The new atom properties encode values that migrate with atoms to new processors and are written to restart files. If you want the new -properties to also be defined for ghost atoms, then use the border +properties to also be defined for ghost atoms, then use the ghost keyword with a value of yes. This will invoke extra communication when ghost atoms are created (at every re-neighboring) to insure the -new properties are also defined for the ghost atoms. +new properties are also defined for the ghost atoms.
IMPORTANT NOTE: The properties for ghost atoms are not updated every timestep, but only once every few steps when neighbor lists are -re-built. Thus the border keyword is suitable for static -properties, like molecule IDs, but not for dynamic properties that -change every step. In that case, the code you add to LAMMPS to change -the properties will also need to communicate their new values, an -operation that can be invoked from within a pair +re-built. Thus the ghost keyword is suitable for static properties, +like molecule IDs, but not for dynamic properties that change every +step. For the latter, the code you add to LAMMPS to change the +properties will also need to communicate their new values to/from +ghost atoms, an operation that can be invoked from within a pair style or fix or compute that you write.
diff --git a/doc/fix_property_atom.txt b/doc/fix_property_atom.txt index 658251cd67..c98be7b38e 100644 --- a/doc/fix_property_atom.txt +++ b/doc/fix_property_atom.txt @@ -77,18 +77,18 @@ seamlessly integrated with the rest of the code. The new atom properties encode values that migrate with atoms to new processors and are written to restart files. If you want the new -properties to also be defined for ghost atoms, then use the {border} +properties to also be defined for ghost atoms, then use the {ghost} keyword with a value of {yes}. This will invoke extra communication when ghost atoms are created (at every re-neighboring) to insure the -new properties are also defined for the ghost atoms. +new properties are also defined for the ghost atoms. IMPORTANT NOTE: The properties for ghost atoms are not updated every timestep, but only once every few steps when neighbor lists are -re-built. Thus the {border} keyword is suitable for static -properties, like molecule IDs, but not for dynamic properties that -change every step. In that case, the code you add to LAMMPS to change -the properties will also need to communicate their new values, an -operation that can be invoked from within a "pair +re-built. Thus the {ghost} keyword is suitable for static properties, +like molecule IDs, but not for dynamic properties that change every +step. For the latter, the code you add to LAMMPS to change the +properties will also need to communicate their new values to/from +ghost atoms, an operation that can be invoked from within a "pair style"_pair_style.html or "fix"_fix.html or "compute"_compute.html that you write. diff --git a/doc/pair_tersoff_zbl.html b/doc/pair_tersoff_zbl.html index f0a6d381dc..5b59312f67 100644 --- a/doc/pair_tersoff_zbl.html +++ b/doc/pair_tersoff_zbl.html @@ -136,14 +136,20 @@ three-body parameters for SiCSi and SiSiC entries will not, in general, be the same. The parameters used for the two-body interaction come from the entry where the 2nd element is repeated. Thus the two-body parameters for Si interacting with C, comes from the -SiCC entry. By symmetry, the twobody parameters in the SiCC and CSiSi -entries should thus be the same. The parameters used for a particular +SiCC entry. + +The parameters used for a particular three-body interaction come from the entry with the corresponding three elements. The parameters used only for two-body interactions (n, beta, lambda2, B, lambda1, and A) in entries whose 2nd and 3rd element are different (e.g. SiCSi) are not used for anything and can be set to 0.0 if desired.
+Note that the twobody parameters in entries such as SiCC and CSiSi +are often the same, due to the common use of symmetric mixing rules, +but this is not always the case. For example, the beta and n parameters in +Tersoff_2 (Tersoff_2) are not symmetric. +
We chose the above form so as to enable users to define all commonly used variants of the Tersoff portion of the potential. In particular, our form reduces to the original Tersoff form when m = 3 and gamma = @@ -154,14 +160,13 @@ different but equivalent form for alloys, which we will refer to as Tersoff_2 potential (Tersoff_2).
LAMMPS parameter values for Tersoff_2 can be obtained as follows: -gamma = 1, just as for Tersoff_1, but now lambda3 = 0 and the value of +gamma = omega_ijk, lambda3 = 0 and the value of m has no effect. The parameters for species i and j can be calculated using the Tersoff_2 mixing rules:
Values not shown are determined by the first atom type. Finally, the -Tersoff_2 parameters R and S must be converted to the LAMMPS +
Tersoff_2 parameters R and S must be converted to the LAMMPS parameters R and D (R is different in both forms), using the following relations: R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the Tersoff_2 parameters. @@ -260,11 +265,11 @@ of Ions in Matter' Vol 1, 1985, Pergamon Press.
-(Albe) J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.: +
(Albe) J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).
-(Tersoff_2) J. Tersoff, Phys Rev B, 39, 5566 (1989) +
(Tersoff_2) J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)