diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index a26934dfb496f2aac3e088879e5117a822badc99..ed4fde60ca8aee3e3987d100335c80f389254e88 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -36,7 +36,7 @@ uses charges on each atom. The "fix qeq/comb"_fix_qeq_comb.html command should be used to perform charge equilibration with the "COMB potential"_pair_comb.html. For more technical details about the charge equilibration performed by fix qeq/reax, see the -"(Aktulga)"_#Aktulga paper. +"(Aktulga)"_#qeq-Aktulga paper. The QEq method minimizes the electrostatic energy of the system by adjusting the partial charge on individual atoms based on interactions @@ -119,6 +119,6 @@ be used for periodic cell dimensions less than 10 angstroms. :link(Nakano) [(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997). -:link(Aktulga) -(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, +:link(qeq-Aktulga) +[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012). diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt index 1e75518273ca6e8504b0d7bd3ffba83bddd17185..0820a00de34ef5c4b742e1ddc3c230435c72b651 100644 --- a/doc/src/pair_polymorphic.txt +++ b/doc/src/pair_polymorphic.txt @@ -52,7 +52,7 @@ to Stillinger-Weber potential ("SW"_#SW) if we set :c,image(Eqs/polymorphic4.jpg) The potential reduces to Tersoff types of potential -("Tersoff"_#Tersoff or "Albe"_#Albe) if we set +("Tersoff"_#Tersoff or "Albe"_#poly-Albe) if we set :c,image(Eqs/polymorphic5.jpg) :c,image(Eqs/polymorphic6.jpg) @@ -63,7 +63,7 @@ The potential reduces to Rockett-Tersoff ("Wang"_#Wang) type if we set :c,image(Eqs/polymorphic6.jpg) :c,image(Eqs/polymorphic8.jpg) -The potential becomes embedded atom method ("Daw"_#Daw) if we set +The potential becomes embedded atom method ("Daw"_#poly-Daw) if we set :c,image(Eqs/polymorphic9.jpg) @@ -218,12 +218,12 @@ F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015). :link(Tersoff) [(Tersoff)] J. Tersoff, Phys. Rev. B, 39, 5566 (1989). -:link(Albe) +:link(poly-Albe) [(Albe)] K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002). :link(Wang) [(Wang)] J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991). -:link(Daw) +:link(poly-Daw) [(Daw)] M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984). diff --git a/doc/src/pair_tersoff_zbl.txt b/doc/src/pair_tersoff_zbl.txt index f19ac6ad42acc53b3304bfac3792fd14d8617355..18e54749aa1752453185ca75bd05897177d1f02c 100644 --- a/doc/src/pair_tersoff_zbl.txt +++ b/doc/src/pair_tersoff_zbl.txt @@ -23,9 +23,9 @@ pair_coeff * * SiC.tersoff.zbl Si C Si :pre [Description:] The {tersoff/zbl} style computes a 3-body Tersoff potential -"(Tersoff_1)"_#Tersoff_1 with a close-separation pairwise modification +"(Tersoff_1)"_#zbl-Tersoff_1 with a close-separation pairwise modification based on a Coulomb potential and the Ziegler-Biersack-Littmark -universal screening function "(ZBL)"_#ZBL, giving the energy E of a +universal screening function "(ZBL)"_#zbl-ZBL, giving the energy E of a system of atoms as :c,image(Eqs/pair_tersoff_zbl.jpg) @@ -146,16 +146,16 @@ 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)"_#Tersoff_2 are not symmetric. +Tersoff_2 "(Tersoff_2)"_#zbl-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 = -1, while it reduces to the form of "Albe et al."_#Albe when beta = 1 +1, while it reduces to the form of "Albe et al."_#zbl-Albe when beta = 1 and m = 1. Note that in the current Tersoff implementation in LAMMPS, m must be specified as either 3 or 1. Tersoff used a slightly different but equivalent form for alloys, which we will refer to as -Tersoff_2 potential "(Tersoff_2)"_#Tersoff_2. +Tersoff_2 potential "(Tersoff_2)"_#zbl-Tersoff_2. LAMMPS parameter values for Tersoff_2 can be obtained as follows: gamma = omega_ijk, lambda3 = 0 and the value of @@ -253,16 +253,16 @@ units. :line -:link(Tersoff_1) +:link(zbl-Tersoff_1) [(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). -:link(ZBL) +:link(zbl-ZBL) [(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press. -:link(Albe) +:link(zbl-Albe) [(Albe)] J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003). -:link(Tersoff_2) +:link(zbl-Tersoff_2) [(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)