forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12766 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
080fe0b70f
commit
b90439226f
Binary file not shown.
|
After Width: | Height: | Size: 5.5 KiB |
|
|
@ -0,0 +1,10 @@
|
|||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
\begin{eqnarray*}
|
||||
F_{i1}^{SRP} & = & F^{SRP}_{ij}(L) \\
|
||||
F_{i2}^{SRP} & = & F^{SRP}_{ij}(1-L)
|
||||
\end{eqnarray*}
|
||||
|
||||
\end{document}
|
||||
|
|
@ -515,7 +515,7 @@ package</A>.
|
|||
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long (go)</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm (o)</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf (o)</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_srp.html">srp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table (o)</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft (o)</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<HR>
|
||||
|
|
|
|||
|
|
@ -846,6 +846,7 @@ package"_Section_start.html#start_3.
|
|||
"sph/rhosum"_pair_sph_rhosum.html,
|
||||
"sph/taitwater"_pair_sph_taitwater.html,
|
||||
"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
|
||||
"srp"_pair_srp.html,
|
||||
"tersoff/table (o)"_pair_tersoff.html,
|
||||
"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,164 @@
|
|||
<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 srp command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<P>pair_style srp cutoff bond_type dist keyword value ...
|
||||
</P>
|
||||
<UL><LI>cutoff = global cutoff for SRP interactions (distance units)
|
||||
|
||||
<LI>bond_type = bond type to apply SRP interactions
|
||||
|
||||
<LI>dist = <I>min</I> or <I>mid</I>
|
||||
|
||||
<LI>zero or more keyword/value pairs may be appended
|
||||
|
||||
<LI>keyword = <I>exclude</I>
|
||||
|
||||
<PRE> <I>exclude</I> value = <I>yes</I> or <I>no</I>
|
||||
</PRE>
|
||||
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
|
||||
pair_coeff 1 1 dpd 60.0 4.5 1.0
|
||||
pair_coeff 1 2 none
|
||||
pair_coeff 2 2 srp 100.0 0.8
|
||||
</PRE>
|
||||
<PRE>pair_style hybrid srp 0.8 1 mid exclude yes
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 1 2 none
|
||||
pair_coeff 2 2 srp 100.0 0.8
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Style <I>srp</I> computes a soft segmental repulsive potential (SRP) that
|
||||
acts between bonds. This potential is useful in preventing bonds from
|
||||
passing through one another when a soft non-bonded potential acts
|
||||
between beads in, for example, DPD polymer chains.
|
||||
An example input script that uses this command is provided
|
||||
in examples/USER/srp.
|
||||
</P>
|
||||
<P>Bonds of type <I>btype</I> interact with one another through a
|
||||
bond-pairwise potential, such that the force on bond <I>i</I> due to bond
|
||||
<I>j</I> is as follows
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/pair_srp1.jpg">
|
||||
</CENTER>
|
||||
<P>where <I>r</I> and <I>rij</I> are the distance and unit vector between the two
|
||||
bonds. The <I>mid</I> option computes <I>r</I> and <I>rij</I> from the midpoint
|
||||
distance between bonds. The <I>min</I> option computes <I>r</I> and <I>rij</I> from
|
||||
the minimum distance between bonds. The force acting on a bond is
|
||||
mapped onto the two bond atoms according to the lever rule,
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/pair_srp2.jpg">
|
||||
</CENTER>
|
||||
<P>where <I>L</I> is the normalized distance from the atom to the point of
|
||||
closest approach of bond <I>i</I> and <I>j</I>. The <I>mid</I> option takes <I>L</I> as
|
||||
0.5 for each interaction as described in <A HREF = "#Sirk">(Sirk)</A>.
