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48
doc/pair_lj.html
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@ -136,6 +136,11 @@ pair_style lj/cut/coul/msm 10.0 8.0
pair_coeff * * 100.0 3.0 pair_coeff * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 pair_coeff 1 1 100.0 3.5 9.0
</PRE> </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 <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_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0 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 distance are computed directly; interactions outside that distance are
computed in reciprocal space. computed in reciprocal space.
</P> </P>
<P>Style <I>lj/cut/tip4p/long</I> implements the TIP4P water model of <P>Styles <I>lj/cut/tip4p/cut</I> and <I>lj/cut/tip4p/long</I> implement the TIP4P
<A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless site located a water model of <A HREF = "#Jorgensen">(Jorgensen)</A>, which introduces a massless
short distance away from the oxygen atom along the bisector of the HOH site located a short distance away from the oxygen atom along the
angle. The atomic types of the oxygen and hydrogen atoms, the bond bisector of the HOH angle. The atomic types of the oxygen and
and angle types for OH and HOH interactions, and the distance to the hydrogen atoms, the bond and angle types for OH and HOH interactions,
massless charge site are specified as pair_style arguments. Style and the distance to the massless charge site are specified as
<I>lj/cut/tip4p/cut</I> is similar to <I>lj/cut/tip4p/long</I>, only it uses a pair_style arguments. Style <I>lj/cut/tip4p/cut</I> uses a cutoff for
cutoff for Coulomb interactions. Coulomb interactions; style <I>lj/cut/tip4p/long</I> is for use with a
long-range Coulombic solver (Ewald or PPPM).
</P> </P>
<P>IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom <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 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. water molecule is 500, then its 2 H atoms must have IDs 501 and 502.
</P> </P>
<P>See the <A HREF = "Section_howto.html#howto_8">howto section</A> for more <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 information on how to use the TIP4P pair styles and lists of
neighobr list cutoff for Coulomb interactions is effectively extended parameters to set. Note that the neighobr list cutoff for Coulomb
by a distance 2*qdist when using the TIP4P pair style, to account for interactions is effectively extended by a distance 2*qdist when using
the offset distance of the fictitious charges on O atoms in water the TIP4P pair style, to account for the offset distance of the
molecules. Thus it is typically best in an efficiency sense to use a fictitious charges on O atoms in water molecules. Thus it is
LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the typically best in an efficiency sense to use a LJ cutoff >= Coulomb
neighbor list. This leads to slightly larger cost for the long-range cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
calculation, so you can test the trade-off for your model. to slightly larger cost for the long-range calculation, so you can
test the trade-off for your model.
</P> </P>
<P>For all of the <I>lj/cut</I> pair styles, the following coefficients must <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 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 type pair. You cannot specify 2 cutoffs for style <I>lj/cut</I>, since it
has no Coulombic terms. has no Coulombic terms.
</P> </P>
<P>For <I>lj/cut/coul/long</I> and <I>lj/cut/coul/msm</I> and <I>lj/cut/tip4p/long</I> <P>For <I>lj/cut/coul/long</I> and <I>lj/cut/coul/msm</I> and <I>lj/cut/tip4p/cut</I>
only the LJ cutoff can be specified since a Coulombic cutoff cannot be and <I>lj/cut/tip4p/long</I> only the LJ cutoff can be specified since a
specified for an individual I,J type pair. All type pairs use the Coulombic cutoff cannot be specified for an individual I,J type pair.
same global Coulombic cutoff specified in the pair_style command. All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
</P> </P>
<HR> <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 * * 100.0 3.0
pair_coeff 1 1 100.0 3.5 9.0 :pre 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
pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0 pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0
pair_coeff * * 100.0 3.0 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 distance are computed directly; interactions outside that distance are
computed in reciprocal space. computed in reciprocal space.
Style {lj/cut/tip4p/long} implements the TIP4P water model of Styles {lj/cut/tip4p/cut} and {lj/cut/tip4p/long} implement the TIP4P
"(Jorgensen)"_#Jorgensen, which introduces a massless site located a water model of "(Jorgensen)"_#Jorgensen, which introduces a massless
short distance away from the oxygen atom along the bisector of the HOH site located a short distance away from the oxygen atom along the
angle. The atomic types of the oxygen and hydrogen atoms, the bond bisector of the HOH angle. The atomic types of the oxygen and
and angle types for OH and HOH interactions, and the distance to the hydrogen atoms, the bond and angle types for OH and HOH interactions,
massless charge site are specified as pair_style arguments. Style and the distance to the massless charge site are specified as
{lj/cut/tip4p/cut} is similar to {lj/cut/tip4p/long}, only it uses a pair_style arguments. Style {lj/cut/tip4p/cut} uses a cutoff for
cutoff for Coulomb interactions. 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 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 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. 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 See the "howto section"_Section_howto.html#howto_8 for more
information on how to use the TIP4P pair style. Note that the information on how to use the TIP4P pair styles and lists of
neighobr list cutoff for Coulomb interactions is effectively extended parameters to set. Note that the neighobr list cutoff for Coulomb
by a distance 2*qdist when using the TIP4P pair style, to account for interactions is effectively extended by a distance 2*qdist when using
the offset distance of the fictitious charges on O atoms in water the TIP4P pair style, to account for the offset distance of the
molecules. Thus it is typically best in an efficiency sense to use a fictitious charges on O atoms in water molecules. Thus it is
LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the typically best in an efficiency sense to use a LJ cutoff >= Coulomb
neighbor list. This leads to slightly larger cost for the long-range cutoff + 2*qdist, to shrink the size of the neighbor list. This leads
calculation, so you can test the trade-off for your model. 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 For all of the {lj/cut} pair styles, the following coefficients must
be defined for each pair of atoms types via the 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 type pair. You cannot specify 2 cutoffs for style {lj/cut}, since it
has no Coulombic terms. has no Coulombic terms.
For {lj/cut/coul/long} and {lj/cut/coul/msm} and {lj/cut/tip4p/long} For {lj/cut/coul/long} and {lj/cut/coul/msm} and {lj/cut/tip4p/cut}
only the LJ cutoff can be specified since a Coulombic cutoff cannot be and {lj/cut/tip4p/long} only the LJ cutoff can be specified since a
specified for an individual I,J type pair. All type pairs use the Coulombic cutoff cannot be specified for an individual I,J type pair.
same global Coulombic cutoff specified in the pair_style command. All type pairs use the same global Coulombic cutoff specified in the
pair_style command.
:line :line