From a58779babf6220e6fd0566c20cff38c311bf47b5 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 13 Mar 2013 15:30:49 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9659 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/pair_lj.html | 48 ++++++++++++++++++++++++++++-------------------- doc/pair_lj.txt | 48 ++++++++++++++++++++++++++++-------------------- 2 files changed, 56 insertions(+), 40 deletions(-) diff --git a/doc/pair_lj.html b/doc/pair_lj.html index 0076b12c29..88da42e1db 100644 --- a/doc/pair_lj.html +++ b/doc/pair_lj.html @@ -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 +
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 
+
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.
 

-
Style lj/cut/tip4p/long implements the TIP4P water model of
-(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), 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
@@ -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.
 

 
See the howto section 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
@@ -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 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.
 

 

 
diff --git a/doc/pair_lj.txt b/doc/pair_lj.txt
index 3b76d70129..418ed9415c 100644
--- a/doc/pair_lj.txt
+++ b/doc/pair_lj.txt
@@ -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