff/mod</I> potential is fitted to both the elastic constants
and melting point by employing the modified Tersoff potential function
form in which the angular-dependent term is improved. The model
performs extremely well in describing the crystalline, liquid, and
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
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.
mapping is not performed. This can be used when a <I>tersoff/mod</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>Tersoff/MOD file in the <I>potentials</I> directory of the LAMMPS distribution
have a ".tersoff_mod" suffix. Lines that are not blank or comments
(starting with #) define parameters for a triplet of elements. The
parameters in a single entry correspond to coefficients in the formula
above:
<P>Tersoff/MOD file in the <I>potentials</I> directory of the LAMMPS
distribution have a ".tersoff.mod" suffix. Lines that are not blank
or comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to coefficients
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>

73
doc/pair_tersoff_mod.txt
View File

@ -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
"(Kumagai)"_#Kumagai based on a 3-body Tersoff potential "(Tersoff_1)"_#Tersoff_1,
"(Tersoff_2)"_#Tersoff_2 with modified cutoff function and angular-dependent
term, giving the energy E of a system of atoms as
The {tersoff/mod} style computes a bond-order type interatomic
potential "(Kumagai)"_#Kumagai based on a 3-body Tersoff potential
"(Tersoff_1)"_#Tersoff_1, "(Tersoff_2)"_#Tersoff_2 with modified
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
continuous second-order differential is employed. The angular-dependent
term g(theta) was modified to increase the flexibility of the potential.
The modified cutoff function f_C proposed by "(Murty)"_#Murty and
having a continuous second-order differential is employed. The
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
melting point by employing the modified Tersoff potential function form
in which the angular-dependent term is improved. The model performs extremely
well in describing the crystalline, liquid, and amorphous phases
"(Schelling)"_#Schelling.
The {tersoff/mod} potential is fitted to both the elastic constants
and melting point by employing the modified Tersoff potential function
form in which the angular-dependent term is improved. The model
performs extremely well in describing the crystalline, liquid, and
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
is used as part of the {hybrid} pair style. The NULL values are
placeholders for atom types that will be used with other potentials.
mapping is not performed. This can be used when a {tersoff/mod}
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.
Tersoff/MOD file in the {potentials} directory of the LAMMPS distribution
have a ".tersoff_mod" suffix. Lines that are not blank or comments
(starting with #) define parameters for a triplet of elements. The
parameters in a single entry correspond to coefficients in the formula
above:
Tersoff/MOD file in the {potentials} directory of the LAMMPS
distribution have a ".tersoff.mod" suffix. Lines that are not blank
or comments (starting with #) define parameters for a triplet of
elements. The parameters in a single entry correspond to coefficients
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).