|
||||
</P>
|
||||
<P>The following coefficients must be defined via the
|
||||
<A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or in
|
||||
the data file or restart file read by the <A HREF = "read_data.html">read_data</A>
|
||||
or <A HREF = "read_restart.html">read_restart</A> commands:
|
||||
</P>
|
||||
<UL><LI><I>C</I> (force units)
|
||||
<LI><I>Rc</I> (distance units)
|
||||
</UL>
|
||||
<P>The last coefficient is optional. If not specified, the global cutoff
|
||||
is used.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Pair style srp considers each bond of type <I>btype</I> as
|
||||
a fictitious particle of type <I>bptype</I>, where <I>bptype</I> is the largest
|
||||
atom type in the system. These "bond particles" are inserted at the
|
||||
beginning of the run, and serve as placeholders that define the
|
||||
position of the bonds. This allows neighbor lists to be constructed
|
||||
and pairwise interactions to be computed in almost the same way as is
|
||||
done for point particles. Because bonds interact only with other
|
||||
bonds, <A HREF = "pair_hybrid.html">pair_style hybrid</A> should be used to turn off
|
||||
interactions between atom type <I>bptype</I> and all other types of atoms.
|
||||
An error will be flagged if <A HREF = "pair_hybrid.html">pair_style hybrid</A> is
|
||||
not used. Further, only bond particles should be given an atom type
|
||||
of <I>bptype</I>; a check is done at the beginning of the run to ensure
|
||||
there are no regular atoms of <I>bptype</I>.
|
||||
</P>
|
||||
<P>The optional <I>exclude</I> keyword determines if forces are computed
|
||||
between first neighbor (directly connected) bonds. For a setting of
|
||||
<I>yes</I> they are, for <I>no</I> they are not.
|
||||
</P>
|
||||
<P>Pair style <I>srp</I> turns off normalization of thermodynamic properties
|
||||
by particle number, as if the command <A HREF = "thermo_modify.html">thermo_modify norm
|
||||
no</A> had been issued. A warning will be given if
|
||||
this setting is overridden in the input script.
|
||||
</P>
|
||||
<P>The pairwise energy associated with style <I>srp</I> is shifted to be zero
|
||||
at the cutoff distance <I>Rc</I>.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
</P>
|
||||
<P>This pair styles does not support mixing.
|
||||
</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. Note that as
|
||||
discussed above, the energy term is already shifted to be 0.0 at the
|
||||
cutoff distance <I>rc</I>.
|
||||
</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.
|
||||
</P>
|
||||
<P>This pair style writes global and per-atom information to <A HREF = "restart.html">binary
|
||||
restart files</A>. Pair srp should be used with <A HREF = "pair_hybrid.html">pair_style
|
||||
hybrid</A>, thus the pair_coeff commands need to be
|
||||
specified in the input script when reading 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>
|
||||
</P>
|
||||
<P>This pair style is part of the USER-MISC package. It is only enabled
|
||||
if LAMMPS was built with that package. See the Making LAMMPS section
|
||||
for more info.
|
||||
</P>
|
||||
<P>This pair style must be used with <A HREF = "pair_hybrid.html">pair_style hybrid</A>.
|
||||
</P>
|
||||
<P>This pair style requires the <A HREF = "newton.html">newton</A> command to be <I>on</I>
|
||||
for non-bonded interactions.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_hybrid.html">pair_style hybrid</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
|
||||
<A HREF = "pair_dpd.html">pair dpd</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>The default keyword value is exclude = yes.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "Sirk"></A>
|
||||
|
||||
<P><B>(Sirk)</B> Sirk TW, Slizoberg YR, Brennan JK, Lisal M, Andzelm JW, J
|
||||
Chem Phys, 136 (13) 134903, 2012.
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,152 @@
|
|||
"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 srp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style srp cutoff bond_type dist keyword value ...
|
||||
|
||||
cutoff = global cutoff for SRP interactions (distance units) :ulb,l
|
||||
bond_type = bond type to apply SRP interactions :l
|
||||
dist = {min} or {mid} :l
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {exclude} :l
|
||||
{exclude} value = {yes} or {no} :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes
|
||||
pair_coeff 1 1 dpd 60.0 4.5 1.0
|
||||
pair_coeff 1 2 none
|
||||
pair_coeff 2 2 srp 100.0 0.8 :pre
|
||||
|
||||
pair_style hybrid srp 0.8 1 mid exclude yes
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 1 2 none
|
||||
pair_coeff 2 2 srp 100.0 0.8 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {srp} computes a soft segmental repulsive potential (SRP) that
|
||||
acts between bonds. This potential is useful in preventing bonds from
|
||||
passing through one another when a soft non-bonded potential acts
|
||||
between beads in, for example, DPD polymer chains.
|
||||
An example input script that uses this command is provided
|
||||
in examples/USER/srp.
