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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10293 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2013-07-23 15:21:46 +00:00
parent ad2266e4bf
commit 21fe3ece38
6 changed files with 104 additions and 14 deletions
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6
doc/fix_tune_kspace.html
View File

@ -97,8 +97,10 @@ called. Reneighboring is required.
<P><A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "boundary.html">boundary</A>
<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_lj.html">pair_style
lj/cut/coul/long</A>, <A HREF = "pair_charmm.html">pair_style
lj/charmm/coul/long</A>, <A HREF = "pair_lj_coul.html">pair_style
lj/coul</A>, <A HREF = "pair_buck.html">pair_style buck/coul/long</A>
lj/charmm/coul/long</A>, <A HREF = "pair_lj_long.html">pair_style
lj/long</A>, <A HREF = "pair_lj_long.html">pair_style
lj/long/coul/long</A>,
<A HREF = "pair_buck.html">pair_style buck/coul/long</A>
</P>
<P><B>Default:</B>
</P>

4
doc/fix_tune_kspace.txt
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@ -92,7 +92,9 @@ called. Reneighboring is required.
"kspace_modify"_kspace_modify.html, "pair_style
lj/cut/coul/long"_pair_lj.html, "pair_style
lj/charmm/coul/long"_pair_charmm.html, "pair_style
lj/coul"_pair_lj_coul.html, "pair_style buck/coul/long"_pair_buck.html
lj/long"_pair_lj_long.html, "pair_style
lj/long/coul/long"_pair_lj_long.html,
"pair_style buck/coul/long"_pair_buck.html
[Default:]

4
doc/kspace_style.html
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@ -307,8 +307,8 @@ non-periodic.
</P>
<P><A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "pair_lj.html">pair_style
lj/cut/coul/long</A>, <A HREF = "pair_charmm.html">pair_style
lj/charmm/coul/long</A>, <A HREF = "pair_lj_coul.html">pair_style
lj/coul</A>, <A HREF = "pair_buck.html">pair_style buck/coul/long</A>
lj/charmm/coul/long</A>, <A HREF = "pair_lj_long.html">pair_style
lj/long/coul/long</A>, <A HREF = "pair_buck.html">pair_style buck/coul/long</A>
</P>
<P><B>Default:</B>
</P>

2
doc/kspace_style.txt
View File

@ -301,7 +301,7 @@ non-periodic.
"kspace_modify"_kspace_modify.html, "pair_style
lj/cut/coul/long"_pair_lj.html, "pair_style
lj/charmm/coul/long"_pair_charmm.html, "pair_style
lj/coul"_pair_lj_coul.html, "pair_style buck/coul/long"_pair_buck.html
lj/long/coul/long"_pair_lj_long.html, "pair_style buck/coul/long"_pair_buck.html
[Default:]

53
doc/pair_coul.html
View File

@ -35,6 +35,14 @@
</H3>
<H3>pair_style coul/wolf/omp command
</H3>
<H3>pair_style tip4p/cut command
</H3>
<H3>pair_style tip4p/long command
</H3>
<H3>pair_style tip4p/cut/omp command
</H3>
<H3>pair_style tip4p/long/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style coul/cut cutoff
@ -42,7 +50,9 @@ pair_style coul/debye kappa cutoff
pair_style coul/dsf alpha cutoff
pair_style coul/long cutoff
pair_style coul/long/gpu cutoff
pair_style coul/wolf alpha cutoff
pair_style coul/wolf alpha cutoff
pair_style tip4p/cut otype htype btype atype qdist cutoff
pair_style tip4p/long otype htype btype atype qdist cutoff
</PRE>
<UL><LI>cutoff = global cutoff for Coulombic interactions
<LI>kappa = Debye length (inverse distance units)
@ -70,6 +80,12 @@ pair_coeff * *
<PRE>pair_style coul/wolf 0.2 9.0
pair_coeff * *
</PRE>
<PRE>pair_style tip4p/cut 1 2 7 8 0.15 12.0
pair_coeff * *
</PRE>
<PRE>pair_style tip4p/long 1 2 7 8 0.15 10.0
pair_coeff * *
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>coul/cut</I> style computes the standard Coulombic interaction
@ -127,6 +143,33 @@ 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>Styles <I>tip4p/cut</I> and <I>tip4p/long</I> implement the coulomb part of
the TIP4P water model of <A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces
a massless site located a short distance away from the oxygen atom
along the bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as
pair_style arguments. Style <I>tip4p/cut</I> uses a global cutoff for
Coulomb interactions; style <I>tip4p/long</I> is for use with a long-range
Coulombic solver (Ewald or PPPM).
</P>
<P>IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
IDs for the O and 2 H atoms must be consecutive, with the O atom
first. This is to enable LAMMPS to "find" the 2 H atoms associated
with each O atom. For example, if the atom ID of an O atom in a TIP4P
water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
</P>
<P>See the <A HREF = "Section_howto.html#howto_8">howto section</A> for more
information on how to use the TIP4P pair styles and lists of
parameters to set. Note that the neighobr list cutoff for Coulomb
interactions is effectively extended by a distance 2*qdist when using
the TIP4P pair style, to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
typically best in an efficiency sense to use a LJ cutoff >= Coulomb
cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
to slightly larger cost for the long-range calculation, so you can
test the trade-off for your model.
</P>
<P>These potentials are designed to be combined with other pair
potentials via the <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>
command. This is because they have no repulsive core. Hence if they
@ -203,15 +246,17 @@ to be specified in an input script that reads a restart file.
<P><B>Restrictions:</B>
</P>
<P>The <I>coul/long</I> style is part of the KSPACE 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
<P>The <I>coul/long</I>, <I>coul/msm</I> and <I>tip4p/long</I> styles are part of the
KSPACE package. They are 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><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_hybrid.html">pair_style
hybrid/overlay</A>
<A HREF = "kspace_style.html">kspace_style</A>
</P>
<P><B>Default:</B> none
</P>

