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Remove some duplicate anchors in documentation

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Richard Berger 2017-03-16 22:36:13 -04:00
parent f893104b18
commit 1bb9c7da42
3 changed files with 16 additions and 16 deletions
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6
doc/src/fix_qeq_reax.txt
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@ -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 command should be used to perform charge equilibration with the "COMB
potential"_pair_comb.html. For more technical details about the potential"_pair_comb.html. For more technical details about the
charge equilibration performed by fix qeq/reax, see 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 The QEq method minimizes the electrostatic energy of the system by
adjusting the partial charge on individual atoms based on interactions 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) :link(Nakano)
[(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997). [(Nakano)] Nakano, Computer Physics Communications, 104, 59-69 (1997).
:link(Aktulga) :link(qeq-Aktulga)
(Aktulga) Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, [(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012). 245-259 (2012).

8
doc/src/pair_polymorphic.txt
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@ -52,7 +52,7 @@ to Stillinger-Weber potential ("SW"_#SW) if we set
:c,image(Eqs/polymorphic4.jpg) :c,image(Eqs/polymorphic4.jpg)
The potential reduces to Tersoff types of potential 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/polymorphic5.jpg)
:c,image(Eqs/polymorphic6.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/polymorphic6.jpg)
:c,image(Eqs/polymorphic8.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) :c,image(Eqs/polymorphic9.jpg)
@ -218,12 +218,12 @@ F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).
:link(Tersoff) :link(Tersoff)
[(Tersoff)] J. Tersoff, Phys. Rev. B, 39, 5566 (1989). [(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, [(Albe)] K. Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B,
66, 035205 (2002). 66, 035205 (2002).
:link(Wang) :link(Wang)
[(Wang)] J. Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991). [(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). [(Daw)] M. S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).

18
doc/src/pair_tersoff_zbl.txt
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@ -23,9 +23,9 @@ pair_coeff * * SiC.tersoff.zbl Si C Si :pre
[Description:] [Description:]
The {tersoff/zbl} style computes a 3-body Tersoff potential 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 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 system of atoms as
:c,image(Eqs/pair_tersoff_zbl.jpg) :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 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, 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 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 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, used variants of the Tersoff portion of the potential. In particular,
our form reduces to the original Tersoff form when m = 3 and gamma = 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, 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 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 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: LAMMPS parameter values for Tersoff_2 can be obtained as follows:
gamma = omega_ijk, lambda3 = 0 and the value of gamma = omega_ijk, lambda3 = 0 and the value of
@ -253,16 +253,16 @@ units.
:line :line
:link(Tersoff_1) :link(zbl-Tersoff_1)
[(Tersoff_1)] J. Tersoff, Phys Rev B, 37, 6991 (1988). [(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 [(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges
of Ions in Matter' Vol 1, 1985, Pergamon Press. 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.: [(Albe)] J. Nord, K. Albe, P. Erhart and K. Nordlund, J. Phys.:
Condens. Matter, 15, 5649(2003). 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) [(Tersoff_2)] J. Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)