|
||||
|
||||
Bonds of type {btype} interact with one another through a
|
||||
bond-pairwise potential, such that the force on bond {i} due to bond
|
||||
{j} is as follows
|
||||
|
||||
:c,image(Eqs/pair_srp1.jpg)
|
||||
|
||||
where {r} and {rij} are the distance and unit vector between the two
|
||||
bonds. The {mid} option computes {r} and {rij} from the midpoint
|
||||
distance between bonds. The {min} option computes {r} and {rij} from
|
||||
the minimum distance between bonds. The force acting on a bond is
|
||||
mapped onto the two bond atoms according to the lever rule,
|
||||
|
||||
:c,image(Eqs/pair_srp2.jpg)
|
||||
|
||||
where {L} is the normalized distance from the atom to the point of
|
||||
closest approach of bond {i} and {j}. The {mid} option takes {L} as
|
||||
0.5 for each interaction as described in "(Sirk)"_#Sirk.
|
||||
|
||||
The following coefficients must be defined via the
|
||||
"pair_coeff"_pair_coeff.html command as in the examples above, or in
|
||||
the data file or restart file read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
{C} (force units)
|
||||
{Rc} (distance units) :ul
|
||||
|
||||
The last coefficient is optional. If not specified, the global cutoff
|
||||
is used.
|
||||
|
||||
IMPORTANT NOTE: Pair style srp considers each bond of type {btype} as
|
||||
a fictitious particle of type {bptype}, where {bptype} is the largest
|
||||
atom type in the system. These "bond particles" are inserted at the
|
||||
beginning of the run, and serve as placeholders that define the
|
||||
position of the bonds. This allows neighbor lists to be constructed
|
||||
and pairwise interactions to be computed in almost the same way as is
|
||||
done for point particles. Because bonds interact only with other
|
||||
bonds, "pair_style hybrid"_pair_hybrid.html should be used to turn off
|
||||
interactions between atom type {bptype} and all other types of atoms.
|
||||
An error will be flagged if "pair_style hybrid"_pair_hybrid.html is
|
||||
not used. Further, only bond particles should be given an atom type
|
||||
of {bptype}; a check is done at the beginning of the run to ensure
|
||||
there are no regular atoms of {bptype}.
|
||||
|
||||
The optional {exclude} keyword determines if forces are computed
|
||||
between first neighbor (directly connected) bonds. For a setting of
|
||||
{yes} they are, for {no} they are not.
|
||||
|
||||
Pair style {srp} turns off normalization of thermodynamic properties
|
||||
by particle number, as if the command "thermo_modify norm
|
||||
no"_thermo_modify.html had been issued. A warning will be given if
|
||||
this setting is overridden in the input script.
|
||||
|
||||
The pairwise energy associated with style {srp} is shifted to be zero
|
||||
at the cutoff distance {Rc}.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair styles does not support mixing.
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
shift option for the energy of the pair interaction. Note that as
|
||||
discussed above, the energy term is already shifted to be 0.0 at the
|
||||
cutoff distance {rc}.
|
||||
|
||||
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.
|
||||
|
||||
This pair style writes global and per-atom information to "binary
|
||||
restart files"_restart.html. Pair srp should be used with "pair_style
|
||||
hybrid"_pair_hybrid.html, thus the pair_coeff commands need to be
|
||||
specified in the input script when reading 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:]
|
||||
|
||||
This pair style is part of the USER-MISC package. It is only enabled
|
||||
if LAMMPS was built with that package. See the Making LAMMPS section
|
||||
for more info.
|
||||
|
||||
This pair style must be used with "pair_style hybrid"_pair_hybrid.html.
|
||||
|
||||
This pair style requires the "newton"_newton.html command to be {on}
|
||||
for non-bonded interactions.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style hybrid"_pair_hybrid.html, "pair_coeff"_pair_coeff.html,
|
||||
"pair dpd"_pair_dpd.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The default keyword value is exclude = yes.
|
||||
|
||||
:line
|
||||
|
||||
:link(Sirk)
|
||||
[(Sirk)] Sirk TW, Slizoberg YR, Brennan JK, Lisal M, Andzelm JW, J
|
||||
Chem Phys, 136 (13) 134903, 2012.
|
||||
Loading…
Reference in New Issue