49
doc/pair_coul.txt
View File

@ -19,6 +19,10 @@ pair_style coul/msm command :h3
pair_style coul/msm/omp command :h3
pair_style coul/wolf command :h3
pair_style coul/wolf/omp command :h3
pair_style tip4p/cut command :h3
pair_style tip4p/long command :h3
pair_style tip4p/cut/omp command :h3
pair_style tip4p/long/omp command :h3
[Syntax:]
@ -27,7 +31,9 @@ pair_style coul/debye kappa cutoff
pair_style coul/dsf alpha cutoff
pair_style coul/long cutoff
pair_style coul/long/gpu cutoff
pair_style coul/wolf alpha cutoff :pre
pair_style coul/wolf alpha cutoff
pair_style tip4p/cut otype htype btype atype qdist cutoff
pair_style tip4p/long otype htype btype atype qdist cutoff :pre
cutoff = global cutoff for Coulombic interactions
kappa = Debye length (inverse distance units)
@ -55,6 +61,12 @@ pair_coeff * * :pre
pair_style coul/wolf 0.2 9.0
pair_coeff * * :pre
pair_style tip4p/cut 1 2 7 8 0.15 12.0
pair_coeff * * :pre
pair_style tip4p/long 1 2 7 8 0.15 10.0
pair_coeff * * :pre
[Description:]
The {coul/cut} style computes the standard Coulombic interaction
@ -112,6 +124,33 @@ 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.
Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of
the TIP4P water model of "(Jorgensen)"_#Jorgensen, which introduces
a massless site located a short distance away from the oxygen atom
along the bisector of the HOH angle. The atomic types of the oxygen and
hydrogen atoms, the bond and angle types for OH and HOH interactions,
and the distance to the massless charge site are specified as
pair_style arguments. Style {tip4p/cut} uses a global cutoff for
Coulomb interactions; style {tip4p/long} is for use with a long-range
Coulombic solver (Ewald or PPPM).
IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
IDs for the O and 2 H atoms must be consecutive, with the O atom
first. This is to enable LAMMPS to "find" the 2 H atoms associated
with each O atom. For example, if the atom ID of an O atom in a TIP4P
water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
See the "howto section"_Section_howto.html#howto_8 for more
information on how to use the TIP4P pair styles and lists of
parameters to set. Note that the neighobr list cutoff for Coulomb
interactions is effectively extended by a distance 2*qdist when using
the TIP4P pair style, to account for the offset distance of the
fictitious charges on O atoms in water molecules. Thus it is
typically best in an efficiency sense to use a LJ cutoff >= Coulomb
cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
to slightly larger cost for the long-range calculation, so you can
test the trade-off for your model.
These potentials are designed to be combined with other pair
potentials via the "pair_style hybrid/overlay"_pair_hybrid.html
command. This is because they have no repulsive core. Hence if they
@ -188,15 +227,17 @@ This pair style can only be used via the {pair} keyword of the
[Restrictions:]
The {coul/long} style is part of the KSPACE 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
The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the
KSPACE package. They are 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.
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_style
hybrid/overlay"_pair_hybrid.html
"kspace_style"_kspace_style.html
[Default:] none