From 1bb9c7da42e58b17849671786d97612a941f1fba Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Thu, 16 Mar 2017 22:36:13 -0400
Subject: [PATCH] Remove some duplicate anchors in documentation
---
doc/src/fix_qeq_reax.txt | 6 +++---
doc/src/pair_polymorphic.txt | 8 ++++----
doc/src/pair_tersoff_zbl.txt | 18 +++++++++---------
3 files changed, 16 insertions(+), 16 deletions(-)
diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt
index a26934dfb4..ed4fde60ca 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 1e75518273..0820a00de3 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 f19ac6ad42..18e54749aa 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)
--
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