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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9659 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2013-03-13 15:30:49 +00:00
parent 0cd14bfb84
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2 changed files with 56 additions and 40 deletions
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48
doc/pair_lj.html
View File

@ -136,6 +136,11 @@ pair_style lj/cut/coul/msm 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</PRE>
<PRE>pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0
</PRE>
<PRE>pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
@ -195,14 +200,15 @@ 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>Style <I>lj/cut/tip4p/long</I> implements 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>lj/cut/tip4p/cut</I> is similar to <I>lj/cut/tip4p/long</I>, only it uses a
cutoff for Coulomb interactions.
<P>Styles <I>lj/cut/tip4p/cut</I> and <I>lj/cut/tip4p/long</I> implement 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>lj/cut/tip4p/cut</I> uses a cutoff for
Coulomb interactions; style <I>lj/cut/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
@ -211,14 +217,15 @@ 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 style. 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.
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>For all of the <I>lj/cut</I> pair styles, the following coefficients must
be defined for each pair of atoms types via the
@ -244,10 +251,11 @@ are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style <I>lj/cut</I>, since it
has no Coulombic terms.
</P>
<P>For <I>lj/cut/coul/long</I> and <I>lj/cut/coul/msm</I> and <I>lj/cut/tip4p/long</I>
only the LJ cutoff can be specified since a Coulombic cutoff cannot be
specified for an individual I,J type pair. All type pairs use the
same global Coulombic cutoff specified in the pair_style command.
<P>For <I>lj/cut/coul/long</I> and <I>lj/cut/coul/msm</I> and <I>lj/cut/tip4p/cut</I>
and <I>lj/cut/tip4p/long</I> only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
</P>
<HR>

48
doc/pair_lj.txt
View File

@ -105,6 +105,11 @@ pair_style lj/cut/coul/msm 10.0 8.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0
@ -164,14 +169,15 @@ specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are
computed in reciprocal space.
Style {lj/cut/tip4p/long} implements 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
{lj/cut/tip4p/cut} is similar to {lj/cut/tip4p/long}, only it uses a
cutoff for Coulomb interactions.
Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement 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 {lj/cut/tip4p/cut} uses a cutoff for
Coulomb interactions; style {lj/cut/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
@ -180,14 +186,15 @@ 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 style. 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.
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.
For all of the {lj/cut} pair styles, the following coefficients must
be defined for each pair of atoms types via the
@ -213,10 +220,11 @@ are specified, they are used as the LJ and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style {lj/cut}, since it
has no Coulombic terms.
For {lj/cut/coul/long} and {lj/cut/coul/msm} and {lj/cut/tip4p/long}
only the LJ cutoff can be specified since a Coulombic cutoff cannot be
specified for an individual I,J type pair. All type pairs use the
same global Coulombic cutoff specified in the pair_style command.
For {lj/cut/coul/long} and {lj/cut/coul/msm} and {lj/cut/tip4p/cut}
and {lj/cut/tip4p/long} only the LJ cutoff can be specified since a
Coulombic cutoff cannot be specified for an individual I,J type pair.
All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
:line