From 20934f12036a6882d8d74bc165483d138345d85d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 28 Jun 2010 23:43:03 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4361 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/pair_hybrid.html | 49 ++++++++++++++++++++++++++++++-------------- doc/pair_hybrid.txt | 49 ++++++++++++++++++++++++++++++-------------- 2 files changed, 68 insertions(+), 30 deletions(-) diff --git a/doc/pair_hybrid.html b/doc/pair_hybrid.html index 8fa5c2ac51..7c95c92cf7 100644 --- a/doc/pair_hybrid.html +++ b/doc/pair_hybrid.html @@ -153,22 +153,41 @@ Pair_style hybrid allows interactions between type pairs 2-2, 1-2, could even add a second interaction for 1-1 to be computed by another pair style, assuming pair_style hybrid/overlay is used.

-

But you cannot exclude the many-body interactions for some subset of -the type pairs within the full set of 1,3,4 interactions, e.g. exclude -1-1 or 1-3 interactions. That is not conceptually well-defined for -many-body interactions, since the potential will typically calculate -energies and foces for small groups of atoms, e.g. 3 or 4 atoms. -Additionally it is non-physical to think of excluding an interaction -between a particular pair of atoms when the potential computes 3-body -or 4-body interactions. +

But you should not, as a general rule, attempt to exclude the +many-body interactions for some subset of the type pairs within the +set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That +is not conceptually well-defined for many-body interactions, since the +potential will typically calculate energies and foces for small groups +of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to +find the additional atoms in the group. It is typically non-physical +to think of excluding an interaction between a particular pair of +atoms when the potential computes 3-body or 4-body interactions.

-

One exception to this rule is that you can still use the neigh_modify -exclude command to exclude certain type pairs from -the neighbor list that will be passed to each sub-style. This would -alter the calculations made by a many-body potential, since it builds -its list of 3-body, 4-body, etc interactions from the pair list, but -you would need to think carefully as to whether it produces a -physically meaningful result for your model. +

However, you can still use the pair_coeff none setting or the +neigh_modify exclude command to exclude certain +type pairs from the neighbor list that will be passed to a manybody +sub-style. This will alter the calculations made by a many-body +potential, since it builds its list of 3-body, 4-body, etc +interactions from the pair list. You will need to think carefully as +to whether it produces a physically meaningful result for your model. +

+

For example, imagine you have two atom types in your model, type 1 for +atoms in one surface, and type 2 for atoms in the other, and you wish +to use a Tersoff potential to compute interactions within each +surface, but not between surfaces. Then either of these two command +sequences would implement that model: +

+
pair_style hybrid tersoff
+pair_coeff * * tersoff SiC.tersoff C C
+pair_coeff 1 2 none 
+
+
pair_style tersoff
+pair_coeff * * SiC.tersoff C C
+neigh_modify exclude type 1 2 
+
+

Either way, only neighbor lists with 1-1 or 2-2 interactions would be +passed to the Tersoff potential, which means it would compute no +3-body interactions containing both type 1 and 2 atoms.

diff --git a/doc/pair_hybrid.txt b/doc/pair_hybrid.txt index 7f2bf9dd59..37eb95c08c 100644 --- a/doc/pair_hybrid.txt +++ b/doc/pair_hybrid.txt @@ -149,22 +149,41 @@ Pair_style hybrid allows interactions between type pairs 2-2, 1-2, could even add a second interaction for 1-1 to be computed by another pair style, assuming pair_style hybrid/overlay is used. -But you cannot exclude the many-body interactions for some subset of -the type pairs within the full set of 1,3,4 interactions, e.g. exclude -1-1 or 1-3 interactions. That is not conceptually well-defined for -many-body interactions, since the potential will typically calculate -energies and foces for small groups of atoms, e.g. 3 or 4 atoms. -Additionally it is non-physical to think of excluding an interaction -between a particular pair of atoms when the potential computes 3-body -or 4-body interactions. +But you should not, as a general rule, attempt to exclude the +many-body interactions for some subset of the type pairs within the +set of 1,3,4 interactions, e.g. exclude 1-1 or 1-3 interactions. That +is not conceptually well-defined for many-body interactions, since the +potential will typically calculate energies and foces for small groups +of atoms, e.g. 3 or 4 atoms, using the neighbor lists of the atoms to +find the additional atoms in the group. It is typically non-physical +to think of excluding an interaction between a particular pair of +atoms when the potential computes 3-body or 4-body interactions. -One exception to this rule is that you can still use the "neigh_modify -exclude"_neigh_modify.html command to exclude certain type pairs from -the neighbor list that will be passed to each sub-style. This would -alter the calculations made by a many-body potential, since it builds -its list of 3-body, 4-body, etc interactions from the pair list, but -you would need to think carefully as to whether it produces a -physically meaningful result for your model. +However, you can still use the pair_coeff none setting or the +"neigh_modify exclude"_neigh_modify.html command to exclude certain +type pairs from the neighbor list that will be passed to a manybody +sub-style. This will alter the calculations made by a many-body +potential, since it builds its list of 3-body, 4-body, etc +interactions from the pair list. You will need to think carefully as +to whether it produces a physically meaningful result for your model. + +For example, imagine you have two atom types in your model, type 1 for +atoms in one surface, and type 2 for atoms in the other, and you wish +to use a Tersoff potential to compute interactions within each +surface, but not between surfaces. Then either of these two command +sequences would implement that model: + +pair_style hybrid tersoff +pair_coeff * * tersoff SiC.tersoff C C +pair_coeff 1 2 none :pre + +pair_style tersoff +pair_coeff * * SiC.tersoff C C +neigh_modify exclude type 1 2 :pre + +Either way, only neighbor lists with 1-1 or 2-2 interactions would be +passed to the Tersoff potential, which means it would compute no +3-body interactions containing both type 1 and 2 atoms. :line